@article {pmid41049421,
year = {2025},
author = {Yan, J and Zhao, J and Naizemuding, P and Zhao, W and Sun, J and Wang, Y and Yang, J and Li, D and Zhang, F and Cao, H},
title = {Unraveling the Anti-Obesity Potential of White Kidney Bean α-Amylase Inhibitors: Mechanistic Insights From Enzyme Kinetics to Gut Microbiota Modulation.},
journal = {Food science & nutrition},
volume = {13},
number = {10},
pages = {e71043},
pmid = {41049421},
issn = {2048-7177},
abstract = {The global rise in obesity, driven largely by excessive carbohydrate consumption, highlights the demand for innovative dietary interventions targeting starch digestion. This study investigates the anti-obesity effects of α-amylase inhibitors (α-AI) extracted from white kidney beans, employing a multidisciplinary strategy encompassing botanical screening, enzyme kinetics, clinical trials, and gut microbiota profiling. Among 10 varieties evaluated, the A10 strain from Jilin Province demonstrated the highest α-AI activity, characterized by noncompetitive inhibition that remains effective across varying starch concentrations. In an 8-week randomized controlled trial, α-AI supplementation significantly reduced body weight, BMI, waist circumference, and hip circumference compared to placebo. Further, 16S rRNA sequencing revealed dual mechanisms: enrichment of SCFA-producing bacteria (e.g., Bifidobacterium and Bacteroides ovatus) and modulation of microbial lipid metabolic pathways. These results highlight α-AI as a dual-action anti-obesity agent, combining direct enzymatic inhibition with microbiome-mediated metabolic effects. By bridging phytochemical characterization with clinical outcomes, this work proposes a novel therapeutic approach that simultaneously targets carbohydrate absorption and gut microbial ecology, supporting the development of standardized α-AI formulations as potential nutraceuticals for metabolic syndrome.},
}

@article {pmid41048979,
year = {2025},
author = {Nurhazli, NAA and Tan, JH and Kamaroddin, MF and Shamsir, MS and Yaakop, AS and Goh, KM},
title = {Microbial Community Profiles of Biofilms from Hot Springs: 16S and 18S rRNA Amplicon Sequencing Data.},
journal = {Data in brief},
volume = {62},
number = {},
pages = {112093},
pmid = {41048979},
issn = {2352-3409},
abstract = {This article presents microbial diversity data from biofilms collected from the sides or outflows of several Malaysian hot springs, with temperatures ranging from 38 to 56 °C and pH values between 7.1 and 8.7. Genomic DNA was extracted from the biofilms and subjected to 16S V3-V4 and 18S V4 amplicon sequencing using the Illumina NovaSeq 6000 platform. Reads were processed with various bioinformatic tools including QIIME2, and eventually, amplicon sequence variants (ASVs) were identified. In almost all analyzed biofilms, approximately 50% of the total ASVs belonged to Cyanobacteriota and Chloroflexota, except for one biofilm, labeled DTO, which was dominated by Pseudomonadata and Cyanobacteriota. Besides bacteria, the data also suggest the presence of various eukaryotic organisms, including small animals such as nematodes, rotifers, and arthropods; fungi and fungus-like organisms such as Ascomycota, Zoopagomycota, Oomycota, and Cryptomycota; as well as photosynthetic eukaryotes from the Viridiplantae group. This dataset serves as a valuable resource for microbial ecology studies in hot spring biofilms and is openly available for reuse, providing a foundation for future research on microbial diversity and functional roles in geothermal ecosystems.},
}

@article {pmid41048492,
year = {2025},
author = {Chen, X and Yu, D and Yan, Y and Yuan, C and He, J},
title = {Soil viruses drive carbon turnover during subtropical secondary forest succession.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633379},
pmid = {41048492},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.

METHODS: We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.

RESULTS: Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.

DISCUSSION: These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.},
}

@article {pmid41048389,
year = {2025},
author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL},
title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20081},
pmid = {41048389},
issn = {2167-8359},
mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; },
abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.},
}

New York City
*Metagenome
*Parks, Recreational
Metagenomics
Humans
*Seawater/microbiology
Microbiota/genetics
*Water Microbiology

@article {pmid41047820,
year = {2025},
author = {Lu, Q and Feng, Y and Wang, H and Zhu, K and Teng, L and Yue, M and Li, Y},
title = {Gut microbiota as a regulator of vaccine efficacy: implications for personalized vaccination.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2563709},
doi = {10.1080/19490976.2025.2563709},
pmid = {41047820},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Vaccine Efficacy ; *Precision Medicine ; Vaccination ; Immunity, Innate ; *Vaccines/immunology ; Animals ; Adaptive Immunity ; },
abstract = {Vaccines are one of the most significant achievements in global health, as they have substantially reduced morbidity and mortality from infectious diseases. However, the vaccine efficacy varies markedly across different populations, particularly among infants, older adults, and people living in low- and middle-income countries. Host-intrinsic factors, such as sex, age, and genetic predisposition, contribute to these heterogeneities. However, accumulating data indicate that the gut microbiota also plays a pivotal role in modulating vaccine efficacy. This review summarizes current knowledge, demonstrating that vaccine efficacy is shaped not only by host biology but also by a dynamic, bidirectional interplay between the gut microbiota and immune system. We discuss how the microbiota influences vaccine outcomes through several mechanisms, including priming the innate immune response, regulating adaptive responses through metabolites, and facilitating antigen cross-reactivity. Furthermore, we examine the potential for microbiota-informed precision vaccinology, which integrates multiomics profiling and artificial intelligence to predict and improve vaccine performance. These advancements establish a framework for personalized vaccine development based on microbial ecology.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Vaccine Efficacy
*Precision Medicine
Vaccination
Immunity, Innate
*Vaccines/immunology
Animals
Adaptive Immunity

@article {pmid41046701,
year = {2025},
author = {Yao, H and Yu, J and Yang, X and Xu, J},
title = {Mechanisms of disruption of the gut-brain axis by environmental endocrine disruptors.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119124},
doi = {10.1016/j.ecoenv.2025.119124},
pmid = {41046701},
issn = {1090-2414},
abstract = {Environmental endocrine disruptors (EEDs) are exogenous chemicals that impair physiological health by disrupting endocrine function. The gut-brain axis represents a complex bidirectional communication network integrating the gut microbiome, immune system, neural signaling, and endocrine pathways to maintain systemic homeostasis. Within this interconnected system, gut microbiota influence mood regulation, immune activity modulates neural processes, and neural signaling governs circadian and sleep cycles. This review explores the multi-system impacts of EEDs across four key physiological domains: (1) gut microbial ecology, (2) immune function, (3) neuroendocrine regulation, and (4) developmental processes. Evidence indicates that EED exposure disrupts intestinal microbial composition, leading to dysbiosis marked by the depletion of beneficial taxa and the expansion of pathogenic species. Concurrently, EEDs impair gut-associated immune cell populations (T cells, B cells, and macrophages), undermining mucosal immunity and increasing susceptibility to inflammatory bowel disease, autoimmune conditions, and gastrointestinal malignancies. At the endocrine level, EEDs interfere with the hypothalamic-pituitary-adrenal and hypothalamic-pituitary-gonadal axes, contributing to hormonal imbalances and impaired reproductive development. Neurochemically, they disrupt the synthesis, release, and degradation of key neurotransmitters, including norepinephrine, dopamine, and serotonin, while exerting direct neurotoxic effects such as cerebrovascular abnormalities and delayed cerebellar myelination. In summary, this review delineates the mechanistic pathways through which EEDs perturb gut-brain axis homeostasis. These insights provide a scientific basis for designing targeted therapeutic interventions and shaping evidence-based public health policies.},
}

@article {pmid41044018,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Soil microbes: below-ground defenders against desertification.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2025.09.014},
pmid = {41044018},
issn = {1872-8383},
abstract = {Soil microbes act as below-ground defenders against desertification by several mechanisms, such as rhizosheath formation, necromass accumulation, biological soil crusts, exopolysaccharide (EPS) production, hyphal networks, and calcium carbonate precipitation. Here, we discuss how soil microbes drive ecosystem recovery in drylands, offering promising, nature-based strategies for restoring soils in the face of desertification.},
}

@article {pmid41041139,
year = {2025},
author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E},
title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1641612},
pmid = {41041139},
issn = {2296-861X},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.

METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000 mg lees/kg body weight for 14 days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.

RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p = 0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p = 0.016) showing both a potentially sex-dependent responses to dietary intervention.

CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.},
}

@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth & development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}

Animals
Larva/microbiology/growth & development
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Metagenome
*Diptera/microbiology/growth & development
Animal Feed/analysis
RNA, Ribosomal, 16S/genetics
Metagenomics
Diet
Phylogeny
Chickens

@article {pmid41037135,
year = {2025},
author = {Cárdenas, P and Carpio-Arias, V and Chávez, M and Benítez, AD and Baldeón, AD and Suárez-Jaramillo, A and Fornasini, M and Robles, J and Loza, G and Baldeón, ME},
title = {Nutritional Status and Fecal Microbiota in School Children from the Galapagos and the Andean Region.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {103},
pmid = {41037135},
issn = {1432-184X},
support = {I+D+I-XVII-2022-03//This work was supported by the Ecuadorian Consortium for the Development of Advanced Internet (CEDIA) and Universidad Internacional del Ecuador, Universidad San Francisco de Quito, and Escuela Superior Politecnica del Chimborazo./ ; },
mesh = {Humans ; Ecuador/epidemiology ; *Feces/microbiology ; *Nutritional Status ; Child ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Intestinal Diseases, Parasitic/epidemiology/microbiology ; },
abstract = {Schoolchildren from the Galapagos and the Andean region present the worst indices of malnutrition in Ecuador and are exposed to distinctive food and water insecurity. We compared the nutritional status, the fecal microbiota composition of schoolchildren from the Galapagos (n = 51; 8.88 ± 2.15 years) and the Andean region (n = 114; 8.69 ± 1.83 years). Children had a nutritional evaluation and provided fecal samples for microbiota analysis by 16S rRNA gene sequencing. Excess weight was more prevalent in Galapagos (41.18%) than in the Andes (24.5%). Additionally, intestinal parasitosis was more prevalent in children from the Andes (76.4%) than in Galapagos (13.0%). Species richness was lower in fecal samples of children from the Galapagos than those from the Andes (Chao1 index p = 0.001). Beta-diversity metrics also showed significant differences between these samples. Bacteroidota and Proteobacteria were enriched in the microbiota of Galapagos children, whereas Firmicutes A and Cyanobacteria were enriched in the Andean children. At the genus level, the top 3 genera present in schoolchildren from the Galapagos were Bacteroides, Phocaeicola, and Escherichia, while in children from the Andes were Cryptobacteroides, Prevotella, and Clostridium. Cyanobacteria were inversely associated with BMI z-score in the Galapagos region (q = 0.009), while, Firmicutes D had a direct relationship with BMI z-score in children from the Andes (q = 0.05). At the genus level, only Butyrivibrio was inversely associated with BMI z-score in children of the Galapagos (q = 0.04). We conclude that schoolchildren with different degrees of malnutrition from two distinct geographical areas have dissimilar fecal microbiota characteristics.},
}

Humans
Ecuador/epidemiology
*Feces/microbiology
*Nutritional Status
Child
Male
Female
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Intestinal Diseases, Parasitic/epidemiology/microbiology

@article {pmid41037127,
year = {2025},
author = {Arunrat, N and Mhuantong, W and Sereenonchai, S},
title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {102},
pmid = {41037127},
issn = {1432-184X},
support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; },
mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; },
abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.},
}

*Soil Microbiology
Thailand
*Bacteria/classification/genetics/metabolism/isolation & purification
Soil/chemistry
*Microbiota
Nitrogen/metabolism
Nitrification
*Agriculture/methods
Nitrogen Fixation
Nitrogen Cycle

@article {pmid41037066,
year = {2025},
author = {Scott, CM and Holman, DB and Gzyl, KE and Ibe, A and Taheri, AE},
title = {Production Systems and Age Influence Fecal Mycobiota Diversity and Composition in Swine.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {104},
pmid = {41037066},
issn = {1432-184X},
mesh = {Animals ; *Feces/microbiology ; Swine/microbiology ; *Fungi/classification/genetics/isolation & purification ; *Animal Husbandry/methods ; *Gastrointestinal Microbiome ; *Mycobiome ; Biodiversity ; DNA, Fungal/genetics ; Age Factors ; Female ; },
abstract = {The gut microbiome is an important factor in animal health and can be influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Bacterial communities of the gut microbiome in many species have been extensively studied, but research on the fungal microbiota remains limited and underrepresented in the literature. The objective of this study was to characterize the fecal mycobiota of swine raised under two different production systems: outdoor pasture-based or conventional indoor systems. Fecal samples from nursery, growing-finishing, and sow pigs from both farming systems were collected, and the mycobiota was profiled using PCR amplification and sequencing of the universal fungal internal transcribed spacer 1 (ITS1) region. A significant difference in fungal community structure was observed between the conventionally raised and pasture-raised pigs, as well as among all three production phases. Four species, Arthrographis kalrae, Enterocarpus grenotii, Pseudallescheria angusta, and Sagenomella oligospora, were differentially abundant between the two farms, all of which had higher relative abundance in the pasture-raised pigs. Additionally, pasture-raised pigs hosted a more diverse fungal community with higher species richness in their gastrointestinal tract. In summary, farming practices and pig age influenced the pig fecal mycobiota.},
}

Animals
*Feces/microbiology
Swine/microbiology
*Fungi/classification/genetics/isolation & purification
*Animal Husbandry/methods
*Gastrointestinal Microbiome
*Mycobiome
Biodiversity
DNA, Fungal/genetics
Age Factors
Female

@article {pmid41036845,
year = {2025},
author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M},
title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0023425},
doi = {10.1128/msphere.00234-25},
pmid = {41036845},
issn = {2379-5042},
abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.},
}

@article {pmid41033533,
year = {2025},
author = {Kim, YJ and Jung, DH and Jung, JH and Seo, DH and Kim, JS and Park, CS},
title = {Genomic and functional characterization of carbohydrate-active enzymes from Ruminococcoides bili FMB-CY1 reveals modular strategy for resistant starch degradation in the human gut.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {147957},
doi = {10.1016/j.ijbiomac.2025.147957},
pmid = {41033533},
issn = {1879-0003},
abstract = {Ruminococcoides bili FMB-CY1, a human gut bacterium, exhibits strong resistant starch (RS)-degrading ability. To elucidate its RS-degradation strategy, we performed comprehensive genomic annotation and biochemical characterization of 19 encoded carbohydrate-active enzymes (CAZymes). Genome analysis revealed glycoside hydrolases (GH13, GH31, GH77), glycosyltransferase (GT35), carbohydrate-binding modules (CBMs), and domains associated with amylosome-like multienzyme complexes, including dockerin and cohesin motifs. All 19 CAZyme genes were heterologously expressed in Escherichia coli, and their enzymatic properties were systematically characterized. Most α-amylases exhibited extracellular activity against raw RS granules, particularly those harboring CBMs. Hydrolysis profiling revealed distinct substrate preferences, leading to functional reannotation of four enzymes. Domain analyses further suggested that select CAZymes form a surface-associated complex analogous to the amylosome. Together, these enzymes suggest a putative RS-degradation system, in which extracellular α-amylases initiate starch breakdown and are followed by pullulanases, glucosidases, and transferases that complete RS degradation. The released sugars support microbial cross-feeding and potentially contribute to host energy metabolism. The study provides molecular insight into RS utilization by Rc. bili FMB-CY1 and identifies enzymatic features relevant to gut microbial ecology and functional food applications targeting RS metabolism.},
}

@article {pmid41031660,
year = {2025},
author = {Wick, LY},
title = {Rebuttal to Correspondence on "DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems".},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12499},
pmid = {41031660},
issn = {1520-5851},
}

@article {pmid41029470,
year = {2025},
author = {Cutajar, S and Braglia, C and Alberoni, D and Mifsud, M and Baffoni, L and Spiteri, J and Di Gioia, D and Mifsud, D},
title = {Gut microbiome of Vespa orientalis: functional insights and potential honey bee pathogen dynamics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {95},
pmid = {41029470},
issn = {2524-4671},
support = {TESS 2022//Tertiary Education Scholarships Scheme by the Ministry for Education, Sport, Youth, Research and Innovation in Malta (TESS 2022)./ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; },
abstract = {Vespa orientalis, the oriental hornet, is an emerging predator of honey bees whose ecological impact and microbial ecology remain poorly understood. Here, we present the first detailed characterisation of its gut microbiota by integrating 16S rRNA gene sequencing, predicted microbial function, pathogen screening, and a three-year beekeeper survey across urban and rural sites in Malta. Hornets were sampled from four locations and classified by observed foraging behaviour, either predation on honey bees or scavenging on cat food.Survey data confirmed consistent V. orientalis sightings and seasonal colony losses, particularly during peak foraging months. Microbiome analysis revealed a conserved core community dominated by Spiroplasma, Arsenophonus, and Rosenbergiella, with overall diversity stable across sites and diets. However, specific taxa varied with foraging behaviour. For example, Arsenophonus was enriched in bee-predating hornets, while Enterobacter and Serratia were more common in scavenging individuals, suggesting environmental and dietary influences on microbiota composition. Predicted functional profiles remained broadly conserved, reflecting robust nutrient metabolism and potential detoxification capabilities, with some variations related to the diet behaviour.Pathogen screening detected Nosema ceranae and Crithidia bombi in a substantial proportion of hornets, including those not observed feeding on bees. Although our findings do not demonstrate pathogen transmission, they support the hypothesis that V. orientalis may act as a transient carrier, potentially contributing to pathogen persistence via environmental exposure.Together, these results reveal the dietary flexibility and microbial flexibility within the gut microbiome of V. orientalis, and highlight its potential involvement in pollinator pathogen dynamics.},
}

@article {pmid41028416,
year = {2025},
author = {Sidharthan, VK and Patel, R and Thiyaharajan, M and Krishnappa, C and Pattanaik, S and Kumar, A},
title = {Metabarcoding reveals unique rhizospheric microbiomes of Rhizophora in Indian Mangroves.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41028416},
issn = {1874-9356},
support = {IFB/T-1/WME/23-1//Indian Council of Forestry Research and Education/ ; },
abstract = {Rhizophora species are ecologically significant true mangroves with a broad tropical distribution. We examined the rhizospheric microbiomes of dominant Rhizophora species from two contrasting Indian mangrove ecosystems-Coringa and Pichavaram-using high-throughput metabarcoding. Soil properties differed significantly between sites: Pichavaram exhibited higher electrical conductivity (24.53 dS/m), organic carbon (1.70%), sodium (8811.86 ppm), sodium adsorption ratio (220.15), and exchangeable sodium percentage (64.27%), while Coringa soils showed higher pH (8.01). Sequencing generated 1.31, 1.24, and 1.22 million high-quality reads for archaea, bacteria, and fungi, respectively. Taxonomic profiling revealed Nitrososphaeria (62.3-91.9%), Gammaproteobacteria (16.8-25.1%), and Sordariomycetes (18.6-27.8%) as dominant classes. Core taxa across both sites included Candidatus Nitrosopumilus, Woeseia, and Aspergillus. Alpha diversity indices (Chao1, Shannon, Simpson) indicated significantly higher bacterial richness and evenness in R. apiculata at Coringa (P < 0.001), while archaeal and fungal diversity showed no marked differences. Beta diversity analysis (PCoA, PERMANOVA) revealed distinct community compositions between Coringa and Pichavaram, with stronger segregation in archaeal and bacterial assemblages than in fungi. Differential abundance analysis identified nine archaeal, fifty-nine bacterial, and three fungal genera enriched between sites, with methanogens (Methanosarcina, Methanocella) predominant in Coringa and halophiles (Halococcus, Haloferax) in Pichavaram. Redundancy analysis showed sodium adsorption ratio as the key determinant of microbial assemblages, while electrical conductivity significantly shaped archaeal and fungal communities. These findings provide the first baseline dataset of the Coringa rhizospheric microbiome and new insights into the microbial ecology of Indian mangroves, with implications for ecosystem functioning, methane emissions, and conservation strategies.},
}

@article {pmid41026240,
year = {2025},
author = {Abdelali, SK and Aissaoui, L and Cano-Argüelles, AL and Piloto-Sardiñas, E and Abuin-Denis, L and Maitre, A and Foucault-Simonin, A and Mateos-Hernández, L and Kratou, M and Wu-Chuang, A and Obregon, D and Cabezas-Cruz, A},
title = {Seasonal Variations in the Microbiome of Hyalomma excavatum Ticks in Algeria.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {96},
pmid = {41026240},
issn = {1432-184X},
mesh = {Animals ; *Seasons ; Algeria ; *Microbiota ; *Ixodidae/microbiology ; Female ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Rickettsia/isolation & purification/genetics ; Biodiversity ; },
abstract = {Ticks are key vectors of zoonotic diseases, with their microbiomes playing a critical role in tick physiology, survival, and vector competence. This study presents the first investigation of the microbiome in Hyalomma excavatum ticks from Algeria, focusing on seasonal variations in bacterial diversity, community composition, and pathogen interactions. Using next-generation sequencing (NGS), the microbiome of 21 female ticks collected during spring, summer, and autumn was analyzed. Beta diversity analysis revealed significant seasonal shifts in microbial community structure, while alpha diversity metrics showed no significant differences in richness and evenness. Co-occurrence network analysis demonstrated seasonal shifts in microbial interactions, particularly between symbionts and pathogens, highlighting Francisella as a key taxon in tick survival and pathogen dynamics. Rickettsia presence varied by season, influencing microbial network stability. These findings underscore the ecological determinants shaping the microbiome and its potential role in pathogen transmission. Understanding seasonal microbiome shifts provides valuable insights for managing tick-borne diseases and could inform the development of targeted, season-specific vector control strategies.},
}

Animals
*Seasons
Algeria
*Microbiota
*Ixodidae/microbiology
Female
*Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 16S/genetics
Rickettsia/isolation & purification/genetics
Biodiversity

@article {pmid41026216,
year = {2025},
author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V},
title = {Aerobiology and Environmental Zonation in Gypsum Caves: A Comparative Study of Culturing and NGS Approaches.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {95},
pmid = {41026216},
issn = {1432-184X},
support = {PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Caves/microbiology ; *Calcium Sulfate/analysis ; *Bacteria/genetics/classification/isolation & purification/growth & development ; High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Microbiota ; Spain ; *Fungi/isolation & purification/genetics/classification ; Geologic Sediments/microbiology ; Phylogeny ; Biodiversity ; },
abstract = {Classical aerobiological studies commonly use high-volume air samplers to quantify and identify cultivable airborne bacteria and fungi. However, this approach introduces a significant bias, as it overlooks the non-cultivable fraction, which likely constitutes a major component of the airborne microbiome. The advent of next-generation sequencing (NGS) has addressed this limitation, enabling a more comprehensive characterization of the cave aerobiome. This study analyzes both cultivable and non-cultivable airborne bacteria from Covadura and C3 caves, located in the Gypsum Karst of Sorbas (SE Spain). A total of 24 bacterial genera were identified using culture-based methods, whereas NGS revealed 749 genera. Culture-based methods using the surface air system (SAS) predominantly recovered Gram-positive spore-forming bacteria from the phyla Bacillota and Actinomycetota, which were largely absent or present in low relative abundances in the NGS datasets. In contrast, NGS revealed a broader diversity, including numerous Gram-negative and rare airborne bacteria not detected by culture. The NGS results from airborne samples showed greater similarity to the microbial communities found in cave biofilms and sediments, suggesting that a portion of airborne bacteria originates from within the cave and is influenced by microclimatic conditions such as ventilation and air stagnation. Although the short-read sequencing approach used in this study has limitations, such as reduced taxonomic resolution compared to the culture-based approach, it remains the most effective tool for capturing the diversity and ecological patterns of airborne microorganisms. The integration of gas tracers and other environmental data allowed the identification of zones within the cave with different ventilation patterns and degrees of isolation, which corresponded to different spatial distributions of airborne bacteria. Our findings underscore that reliable aerobiological studies in caves require the combination of non-culture dependent-based sequencing approaches and environmental monitoring to fully understand the origin, diversity, and ecological dynamics of airborne microbial communities.},
}

*Caves/microbiology
*Calcium Sulfate/analysis
*Bacteria/genetics/classification/isolation & purification/growth & development
High-Throughput Nucleotide Sequencing/methods
*Air Microbiology
*Microbiota
Spain
*Fungi/isolation & purification/genetics/classification
Geologic Sediments/microbiology
Phylogeny
Biodiversity

@article {pmid41026209,
year = {2025},
author = {Gutiérrez-Pavón, AJ and Pereyra, MM and Chacón, FI and Monroy-Morales, E and Rebollar, EA and Dib, JR and Serrano, M and Romero-Contreras, YJ},
title = {Bacteria from the Amphibian Skin Inhibit the Growth of Phytopathogenic Fungi and Control Postharvest Rots.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {101},
pmid = {41026209},
issn = {1432-184X},
support = {PICT-2021-GRF-TII-0020//Agencia Nacional de Promoción Científica y Tecnológica/ ; N203023//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica/ ; },
mesh = {Animals ; *Plant Diseases/microbiology/prevention & control ; Botrytis/growth & development ; *Skin/microbiology ; Penicillium/growth & development ; *Antibiosis ; *Bacteria/isolation & purification/metabolism ; Fruit/microbiology ; *Biological Control Agents ; Solanum lycopersicum/microbiology ; Alternaria/growth & development ; *Anura/microbiology ; Citrus/microbiology ; *Fungi/growth & development ; Volatile Organic Compounds/pharmacology ; Aspergillus niger/growth & development ; Pest Control, Biological ; },
abstract = {Postharvest diseases caused by phytopathogenic fungi represent one of the main challenges in the agricultural industry, leading to significant losses in fruit production. Although chemical treatments have been widely used for the control of these pathogens, the emergence of resistant strains and concerns regarding food safety and environmental impact have driven the search for novel effective and eco-friendly alternatives, such as the use of biological control agents (BCAs). Previously, we demonstrated that bacteria isolated from frog skin inhibit the growth of the phytopathogenic fungus Botrytis cinerea. Based on these findings, in this study we aimed to investigate the biocontrol potential of three bacterial isolates obtained from the skin of the frog Craugastor fitzingeri. Dual culture assays showed that these bacteria strongly inhibited the mycelial growth of several postharvest fungal phytopathogens, including Penicillium digitatum, P. italicum, Alternaria alternata, Aspergillus niger, and Alternaria solani. This antagonistic activity was further confirmed through assays using bacterial filtrates (BFs) and volatile organic compounds (VOCs), effectively delaying or suppressing fungal development under in vitro conditions. Additionally, in vivo experiments on citrus fruits, tomato, and blueberry demonstrated that treatments with bacterial cell suspensions or BFs significantly reduced disease incidence caused by P. digitatum, A. alternata, and B. cinerea. However, no inhibitory effects were observed against Geotrichum citri-aurantii, Fusarium sp., Fusarium oxysporum, and Phytophthora capsici, suggesting a degree of specificity. Our findings highlight the potential of frog skin-associated bacteria as a novel source of BCAs for the sustainable management of postharvest diseases in fruits.},
}

Animals
*Plant Diseases/microbiology/prevention & control
Botrytis/growth & development
*Skin/microbiology
Penicillium/growth & development
*Antibiosis
*Bacteria/isolation & purification/metabolism
Fruit/microbiology
*Biological Control Agents
Solanum lycopersicum/microbiology
Alternaria/growth & development
*Anura/microbiology
Citrus/microbiology
*Fungi/growth & development
Volatile Organic Compounds/pharmacology
Aspergillus niger/growth & development
Pest Control, Biological

@article {pmid41026187,
year = {2025},
author = {Cheng, P and Liu, F and Li, L and Wu, S and Xiao, W and Zong, Q and Liu, T and Peng, Y},
title = {Impact of Tebuconazole On the Development and Symbiotic Microbial Communities of Pardosa Pseudoannulata.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {97},
pmid = {41026187},
issn = {1432-184X},
mesh = {*Triazoles/toxicity ; *Symbiosis/drug effects ; Animals ; *Microbiota/drug effects ; Bacteria/drug effects/classification/genetics/isolation & purification ; *Fungi/drug effects/classification/genetics ; *Fungicides, Industrial/toxicity ; *Spiders/microbiology/drug effects/growth & development/physiology ; RNA, Ribosomal, 16S/genetics ; Animals, Poisonous ; },
abstract = {Tebuconazole is a widely used triazole fungicide to control fungal diseases. While there have been reported side effects on non-target arthropods, its ecological risks to natural enemies remain poorly understood. In this study, we evaluated the developmental toxicity and symbiotic microorganism responses of the wolf spider Pardosa pseudoannulata, an important predator in rice ecosystems, following exposure to tebuconazole. The results indicated that tebuconazole did not significantly increase the mortality rate of spiderlings; however, it did lead to a significant decrease in spiderling body weight, as well as the length and width of the carapace. High-throughput sequencing of the 16S rRNA gene V3-V4 regions and the ITS region revealed that tebuconazole significantly reduced bacterial diversity indices in the short term, with a gradual recovery over time. In contrast, the impact on the fungal community was continuous and irreversible, with a significant decrease in the Shannon index observed after 15 days. At the genus level, the relative abundances of Cupriavidus and Staphylococcus in the bacterial community decreased significantly after tebuconazole exposure, while Stenotrophomonas increased. In the fungal community, Fungi_gen_Incertae_sedis decreased significantly, and Simplicillium increased. Our findings highlight the ecological risks of fungicide exposure to beneficial predators and underscore the importance of considering symbiotic microbiota in pesticide risk assessments.},
}

*Triazoles/toxicity
*Symbiosis/drug effects
Animals
*Microbiota/drug effects
Bacteria/drug effects/classification/genetics/isolation & purification
*Fungi/drug effects/classification/genetics
*Fungicides, Industrial/toxicity
*Spiders/microbiology/drug effects/growth & development/physiology
RNA, Ribosomal, 16S/genetics
Animals, Poisonous

@article {pmid41026185,
year = {2025},
author = {Borja-Martínez, G and de León-Lorenzana, A and Yanez-Montalvo, A and Hernández-Canchola, G and Falcón, LI and Vázquez-Domínguez, E},
title = {Evolutionary and Ecological Drivers of Gut Microbiota in Wild Rodent Species from the Yucatán Peninsula.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {100},
pmid = {41026185},
issn = {1432-184X},
support = {887756//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT)/ ; IV200421//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica-DGAPA/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mexico ; *Rodentia/microbiology/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Biological Evolution ; Biodiversity ; Symbiosis ; },
abstract = {The host-microbiome association is considered a coevolutionary process, in which the microbiome provides important functions for host development, physiology and health. However, the ecological and evolutionary forces shaping the diversity and structure of the bacterial communities that form the microbiome are still being elucidated. We assessed the composition of gut microbiota in six rodent species from three geographic regions across the Yucatán peninsula, Mexico. We evaluated the contribution of host species identity, phylogenetic relationships, and geography to the rodents' gut microbiota, using 16S rRNA V4 sequences. We performed a comprehensive set of analytical approaches, including Hill numbers, machine learning, and phylogenetic comparative frameworks. Our results show that phylosymbiosis is one of the main mechanisms driving microbiota dissimilitude across species and specific microbiota diversity traits. Additionally, the microbial pool in each region was geographically differentiated, shaped by the rodent community ensemble, while ecological filtering rendered a microbial pool characteristic of each species. The environment also played a significant role for some species like Heteromys gaumeri, while dietary habits showed a stronger signal for Oryzomys couesi. Rodents with more specialized habits like Ototylomys phyllotis (semi-arboreal, folivorous) had higher bacterial diversity. The abundance of eight bacterial families determined key differences of the gut microbiota which, in addition to phylogeny and geography, are associated with distinct diet and metabolic functions among rodents. Distinct metabolic functions were related, among others, to toxins metabolism and digestion of complex food components. Overall findings show that both evolutionary and ecological drivers influence these rodents gut microbial structure and composition.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mexico
*Rodentia/microbiology/classification
Phylogeny
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Biological Evolution
Biodiversity
Symbiosis

@article {pmid41026172,
year = {2025},
author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y},
title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {98},
pmid = {41026172},
issn = {1432-184X},
support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; },
abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.},
}

Animals
*Gastrointestinal Microbiome
*Bacteriophages/genetics/classification/physiology/isolation & purification
*Bacteria/classification/genetics/isolation & purification/virology
*Ecosystem
RNA, Ribosomal, 16S/genetics
*Antelopes/microbiology/virology
Metagenome
Feces/microbiology

@article {pmid41026164,
year = {2025},
author = {Yeo, IC and Shim, KY and Min, JO and Kim, JH and Ha, SY and Jeong, CB},
title = {Vertical Structure and Functional Diversity of Microbial Communities in the Ross Sea, Antarctica.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {99},
pmid = {41026164},
issn = {1432-184X},
support = {KIMST RS-2022-KS221661//Korea Institute of Marine Science and Technology promotion/ ; NRF-2022R1C1C1010575//National Research Foundation of Korea/ ; },
mesh = {Antarctic Regions ; *Seawater/microbiology/chemistry ; *Microbiota ; *Biodiversity ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {The Ross Sea, Antarctica, encompasses distinct water masses, each characterized by unique physicochemical conditions influencing microbial community composition and functional diversity. This study examined microbial communities across five stations covering various water masses, including Antarctic Surface Water (AASW), Circumpolar Deep Water (CDW), and Shelf Water (SW). Despite limited horizontal variability, significant vertical structuring was observed, potentially driven by vertical microbial dispersal from surface waters. Surface communities exhibited lower alpha diversity due to abundant labile organic matter favoring fast-growing heterotrophic taxa, whereas deeper communities displayed increased microbial richness, reflecting adaptation to more refractory organic matter. Functional diversity revealed distinct depth-related patterns, with metabolic pathways associated with organic matter predominantly enriched in surface layers. Concurrently, rare taxa became more abundant with depth, emphasizing their potential role as keystone organisms in deep-ocean nutrient cycling. These findings highlight the critical role of vertical microbial connectivity and organic matter composition in shaping microbial community structure and functional specialization, contributing significantly to our understanding of microbial-mediated biogeochemical processes in polar marine ecosystems.},
}

Antarctic Regions
*Seawater/microbiology/chemistry
*Microbiota
*Biodiversity
*Bacteria/classification/genetics/isolation & purification/metabolism
Ecosystem
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid41025798,
year = {2025},
author = {Damashek, J and Sheik, CS and Petro, C and Reeder, CF and Chowdhury, S and Kramer, BJ and DeVilbiss, SE and Pierella Karlusich, JJ and Marks, JC and Valdespino-Castillo, PM and Furey, PC and Berberich, ME and Marcarelli, AM and Scott, JT and Fulweiler, RW},
title = {DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0089725},
doi = {10.1128/mra.00897-25},
pmid = {41025798},
issn = {2576-098X},
abstract = {Microbial nitrogen fixation (diazotrophy) is a critical ecological process. We curated DiazoTIME (Diazotroph Taxonomic Identity and MEtabolism), a comprehensive database of diazotroph genomes including taxonomic annotation and metabolic prediction. DiazoTIME is unique among databases for classifying diazotrophs because it resolves both taxonomy and metabolic functionality.},
}

@article {pmid41025789,
year = {2025},
author = {Hodgskiss, LH and Kerou, M and Luo, Z-H and Bayer, B and Maier, A and Weckwerth, W and Nägele, T and Schleper, C},
title = {Metabolic response of a chemolithoautotrophic archaeon to carbon limitation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0073225},
doi = {10.1128/msystems.00732-25},
pmid = {41025789},
issn = {2379-5077},
abstract = {The ubiquitously distributed ammonia-oxidizing archaea generate energy from ammonia and build cell mass from inorganic carbon sources, thereby contributing to both the global nitrogen and carbon cycles. However, little is known about the regulation of their predicted core carbon metabolism. A thermodynamic model for Nitrososphaera viennensis was developed to estimate the consumption of inorganic carbon in relation to ammonia consumed for energy and was tested experimentally by growing cells in carbon-limited and excess conditions. A combined proteomic and metabolomic approach to the experimental conditions revealed distinct metabolic adaptation depending on the amount of carbon supplied, either in a catalase or pyruvate background as a reactive oxygen species scavenger. Integration of protein and metabolite dynamics revealed a cellular strategy under carbon limitation to maintain a pool of amino acids and an upregulation of proteins necessary for translation initiation to stay primed for protein synthesis. The combination of modeling and functional genomics fills gaps in the understanding of the central metabolism and its regulation in a chemolithoautotrophic, ammonia-oxidizing archaeon, even in the absence of available genetic tools.IMPORTANCELittle is known about the regulation of carbon metabolism within ammonia-oxidizing archaea (AOA), a widespread clade that plays a critical role in the global nitrogen cycle while also fixing inorganic carbon. To address this missing knowledge, the soil AOA Nitrososphaera viennensis was subjected to various levels of inorganic carbon and analyzed via a systems biology approach to better understand how its core metabolism is regulated. The results demonstrate a strong dependence on the carbon fixation cycle and highlight key connection points between the core metabolic pathways. The analysis additionally revealed tight control on translational processes and elucidated unique cellular responses when the organism was exposed to either exogenous catalase or pyruvate to relieve oxidative stress from reactive oxygen species. The presented data highlight metabolic responses of N. viennensis and provide a better understanding of how the organism, and likely other AOA, respond to various environmental conditions.},
}

@article {pmid41024334,
year = {2025},
author = {Zhan, J and Zhang, L and Lai, S and Guo, J and Lin, T and Liu, G and Rensing, C and Liu, X and Zhou, S},
title = {Fe(III)-dependent Nrf activity determines nitrate reduction partitioning in nitrate-reducing communities.},
journal = {mBio},
volume = {},
number = {},
pages = {e0222025},
doi = {10.1128/mbio.02220-25},
pmid = {41024334},
issn = {2150-7511},
abstract = {Identifying the factors that affect the nitrate reduction partitioning between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification is crucial for mitigating nitrogen loss in ecosystems. Conventionally, the nutrient status of the environment (e.g., the carbon-to-nitrogen ratio) is recognized as the key determinant of nitrogen conversion pathways. Here, we report that the availability of Fe(III) regulates the nitrate reduction partitioning in Geobacter metallireducens and Alcaligenes faecalis co-culture. We controlled the availability of Fe(III) in the coculture medium and tracked nitrogen conversion dynamics and community composition. The results demonstrated that the coculture performed DNRA, contributed mainly by G. metallireducens under Fe(III)-replete conditions, while performing interspecies synergistic denitrification between both species under Fe(III)-depleted conditions. Nitrate/nitrite reductase activity calculations and mutation analyses indicated that nitrate reduction partitioning in the coculture was governed by the nitrite reductase (Nrf) activity of G. metallireducens, which was Fe(III)-dependent. Further validation in urban river water confirmed that Fe(III) supplementation significantly enhances DNRA activity. Our findings establish Fe(III) as a previously unrecognized regulator of microbial nitrogen retention, showing insights into strategies for managing nitrogen fluxes in agricultural and aquatic systems.IMPORTANCENitrogen is essential for life, but its loss from ecosystems through microbial processes like denitrification harms agricultural productivity and contributes to greenhouse gas emissions. Retaining nitrogen as ammonium via microbial dissimilatory nitrate reduction to ammonium (DNRA) could mitigate these issues, but the factors governing microbial prioritization of DNRA over denitrification remain unclear. Our study reveals that Fe(III) plays a critical, previously unrecognized role in steering this process. We show that Fe(III) availability determines whether the nitrate-reducing community conserves nitrogen as ammonium or releases it as gas, with implications for managing nitrogen in soils and waterways. By demonstrating Fe(III)'s ability to enhance nitrogen retention in environmental systems like urban rivers, our findings offer a new lever for sustainable agriculture and pollution control. This work bridges microbial ecology and environmental management, highlighting how trace metals shape nutrient cycles in ways that can be harnessed to protect ecosystem health.},
}

@article {pmid41023320,
year = {2025},
author = {Musiałowski, M and Mierzwa-Hersztek, M and Gondek, K and Dębiec-Andrzejewska, K},
title = {A novel two-step metabarcoding approach improves soil microbiome biodiversity assessment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33697},
pmid = {41023320},
issn = {2045-2322},
support = {LIDER/13/0051/L-11/NCBR/2020//Narodowe Centrum Badań i Rozwoju,Poland/ ; LIDER/13/0051/L-11/NCBR/2020//Narodowe Centrum Badań i Rozwoju,Poland/ ; },
mesh = {*Soil Microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Bacteria/genetics/classification ; Phylogeny ; },
abstract = {The foundation of microbial ecology research is Next-Generation Sequencing (NGS), which allows for reconstruction of the soil microbiome taxonomical structure and the calculation of biodiversity metrics. However, obtaining reliable data on soil biodiversity poses several challenges, with accurate primer selection being one of the most critical. While 16S rDNA primers are widely used for their ability to broadly target bacterial communities, they can introduce biases. These primers may preferentially amplify certain bacterial groups, leading to a skewed representation of the microbial diversity in soil samples. To overcome the bias, we developed a novel, Two-Step Metabarcoding (TSM) approach to obtain more accurate and detailed data on soil microbiome structure and biodiversity. The first step involved sequencing of amplicons generated using universal 16S rDNA primers, provided an initial overview of the microbial community, and allowed the identification of key taxonomical groups. In the second step, we employed sequencing of amplicons generated with taxa-specific primers designed for the most abundant phyla in the community. We used the obtained data for a more reliable reconstruction of microbiome taxonomic structure and biodiversity. This two-step approach ensures a thorough exploration of the soil microbiome and promises to enhance our understanding of soil microbial dynamics and ecology.},
}

*Soil Microbiology
*Biodiversity
*DNA Barcoding, Taxonomic/methods
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
*Bacteria/genetics/classification
Phylogeny

@article {pmid41018004,
year = {2025},
author = {Neilson, R and King, D and Giles, ME},
title = {The microbiome associated with Trichodorus primitivus is enriched with Janthinobacterium compared to soil.},
journal = {Journal of nematology},
volume = {57},
number = {1},
pages = {20250043},
pmid = {41018004},
issn = {0022-300X},
abstract = {Although soil biota mediates many key processes that deliver multiple environmental benefits, interactions between soil biota are not well characterized. In an ecological context, studies to date on the associations between nematodes and bacteria have mostly focused on either intracellular bacteria or bacteria that have a potential role in crop pathogenesis by endoparasitic nematode species, that is, those species that have a component of their life cycle within the plant host. Moreover, evolutionary studies have utilized the model nematode species, Caenorhabditis elegans, for studies on survival, behavior, and fecundity. In this study, we characterize the bacterial communities associated with an ectoparasitic nematode species, Trichodorus primitivus, whose complete life cycle is external to the plant host. Compared to the soil from which the nematodes were extracted, the diversity of bacterial communities associated with T. primitivus was reduced. By contrast, the nematode-associated bacterial community was significantly enriched with Janthinobacterium, a known antagonist of soilborne pathogens. This study advances knowledge on the interactions between bacteria and ectoparasitic nematodes, which could help inform the future development of novel strategies for nematode control.},
}

@article {pmid41017558,
year = {2025},
author = {Han, P and Liu, C and Abdal-Hay, A and Reed, S and Liaw, A and Wang, J and Ning, Y and Ivanovski, S},
title = {Proteome and microbiome profiles of polymicrobial salivary biofilms on 3D MEW fibrous scaffolds: biomimetic ECM-inspired structures.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5tb01410g},
pmid = {41017558},
issn = {2050-7518},
abstract = {Replicating the structural complexity of polymicrobial oral biofilms in vitro remains a significant challenge in biomaterials research. Nevertheless, developing clinically relevant biofilm models is crucial for advancing our understanding of biofilm-host interactions and elucidating how biomaterials influence microbial composition, behaviour, and overall biofilm dynamics. In this work, 3D biomimetic fibrous scaffolds made from medical-grade polycaprolactone (mPCL) were fabricated using the melt electrowriting (MEW) technique. The effects on biofilm viability, activity, microbiome, and proteome profiles were assessed on 3D fibrous scaffolds and conventional 2D tissue culture plates (TCP). Human saliva was cultured on MEW mPCL (3D BF) and TCP (2D BF) for 4 days, followed by microbiome profiling via 16S rRNA sequencing and proteomic analysis using LC-MS/MS, SWATH with GO and KEGG pathway enrichment. The results demonstrated that 3D MEW mPCL scaffolds enhanced biofilm biomass, thickness, and viability. Microbiome analysis revealed that 3D BF was enriched with both commensals and pathogens, including Veillonella, Peptostreptococcus, Porphyromonas gingivalis, and Treponema denticola, alongside probiotic species like Lactobacillus acidophilus. Pooled proteomic data from three technical repeats, along with GO and KEGG analyses, revealed a functionally dynamic biofilm ecosystem characterised by elevated expression of proteins involved in glycolysis, the TCA cycle, and nucleotide metabolism, highlighting pathways essential for biofilm survival, stress adaptation, and host interaction. These 'proof-of-concept' findings highlight the potential of 3D MEW fibrous mPCL scaffolds as a biomimetic 3D platform capable of accurately recapitulating the dynamic spatial and metabolic complexity of oral biofilms, thereby facilitating innovative investigations into microbial ecology, host-pathogen interactions, and the accelerated development of targeted antimicrobial therapies.},
}

@article {pmid41016925,
year = {2025},
author = {Li, C and Wu, M and Tang, W and Yu, B and Saiz-Lopez, A and Poulain, A and Bank, MS and Zhou, Q and Bodelier, PLE and Yan, Z and Frey, B and Hu, H and Chen, J and Jiang, Y and Zhong, H},
title = {Aligning global mercury mitigation with climate action.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7826},
pmid = {41016925},
issn = {2041-1723},
support = {42107223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41673075//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Mercury/analysis/toxicity ; *Climate Change ; Greenhouse Gases/metabolism/analysis ; Humans ; *Environmental Pollution/prevention & control ; Microbiota/drug effects ; *Environmental Pollutants/analysis ; },
abstract = {Environmental mercury (Hg) pollution affects microbial community structure and functions. Yet, whether and how this influence cascades through microbe-mediated cycling of major greenhouse gases (GHGs) remains poorly understood. This Perspective synthesizes emerging evidence on the Hg-microbe-GHG nexus, exploring the possibility that global Hg emission reductions, while critical for human and planetary health, may cause alterations to microbe-mediated GHG fluxes. Significant knowledge gaps persist, however, regarding the Hg-microbe-GHG nexus, particularly concerning the magnitude and direction of the nexus's net impact on climate and global environmental change. To bridge these gaps, we propose a three-step roadmap aimed at disentangling the potential impacts of global Hg emission mitigation strategies on microbial communities, associated GHG emissions, and subsequent climate change. Collectively, these joint efforts from scientists, industry, community stakeholders, and policymakers are critical to harmonizing global Hg mitigation efforts with climate action and to ensuring a sustainable future for Earth systems and their inhabitants.},
}

*Mercury/analysis/toxicity
*Climate Change
Greenhouse Gases/metabolism/analysis
Humans
*Environmental Pollution/prevention & control
Microbiota/drug effects
*Environmental Pollutants/analysis

@article {pmid41016813,
year = {2025},
author = {Lee, HH},
title = {Iodine Biogeochemical Cycle and Microbial Bioremediation of Radioactive Iodine-129.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2508018},
doi = {10.4014/jmb.2508.08018},
pmid = {41016813},
issn = {1738-8872},
mesh = {*Biodegradation, Environmental ; *Iodine Radioisotopes/metabolism ; *Bacteria/metabolism ; *Iodine/metabolism ; Oxidation-Reduction ; Humans ; Hydrocarbons, Iodinated ; },
abstract = {Iodine is an essential biophilic element that plays pivotal roles in both environmental systems and human physiology, particularly as a key constituent of thyroid hormones and a regulator of atmospheric ozone. In contrast, its radioactive isotope, iodine-129 (I-129), predominantly generated through anthropogenic nuclear activities, represents a persistent environmental and public health concern. With an exceptionally long half-life of approximately 15.7 million years and high environmental mobility, especially in groundwater, combined with a strong tendency to bioaccumulate in the human thyroid, I-129 poses a disproportionate and long-term radiological hazard in contaminated sites. The biogeochemical cycling of iodine involves intricate interconversions among multiple oxidation states and phases across the lithosphere, hydrosphere, atmosphere, and biosphere. Microorganisms are central to these processes, mediating oxidation, reduction, methylation, accumulation, and sorption. While microbial methylation can increase I-129 mobility via the production of volatile methyl iodide, other microbial pathways, notably biosorption and binding to organic matter, provide promising mechanisms for immobilization and natural attenuation. Microbial bioremediation offers a sustainable and cost-effective alternative or complement to conventional physicochemical methods for managing radioactive contaminants. Strategies such as bioreduction, biosorption, bioaccumulation, and biomineralization exploit the metabolic versatility of microorganisms to alter radionuclide speciation, solubility, and mobility. However, practical application to I-129 remains challenging due to its extreme persistence, environmental variability, and uncertainties in predicting its long-term geochemical fate. Effective management of I-129 contamination will require an integrated, multidisciplinary approach that combines advanced microbial ecology insights, optimized biotechnological processes, and long-term monitoring frameworks.},
}

*Biodegradation, Environmental
*Iodine Radioisotopes/metabolism
*Bacteria/metabolism
*Iodine/metabolism
Oxidation-Reduction
Humans
Hydrocarbons, Iodinated

@article {pmid41016251,
year = {2025},
author = {Schubert, K and Shosanya, T and García-Bayona, L},
title = {The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.},
journal = {Current opinion in microbiology},
volume = {88},
number = {},
pages = {102675},
doi = {10.1016/j.mib.2025.102675},
pmid = {41016251},
issn = {1879-0364},
abstract = {The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.},
}

@article {pmid41013679,
year = {2025},
author = {Ramljak, A and Jurburg, S and Chatzinotas, A and Lučić, M and Žižek, M and Babić, I and Udiković-Kolić, N and Petrić, I},
title = {Identifying the drivers of microbial community changes and interactions in polluted coastal sediments.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {117},
pmid = {41013679},
issn = {2524-6372},
support = {IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; },
abstract = {Despite over three decades of research into the composition and distribution of microbial communities, gaps remain in our mechanistic understanding of microbial community assembly processes, especially in benthic communities in coastal zones continuously exposed to anthropogenic pressures. We analyzed the microbial communities (prokaryotes, fungi, and protists) in sediment samples from ports and bays located along the Adriatic coast chronically exposed to chemical and nutrient pollution, and explored how selective pressures (pollutants, nutrients, and environmental conditions) and dispersal shape these communities. We found that biogeographic factors (i.e. location) play a key role in structuring microbial communities, with benthic fungi also being shaped by the presence of pollutants and nutrients. Strong correlations between nutrient loads and pollutants were observed, along with weakened interactions between microbial communities, particularly between prokaryotes and protists, in the presence of specific pollutants (bismuth, cadmium, copper, zinc, mercury). These results are an important step in disentangling the complex interactions between pollutants and microbial community dynamics in aquatic ecosystems. Further research is needed to assess how these shifts in microbial community dynamics may affect ecosystem services in vulnerable coastal zones.},
}

@article {pmid41012703,
year = {2025},
author = {Johnson, ML and Boezen, D and Grum-Grzhimaylo, AA and van der Vlugt, RAA and de Visser, JAGM and Zwart, MP},
title = {Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses.},
journal = {Viruses},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/v17091275},
pmid = {41012703},
issn = {1999-4915},
support = {016.VIDI.171.061/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Genome, Viral ; *Plant Viruses/genetics/physiology ; Host Specificity ; Metagenomics ; Plant Diseases/virology ; Plants/virology ; },
abstract = {BACKGROUND: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form.

METHODS: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose-response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data.

RESULTS: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses.

CONCLUSIONS: Our analyses also suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus-host systems demands pluralistic explanatory frameworks.},
}

*Genome, Viral
*Plant Viruses/genetics/physiology
Host Specificity
Metagenomics
Plant Diseases/virology
Plants/virology

@article {pmid41011533,
year = {2025},
author = {Dai, X and He, Y and Su, Y and Mo, H and Li, W and Li, W and Zi, S and Liu, L and Di, Y},
title = {Pathogen Identification, Antagonistic Microbe Screening, and Biocontrol Strategies for Aconitum carmichaelii Root Rot.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092202},
pmid = {41011533},
issn = {2076-2607},
support = {202403AP140013//The Sino-Vietnamese International Joint Laboratory for Characteristic & Cash Crops Green De-velopment of Yunnan Province/ ; Yunnan Academic Degrees Committee Document [2024] No. 19//The Construction Project for Postgraduate Tutor Team of Yunnan Province in 2024/ ; 2024J0486//Scientific Research Fund of the Educational Department of Yunnan Province/ ; },
abstract = {The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch's postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management.},
}

@article {pmid41011501,
year = {2025},
author = {Dai, L and Hao, X and Niu, T and Liu, Z and Wang, Y and Geng, X and Cai, Q and Wang, J and Ren, Y and Liu, F and Liu, H and Li, Z},
title = {Analysis of Microbial Community Structure and Diversity in Different Soil Use Types in the Luo River Basin.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092173},
pmid = {41011501},
issn = {2076-2607},
support = {30803302//Henan Provincial Finance Forest and Grass Science and Technology (Intermediate Trial) Promo-tion Demonstration Project "Introduction and Cultivation of desia polycarpa Maxim. 'Yulu/ ; 2025-2627//Henan Province Science and Technology Research Project "Innovative Utilization of Germplasm Resources and Breeding of Excellent New Varieties of desia polycarpa Maxim."/ ; },
abstract = {The Luohe River boasts a profound historical heritage. Due to long-term impacts of human activities along its banks, significant variations in soil environmental conditions may exist across different land use types within the region. This study focused on four land use types (farmland, bamboo forest, grassland, and abandoned land) in Luoning County of the Luohe River Basin and employed high-throughput sequencing technology to analyze the characteristics of soil microbial communities and differences in soil nutrients. The results showed the following: There were significant differences in soil nutrients and microbial diversity among different land use types. Specifically, the organic matter content in farmland was significantly higher than that in bamboo forests (p < 0.05), and the available phosphorus content in farmland was significantly higher than that in abandoned land (p < 0.05); the abandoned land had a significant advantage in alkali-hydrolyzable nitrogen and available potassium contents (p < 0.05) but the lowest soil water content (p < 0.05). Microbial diversity indices indicated that Pielou's evenness index (Pieloue) in farmland was significantly higher than that in grassland. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Actinobacteria. At the genus level, available potassium was the key factor affecting the top 20 dominant bacterial genera. Redundancy Analysis (RDA) showed that pH was the core environmental variable driving the variation of bacterial community structure. Metabolic pathway analysis revealed that biosynthetic metabolism was the main pathway, and grassland exhibited outstanding performance in the secondary metabolite synthesis pathway. The results of this study fill the gap in soil microbial ecology research in this region and provide a theoretical basis for the sustainable utilization of land resources and agricultural ecological management in the Luohe River Basin.},
}

@article {pmid41011387,
year = {2025},
author = {Wang, Y and Deng, C and Sui, M and Wei, P and Duan, B and Li, Z and Zou, F},
title = {Acute Toxoplasma gondii Infection Drives Gut Microbiome Dysbiosis and Functional Disruption in Mice as Revealed by Metagenomic Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092056},
pmid = {41011387},
issn = {2076-2607},
support = {202449CE340019//the Yunnan Key Laboratory of Veterinary Etiological Biology/ ; U2202201//the NSFC-Yunnan Joint Fund/ ; 202401AT070440//the Yunnan Fundamental Research Projects/ ; 2024Y339//the Scientific Research Fund of Education Department of Yunnan Province/ ; No.XXX//the Yunnan Provincial University Key Industry Service Science and Technology Program/ ; },
abstract = {Toxoplasma gondii is a widely distributed intracellular parasite that disrupts host immune and metabolic homeostasis. Although accumulating evidence highlights the role of gut microbiota in parasitic infections, the effects of acute T. gondii infection on host gut microbial ecology remain poorly understood. In this study, metagenomic sequencing technology was used to systematically analyze the composition and functional alterations of the ileal microbiota in BALB/c mice on day 10 post-infection. Compared to uninfected controls, T. gondii infected mice exhibited a significant reduction in microbial diversity and a pronounced shift in community structure. Notably, there was an expansion of Proteobacteria, particularly the Enterobacteriaceae family, alongside a marked decline in beneficial taxa such as Actinobacteria and Bacillota. Functional annotation using the KEGG and CAZy databases revealed enrichment of metabolic pathways related to glycolysis/gluconeogenesis, O-antigen nucleotide sugar biosynthesis, bacterial secretion systems, and biofilm formation-Escherichia coli in the infected microbiota. These findings provide novel insights into the dysbiosis of gut microbiota and host-microbe interactions during acute T. gondii infection.},
}

@article {pmid41010480,
year = {2025},
author = {Duysburgh, C and Fiore, W and Marzorati, M},
title = {Survival and Impact on Microbial Diversity of Lacticaseibacillus paracasei DG in a Simulation of Human Intestinal Microbial Ecosystem.},
journal = {Nutrients},
volume = {17},
number = {18},
pages = {},
doi = {10.3390/nu17182952},
pmid = {41010480},
issn = {2072-6643},
support = {N/A//Alfasigma S.p.A./ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; *Lacticaseibacillus paracasei/physiology/growth & development/metabolism ; Microbial Viability ; Hydrogen-Ion Concentration ; Fatty Acids, Volatile/metabolism ; Colon/microbiology ; Lactic Acid/metabolism ; Feces/microbiology ; },
abstract = {Background/Objectives: The probiotic Lacticaseibacillus paracasei DG (LpDG) has shown promising results for various gastrointestinal diseases. This study evaluated the survival, metabolic activity, and impact on colonic microbiota of LpDG in an in vitro gastrointestinal tract simulation. Methods: Encapsulated LpDG was tested under simulated fed, fasted, and shortened fasted conditions compared with a blank control in a modified Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) reactor. Capsule integrity, and cell culturability and viability were assessed at the end of each digestion phase. Metabolic activity (pH, total gas production, and concentrations of short-chain fatty acids, lactate, and ammonium) was assessed after a 24 h colonic incubation with a faecal inoculum. The impact of LpDG on the colonic microbial community was analysed by quantitative polymerase chain reaction and shallow shotgun sequencing. Results: The capsule was completely degraded at the end of the jejunum under all conditions. A low pH had a minimal impact on LpDG culturability and viability. Compared with blank control, LpDG remained metabolically active in the microbial community following a 24 h colonic incubation (LpDG [0-24 h] vs. blank control [0-24 h]: ΔpH, decreased [0.29-0.38 vs. 0.12-0.34]; Δlactic acid, decreased [1.52-1.69 mM vs. 0.13-0.21 mM]; and Δbutyrate, increased [7.49-10.52 mM vs. 5.19-7.76 mM]). Under fed conditions, treatment with LpDG compared with blank control significantly decreased levels of Escherichia coli and Blautia wexlerae and increased Clostridiaceae, Eubacteriaceae, and Lachnospiraceae. Conclusions: LpDG remains viable and metabolically active in the gastrointestinal tract, positively affecting intestinal microbiota and metabolite production.},
}

Humans
*Gastrointestinal Microbiome
*Probiotics
*Lacticaseibacillus paracasei/physiology/growth & development/metabolism
Microbial Viability
Hydrogen-Ion Concentration
Fatty Acids, Volatile/metabolism
Colon/microbiology
Lactic Acid/metabolism
Feces/microbiology

@article {pmid41009926,
year = {2025},
author = {Dealis Gomes, ML and Afonso, L and Basso, KR and Alves, LC and Macías, EJN and Yamada-Ogatta, SF and Guidi, AC and de Mello, JCP and Andrade, FG and Cabeça, LF and Cely, MVT and Andrade, G},
title = {Liposomal Fluopsin C: Physicochemical Properties, Cytotoxicity, and Antibacterial Activity In Vitro and over In Vivo MDR Klebsiella pneumoniae Bacteremia Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/antibiotics14090948},
pmid = {41009926},
issn = {2079-6382},
support = {439754/2018-6 (AMR MCTIC)//Brazilian National Council for Scientific and Technological Development (CNPq)/ ; 406016/2022-4, PPSUS-Aracauria Foundation-PR//Brazilian National Council for Scientific and Technological Development (CNPq)/ ; },
abstract = {Introduction: Antimicrobial resistance has become a global concern, and few new antimicrobials are currently being developed. Fluopsin C has proven broad-spectrum activity, being a promising candidate for new antimicrobial development. To optimize antimicrobial activity, this research aimed at fluopsin C (Flp) encapsulation in liposomes to achieve controlled release and reduce cytotoxicity. Methods: Liposomal formulations were prepared by extruding formulations based on soy phosphatidylcholine (SPC) or poly (ethylene glycol)-distearoylphosphatidylethanolamine (DSPE-PEG) plus cholesterol, and were characterized by their size, polydispersity index, zeta potential, encapsulation efficiency, shelf-life stability, in vitro release profile, cytotoxicity, and antimicrobial activity against Klebsiella pneumoniae in vitro and in vivo. Results: The results indicated that the DSPE-PEG DMSO+Flp formulation presented superior physicochemical stability and unaltered antimicrobial activity. In vitro, CC50 decreased by 54%. No lethal dose was obtained in mice within the concentration range tested. The most effective doses in vivo were 2 × 2 mg/kg for free fluopsin C and 1 × 2 mg/kg for DSPE-PEG DMSO+Flp, resulting in a 40% reduction in mortality from bacteremia. Only discrete inflammatory infiltration was detected in the liver, while kidney necrosis ranged from discrete to moderate. Encapsulation of fluopsin C in liposomes showed promising features supporting to use against infections by MDR K. pneumoniae.},
}

@article {pmid41009119,
year = {2025},
author = {Kiewra, D and Ojrzyńska, H and Czułowska, A and Dyczko, D and Jawień, P and Plewa-Tutaj, K},
title = {Dermacentor reticulatus (Fabricius, 1794) in Southwestern Poland: Changes in Range and Local Scale Updates.},
journal = {Insects},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/insects16090935},
pmid = {41009119},
issn = {2075-4450},
abstract = {The ornate dog tick Dermacentor reticulatus is a key vector of several pathogens and has been expanding its range across Europe, raising concerns about the associated veterinary and public health risks. This study aimed to assess the current distribution and local-scale expansion of D. reticulatus in southwestern Poland, particularly in and around the city of Wrocław. In 2024, host-seeking ticks were collected using the flagging method at 80 sites, including 30 previously monitored locations and 50 newly designated ones, selected based on land cover analysis and field verification. Spatial statistics and kriging method were applied to evaluate changes in the tick's range compared to data from 2014-2019. The presence of D. reticulatus was confirmed at 68 sites, including 13 located beyond the previously estimated range. A shift in the mean center of tick occurrence toward the southeast was observed, along with an increase in the compact area of occurrence. The results indicate a continued expansion of D. reticulatus in the region, with urbanization and landscape structure likely influencing its spread. These findings underscore the importance of local-scale surveillance and spatial modeling in assessing the risk of tick-borne diseases.},
}

@article {pmid41006295,
year = {2025},
author = {van Galen, LG and Smith, GR and Margenot, AJ and Waldrop, MP and Crowther, TW and Peay, KG and Jackson, RB and Yu, K and Abrahão, A and Ahmed, TA and Alatalo, JM and Anslan, S and Anthony, MA and Araujo, ASF and Ascher-Jenull, J and Bach, EM and Bahram, M and Baker, CCM and Baldrian, P and Bardgett, RD and Barrios-Garcia, MN and Bastida, F and Beggi, F and Benning, LG and Bragazza, L and Broadbent, AAD and Cano-Díaz, C and Cates, AM and Cerri, CEP and Cesarz, S and Chen, B and Classen, AT and Dahl, MB and Delgado-Baquerizo, M and Eisenhauer, N and Evgrafova, SY and Fanin, N and Fornasier, F and Francisco, R and Franco, ALC and Frey, SD and Fritze, H and García, C and García-Palacios, P and Gómez-Brandón, M and Gonzalez-Polo, M and Gozalo, B and Griffiths, R and Guerra, C and Hallama, M and Hiiesalu, I and Hossain, MZ and Hu, Y and Insam, H and Jassey, VEJ and Jiang, L and Kandeler, E and Kohout, P and Kõljalg, U and Krashevska, V and Li, X and Lu, JZ and Lu, X and Luo, S and Lutz, S and Mackie-Haas, KA and Maestre, FT and Malmivaara-Lämsä, M and Mangelsdorf, K and Manjarrez, M and Marhan, S and Martin, A and Mason, KE and Mayor, J and McCulley, RL and Moora, M and Morais, PV and Muñoz-Rojas, M and Murugan, R and Nottingham, AT and Ochoa, V and Ochoa-Hueso, R and Oja, J and Olsson, PA and Öpik, M and Ostle, N and Peltoniemi, K and Pennanen, T and Pescador, DS and Png, GK and Poll, C and Põlme, S and Potapov, AM and Priemé, A and Pritchard, W and Puissant, J and Rocha, SMB and Rosinger, C and Ruess, L and Sayer, EJ and Scheu, S and Sinsabaugh, RL and Slaughter, LC and Soudzilovskaia, NA and Sousa, JP and Stanish, L and Sugiyama, SI and Tedersoo, L and Trivedi, P and Vahter, T and Voriskova, J and Wagner, D and Wang, C and Wardle, DA and Whitaker, J and Yang, Y and Zhong, Z and Zhu, K and Ziolkowski, LA and Zobel, M and van den Hoogen, J},
title = {A global database of soil microbial phospholipid fatty acids and enzyme activities.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1568},
pmid = {41006295},
issn = {2052-4463},
support = {DEB-1845544//National Science Foundation (NSF)/ ; DEB-1926335//National Science Foundation (NSF)/ ; DGE 1450271//National Science Foundation (NSF)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; 305069/2018-7//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; CZ.02.01.01/00/22_008/0004635//Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; PICT 2014-2838//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)/ ; 315260_149807//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; BIPD_01_2021_FCT-PTDC/BIA-CBI/2340/2020, UIDB/05937/2020, UIDP/05937/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816, Ei 862/29-1 and Ei 862/31-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 316045089//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315415//Academy of Finland (Suomen Akatemia)/ ; PTDC/BIA-CBI/2340/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; ANR; MIXOPEAT; ANR-17-CE01-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 31872994//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41922056//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32101286//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32061143027//National Natural Science Foundation of China (National Science Foundation of China)/ ; CIDEGENT/2018/041//Generalitat Valenciana (Regional Government of Valencia)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; NE/T012226//National Eye Research Centre (NERC)/ ; PRG1065, PRG1789, PSG784//Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council)/ ; 2021M693360//China Postdoctoral Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Phospholipids ; *Fatty Acids ; *Databases, Factual ; *Enzymes ; Soil/chemistry ; Ecosystem ; },
abstract = {Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.},
}

*Soil Microbiology
*Phospholipids
*Fatty Acids
*Databases, Factual
*Enzymes
Soil/chemistry
Ecosystem

@article {pmid41005096,
year = {2025},
author = {Wang, J and Hao, J and Jing, W and Gao, Y and Qiu, S},
title = {Effects of polyethylene terephthalate microplastics on performance of sequencing-batch membrane bioreactor for simulated municipal wastewater treatment.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139956},
doi = {10.1016/j.jhazmat.2025.139956},
pmid = {41005096},
issn = {1873-3336},
abstract = {Municipal wastewater treatment plants (WWTPs) are recognized as key recipients of microplastics (MPs), with polyethylene terephthalate (PET) being among the most prevalent types in sewage. However, the systemic impact of PET MPs on integrated biological-membrane systems-especially their role in microbial ecology and membrane fouling-remains poorly understood. Therefore, the influence of PET MPs on the performance, microbial community and membrane fouling in a sequencing-batch membrane bioreactor (SMBR) was evaluated in this study. Based on the results, adding PET MPs decreased the MLSS from around 5000 mg/L to 4500 mg/L whereas the MLVSS/MLSS remain basically consistent. The SV30 and SVI increased rapidly to 76 % and 173.2 mL/g on the 3rd day (from 64 % and 128.3 mL/g on the 1st day) of adding PET MPs, however, they could be restored in the following days. For pollutants removal, the COD and NH4[+]-N removal were initially negatively affected but gradually recovered after several days of operation. The addition of PET MPs enhanced denitrification, resulting in a decrease in the effluent TN concentration from 15.1 ± 4.9 mg/L to 10.4 ± 4.4 mg/L. PET MPs changed microbial community structure and decreased the abundance of dominant bacteria and species diversity in activated sludge. Arenimonas and Sphingopyxis had strong relationships with PET MPs addition. PET MPs addition exacerbated membrane biofouling, and the microbial diversity on membrane at was basically consistent with activated sludge whereas the abundance changed significantly. This research provides a comprehensive understanding of how PET MPs affect the performance of integrated biological-membrane systems.},
}

@article {pmid41000638,
year = {2025},
author = {Flores, C and Seekatz, AM},
title = {Reduced carbohydrate complexity alters gut microbial structure independent of total carbohydrate intake.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.20.677466},
pmid = {41000638},
issn = {2692-8205},
abstract = {Dietary habits have dramatically altered over recent decades, yet the impact of simplified carbohydrate intake on the gut microbiome's complexity and function remains poorly understood. This study investigates how the variety of dietary carbohydrates - not just their amount - shapes gut microbial diversity and resilience in C57BL/6 mice. Over eight weeks, mice consumed diets varying in carbohydrate complexity but matched for total carbohydrate content. Using 16S rRNA sequencing, we found that reduced carbohydrate diversity led to significant declines in microbial diversity and taxonomic redundancy among important bacterial groups, such as unclassified Lachnospiraceae, Ruminococcaceae, and Muribaculaceae, despite no immediate changes in host physiology. Concurrently, Akkermansia increased under low-complexity diets, suggesting a shift toward mucin degradation when complex polysaccharides are scarce. These changes indicate that loss of carbohydrate complexity narrows microbial niches, potentially disrupting metabolic interactions and functional stability of the gut ecosystem. Given the widespread adoption of processed, low-fiber diets in modern societies, these findings emphasize the importance of macronutrient complexity in maintaining gut microbial health. While short-term host effects were minimal, the microbial shifts observed could presage long-term consequences for gut resilience and disease susceptibility. This study underscores the need to consider carbohydrate diversity in dietary recommendations and microbial ecology research to safeguard gut health in the face of global dietary simplification.},
}

@article {pmid41000006,
year = {2025},
author = {Hodgson, RJ and Cando-Dumancela, C and Davies, T and Dinsdale, EA and Doane, MP and Edwards, RA and Liddicoat, C and Peddle, SD and Ramesh, SA and Robinson, JM and Breed, MF},
title = {Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70205},
pmid = {41000006},
issn = {1365-3040},
support = {//This metagenomics sequencing for this project was supported by the Flinders University Accelerator for Microbiome Exploration. We also received funding from the Holsworth Wildlife Research Endowment with the Ecological Society of Australia, the Conservation Biology Grant 2022 with the Biological Society of South Australia and Nature Conservation Society of South Australia and the Lirabenda Wildlife Research Fund from the Field Naturalists Society of South Australia. We also received support from the Australian Research Council (grant numbers LP190100051 and LP190100484) and the New Zealand Ministry of Business Innovation and Employment (grant UOWX2101)./ ; },
abstract = {The interactions between native plants and soil microbiota are not well characterised, despite growing recognition of their importance for host plant fitness and ecological functioning. We used shotgun metagenomics to examine microbial taxonomic and functional colonisation patterns in wild populations of the pan-palaeotropical C4 grass, Themeda triandra, across a globally representative aridity gradient (aridity index 0.318-0.903). We investigated these patterns through the two-step selection process whereby microbes are recruited from bulk soils into rhizospheres (soil on the root surface), and root interiors (endospheres). We provide clear evidence of this process through decreasing microbial taxonomic diversity from bulk soil to T. triandra roots. Surprisingly, microbial functional potential showed the opposite trend: the diversity of potential functions (exponent of Shannon's diversity) increased from bulk soil to the rhizosphere and endosphere, but functional richness did not. Finally, we found that increasing aridity was associated with rhizospheres that were more compositionally similar, yet remained highly diverse in functional potential. Overall, aridity is strongly associated with the root-associated microbiome of T. triandra, selecting for microbiota that likely support plant resilience under dry conditions. Furthermore, microbial functional potential closely tracks taxonomic composition and aridity trends, highlighting how native plants can shape their microbial communities.},
}

@article {pmid40999741,
year = {2025},
author = {Sun, J and Huang, H and Li, J and Xu, J and Jia, J and Li, W and Cheng, J and Zhu, D and Liu, M and Yuan, M and Xiao, S and Xue, C},
title = {Mitochondrial iron transporter ClMrs3/4 regulates iron homeostasis to modulate nitric oxide balance facilitating appressorial development in Curvularia lunata.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70594},
pmid = {40999741},
issn = {1469-8137},
support = {2024YFD1400304//National Key Research & Development Program of China/ ; 2023JH101300163/2022JH2/101300168//Liaoning Provincial Applied Basic Research Program/ ; 2024JH1/11700007-3//Liaoning Provincial Key Projects of Science and Technology/ ; JYTYB2024053//Basic Research Project of the Department of Education of Liaoning Province/ ; },
abstract = {Iron is indispensable for the vast majority of organisms, and iron homeostasis plays a pivotal role in both the physiology and pathogenesis of fungal pathogens. However, the underlying mechanisms by which iron homeostasis modulates fungal pathogenesis remain to be fully elucidated. We therefore focused on investigating the functions of mitochondrial iron transporter ClMrs3/4 in virulence. We conducted targeted gene deletions, expression analyses, biochemistry, and pathogenicity assays, demonstrating that ClMrs3/4 regulates appressorial development via maintenance of cellular iron balance in Curvularia lunata. ClMrs3/4 modulates virulence by influencing appressorial development in C. lunata, which is dependent on iron homeostasis. ClMrs3/4 controls nitric oxide (NO) balance via the nitrate (NO3 [-]) assimilation pathway by modulating cytoplasmic iron levels, a process crucial for turgor pressure accumulation within the appressoria independent of mitochondrial and cytoplasmic Fe-S cluster biosynthesis. Our findings underscore the conserved role of Mrs3/4 in iron homeostasis among pathogenic fungi and propose a novel mechanism by which iron homeostasis regulates virulence, particularly through the NO3 [-] assimilation pathway mediated by cytoplasmic iron levels to regulate appressorial development.},
}

@article {pmid40998779,
year = {2025},
author = {Li, Y and Sun, M and Raaijmakers, JM and Mommer, L and Zhang, F and Song, C and Medema, MH},
title = {Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8400},
pmid = {40998779},
issn = {2041-1723},
support = {24.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
mesh = {*Rhizosphere ; *Bacteria/genetics/metabolism/classification ; *Plant Roots/microbiology ; Soil Microbiology ; Microbiota/genetics ; *Multigene Family ; *Plants/microbiology ; Machine Learning ; Algorithms ; },
abstract = {Plants release a substantial fraction of their photosynthesized carbon into the rhizosphere as root exudates that drive microbiome assembly. Deciphering how plants modulate the composition and activities of rhizosphere microbiota through root exudates is challenging, as no dedicated computational methods exist to systematically identify microbial root exudate catabolic pathways. Here, we integrate published information on catabolic genes in bacteria that contribute to their rhizosphere competence and develop the rhizoSMASH algorithm for genome-synteny-based annotation of rhizosphere-competence-related catabolic gene clusters (rCGCs) in bacteria with 58 curated detection rules. Our analysis reveals heterogeneity in rCGC prevalence both across and within plant-associated bacterial taxa, indicating extensive niche specialization. Furthermore, we demonstrate the predictive value of the presence or absence of rCGCs for rhizosphere competence in machine learning with two case studies. rhizoSMASH provides an extensible framework for studying rhizosphere bacterial catabolism, facilitating microbiome-assisted breeding approaches for sustainable agriculture.},
}

*Rhizosphere
*Bacteria/genetics/metabolism/classification
*Plant Roots/microbiology
Soil Microbiology
Microbiota/genetics
*Multigene Family
*Plants/microbiology
Machine Learning
Algorithms

@article {pmid40997605,
year = {2025},
author = {Wu, G and Ding, Z and Wang, J and Xie, J},
title = {Frontier research on the risk of spoilage microorganisms in refrigerated marine fish: From regional to global perspectives.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111465},
doi = {10.1016/j.ijfoodmicro.2025.111465},
pmid = {40997605},
issn = {1879-3460},
abstract = {Microbial spoilage is creating safety risks and significant wastage of refrigerated marine fish. Spoilage microorganisms possess distinct physiological adaptations that enable them to contribute to the spoilage of refrigerated marine fish, thereby complicating the accuracy of microbial risk predictions and the efficacy of control strategies. This review integrates research findings from diverse geographical regions to elucidate mechanisms of microbial spoilage and underscores the ongoing challenges in cross-regional collaborative studies. Omics serve as guiding tools for elucidating the molecular mechanisms by which metabolite mediate spoilage microorganisms-induced deterioration of flavor, texture, and safety. Quantitative Microbial Risk Assessment (QMRA) provides a critical framework for risk prediction, with its future development being intrinsically linked to the integration of omics data, rapid fluorescence sensing, and artificial intelligence (AI) for enhanced prediction and modeling. In conclusion, this review underscores the critical role of spoilage microorganisms in the deterioration of refrigerated marine fish, highlights the complex interplay between microbial ecology, cold adaptation, and spoilage potential, and emphasizes the necessity for collaborative global efforts. Advancing research on native microbial communities, molecular spoilage mechanisms, and AI-powered QMRA frameworks is paramount for reducing food waste, enhancing food safety risk assessment, and the sustainable development of preservation technology.},
}

@article {pmid40996662,
year = {2025},
author = {Rév, A and Parádi, I and Füzy, A and Juhász, P and Kocsis, K and Cseresnyés, I and Takács, T},
title = {Improvement of soil fertility and enzymatic activity by wastewater sludge compost and arbuscular mycorrhizal fungi in giant reed's rhizosphere.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {40996662},
issn = {2676-8607},
support = {SA-26/2021//Eötvös Loránd Research Network/ ; },
abstract = {The effect of low-dose, commercially available wastewater sludge compost (WSC; 15 t ha[-1]) treatment was examined with or without arbuscular mycorrhizal fungal (AMF) inoculation on the nutritional status, heavy metal (HM) concentration and the rhizosphere activity of giant reed (Arundo donax L. var. BL clone (Blossom)) plants. Funneliformis mosseae (BEG12; AMF1), F. geosporum (BEG11; AMF2) or their combination (AMFmix) were applied as AMF treatments in a short-term pot experiment. The physiological and growth parameters of the host plants, the AMF root colonization and the microbiological enzyme activity of the mycorrhizosphere were examined. We assumed that the combined treatment (WSC + AMF) enhances the fertility of low-fertility acidic sandy soil. Neither the WSC treatment nor the AMF inoculations changed the extent of root colonization. Based on the results of root electrical capacitance and the phosphorous uptake, plant nutritional status was improved by WSC addition, without any negative impacts among the measured parameters. AMF treatments increased the enzyme activity in the soil and decreased the concentrations of the potentially toxic HMs (Cu, Mn, Pb, Zn) in roots, but that mitigation of Cu and Zn was compensated in shoots. According to the results of MicroResp™ measurements, the catabolic activity profile of the soil microbial community was changed in case of the AMF2 treatment. The efficient regulatory mechanism of giant reed might be able to adjust optimal/maximal colonization rate, and to select the preferential AMF partners, this supposed mechanism might be responsible for its invasiveness and tolerance to a wide range of environmental conditions.},
}

@article {pmid40996559,
year = {2025},
author = {Han, SI and Kim, JO and Lee, YR and Ekpeghere, KI and Koh, SC and Whang, KS},
title = {Correction: Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {10},
pages = {157},
doi = {10.1007/s10482-025-02169-7},
pmid = {40996559},
issn = {1572-9699},
}

@article {pmid40995846,
year = {2025},
author = {Stephenson, T and Crowder, DW and Osburn, E and Strickland, M and Jones, M and Bartel, S and Kittipalawattanapol, K and Cunningham, CX and Hudiburg, T and Storfer, A and Piaskowski, J and Lynch, L},
title = {Apex Scavenger Declines Have Cascading Effects on Soil Biogeochemistry and Ecosystem Processes.},
journal = {Global change biology},
volume = {31},
number = {9},
pages = {e70520},
doi = {10.1111/gcb.70520},
pmid = {40995846},
issn = {1365-2486},
support = {DEB-2054716//National Science Foundation/ ; },
mesh = {Animals ; *Soil/chemistry ; *Soil Microbiology ; *Food Chain ; *Marsupialia/physiology ; *Ecosystem ; Seasons ; Microbiota ; },
abstract = {Global apex scavenger declines strongly alter food web dynamics, but studies rarely test whether trophic downgrading impacts ecosystem functions. Here, we leverage a unique, disease-induced gradient in Tasmanian devil (Sarcophilus harrisii) population densities to assess feedbacks between carcass persistence, subordinate scavenger guilds, and biogeochemical cycling. We further explored interkingdom and seasonal interactions by manipulating carcass access and replicating experiments in warmer, drier summer versus cooler, wetter winter periods. We show Tasmanian devil declines significantly extend carcass persistence and increase the flux of carcass-derived nutrients belowground (e.g., by 18-134-fold for ammonium). Greater nutrient availability reduces soil microbiome diversity by up to 26%, increasing the relative abundance of putative zoonotic pathogens. Nutrient subsidies also shift microbial communities toward faster-growing taxa that invest less energy in resource acquisition, with implications for soil carbon sequestration. Rates of carcass decomposition were reduced in the winter, dampening soil biogeochemical responses and interkingdom competition. Notably, while less efficient scavenger guilds clearly facilitate carcass consumption, they were not able to fill the functional role of apex scavengers. Our study illustrates how trophic downgrading effects can ripple across all levels of ecological organization.},
}

Animals
*Soil/chemistry
*Soil Microbiology
*Food Chain
*Marsupialia/physiology
*Ecosystem
Seasons
Microbiota

@article {pmid40993772,
year = {2025},
author = {Dubey, JP and Alić, A and Hodžić, A and Lopez-Flores, J and Baneth, G},
title = {Hepatozoon infections in domestic and wild Carnivora: etiology, prevalence, clinical disease, diagnosis and treatment, and redescription of Hepatozoon silvestris, H. martis, and H. ursi.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {391},
pmid = {40993772},
issn = {1756-3305},
mesh = {Animals ; Prevalence ; *Coccidiosis/veterinary/diagnosis/epidemiology/parasitology/drug therapy/therapy ; *Eucoccidiida/classification/isolation & purification ; *Carnivora/parasitology ; Animals, Wild/parasitology ; Animals, Domestic/parasitology ; Life Cycle Stages ; },
abstract = {Hepatozoon spp. are common pathogens in dogs and other Carnivora in many parts of the world, especially in the tropics. There is considerable taxonomic debate concerning the Hepatozoon species infecting Carnivora. Morphological descriptions of several Hepatozoon species are inadequate and their validity is questionable. Additionally, different terminology has been used for the description of life cycle stages. Here, we provide a comprehensive review of the Hepatozoon species in the Carnivora, using a uniform terminology. Worldwide prevalence of clinical and subclinical Hepatozoon infections for the past century is tabulated and critically evaluated. We also review the epizootiology, clinical signs, diagnosis, and treatment of hepatozoonosis in the Carnivora. The morphology and life cycles of seven valid species with known merogonic stages (Hepatozoon americanum, H. canis, H. felis, H. martis, H. rufi, H. silvestris, H. ursi) are summarized in a table using standard terminology. Additional information on H. apri, H. martis, and H. silvestris life cycle stages is provided. Information lacking for H. procyonis, H. luiperdjie and H. ingwe is discussed. The relevance of H. mustelis, H. banethi and H. ewingi is discussed and they are considered as invalid species. For the benefit of future researchers, worldwide reports of prevalence, clinical disease, diagnosis, and treatment of Hepatozoon infections in domestic and wild Carnivora for the past century are summarized in tables alphabetically and chronologically for each country. Co-infections of H. canis, H. americanum, H. felis, and H. silvestris are summarized and discussed. The role of Hepatozoon infections causing clinical illness in wild Carnivora is discussed, particularly for red foxes, coyotes, and mustelids.},
}

Animals
Prevalence
*Coccidiosis/veterinary/diagnosis/epidemiology/parasitology/drug therapy/therapy
*Eucoccidiida/classification/isolation & purification
*Carnivora/parasitology
Animals, Wild/parasitology
Animals, Domestic/parasitology
Life Cycle Stages

@article {pmid40993491,
year = {2025},
author = {Sun, S and Qiao, Z and Tikhonenkov, DV and Gong, Y and Li, H and Li, R and Sun, K and Huo, D},
title = {Temporal Dynamics and Adaptive Mechanisms of Microbial Communities: Divergent Responses and Network Interactions.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {94},
pmid = {40993491},
issn = {1432-184X},
support = {24-44-00093//Russian Science Foundation/ ; 32361133561//National Natural Science Foundation of China/ ; 2021M703430//China Postdoctoral Science Foundation/ ; },
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Ecosystem ; *Rivers/microbiology ; *Eukaryota/genetics/classification/physiology ; Water Microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Microbial communities are vital to aquatic ecosystems, driving biogeochemical cycles, nutrient recycling, and overall ecosystem functioning. However, their instant feedback, particularly in response to environmental fluctuations, remain insufficiently understood. In this study, we investigated the interaction of prokaryotic and eukaryotic microbial communities in riverine ecosystems under temporal dynamics using high-throughput sequencing and co-occurrence network analysis. We observed distinct patterns, with eukaryotic communities showing a consistent increase in alpha diversity, while prokaryotic communities exhibited more variable and directional shifts over time. Two key phases were identified: a dynamic phase characterized by rapid changes in both alpha and beta diversity and a stabilization phase where community composition became more stable, with increased evenness. Co-occurrence network analysis revealed a transition from a modular structure in the dynamic phase to a more centralized and highly connected network in the stabilization phase. While modularity can enhance stability by localizing perturbations within distinct subnetworks, increased centralization and connectivity may weaken this stabilizing effect, potentially making the network less resilient to environmental fluctuations. Our findings provide new insights into the adaptive mechanisms that sustain microbial community stability and resilience in dynamic aquatic ecosystems, emphasizing the importance of diversity and network structure in maintaining ecological stability.},
}

*Microbiota
*Bacteria/classification/genetics/isolation & purification
Biodiversity
Ecosystem
*Rivers/microbiology
*Eukaryota/genetics/classification/physiology
Water Microbiology
High-Throughput Nucleotide Sequencing

@article {pmid40991823,
year = {2025},
author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK},
title = {Microbes without borders: uniting societies for climate action.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf199},
pmid = {40991823},
issn = {1751-7370},
}

@article {pmid40991432,
year = {2025},
author = {van Gestel, J and Koo, BM and Stürmer, VS and Garriga-Canut, M and Wagner, J and Zanon, A and Gross, CA},
title = {Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {39},
pages = {e2518989122},
doi = {10.1073/pnas.2518989122},
pmid = {40991432},
issn = {1091-6490},
support = {101116560//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; P400PB_186789//Swiss National Science Foundation (Postdoc.Mobility)/ ; R35GM118061//HHS | National Institutes of Health (NIH)/ ; },
mesh = {*Bacillus subtilis/genetics/physiology/growth & development ; *Dictyostelium/physiology ; *Adaptation, Physiological ; Bacterial Proteins/metabolism/genetics ; Phenotype ; },
abstract = {Single-cell eukaryotic predators in the soil are a primary cause of bacterial cell death. Yet, most functional genomic studies on soil bacteria have been performed without predation, thereby selecting for phenotypes impacting growth rather than survival and biasing our view on the ecological factors driving genomic evolution. Here, we study how predation by the ubiquitous amoebal predator Dictyostelium discoideum affects Bacillus subtilis' growth and survival using both a genome-scale mutant screen and de novo evolution of resistance. We show that predation-related genes (many not previously identified) promote survival by enabling filament or aggregate formation, thereby outsizing D. discoideum and slowing or preventing ingestion. Importantly, we find that predation resistance is costly, causing a trade-off between growth and survival. B. subtilis navigates this trade-off through switch-like adaptations, where cells switch back-and-forth between a slow-growing resistant state and a fast-growing susceptible state. These behaviors are controlled through both genotypic and phenotypic switches, with a central role for the Spo0A phosphorylation cascade, whose ancestral function may have been to evade or slow predation. Taken together, we uncover how the antagonist selection pressure imposed by predation is an important ecological driver of phenotypic heterogeneity in B. subtilis.},
}

*Bacillus subtilis/genetics/physiology/growth & development
*Dictyostelium/physiology
*Adaptation, Physiological
Bacterial Proteins/metabolism/genetics
Phenotype

@article {pmid40990948,
year = {2025},
author = {Basu, A and Mondal, S and Roy, A and Tewari, S and Chattopadhyay, S and Ghosh, A and Sil, AK},
title = {Paraclostridium sp. AKS46 vesicles facilitate extracellular electron transport.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf239},
pmid = {40990948},
issn = {1365-2672},
abstract = {AIMS: Paraclostridium sp. AKS46 was shown to have high exoelectrogenic activity. The current study investigated whether membrane vesicles (MVs) contribute to this electrogenic activity of this organism.

METHODS AND RESULTS: To examine the contribution of MVs to electrogenic activity, formation of MVs was first investigated by microscopic analyses of AKS46 cells at different time points of growth. The results showed increasing MV formation with time, especially in electrode-attached cells. To test electrogenic activity, the redox property and the electrochemical activity of the vesicles were examined. To this end, purified AKS46 vesicles demonstrated robust redox activities, and cyclic voltammetry and electrochemical impedance spectroscopy revealed high electrochemical properties of purified vesicles. Furthermore, proteomic analysis of the vesicles identified the presence of redox-active proteins, particularly flavoproteins, which might significantly contribute to electron carrier properties. AKS46 MVs also harbour enzymes involved in CO2 and nitrogen fixation, suggesting their roles in nutrient cycling and maintaining microbial ecology.

CONCLUSION: The exoelectrogenic gram-positive bacteria Paraclostridium sp. AKS46 produces extracellular vesicles packed with electron-rich molecules and thus, these vesicles act as electron transporters. The work highlights a vesicle-mediated mechanism for energy harvesting from waste degradation in microbial fuel cells.},
}

@article {pmid40990516,
year = {2025},
author = {Wang, Y and Xu, J and Liu, Y and Liu, L and Xiao, S and Wang, X and Zhang, J and Huang, S and Zheng, Q},
title = {Ocean currents and environmental gradients shape prokaryotic community structure and function in the South China Sea.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0102025},
doi = {10.1128/spectrum.01020-25},
pmid = {40990516},
issn = {2165-0497},
abstract = {UNLABELLED: The South China Sea (SCS) is characterized by complex hydrodynamic conditions that influence the structure and function of prokaryotic microbial communities. This study conducted a comprehensive analysis of prokaryotic diversity, community assembly, and functional potential across various water masses within the SCS. Using 16S rRNA gene sequencing and co-occurrence network analyses, we found that geographic distance and environmental gradients, particularly temperature and nutrient levels, significantly impacted community composition. Our findings indicate that ecological drift is the primary mechanism governing community assembly, with spatial turnover primarily driven by the dispersal of microorganisms facilitated by ocean currents. Distinct modules in co-occurrence networks were associated with specific environmental factors, reflecting potential environmental selection processes along the SCS current. Keystone species and biomarkers identified through network analysis and random forest modeling exhibited varying associations with environmental variables, highlighting their adaptability to changing conditions. This work underscores the importance of ocean currents and environmental factors in shaping prokaryotic community dynamics and provides insights into microbial biogeography and ecosystem function in the SCS.

IMPORTANCE: Microorganisms, especially prokaryotes, are fundamental in sustaining marine ecosystems through nutrient cycling and organic matter decomposition. However, understanding what shapes their diversity and distribution remains challenging. Our study highlights the significant role ocean currents and environmental conditions play in influencing prokaryotic communities in the South China Sea-a critical marine environment due to its dynamic currents and ecological complexity. We found that currents facilitate microbial dispersal, shaping community composition over vast areas, while temperature gradients act as key selective pressures, determining which species thrive. Additionally, we reveal that both predictable environmental selection and random ecological drift significantly contribute to community structuring. By identifying keystone microbes and biomarkers sensitive to environmental change, our work offers essential insights into marine microbial ecology. These findings are crucial for predicting how microbial communities, and thus ocean health and productivity, respond to ongoing environmental changes.},
}

@article {pmid40989908,
year = {2025},
author = {Lopez-Alforja, X and Sà, EL and Quiroga, MV and Pernice, MC and Cardelús, C and Balagué, V and Gasol, JM and Coutinho, FH and Massana, R and Vaqué, D},
title = {Long-term decline of marine viruses associated with warming and oligotrophication at a NW Mediterranean coastal site.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf150},
pmid = {40989908},
issn = {2730-6151},
abstract = {Viruses play key roles in controlling microbial abundance and community composition, nutrient cycling, and productivity in marine systems. Rising ocean temperatures, alongside increasing oligotrophy, are expected to alter the availability of inorganic nutrients and oxygen-key environmental factors that shape microbial community structure and virus-host interactions. While many studies have investigated viral abundances and community structure across spatial gradients, less is known about their long-term temporal variations, which is particularly relevant in the current context of global change. To address this gap, we analyzed two decades of surface water data from the Blanes Bay Microbial Observatory, located at the North-Western Mediterranean, to describe how biotic and abiotic variables influence temporal dynamics of viral abundances and community composition. Statistical tools for time series, including GAMMs, anomaly analysis, and neural networks, allowed us to demonstrate that viral abundance follows strong seasonality and a clear decrease starting midway (ca. 2011) through the sampled period (2005-2022). Fingerprint analysis evidenced that viral community composition was significantly influenced by seasonality and some environmental and biotic factors, with strong differences in viral communities between summer and winter months. Our analyses revealed that over the last 18 years, the abundance of most microbial groups, including viruses and their potential hosts, has declined, coinciding with an increase in seawater temperature and transparency, as well as a notable decrease in nutrient concentrations and phytoplankton biomass. We identified the ongoing shift toward more oligotrophic conditions as a potential driver of the observed decline in viral abundance, particularly in the last decade.},
}

@article {pmid40989192,
year = {2025},
author = {Alfahl, Z and O'Connor, L and Morris, D and Smith, TJ and O'Dwyer, J and Hynds, PD and Cormican, M and Burke, LP},
title = {A novel enrichment-free, low-volume filtration and rapid lysis (ELR) method in combination with real-time PCR for detection of Shiga toxin-producing Escherichia coli (STEC) in water.},
journal = {Access microbiology},
volume = {7},
number = {7},
pages = {},
pmid = {40989192},
issn = {2516-8290},
abstract = {Consequences of Shiga toxin-producing Escherichia coli (STEC) infection can range in severity from asymptomatic infection to haemolytic uraemic syndrome, renal failure and death. Groundwater-derived drinking water is an important route for STEC transmission. Detection of STEC in water is crucial for timely response and public health interventions; however, currently used culture-based methods are time-consuming and laborious. Therefore, there is a need for rapid methods that maintain high sensitivity and specificity [1]. We describe a novel, sensitive, enrichment-free water filtration method using a convenient sample volume (100 ml) to detect DNA markers of STEC serogroups and virulence factors within 6 h. Quantitative real-time PCR (qPCR) was used to detect and quantify the most common STEC infection-associated serogroups globally, O157 and O26. Real-time PCR was used to detect genetic determinants of STEC virulence (stx1, stx2 and eae genes) and specific marker genes for the clinically relevant serogroups O111, O103, O145 and O104. Results showed that the novel method can detect as low as 5 c.f.u. ml[-1] of STEC in water. The limit of detection for O157 and O26 qPCR assays was two and six copies, respectively. Groundwater and surface water samples (n=28) were collected and processed using the novel method. STEC O157 and O26 serogroups were detected in 23 out of 28 (82.1%) samples (mean 5.2×10[4] copies/reaction) and 19 out of 28 (67.9%) samples (mean 7.83×10[4] copies/reaction), respectively. Shiga toxin genes stx1 or stx2 were detected in 15 out of 28 (53.6%) and 9 out of 28 (32.1%) samples, respectively. The virulence factor intimin gene eae was detected in 24 out of 28 (85.7%) samples. STEC serogroups O111, O103, O145 and O104 were detected in 15 out of 28 (53.6%), 10 out of 28 (35.7%), 11 out of 28 (39.3%) and 15 out of 28 (53.6%) samples, respectively. This novel method reproducibly detects low copies of STEC in low-volume fresh water and has the potential to be used for the detection and quantification of waterborne bacterial pathogens.},
}

@article {pmid40987850,
year = {2025},
author = {Laso-Pérez, R},
title = {Deep-mining the archaeal proteome for antibiotics.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40987850},
issn = {2058-5276},
}

@article {pmid40987416,
year = {2025},
author = {Liaqat, F and Khazi, MI and Ismail, W},
title = {Microbial transport systems of organic sulfur compounds: Diversity and implications for biocatalysis, healthcare, and environmental biotechnology.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108718},
doi = {10.1016/j.biotechadv.2025.108718},
pmid = {40987416},
issn = {1873-1899},
abstract = {The global sulfur cycle plays a vital role in human health, global warming and biogeochemistry. Organic sulfur compounds constitute a substantial sulfur reservoir and serve as an energy and/or carbon source for prokaryotes. In addition, microbial interactions with organic sulfur compounds are pivotal for several biotechnological applications in petroleum biorefining, industrial biocatalysis, bioremediation, healthcare, and plant growth promotion. Microbial degradation of organic sulfur compounds is hindered by slow degradation rates, substrate specificity, toxicity of by-products, and challenges in scalability and efficiency. While degradation pathways of some organic sulfur compounds have been elucidated, transport systems involved in their uptake and efflux remain less explored. Regulating the uptake and efflux of organic sulfur compounds in microorganisms can help overcome several of the limitations associated with their transformation. Membrane transporters are not only crucial for uptake and efflux of organic sulfur compounds but also play a key role in stress tolerance by facilitating the excretion of toxic metabolites. Understanding the intricacies of these transporters provides valuable insights into microbial ecology and the development of strategies for harnessing microbial sulfur metabolism for important biotechnological applications. This review systematically presents the diversity, mechanisms, and potential evolution pathways of microbial membrane transporters involved in organic sulfur compounds acquisition. Furthermore, it highlights and discusses advances in the characterization of transporter systems and current limitations in using transporter systems for fuel biodesulfurization and organic sulfur compound degradation. Eventually, we explore the implications of organic sulfur compounds transporters in biotechnology and identify future research directions toward leveraging the biotechnological potential of microbial sulfur metabolism, fueled by advanced techniques of systems microbiology, metabolic engineering, as well as artificial intelligence.},
}

@article {pmid40986398,
year = {2025},
author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK},
title = {Microbes without borders: uniting societies for climate action.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {10},
pages = {},
doi = {10.1093/femsec/fiaf084},
pmid = {40986398},
issn = {1574-6941},
}

@article {pmid40985999,
year = {2025},
author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK},
title = {Microbes without borders: uniting societies for climate action.},
journal = {mBio},
volume = {},
number = {},
pages = {e0213625},
doi = {10.1128/mbio.02136-25},
pmid = {40985999},
issn = {2150-7511},
abstract = {The climate crisis is one of the greatest challenges of our time, yet the role of microorganisms remains underrecognized in climate science and policy. Microbes are highly sensitive to environmental change and regulate essential biogeochemical processes, while also offering solutions for reducing emissions, restoring ecosystems, and enhancing resilience. Microbiology societies from five continents recently convened in Washington, DC, for the inaugural Global Strategy Meeting on Microbes and Climate Change. The gathering launched a global alliance to position microbial science as a pillar of climate action and identified four priorities: building a coalition, embedding microbes in climate frameworks, transforming communication, and advancing real-world demonstration projects. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.},
}

@article {pmid40985636,
year = {2025},
author = {Grosso Giordano, F and Mariën, Q and De Belie, N and Rodriguez-Navarro, C and Boon, N},
title = {Characterization of isolates used in bacterial-based strategies for accelerated carbonation of lime mortars.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/aem.00683-25},
pmid = {40985636},
issn = {1098-5336},
abstract = {Portland cement largely replaced hydraulic lime over the past century because of its rapid hardening. Achieving earlier hardening in lime through faster carbonation is thus essential to help overcome one of lime's limiting qualities. Here, we isolated two alkaliphilic bacteria, Shouchella clausii and Shouchella patagoniensis, from a lime mortar wall. S. clausii was then further grown in high pH (>11) by adaptive laboratory evolution to acclimate a third isolate. Bacterial suspensions of all three isolates were followed for 14 days in serum bottles at pH 11, and gas composition of the headspace, intact/damaged cell populations, and pH were measured. In parallel, lime mortar samples were incubated in a closed environment with bacterial suspension of the isolates and analyzed with thermogravimetric analysis after 7 and 14 days to quantify carbonation. S. patagoniensis produced more CO2, close to the estimated maximum CO2 uptake rate of lime, and carbonated the lime mortars to a larger extent than the other isolates. Finally, the bacterial suspensions were directly mixed with lime. A linear and homogeneous carbonation of the paste samples was measured compared to water-based pastes, and the development of Liesegang patterns was observed upon phenolphthalein spreading. All this indicated that the organic addition altered the carbonation dynamics of the material, although bacteria did not accelerate carbonation relative to media alone and inhibited it relative to water-based paste. Still, a relationship between bacterial activity, CO2 emission, and carbonation rate was established, but practical aspects of bacterial delivery into lime must be addressed.IMPORTANCEPortland cement is the dominant binder used in most construction today, but until last century, lime was the ubiquitous construction material. The increase in use of cement has sprung from its higher strength and faster hardening; yet, lime still remains a relevant material, particularly in masonry structures and the built heritage. As such, novel lime materials are necessary to tackle some of the current limitations of lime, such as earlier hardening, which would not only make lime easier to work with but would also limit failure due to environmental conditions. As existing strategies to speed up lime hardening have had limited uptake due to their reliance on expensive and often toxic chemicals, the need for novel solutions is in place. We show that bacterial-based strategies could be a viable option to go beyond the limitations of current strategies, but limitations are in place.},
}

@article {pmid40985445,
year = {2025},
author = {Shen, K and Tang, Y and Shi, J and Hu, Z and He, M and Li, J and Wang, Y and Shao, M and Liu, H},
title = {Relationship Between Aquatic Fungal Diversity in Surface Water and Environmental Factors in Yunnan Dashanbao Black-Necked Crane National Nature Reserve, China.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/jof11070526},
pmid = {40985445},
issn = {2309-608X},
support = {2024//Yunnan Provincial Department of Education Scientific and Technological Innovation Team for Development and Utilization of Gastrodia Resources/ ; 202110BA070001-059//Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities' Association/ ; 2023-3//Zhaotong "Xingzhao Talent Support Program" Team Project/ ; },
abstract = {Aquatic fungi serve as core ecological engines in freshwater ecosystems, driving organic matter decomposition and energy flow to sustain environmental balance. Wetlands, with their distinct hydrological dynamics and nutrient-rich matrices, serve as critical habitats for these microorganisms. As an internationally designated Ramsar Site, Yunnan Dashanbao Black-Necked Crane National Nature Reserve in China not only sustains endangered black-necked cranes but also harbors a cryptic reservoir of aquatic fungi within its peat marshes and alpine lakes. This study employed high-throughput sequencing to characterize fungal diversity and community structure across 12 understudied wetland sites in the reserve, while analyzing key environmental parameters (dissolved oxygen, pH, total nitrogen, and total phosphorus). A total of 5829 fungal operational taxonomic units (OTUs) spanning 649 genera and 15 phyla were identified, with Tausonia (4.17%) and Cladosporium (1.89%) as dominant genera. Environmental correlations revealed 19 genera significantly linked to abiotic factors. FUNGuild functional profiling highlighted saprotrophs (organic decomposers) and pathogens as predominant trophic guilds. Saprotrophs exhibited strong associations with pH, total nitrogen, and phosphorus, whereas pathogens correlated primarily with pH. These findings unveil the hidden diversity and ecological roles of aquatic fungi in alpine wetlands, emphasizing their sensitivity to environmental gradients. By establishing baseline data on fungal community dynamics, this work advances the understanding of wetland microbial ecology and informs conservation strategies for Ramsar sites.},
}

@article {pmid40983756,
year = {2025},
author = {Dong, S and Wang, S and Li, L and Yu, J and Zhang, Y and Xue, JY and Chen, H and Ma, J and Zeng, Y and Cai, Y and Huang, W and Zhou, X and Wu, J and Li, J and Yao, Y and Hu, R and Zhao, T and Villarreal A, JC and Dirick, L and Liu, L and Ignatov, M and Jin, M and Ruan, J and He, Y and Wang, H and Xu, B and Rozzi, R and Wegrzyn, J and Stevenson, DW and Renzaglia, KS and Chen, H and Zhang, L and Zhang, S and Mackenzie, R and Moreno, JE and Melkonian, M and Wei, T and Gu, Y and Xu, X and Rensing, SA and Huang, J and Long, M and Goffinet, B and Bowman, JL and Van de Peer, Y and Liu, H and Liu, Y},
title = {Bryophytes hold a larger gene family space than vascular plants.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40983756},
issn = {1546-1718},
abstract = {After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes' rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.},
}

@article {pmid40981669,
year = {2025},
author = {Riisgaard-Jensen, M and Valença, RM and Peces, M and Nielsen, PH},
title = {Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf213},
pmid = {40981669},
issn = {1751-7370},
abstract = {The link between the sewer microbiome and microbial communities in activated sludge wastewater treatment plants is currently poorly understood despite the systems being directly interconnected. Microbial immigration from wastewater has been identified as a key factor determining activated sludge community assembly. Here, we present the first comprehensive study of the sewer microbiome and hypothesize that it harbors a process-critical activated sludge microbes, thus critical for activated sludge community assembly and performance. We integrated species-level microbial analyses of biofilm, sediment, and sewer wastewater in domestic gravity and pressure sewers in Aalborg, Denmark, with samples from influent wastewater and activated sludge from two downstream wastewater treatment plants. By tracing the sources of incoming bacteria and determining their growth fate in the activated sludge, we confirmed the hypothesis that most activated sludge process-critical bacteria were part of the sewer microbiome. Within the sewer system, a gradient was observed, from dominance of gut-bacteria in the wastewater upstream to prevalence of biofilm and sediment bacteria downstream at the wastewater treatment plants inlet, with the relative ratio strongly affected by rain events. A holistic understanding of the sewer system and activated sludge is essential, as the sewers hold massive amounts of active biomass serving as a major microbial source for community composition and dynamics in wastewater treatment plants. Sewer systems should be recognized as a crucial environmental filtration step, and the sewer microbiome as an important source community for activated sludge, helping to explain the observed regional and global differences in activated sludge community structure.},
}

@article {pmid40981467,
year = {2025},
author = {Qiao, Y and Wang, L and Wang, S and Li, S and Wang, F and Wang, B and Lin, S and Liu, Y},
title = {Bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity of the algae-associated microbiome throughout the growth cycle of Alexandrium pacificum.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0135925},
doi = {10.1128/aem.01359-25},
pmid = {40981467},
issn = {1098-5336},
abstract = {The algae-associated microbiome represents a consortium that has been chronically domesticated by specific algae, maintaining a close relationship with the host population. Although the microbes associated with dinoflagellates have garnered significant attention in recent years, the interactions and contributions of microbial generalists and specialists through the growth cycle of a bloom-forming dinoflagellate remain largely unexplored. Herein, the ecological and evolutionary characteristics of free-living generalists and specialists within bacterial and fungal communities were investigated during the growth process of Alexandrium pacificum cultured in the laboratory for years without antibiotic treatment. From an ecological perspective, bacterial generalists and fungal specialists dominated the community, indicating different microbial niche patterns between the bacterial and fungal consortia. Furthermore, microbial specialists were more susceptible to disturbance from algal proliferation, as evidenced by greater community dissimilarity and determinacy-dominated assembly processes. Compared with their counterparts, the molecular networks of bacterial generalists and fungal specialists were more complex and robust, suggesting that they significantly contributed to resistance to environmental stress and functional maintenance. Evolutionarily speaking, bacterial generalists and fungal specialists showed much higher diversification potential, and others featured higher extinction rates. Despite these differences, a continuous transition from the former two to their counterparts was observed, alleviating the "Matthew effect" in the biological world for ecological trade-offs. Collectively, these findings emphasize that bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity during the growth process, which expands the current understanding of the maintenance mechanisms of the diversity and community of phytoplankton-associated microbes in the face of disturbance from bloom-forming dinoflagellates.IMPORTANCELike the microbes residing in the rhizosphere and human gut, bacteria that coexist chronically with microalgae exemplify a relationship, forming potentially intimate partnerships with the host. However, studies on the ecological significance of algae-associated microbiomes with different niches under the interference of bloom-forming species are still lacking. This work investigated the ecological interactions and contributions of generalists and specialists within algae-associated bacterial and fungal communities across the growth cycle of Alexandrium pacificum for the first time. These results increase the understanding of the microbial ecology of algae-associated microbes in the context of interference from the proliferation of harmful algal bloom species.},
}

@article {pmid40981420,
year = {2025},
author = {Wing, AJ and Hegarty, B and Bastien, GE and Denef, VJ and Evans, J and Dick, GJ and Duhaime, MB},
title = {Tracking putative Microcystis viruses and virus-host associations across distinct phases of a Microcystis-dominated bloom.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057525},
doi = {10.1128/msystems.00575-25},
pmid = {40981420},
issn = {2379-5077},
abstract = {Viruses significantly impact microbial community composition and function. Yet their role in the fate of freshwater cyanobacterial harmful algal blooms (cHABs), an increasing threat to freshwater systems, remains poorly understood. Here, we address this with a metagenomic analysis of viruses of bloom-forming Microcystis aeruginosa through a seasonal cHAB in the western basin of Lake Erie. We identified globally distributed Microcystis viruses in Lake Erie based on sequence homology to well-studied isolates. A machine-learning model was then used to predict associations between uncharacterized viral populations and the Microcystis and non-Microcystis hosts of the cHAB. Size fractionation of water samples allowed us to identify significant fraction-specific trends in Microcystis viral diversity that corresponded with Microcystis genetic diversity. Viral diversity was highest in the non-colony-associated fraction and lowest in the colony-associated fraction, suggesting that colony formation may lead to bottlenecks in viral diversity in cHABs. Significant turnover of predicted Microcystis virus populations was observed through time, but not between stations miles apart. The virus-host networks revealed extensive interconnectivity and the potential for virus-mediated cross-species genetic exchange. The networks predicted that Lake Erie Microcystis viruses infect hosts spanning phyla, in agreement with lab studies in other systems but challenging previous notions of "narrow" host-virus associations in this genus. Abundant Microcystis virus genes revealed a potential role in key metabolic pathways and host adaptation. These findings advance our understanding of Microcystis viruses and their potential influence on host metabolism, species interactions, and coevolution in Microcystis-dominated cHABs.IMPORTANCEUnderstanding associations between viruses, their hosts, and environmental factors is key for identifying the mechanisms behind the rise and fall of cyanobacterial harmful algal blooms. This study explores the diversity and host ranges of viruses predicted to infect Microcystis, reporting how these properties vary over time, across sample stations in western Lake Erie, and among different filter size fractions. We found that Microcystis virus diversity is highest in non-colony-associated fractions and the lowest in colony-associated fractions, suggesting a link between Microcystis colony formation and reduced viral diversity. We identify abundant genes belonging to predicted Microcystis viruses and their potential roles in key metabolic pathways and adaptation to environmental changes. These findings enhance our understanding of the interplay among viruses, Microcystis, and co-occurring bacteria in cHABs, offering insights into the mechanisms driving bloom dynamics, species interactions, and coevolutionary processes.},
}

@article {pmid40980873,
year = {2025},
author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR},
title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0060125},
doi = {10.1128/msystems.00601-25},
pmid = {40980873},
issn = {2379-5077},
abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.

IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.},
}

@article {pmid40980756,
year = {2025},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {40980756},
issn = {2331-8422},
abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologs or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems including human microbiomes, soil, oceans, and extreme environments, and discuss what is known, and still unknown, about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization, and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation, and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.},
}

@article {pmid40980429,
year = {2025},
author = {Rahman, MS and Chlingaryan, A and Thomson, PC and Islam, MR and Lees, AM and Gregorini, P and Pereira, FC and Clark, CEF},
title = {In vitro simulation of drinking events in cattle.},
journal = {MethodsX},
volume = {15},
number = {},
pages = {103593},
pmid = {40980429},
issn = {2215-0161},
abstract = {Drinking causes a rapid decline in reticulorumen temperature (RT) followed by an exponential recovery, which may potentially impact the reticulorumen ecosystem. However, the nexus between drinking events and their effects on ruminal fermentation and microbial diversity has not yet been studied, either in vitro or in vivo. Although artificial (in vitro) rumen systems are widely used in ruminant research to simulate the reticulorumen environment, no such simulation has been described to consider the impact of drinking events on the reticulorumen environment. Therefore, we have developed a method for the in vitro simulation of drinking events in the fermentation jar where the jar temperature was considered a proxy for RT is reduced by adding a measured amount of cold water to the water bath, and the subsequent recovery period is achieved following a temperature profile regulated by a heating immersion circulator. This method enables the replication of RT fluctuations from drinking events, allowing for the monitoring of their impact on fermentation characteristics and microbial ecology in future research. The features of this method are: Creation of a hypothetical drinking event Estimation of volume and temperature of cold water for a drinking event Establishing a temperature profile to regulate the recovery period.},
}

@article {pmid40978322,
year = {2025},
author = {Phonlamai, A and Khetkorn, W and Thongpool, V and Panyachanakul, T and Suriyachadkun, C and Kitpreechavanich, V and Sakdapetsiri, C and Lomthong, T},
title = {Profiling of the bacterial community and the degradative capability of newly isolated poly(lactic acid) (PLA)- and poly(butylene succinate) (PBS)-degrading bacteria from coastal samples.},
journal = {3 Biotech},
volume = {15},
number = {10},
pages = {352},
pmid = {40978322},
issn = {2190-572X},
abstract = {UNLABELLED: The coastal area of Thailand is a tropical marine environment with high microbial diversity, providing favorable conditions for microorganisms capable of degrading bioplastics. The current study aimed to investigate the bacterial community profiling of four samples collected from a coastal area in Thailand and to isolate the potential thermophilic bacteria with the ability to produce bioplastic-degrading enzymes. Our analysis revealed site-specific predominant genera: Brevibacillus in seawater (64.34 ± 0.27%), Pseudomonas in plastic waste (39.69 ± 3.77%), Pseudoalteromonas in soil (54.83 ± 2.40%), and Psychrobacter in moss rock (41.01 ± 1.67%). The thermophilic bacteria, including 6 poly(lactic acid) (PLA)- and 3 poly(butylene succinate) (PBS)-degrading bacteria, were isolated using a two-step technique in an emulsified polymer medium. These nine isolates were classified into five species across four genera: Brevibacillus gelatini, Microbispora rosea, Actinomadura keratinilytica, Paenibacillus thermoaerophilus, and P. ginsengihumi. Among these, Actinomadura keratinilytica LDF1 and M. rosea BS2-4 exhibited the highest enzymatic activities for PLA and PBS degradation (0.87 ± 0.11 U/mL and 0.31 ± 0.03 U/mL, respectively). Scanning electron microscopy confirmed the degradation capabilities of these strains in culture medium. Crude enzyme from the LDF1 strain demonstrated versatility in degrading various types of PLA, including PLA film, PLA powder, commercial cup, and commercial cutlery, while the strain BS2-4 enzyme effectively degraded PBS in film, powder, commercial cup, and commercial drinking straw. These findings advance our understanding of coastal microbial ecology and also highlight the potential of indigenous bacteria for bioplastic waste management, contributing to sustainable environmental solutions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04521-0.},
}

@article {pmid40976393,
year = {2025},
author = {Cui, J and Dörmann, P},
title = {Microbial degradation of hydrocarbons from petroleum assisted by biosurfactants: pathways and bioremediation potential.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2025.09.011},
pmid = {40976393},
issn = {1638-6183},
abstract = {Petroleum pollution from oil extraction, transportation, and industrial activities poses significant threats to marine ecosystems and socioeconomic stability due to the high toxicity of alkanes and polycyclic aromatic hydrocarbons (PAHs) to many organisms. Traditional remediation methods, including physical removal and chemical oxidation, are often costly and ecologically disruptive. Microbial degradation, facilitated by hydrocarbonoclastic bacteria like Pseudomonas aeruginosa and Alcanivorax borkumensis, offers a sustainable alternative by converting hydrocarbons into non-toxic CO2 and water. This review examines the degradation pathways of aliphatic and aromatic hydrocarbons by these bacteria, highlighting key enzymatic mechanisms and the pivotal role of biosurfactants-specifically rhamnolipids, and glycine-glucolipid-in enhancing hydrocarbon bioavailability. It also delves into the biosynthesis of these biosurfactants, along with the involvement of non-ribosomal peptide synthetases (NRPS) in producing lipopeptide biosurfactants such as surfactin. Additionally, the review addresses the challenges associated with scaling up biosurfactant production for bioremediation applications. Through a synopsis of recent research, this work proposes strategies to optimize biosurfactant efficacy, contributing to environmental sustainability and advancing the field of microbial ecology.},
}

@article {pmid40976174,
year = {2025},
author = {Allouche, M and Bouzidi, I and Lassoued, A and Sellami, B and Derguini, A and Idres, T and Badraoui, R and Ben Hamadi, N and Chaudhary, AA and Bendif, H and Pacioglu, O and Abd-Elkader, OH and Boufahja, F and Plavan, G},
title = {How do polyethylene microplastics, ibuprofen, and sediment mud levels influence meiobenthic features and their interactions with CeO2-doped ZnO nanoparticles? Answers through nematode taxon/functional traits, allometry of Metoncholaimus pristiurus, and computational analyses.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107564},
doi = {10.1016/j.marenvres.2025.107564},
pmid = {40976174},
issn = {1879-0291},
abstract = {Microplastic pollution and pharmaceutical contaminants represent growing environmental threats, particularly in aquatic ecosystems. This research examines the individual and combined effects of polyethylene microplastics, sediment particles, and ibuprofen on meiobenthic species, specifically free-living nematodes. Abundance changes, species diversity, and functional characteristics were monitored during a 30-day microcosm experiment. The binding affinities and molecular interactions of both contaminants with germ-line development protein 3 (GLD-3) and sex-determining protein (SDP) have been assessed using computational modeling assays. The results indicate that contamination significantly alters nematode communities, with pronounced declines in sensitive species such as Dorylaimopsis timmi and Halalaimus longicaudatus. At the same time, opportunistic taxa like Paramonhystera pellucida and Parodontophora beviseta exhibited increased abundance, resulting in a worldwide reduction of nematofauna (432 individuals in controls compared to 233-322 individuals in treated communities). The experimental results and computational assays supported each other. Furthermore, the strongest negative effects were observed in combined polyethylene-ibuprofen treatments, suggesting a synergistic interaction that enhances toxicity. Polyethylene microplastics appear to modulate the bioavailability and toxicity of ibuprofen, potentially exacerbating its impact on benthic communities. According to regressions linking body dimensions, the combination of polyethylene microplastics and ibuprofen with ZnO-CeO2 (slopes: 0.53629 and 0.31718, respectively) nanoparticles enhanced the growth rate of the nematode Metoncholaimus pristiurus, compared to the control group (slopes: 0.05775).},
}

@article {pmid40976099,
year = {2025},
author = {Saci, S and Nabti, EH and Sebbane, H and Issad, HA and Boufahja, F and De Martino, L and Nocera, FP and Bendif, H and Derguini, A and Hamadi, NB and Chaudhary, AA and Rebai, A and Cruz, C and Idres, T and Houali, K},
title = {Exploring Thymus vulgaris Extract as a Phytotherapeutic Agent: A Multifaceted Approach to tackle Avian Colibacillosis and Drug Resistance.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105794},
doi = {10.1016/j.psj.2025.105794},
pmid = {40976099},
issn = {1525-3171},
abstract = {Avian colibacillosis remains a major threat to poultry production and food security, whereas its antibiotic-based control accelerates antimicrobial resistance. This study investigated the antibacterial potential of the hydroethanolic extract of Thymus vulgaris, alone and in combination with antibiotics, against avian pathogenic Escherichia coli (APEC). The phytochemical composition of the extract was analyzed by HPLC, while its antibacterial activity was assessed using agar diffusion and minimum inhibitory concentration (MIC) assays. Antibiotic-extract interactions were evaluated by the checkerboard method, and mechanisms of action were explored through assays targeting membrane permeability, proton pump inhibition, catalase inhibition, oxidative stress, and biofilm formation. Its antioxidant, anti-inflammatory, and cytotoxic activities were also evaluated. HPLC analysis revealed 16 phenolic compounds, including rosmarinic, ferulic, and salicylic acids, as well as flavonoids such as quercetin and luteolin, with an extraction yield of 15% ± 0.55. The extract displayed significant antibacterial activity (MIC: 5.46-10.93 mg/ml, p < 0.05). In synergy tests, the extract enhanced ampicillin efficacy 4-8-fold and showed additive effects with ciprofloxacin and tetracycline (2-4-fold). Mechanistic assays demonstrated disruption of bacterial membranes (32.66% electrolyte leakage, p < 0.05), inhibition of H[+]-ATPase proton pumps (p < 0.05), catalase activity reduction by 79.2% (p < 0.05), >50% decrease in cell hydrophobicity, and inhibition of biofilm formation (49.07-72.47%), alongside eradication of mature biofilms (41.89-64.67%) (p < 0.05). Beyond antimicrobial effects, the extract exhibited notable antioxidant capacity. In DPPH radical scavenging, the extract showed an IC50 of 9.76 ± 0.228 μg/ml (p < 0.05), while in the TAC assay, it reached 467.25 ± 1.889 μg/ml (p < 0.05), and it reduced ampicillin-induced lipid peroxidation by 42.85% (p < 0.05). Anti-inflammatory testing revealed inhibition of protein denaturation (4.95-52.48% at 15-2000 µg/ml, p < 0.05), although weaker than aspirin. Hemolysis assays confirmed the extract was non-hemolytic at concentrations up to 11 mg/ml (p < 0.05). In conclusion, Thymus vulgaris extract demonstrated safe, multi-target bioactivity, supporting its potential as a promising alternative to combat avian colibacillosis and antimicrobial resistance.},
}

@article {pmid40975416,
year = {2025},
author = {Bi, Z and Wang, X and Fu, H and Huang, Y},
title = {Carbon source shaped microbial ecology, metabolism and performance in biofilm system for simultaneous phosphorus recovery and nitrogen removal.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122800},
doi = {10.1016/j.envres.2025.122800},
pmid = {40975416},
issn = {1096-0953},
abstract = {The application of biofilm-based phosphorus enrichment technology has been hampered by the limited information on the performance, microbial interactions and metabolic patterns of dominant functional bacteria, especially those fed with complex carbon sources conditions. In this study, three representative carbon sources contained in real sewage, i.e., volatile fatty acids (VFAs), glucose, and amino acids were selected as the complex carbon sources. The comparison in phosphorus removal/enrichment performance, carbon utilization, and metabolic characteristics were performed during the biofilm system changed the sole carbon source (acetate sodium) feeding to complex carbon source feeding gradually. The performance reduction and instability were observed in initial stage of complex carbon source feeding, while the phosphorus removal/enrichment efficiency improved significantly after long-term acclimation by extending the anaerobic HRT. The concentration of phosphorus enrichment solution exceeded 50 mg/L, meanwhile the total nitrogen and total phosphorus removal efficiencies over 82% and 97%, respectively. Intriguing, intracellular organic phosphorus (OP) contents fluctuated with phosphorus uptake and release, which may be a hint of the important role of OP in PAOs energy conversion. Complex carbon sources induced the succession of biofilm community, especially the enrichment of hydrolytic fermentation bacteria, and a more intricate microbial interaction network among functional microbiota. The co-occurrence of the EMP and ED pathways during glycolysis implied more extensive carbon utilization pathways, and amino acids was speculated to complement intracellular energy metabolism via the tricarboxylic acid cycle (TCA). This study demonstrated that the biofilm systems have great potential to simultaneously achieve phosphorus removal and enrichment by using complex carbon sources in sewage wastewater.},
}

@article {pmid40972460,
year = {2025},
author = {Arulananthan, A and Scholz, B and Karsten, U and Grossart, HP and Sigurbjörnsdóttir, A and Rolfsson, Ó and Joerss, H and Duarte, B and Vilhelmsson, OÞ},
title = {Arctic and sub-Arctic marine diatom responses to PFAS exposure: Understanding physiological changes and resilience.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {289},
number = {},
pages = {107562},
doi = {10.1016/j.aquatox.2025.107562},
pmid = {40972460},
issn = {1879-1514},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants widely detected across diverse ecosystems. Despite regulatory bans on several PFAS compounds, PFAS remain prevalent in remote areas like the Arctic, raising significant ecological health concerns. This study addresses a critical knowledge gap regarding the effects of PFAS on unicellular primary producers, with a focus on diatom physiology and fitness. Two ecologically important Arctic and sub-Arctic diatom species, Cylindrotheca closterium and Thalassiosira pseudonana, as well as legacy long-chain PFAS, and two emerging PFAS replacements were investigated. Exposures were conducted for 10 days at three concentrations (100 mg/L, 1 mg/L, and 0.9 ng/L). Following the 10 d (short-term) toxicity assessment, one PFAS mixture was exposed for 28 days (long-term) at an environmentally relevant concentration of 0.9 ng/L. Physiological and biochemical responses, including growth, photosynthetic capacity, stress biomarkers, and metabolic changes, were assessed. Results revealed distinct impacts of PFAS on individual PFAS and their mixtures. Perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorododecanoic acid (PFDoA), perfluorotridecanoic acid (PFTrDA), and perfluorotetradecanoic acid (PFTeDA) often exhibited the most detrimental effects on both species relative to controls. PFAS mixtures exhibited synergistic impacts, with increasing effects as the number of PFAS compounds increased. Both diatoms exhibited significant reductions in growth and photochemical efficiency of photosystem II, along with elevated proline and total antioxidant activity, during short-term exposure to PFAS. During the long-term experiment, after the exponential growth phase (after 14 d), growth rates were not significantly different from those of the controls, suggesting potential compensatory responses over time. Despite the mild growth inhibition, enhanced biochemical activity relative to controls indicates sustained metabolic adjustment under prolonged PFAS exposure. These findings emphasize the potential impacts of PFAS, specially in mixtures, on disrupting primary producers in cold marine ecosystems, highlighting the need to assess the cumulative effects of pollutants on foundational Arctic biota.},
}

@article {pmid40972045,
year = {2025},
author = {Feliu-Paradeda, L and Puig, S and Bañeras, L},
title = {Electron conductive compounds alter fermentative pathways and cooperation in Clostridium carboxidivorans and Clostridium acetobutylicum in co-culture.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf090},
pmid = {40972045},
issn = {1574-6941},
abstract = {The addition of conductive materials promotes interactions between bacteria as they facilitate the exchange of reducing equivalents among cells. In this work, the impact of electron conductive compounds (magnetite, activated carbon or iron salts) was investigated on a Clostridium acetobutylicum/Clostridium carboxidivorans co-culture. Co-culturing both species with soluble iron salts or magnetite significantly improved carbon recovery in liquid end-products (75-85% of added carbon) compared to control and activated carbon supplementation (50-55% of added carbon). The addition of magnetite enhanced the production of longer-chain acids and alcohols (C4 and C6) when compared to all other treatments and reached the highest production after 44 h of fermentation. This effect was not observed in C. carboxidivorans nor in C. acetobutylicum pure cultures, advocating for a cooperation between the two species. Among comparisons to the behaviour observed in pure cultures, we suggest magnetite was first used as a sink of reduced equivalents produced by C. carboxidivorans and later as a source of energy for C. acetobutylicum for the production of elongated short-chain fatty acids and alcohols. We propose that adding magnetite (iron) could be an effective strategy to enhance alcohol production in synthetic clostridia consortia.},
}

@article {pmid40970936,
year = {2025},
author = {Uddin, MR and Saifullah, S},
title = {Type II toxin-antitoxin systems as stress-responsive survival circuits in archaea and bacteria.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {269},
pmid = {40970936},
issn = {1432-072X},
support = {23-FoBST-02//Research Cell, JUST/ ; },
mesh = {*Toxin-Antitoxin Systems/genetics ; *Archaea/genetics/physiology/metabolism ; *Bacteria/genetics/metabolism ; *Stress, Physiological ; Bacterial Proteins/genetics/metabolism ; DNA Repair ; Phylogeny ; *Antitoxins/genetics/metabolism ; Bacterial Toxins/genetics/metabolism ; Biofilms/growth & development ; },
abstract = {Simple early lifeforms with relatively small genomes were evolved with certain genetic circuitry to better their stress-response mechanism which significantly enhances their survival during stress, hypothetically. In this review, we conducted a comprehensive investigation to identify survival-focused genetic circuitry in microorganisms, focusing on type II toxin-antitoxin (TA) systems, particularly sought after due to their ubiquitousness in nature, composed of two functionally coordinated genes: one that transiently inhibits reproduction during stress and another that represses this inhibition under normal conditions, while simultaneously promoting DNA repair under stress. Our comprehensive analysis of 22 type II TA systems reveals diverse roles, including dormancy induction, biofilm formation, pathogenicity and DNA repair. While canonical modules such as HigAB and RelBE are well-characterized, others like ParDE, Kid-Kis, and YafO-YafN remain understudied in the context of dormancy or biofilm involvement. Additionally, systems such as DarT-DarG, YafQ-DinJ and CcdB-CcdA have been implicated in DNA repair pathways, suggesting broader functional repertoires beyond growth inhibition. Phylogenetic analyses further reveal that TA systems such as VapC-VapB and MazF-MazE are widely distributed among bacteria, archaea, and cyanobacteria, including lineages thriving in extreme environments like deep-sea hydrothermal vents, which are considered potential sites for the emergence of early life. The presence of TA loci in ancient microorganisms like Methanocaldococcus jannaschii and Microcystis aeruginosa hints at their ancient origin and possible role in microbial survival on early Earth. This review synthesizes current knowledge on type II TA systems as stress-responsive survival circuits and highlights their significance in microbial ecology, evolution, and adaptation.},
}

*Toxin-Antitoxin Systems/genetics
*Archaea/genetics/physiology/metabolism
*Bacteria/genetics/metabolism
*Stress, Physiological
Bacterial Proteins/genetics/metabolism
DNA Repair
Phylogeny
*Antitoxins/genetics/metabolism
Bacterial Toxins/genetics/metabolism
Biofilms/growth & development

@article {pmid40970741,
year = {2025},
author = {Lee, W and Kim, G and Park, T},
title = {Refining microbial biomarker identification in rumen microbiome studies: a viability PCR-based approach.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0142925},
doi = {10.1128/aem.01429-25},
pmid = {40970741},
issn = {1098-5336},
abstract = {The rumen microbiome significantly affects host performance, influencing feed efficiency, nitrogen utilization, and methane emission. However, conventional DNA-based marker gene sequencing cannot distinguish between viable and non-viable microbes, leading to inaccurate microbiota analyses. Viability PCR (v-PCR) with propidium monoazide (PMA) can inhibit DNA amplification from membrane-compromised cells, allowing the detection of viable microbes in rumen cultures. Therefore, this study aims to identify conditions for applying PMA in rumen culture experiments using qPCR and to examine its effect on the rumen microbial community using 16S rRNA gene sequencing in standard in vitro experiments. PMA treatment conditions were applied using a fivefold inoculum dilution, 100 µM PMA concentration, 30 min dark incubation, and 20 min light exposure, validated by a decrease in absolute abundance in heat-treated samples. When applied to in vitro rumen experiments, PMA treatment reduced bacterial evenness and induced shifts in key bacterial and archaeal taxa. Additionally, it affected major functional profiles of the microbiota. PMA treatment increased the relative abundance of Ruminobacter [log fold change (LFC) = 0.52] and Succinivibrio (LFC = 0.68) at 0 h (no incubation), along with Ruminobacter (LFC = 0.83) after 24 h of incubation, while decreasing that of Xylanibacter (LFC = -0.39) at 24 h. These shifts align with those of RNA-based studies showing higher Succinivibrionaceae abundance than Prevotellaceae, supporting the effectiveness of PMA in capturing active microbial dynamics. PMA-based v-PCR offers a reliable alternative to RNA-based methods, improving microbial community assessments and facilitating the identification of viability-associated microbial biomarkers in rumen studies.IMPORTANCEThis study identifies the optimal conditions for applying propidium monoazide (PMA) in in vitro rumen experiments to selectively amplify DNA from viable microorganisms while suppressing amplification from nonviable ones. PMA-based viability PCR (v-PCR) improves the accuracy of microbial community analysis by selectively detecting viable microorganisms, addressing the limitations of conventional DNA-based methods. Additionally, this approach provides a potential cost-effective alternative to RNA-based analyses, offering a practical tool for studying rumen microbial ecology.},
}

@article {pmid40970700,
year = {2025},
author = {Havlena, ZE and Lucero, K and Graham, HV and Stern, JC and Wankel, SD and Mainiero, M and Jones, DS},
title = {Microbial ecology of acidic, biogenic gypsum: community structure and distribution of extremophiles on freshly formed and relict sulfate deposits in a hydrogen sulfide-rich cave.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0139725},
doi = {10.1128/aem.01397-25},
pmid = {40970700},
issn = {1098-5336},
abstract = {UNLABELLED: Sulfate minerals are abundant on the Martian surface, and many of these evaporite deposits are thought to have precipitated from acidic fluids. On Earth, gypsum (CaSO4•2H2O) and other sulfates sometimes form under acidic conditions, so exploring the extremophilic life that occurs in these mineral environments can help evaluate the astrobiological potential of acid sulfate depositional settings. Here, we characterized the microbial communities associated with acidic gypsum deposits in a sulfuric acid cave, where sulfate precipitation is driven by sulfide-oxidizing bacteria and archaea. We used 16S rRNA gene sequencing and cell counts to characterize gypsum-associated microorganisms in freshly formed and relict deposits throughout the cave, to test how microbial community composition and abundance would vary with distance from the sulfidic water table and with the concentration of H2S(g) and other gases in the cave atmosphere. We found that actively forming gypsum in the lower cave levels was colonized by low-diversity communities that have few cells compared to other environments in the cave. The most abundant taxa were Acidithiobacillus, Metallibacterium, Mycobacteria, and three different Thermoplasmatales-group archaea, which occupied distinct niches based on proximity to sulfidic streams and the concentration of gases in the cave air. By contrast, deposits in older cave levels had more diverse communities that were distinct from those associated with freshly formed gypsum and likely represent a community reliant on different energy resources. These findings show that acidic sulfate deposits serve as habitats for extremophilic microorganisms and broaden our knowledge of the life associated with terrestrial sulfates.

IMPORTANCE: Gypsum and other sulfate salts are common on Mars, and many of these deposits are thought to have formed from acidic fluids early in the planet's history. Understanding the life that survives and thrives in similar environments on Earth is therefore crucial for evaluating whether these Martian sulfates are or ever were habitable. One such environment where acidic gypsum occurs is in sulfuric acid caves, where extremophilic microorganisms drive the precipitation of sulfate minerals by oxidizing hydrogen sulfide gas from the cave atmosphere. Here, we characterized the communities of microorganisms on freshly formed and ancient gypsum in the Frasassi Caves and found that the gypsum deposits hosted microbial communities that changed based on chemical energy availability and the age of the gypsum. Our findings underscore the importance of chemical and microbiological interactions in shaping habitable niches and provide context for searching for past or present life in acidic Martian sulfates.},
}

@article {pmid40969862,
year = {2025},
author = {Wang, H and Lindemann, E and Liebmann, P and Varsadiya, M and Svenning, MM and Waqas, M and Petters, S and Richter, A and Guggenberger, G and Barta, J and Urich, T},
title = {Methane-cycling microbiomes in soils of the pan-Arctic and their response to permafrost degradation.},
journal = {Communications earth & environment},
volume = {6},
number = {1},
pages = {748},
pmid = {40969862},
issn = {2662-4435},
abstract = {The methane-cycling microbiomes play crucial roles in methane dynamics. However, little is known about their distributions on a pan-Arctic scale as well as their responses to the widespread permafrost degradation. Based on 621 datasets of 16S rRNA gene amplicons from intact permafrost soils across the pan-Arctic, we identified only 22 methanogen and 26 methanotroph phylotypes. Their relative abundances varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations. Remarkably, the permafrost soil methane filter was almost exclusively dominated by some obligate methanotroph (Methylobacter-like) phylotypes. However, a case study in Alaska suggests that atmospheric methane oxidizing bacteria (Methylocapsa-like phylotypes) dominated methanotrophs in a drier condition after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic methane dynamics in a warming climate and that under future dry conditions, increased atmospheric methane uptake in Arctic upland soils may occur.},
}

@article {pmid40968530,
year = {2025},
author = {Popov, IV and Chikindas, ML and Venema, K and Ermakov, AM and Popov, IV},
title = {KEGGaNOG: A Lightweight Tool for KEGG Module Profiling From Orthology-Based Annotations.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70269},
doi = {10.1002/mnfr.70269},
pmid = {40968530},
issn = {1613-4133},
support = {23-14-00316//Russian Science Foundation/ ; },
abstract = {Functional interpretation of bacterial genomes and metagenomes is essential for applications ranging from microbial ecology to probiotic development. KEGGaNOG is a lightweight and scalable Python tool that enables pathway-level profiling by translating orthology-based annotations into KEGG module completeness scores. KEGGaNOG accepts input from eggNOG-mapper annotations and supports both individual genome and multi-sample analyses. It calculates completeness scores for KEGG modules using internally integrated KEGG-Decoder logic and offers a suite of visualization options, including heatmaps, grouped summaries, barplots, radar plots, and correlation networks. We demonstrate its use on 11 well-characterized bacterial genomes, including several probiotic strains. KEGGaNOG accurately captured core biosynthetic capabilities and highlighted functionally informative differences across samples, such as vitamin biosynthesis, stress-response pathways, and transport systems. KEGGaNOG provides a practical framework for high-throughput functional annotation and comparative metabolic profiling in bacterial genomics and microbiome research. It is particularly well suited for preliminary analysis of novel or uncharacterized strains and is applicable to both isolate and metagenome-derived data. In the context of probiotic research, KEGGaNOG supports mechanistic exploration and strain selection by linking genomic content to functional capacity in a reproducible and interpretable manner.},
}

@article {pmid40968492,
year = {2025},
author = {Dong, X and Chu, Y and Tong, Z and Yi, X and Sun, M and Meng, D and Gao, T and Wang, M and Duan, J},
title = {The adsorption mechanism of tembotrione on modified biochar and its impact on soil microbial communities.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70225},
pmid = {40968492},
issn = {1526-4998},
support = {2023YFD1400900//National Key Research and Development Program of China/ ; 32372609//National Natural Science Foundation of China/ ; 32302414//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Tembotrione, a triketone herbicide with high mobility and persistence, poses significant environmental risks by disrupting soil microbial ecology and threatening crop rotation systems. This study investigates the adsorption mechanism and ecological benefits of hydrogen peroxide-modified biochar (HPBC-700) for mitigating tembotrione contamination in soil environments.

RESULTS: The oxidative modification introduces abundant oxygen-containing functional groups, including hydroxyl, carboxyl, and carbonyl, which substantially enhance the biochar's adsorption capacity and surface reactivity. Density Functional Theory (DFT) calculations and non-covalent interaction analyses reveal that hydrogen bonding and π-π stacking are the dominant adsorption mechanisms. Among the functional groups, carboxyl contributes the strongest binding due to its ability to form dual hydrogen-bond interactions. In addition to physically immobilizing the herbicide, HPBC-700 improves soil microbial diversity and enriches degradation-related functional taxa, particularly Proteobacteria and Acinetobacter, thereby alleviating pesticide-induced ecological stress.

CONCLUSION: These findings highlight the dual function of HPBC-700 as both an efficient adsorbent and a regulator of soil microbiomes, providing a sustainable strategy for pesticide remediation and agroecosystem restoration. This work advances the understanding of biochar-pesticide interactions and offers new insights into integrating chemical immobilization with ecological recovery for effective soil pollution control. © 2025 Society of Chemical Industry.},
}

@article {pmid40968405,
year = {2025},
author = {Trubl, G and Probst, AJ},
title = {Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70177},
doi = {10.1111/1462-2920.70177},
pmid = {40968405},
issn = {1462-2920},
support = {SCW1632//U.S. Department of Energy Office of Biological and Environmental Research through the Genomic Science Program and the Lawrence Livermore National Laboratory/ ; CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; 426547801//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Terminology as Topic ; *Ecology ; *Microbiota ; *Microbiology ; Communication ; },
abstract = {The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.},
}

*Terminology as Topic
*Ecology
*Microbiota
*Microbiology
Communication

@article {pmid40967376,
year = {2025},
author = {Huang, M and Lian, Y and Xie, C},
title = {A rare case of recurrent abdominal pain with facial edema.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.09.019},
pmid = {40967376},
issn = {1528-0012},
}

@article {pmid40969174,
year = {2024},
author = {Matz, LM and Shah, NS and Porterfield, L and Stuyck, OM and Jochum, MD and Kayed, R and Taglialatela, G and Urban, RJ and Buffington, SA},
title = {Gut pathobiont enrichment observed in a population predisposed to dementia, type 2 diabetics of Mexican descent living in South Texas.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {},
pmid = {40969174},
issn = {2813-4338},
abstract = {Type 2 diabetes (T2D) is a common forerunner of neurodegeneration and accompanying dementia, including Alzheimer's Disease (AD), yet the mechanisms underlying this comorbidity remain unresolved. Individuals of Mexican descent living in South Texas have increased prevalence of comorbid T2D and early onset AD, despite low incidence of the APOE-ε4 risk variant among the population and an absence of a similar predisposition among relatives residing in Mexico - suggesting a role for environmental factors in coincident T2D and AD susceptibility. We therefore sought to test if differences in gut community structure could be observed in this population prior to any AD diagnosis. Here, in a small clinical trial (ClinicalTrials.gov Identifier NCT04602650), we report evidence for altered gut microbial ecology among subjects of Mexican descent living in South Texas with T2D (sT2D) compared to healthy controls without T2D (HC), despite no differences in expressed dietary preferences. We performed metataxonomic 16S rRNA gene amplicon sequencing of study participant stool samples. Although no significant decrease in microbial alpha diversity was observed between sT2D gut communities versus those of HC, body mass index was identified as a driver of gut community structure. Intriguingly, we observed a significant negative association of Faecalibacterium with T2D and an increase in the abundance of pathobionts Escherichia-Shigella, Enterobacter, and the erysipelotrichial species Clostridia innocuum among sT2D gut microbiota, as well as differentially abundant gene and metabolic pathways. Future large-scale, longitudinal sequencing efforts of the gut microbiome of individuals with T2D who go onto develop AD might identify key actors among "disease state" microbiota that contribute to increased susceptibility to comorbid dementia among type 2 diabetics. Finally, we identified candidate microbiome-targeted approaches for the treatment of T2D.},
}

@article {pmid40966281,
year = {2025},
author = {Dai, J and Chen, C and Zhai, ZQ and Gao, AX and Johnson, DR and Kopittke, PM and Zhao, FJ and Wang, P},
title = {The balance between microbial arsenic methylation and demethylation in paddy soils underpins global arsenic risk and straighthead disease in rice.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {38},
pages = {e2508311122},
doi = {10.1073/pnas.2508311122},
pmid = {40966281},
issn = {1091-6490},
support = {42325701 W2411035//National natural science foundation of china/ ; },
mesh = {*Oryza/microbiology/metabolism ; *Arsenic/metabolism/toxicity ; *Soil Microbiology ; Methylation ; Soil/chemistry ; *Plant Diseases/microbiology ; *Soil Pollutants/metabolism ; Bacteria/metabolism/genetics ; Cacodylic Acid/metabolism ; Food Contamination/analysis ; },
abstract = {Arsenic contamination in rice poses a global challenge to food safety and agricultural productivity, as toxic methylated arsenic species-dimethylarsinic acid (DMA) and its highly toxic derivative, methylated monothioarsenate (DMMTA)-accumulate in rice grains. These arsenic species endanger human health and trigger rice straighthead disease, a crop disorder that drastically reduces yields. However, the microbial ecological processes driving arsenic speciation in paddy soils, and their link to striking geographic disparities in rice arsenic speciation profiles and disease prevalence, remain poorly understood. Here, we integrate soil chronosequences spanning 1 to 2,000 y of rice cultivation, a global metagenomic survey of 801 paddy soils, controlled incubations, and field surveys to demonstrate that the balance between arsenic-methylating and arsenic-demethylating microbes is the key determinant of rice grain arsenic speciation and straighthead disease susceptibility. We show that young and moderate-age paddy soils (<700 y), common in regions such as the Americas and Europe, are enriched in arsenic-methylating bacteria, leading to elevated DMA and DMMTA in soils and rice grains. In contrast, ancient paddies in Southeast Asia harbor robust populations of DMA-demethylating methanogenic archaea that effectively mitigate the buildup of these toxic arsenic species. We identify core microbial taxa whose abundances serve as predictive biomarkers and construct a global risk map linking a high methylator-to-demethylator ratio in soils with increased straighthead disease incidence. These findings advance our understanding of arsenic biogeochemistry in agroecosystems and establish a predictive framework for identifying regions at elevated risk of arsenic-induced crop disorders and food contamination.},
}

*Oryza/microbiology/metabolism
*Arsenic/metabolism/toxicity
*Soil Microbiology
Methylation
Soil/chemistry
*Plant Diseases/microbiology
*Soil Pollutants/metabolism
Bacteria/metabolism/genetics
Cacodylic Acid/metabolism
Food Contamination/analysis

@article {pmid40965595,
year = {2025},
author = {Nieto, EE and Ghanem, N and Cammarata, RV and Borim Corrêa, F and Coppotelli, BM and Chatzinotas, A},
title = {Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk.},
journal = {Biodegradation},
volume = {36},
number = {5},
pages = {86},
pmid = {40965595},
issn = {1572-9729},
mesh = {*Phenanthrenes/metabolism ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Bacteriophages/genetics/isolation & purification/physiology/metabolism ; Soil Pollutants/metabolism ; *Burkholderiaceae/virology/metabolism ; Genome, Viral ; Soil Microbiology ; },
abstract = {Phages are a major cause of bacterial mortality, affecting bacterial diversity and ecosystem functioning. However, the impact of phage-host interactions in contaminated environments and their role in pollutant biodegradation have largely been overlooked. We isolated and characterized a novel phage that infects the PAH-degrading bacterium Paraburkholderia caledonica Bk from a polycyclic aromatic hydrocarbon (PAH)-contaminated soil and investigated the effect of different multiplicity of infection (MOI) ratios on the degradation efficiency of phenanthrene. The phage IPK is a temperate phage with a wide pH and temperature tolerance and a burst size of 80 PFU ml[-][1]. The phage was classified as a member of the Caudoviricetes and is related to Pseudomonas and Burkholderia phages. However, its low intergenomic similarity indicates that it is a new species. Three auxiliary metabolic genes (AMGs) related to amino acid metabolism and to bacterial growth regulation were identified in the phage genome. The highest multiplicity of infection (MOI 10) showed a rapid recovery of the host density and greater phenanthrene degradation than MOIs ranging from 0.01 to 1. This work highlights the important role of phage-host interactions in modulating the efficiency of pollutant degradation, which could be a key for improving the establishment of inoculants in bioremediation processes.},
}

*Phenanthrenes/metabolism
Biodegradation, Environmental
*Polycyclic Aromatic Hydrocarbons/metabolism
*Bacteriophages/genetics/isolation & purification/physiology/metabolism
Soil Pollutants/metabolism
*Burkholderiaceae/virology/metabolism
Genome, Viral
Soil Microbiology

@article {pmid40965271,
year = {2025},
author = {Dell'Acqua, AN and Scicchitano, D and Simoncini, N and Mercanti, I and Leuzzi, D and Turroni, S and Corlatti, L and Rampelli, S and Colonna, M and Corinaldesi, C and Candela, M and Palladino, G},
title = {Ski Tourism Shapes the Snow Microbiome on Ski Slopes in the Italian Central Alps.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70195},
doi = {10.1111/1758-2229.70195},
pmid = {40965271},
issn = {1758-2229},
mesh = {Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Skiing ; *Snow/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; *Tourism ; Humans ; Viruses/classification/genetics/isolation & purification ; Metagenomics ; Seasons ; },
abstract = {Winter sports exert significant anthropogenic pressures on the snow microbiome, affecting the entire alpine ecosystem. The massive usage of artificial snow, human occupation, and the release of xenobiotics like microplastics or ski wax components on ski tracks can profoundly alter snow microbial ecology. Here, we reconstructed the temporal dynamics of the snow microbiome at three sites in the Italian Alps: inside and outside a ski track at the impacted site of Santa Caterina Valfurva and near Cancano lake as an unimpacted control. Using epifluorescence microscopy, 16S rRNA amplicon sequencing, and inferred metagenomics, we found that the snow microbiome inside the track presented a higher load of prokaryotes and viruses. Notably, N2-fixing microorganisms from cryospheric environments and host-associated taxa, like Terrisporobacter, Clostridium sensu stricto, Enterococcus, and Muribaculaceae, and the opportunistic pathogen Citrobacter characterised the impacted site. These microorganisms could originate from the river water used to produce artificial snow during winter. Our findings highlight the complexity and multifunctionality of the snow microbiome, where microorganisms with different ecological propensities can coexist, and the detectable impact of ski tourism, which enriches host-associated and xenobiotic-degrading microorganisms. This underscores the need for systematic monitoring and protection of the snow microbiome in the Alpine environment from anthropogenic threats.},
}

Italy
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Skiing
*Snow/microbiology/virology
RNA, Ribosomal, 16S/genetics
*Tourism
Humans
Viruses/classification/genetics/isolation & purification
Metagenomics
Seasons

@article {pmid40965193,
year = {2025},
author = {Armin, G and Boros, G and Kis, M and Burányi, M and Horváth, H and Krassován, K and Masuda, T and Bernát, G and Inomura, K},
title = {The effect of temperature on phytoplankton physiology: a mesocosm and modeling study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0045725},
doi = {10.1128/spectrum.00457-25},
pmid = {40965193},
issn = {2165-0497},
abstract = {Strategies that focus on reducing nutrient loading to freshwater lakes have historically been successful in improving water quality by curbing large phytoplankton blooms. However, as waters warm, little is known about the resultant phytoplankton physiology and ensuing perturbations in the food web that may occur. Here, we designed a mesocosm experiment to investigate the impact of warming water on phytoplankton physiology and further validate a previously developed, coarse-grained model that predicts the key aspects of phytoplankton physiology, including elemental stoichiometry and macromolecular allocation, across varying temperatures. We found that higher temperatures double the maximum cellular density (cells L[-1]) of phytoplankton, suggesting that high temperature stimulates cell division over maximizing carbon storage. Also, the cells in warmer waters dedicate fewer resources to proteins and RNA production, leading to higher fractions of carbon allocated to storage. This work illustrates the potential impact warming waters may have on the ecosystem, as higher fractions of carbohydrates are often associated with less nutritious food for higher trophic levels.IMPORTANCEWe take a novel approach to investigating the impact of warming on phytoplankton physiology by utilizing mesocosms and a coarse-grained cellular model. Previous work in this field tends to use idealized laboratory experiments, mesocosms, or models alone. By synthesizing model and mesocosm results, we test the model's ability to capture physiology in semi-natural environments. We conducted this experiment under phosphorus limitation and saw high cell densities in the heated, treatment tanks. Thus, warming waters may negate some successful management practices that curb eutrophication. With increased temperatures, we also observed increased N:P values in both the experimental and model results, which may be due to the combined effects of a lack of P storage, fewer enzymes required, and a corresponding decrease in RNA production. Our model predictions closely aligned to mesocosm observations, suggesting the capability of our model to represent lower trophic organisms in ecosystem models.},
}

@article {pmid40965139,
year = {2025},
author = {Kim, M and Kamagata, Y and Park, S-J},
title = {Genomics and physiological characterizations of an acidotolerant nitrite-oxidizing Nitrospira enriched from freshwater pond.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0152225},
doi = {10.1128/aem.01522-25},
pmid = {40965139},
issn = {1098-5336},
abstract = {Nitrite-oxidizing bacteria (NOB) play a crucial role in global nitrogen cycling, yet their presence and adaptations in acidic environments remain poorly understood. This study unveils the cultivation and characterization of a novel acid-tolerant NOB, NS4 culture, affiliated with lineage II (Nitrospira_D) within the genus Nitrospira. Enriched and isolated from a freshwater pond sediment, NS4 culture exhibits remarkable physiological and genomic traits that shed light on NOB survival strategies in low pH conditions. NS4 culture demonstrates the optimal growth at pH 6 and 0.5 mM nitrite concentration, with a maximum growth rate of 0.62 day[-1]. Kinetic analyses reveal a high affinity for nitrite (Km(app) = 4.02 µM), suggesting adaptation to oligotrophic environments. Phylogenomic and genomic-relatedness analyses position NS4 culture as a novel member within the genus Nitrospira, for which we propose as "Candidatus Nitrospira acidotolerans." Genomic investigations indicate the presence of a complete reductive tricarboxylic acid cycle and genes for nitrite oxidation, confirming its chemolithoautotrophic lifestyle. Intriguingly, NS4 genome lacks complete pathways for cobalamin biosynthesis, implying a potential dependence on symbiotic partners for this essential cofactor. The NS4 genome harbors genes associated with acid resistance, including chaperones, transporters, and amino acid metabolism, suggesting a genetic potential for adaptation or resistance to low pH conditions. This discovery expands our understanding of NOB diversity and adaptability, offering insights into nitrogen cycling in acid-impacted ecosystems. The physiological and genomic traits of this acid-tolerant NOB open new insights for exploring the ecological significance of NOB in previously overlooked acidic habitats.IMPORTANCENitrite-oxidizing bacteria (NOB) are integral to the global nitrogen cycle, yet their adaptations to acidic environments remain poorly understood. This study introduces Candidatus Nitrospira acidotolerans, an acid-tolerant NOB highly enriched from freshwater pond sediment. By combining physiological and genomic analyses, this work reveals unique adaptations that enable survival and nitrite oxidation under low pH conditions. Notably, the NS4 culture demonstrates high nitrite affinity and resistance to acidic stress, suggesting its ecological significance in acid-impacted ecosystems. Additionally, NS4 genomic traits reveal genetic potential of metabolic dependencies, including reliance on symbiotic partners for cobalamin synthesis. These findings expand our understanding of NOB diversity and their role in nitrogen cycling under extreme conditions, offering novel insights into microbial ecology and potential applications in managing nitrogen processes in acidic environments.},
}

@article {pmid40961788,
year = {2025},
author = {Kotowska, D and Báldi, A and Dobosy, P and Felföldi, T and Garamszegi, LZ and Horváth, Z and Kröel-Dulay, G and Ódor, P and Valkó, O and Batáry, P},
title = {Aligning land use with sustainability: Context-sensitive pathways forward.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127252},
doi = {10.1016/j.jenvman.2025.127252},
pmid = {40961788},
issn = {1095-8630},
abstract = {The concept of sustainable development states that economic, social, and technological progress needs to be harmonised with nature. However, with the rate of global environmental deterioration now higher than at any time in human history and an ever-increasing human population, sustainability slips out of reach. One of the central processes and key issues in attaining sustainability is human use of and interaction with land resources. These can be described by two main processes that often go hand in hand: land conversion and land-use intensification. As these two phenomena accelerate, the level of disturbance in the environment increases, transforming natural ecosystems into altered, novel ecosystems or intensively used ecosystems. Depending on the degree of human-induced land alterations, different actions are needed to achieve and maintain sustainability. Conservation and prevention are necessary in natural areas with a low level of anthropogenic pressures. In areas that have already been disturbed by humans, sustainable management allows for a harmonious coexistence between humans and nature. Restoration and mitigation can help address the negative impacts of the most altered habitats. Sustainability, however, is not a fixed target but a dynamic condition shaped by evolving local contexts and global drivers. We advocate for transformative change grounded in flexible, context-sensitive land-use strategies that integrate ecological resilience, participatory governance, and institutional adaptability. With such systemic shifts, land systems can become catalysts for long-term sustainability.},
}

@article {pmid40832858,
year = {2025},
author = {Gregor, R and Vercelli, GT and Szabo, RE and Gralka, M and Reynolds, RC and Qu, EB and Levine, NM and Cordero, OX},
title = {Vitamin auxotrophies shape microbial community assembly on model marine particles.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf184},
pmid = {40832858},
issn = {1751-7370},
support = {542395//Simons Collaboration on Principles of Microbial Ecosystems/ ; 653410//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; OCE-2019589//Center for Chemical Currencies of a Microbial Planet Postdoctoral Fellowship/ ; #031//NSF Center for Chemical Currencies of a Microbial Planet/ ; },
mesh = {*Seawater/microbiology/chemistry ; *Bacteria/metabolism/classification/isolation & purification/genetics ; *Vitamins/metabolism ; Polysaccharides/metabolism ; *Microbiota ; },
abstract = {Microbial community assembly is governed by the flow of carbon sources and other primary metabolites between species. However, central metabolism represents only a small fraction of the biosynthetic repertoire of microbes: metabolites such as antimicrobial compounds, signaling molecules, and co-factors are underexplored in their potential to shape microbial communities. Here, we focus on B vitamin exchange in marine bacterial communities that degrade polysaccharides, a key component of particulate organic matter. We found that in a screen of 150 natural isolates, almost a third were auxotrophs for one or more B vitamins. By measuring physiological parameters such as uptake affinities and comparing those to ambient seawater concentrations, we showed that marine bacteria live at the edge of vitamin limitation in the environment. To understand how auxotrophs survive in the open oceans, we used our experimental data to model vitamin cross-feeding on particles through both secretion and lysis. Our results highlight the importance of vitamin auxotrophies in shaping microbial community assembly and succession, adding another layer of complexity to the trophic structure of particle-associated communities.},
}

*Seawater/microbiology/chemistry
*Bacteria/metabolism/classification/isolation & purification/genetics
*Vitamins/metabolism
Polysaccharides/metabolism
*Microbiota

@article {pmid40959279,
year = {2025},
author = {Liu, X and Chen, Z and Lin, J and Lian, Y and Gan, W and Liu, H and Huang, X and Mei, J and Ma, T and Lu, Z and Zeng, W and Gong, Y and Chen, S and He, W},
title = {DLGAP5 Promotes Acute Liver Injury via Hepatocyte Pyroptosis-Driven Macrophage Metabolic Reprogramming and M1 Polarization.},
journal = {International journal of biological sciences},
volume = {21},
number = {12},
pages = {5563-5585},
pmid = {40959279},
issn = {1449-2288},
mesh = {Animals ; *Pyroptosis/physiology/genetics ; *Hepatocytes/metabolism ; Mice ; *Macrophages/metabolism ; Methyltransferases/metabolism/genetics ; Mice, Inbred C57BL ; Mice, Knockout ; Male ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; Inflammasomes/metabolism ; Metabolic Reprogramming ; },
abstract = {Pyroptosis is a novel programmed cell death that exists in inflammatory diseases and methyltransferase-like 3 (METTL3) is a core N6-methyladenosine (m6A) modified methyltransferase that has been shown to regulate cell fate. However, the role of pyroptosis in acute liver injury (ALI) is still unknown and whether it is regulated by m6A modification needs to be elucidated. Here, Mettl3 mutant and Nlrp3 knockout mouse were constructed, CCl4- and TAA-induced ALI models were established and primary cells were isolated, and cell pyroptosis and m6A modification were evaluated. We found that hepatocyte pyroptosis is a key characteristic of ALI, and METTL3-mediated m6A modification was upregulated in hepatocytes during ALI. Inhibition of METTL3-mediated m6A modification alleviated hepatocyte pyroptosis and ALI. Through MeRIP-seq analysis and verification, Dlgap5 was determined as the target of METTL3-mediated m6A modification, which was regulated in an IGF2BP2-dependent manner. Mechanistically, METTL3 can bind to DLGAP5, and then DLGAP5 promoted pyroptosis through NF-κB-dependent NLRP3 inflammasome activation and direct potentiation of inflammasome structure formation and assembly. Mettl3 mutation or AT9283-mediated DLGAP5 inhibition alleviated pyroptosis and ALI. The effects of hepatocyte pyroptosis on cell interaction were then explored and we revealed that NLRP3 inflammasome and interleukin releasing by the GSDMD-N-dependent membrane pores from pyroptotic hepatocytes activated macrophage metabolic reprogramming and M1 polarization, further exacerbating ALI. Nlrp3 deficiency alleviated ALI by suppressing hepatocyte pyroptosis and blocking communication between macrophages and hepatocytes. Our findings indicate the potential mechanisms of ALI from an intercellular communication perspective, and targeted-inhibition of DLGAP5 and -blockade of hepatocyte-macrophage interaction provide promising strategies for ALI treatment.},
}

Animals
*Pyroptosis/physiology/genetics
*Hepatocytes/metabolism
Mice
*Macrophages/metabolism
Methyltransferases/metabolism/genetics
Mice, Inbred C57BL
Mice, Knockout
Male
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics
Inflammasomes/metabolism
Metabolic Reprogramming

@article {pmid40958166,
year = {2025},
author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG},
title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70178},
doi = {10.1111/1462-2920.70178},
pmid = {40958166},
issn = {1462-2920},
support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; },
abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.},
}

*Metagenome
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism
Soil Microbiology
Phylogeny
*Microbiota/genetics
Computational Biology/methods
*Bacterial Proteins/genetics/chemistry
*Databases, Protein
Protein Conformation

@article {pmid40957333,
year = {2025},
author = {Sánchez, N and Merbach, I and Drabesch, S and Blagodatskaya, E and Jamoteau, F and Keiluweit, M and Bachelder, J and Tarkka, M and Muehe, EM},
title = {Bioavailability and phyto-extractability of metals in a peat-amended agricultural soil under climate stress.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127167},
doi = {10.1016/j.jenvman.2025.127167},
pmid = {40957333},
issn = {1095-8630},
abstract = {Climate-induced mobilization of harmful metals in soils with a pH below 7 threatens food safety through plant uptake. While organic amendments like peat are known to immobilize metals, it remains unclear how their immobilization effectiveness changes under future climate scenarios and whether there is an optimal amendment threshold before immobilization turns into re-mobilization. This study assessed how varying peat input levels (3, 5 and 8 %) and projected climatic conditions (+4 °C, +320 ppmv CO2) affect metal fractionation, bioavailability, and uptake by a metal-tolerant plant in historically contaminated soils. Intermediate 5 % peat levels enhanced metal immobilization via organic matter complexation, reducing exchangeable Zn and Cd ∼2-fold compared to 3 % peat, despite acidification. At high 8 % peat input, a 0.65-unit pH decline and increased dissolved organic matter reversed this trend, increasing exchangeable Zn and Cd > 2-fold relative to 5 % peat. Chemical equilibrium modeling (WHAM VII) confirmed greater metal complexation with dissolved organic matter at higher 5-8 % peat levels. Under future climatic conditions-elevated temperature and CO2-metal immobilization improved at low 3 % peat input, likely due to stable organic matter and functional group buffering. Nevertheless, metal re-mobilization occurred at higher peat inputs, likely due to enhanced peat decomposition. Despite these variations, plant Cd uptake remained low across peat and climate treatments. This emphasizes peat's protective role against Cd while maintaining the plant's nutritional status for Zn. This study highlights the dual effects of peat amendments: intermediate levels optimize metal immobilization, but excessive amendments may destabilize harmful metals, especially under future conditions.},
}

@article {pmid40954372,
year = {2025},
author = {Jauri, PV and Silva, C and Massa, AM},
title = {Early shifts in soil microbial community structure and functions upon application of a biofertilizer in a kaki (Diospyros kaki) orchard.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40954372},
issn = {1874-9356},
abstract = {Biofertilizers are key tools for sustainable agriculture and soil health Maintenance, yet their specific effects on soil functions and microbiota remain unclear. In order to address this, we aimed to evaluate how a biofertilizer alters soil microbial communities, physicochemical properties, and functions after 18 months of periodical use in a kaki monoculture. We found that the biofertilizer indirectly reshaped microbial community structure-especially bacterial diversity-likely through interactions with the native microbiome. Functional changes included increased microbial biomass, nitrogen mineralization, and dehydrogenase activity, with reduced acid phosphatase activity. The composition of bacterial and fungal communities exhibited significant differences between biofertilizer-treated soils and control soils across most evaluated taxonomic levels. Biodiversity was altered with biofertilizer application in bacterial communities, while fungal communities were less affected. Microbial co-occurrence networks differed between the two soil treatments, although a few patterns were consistent among treated and control soils. A novel contribution of this work is the integration of co-occurrence network analysis with microbial functional traits, revealing that core microbial networks linked to nitrogen and phosphate cycling persist despite disturbance. These findings highlight the role of microbial biodiversity and community assembly in sustaining soil functions under biofertilizer application.},
}

@article {pmid40952163,
year = {2025},
author = {Nir, I and Armoza-Zvuloni, R and Barak, H and De Los Ríos, A and McKay, CP and Kushmaro, A},
title = {The Biology, Microclimate, and Geology of a Distinctive Ecosystem Within the Sandstone of Hyper-Arid Timna Valley, Israel.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70188},
doi = {10.1111/1758-2229.70188},
pmid = {40952163},
issn = {1758-2229},
support = {PID2023-147027NB-I00B//Agencia Estatal de Investigación. Write: Agencia Estatal de Investigacion (AEI), MICINN/ ; EXO-92-4//NASA AMES/ ; 3-17370//Minstry of Science and Technology (MOST), Israel/ ; },
abstract = {Microbial endolithic communities in the sandstone rocks of the southern Negev Desert, particularly in Timna Park, were initially discovered by Imre Friedmann and Roseli Ocampo-Friedmann in their pioneering study about 50 years ago. Nonetheless, this harsh microecosystem, dominated by cyanobacterial taxa, raises questions about the adaptive mechanisms that enable the survival of these microorganisms. The present study provides comprehensive data, including extensive precipitation records for the Timna Valley, and multi-year microclimatic data from a colonised site. It includes examinations of rock structure, as well as microscopic and metagenomic analysis. Our findings point to a distinct bacterial endolithic population dominated by the cyanobacterial genus Chroococcidiopsis. Although the taxa are well known, we show here how their exclusive persistence is driven by the sandstone's fine porosity and thermal properties, combined with rare, low-volume precipitation. This highly selective microenvironment highlights how specific rock and climate interactions can filter microbial diversity in hyper-arid deserts. Additionally, it demonstrates an adaptation strategy based on both short-term and decadal-scale dormancy. Thus, it offers new insights for the survival of these unique ecosystems and provides valuable perspectives for astrobiology and the search for evidence of microbial life on Mars.},
}