@article {pmid40361556,
year = {2025},
author = {Li, J and Wu, J and Tu, M and Xiao, X and Hu, K and Li, Q and Zhao, N and Liu, A and Ao, X and Hu, X and Liu, S},
title = {Interaction Between Lactic Acid Bacteria and Acetic Acid Bacteria in Sichuan Bran Vinegar: Impact on Their Growth and Metabolites.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091471},
pmid = {40361556},
issn = {2304-8158},
support = {2024NSFSC2079//Science and Technology Department of Sichuan Province/ ; },
abstract = {Microbial interactions are essential for maintaining the stability and functionality of microbiota in fermented foods. In this study, representative strains of predominant lactic acid bacteria and acetic acid bacteria in Sichuan bran vinegar were selected, and their interactions in a simulated solid-state fermentation system were investigated. The results reveal that the biomass of A. pasteurianus LA10 significantly increased in both the co-culture and the pure culture, whereas the biomass of L. amylovorus LL34 in the co-culture (6.44 ± 0.30 lg CFU/g) was significantly lower than that in the pure culture (7.28 ± 0.30 lg CFU/g) (p < 0.05), indicating a partially harmful symbiosis between these two strains. The metabolic analysis shows that total acid (21.82 mg/g) and acetic acid (9.53 mg/g) contents in the co-culture were lower than those in the pure culture of LA10, suggesting that LL34 inhibited the acid-producing activity of LA10 to some extent. The interaction between the two bacteria also influenced the production of volatile compounds and non-volatile compounds, as revealed by GC-MS and untargeted UHPLC-MS/MS, respectively. Significant enrichment of acid and amino acid metabolism pathways was observed in the co-culture, revealing the impact of bacterial interactions on flavor development. This study provides valuable insights into the advancement of vinegar brewing technology.},
}

@article {pmid40360784,
year = {2025},
author = {Voolstra, CR and Schlotheuber, M and Camp, EF and Nitschke, MR and Szereday, S and Bejarano, S},
title = {Spatially restricted coral bleaching as an ecological manifestation of within-colony heterogeneity.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {740},
pmid = {40360784},
issn = {2399-3642},
support = {468583787//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Anthozoa/physiology/microbiology ; Coral Reefs ; *Coral Bleaching ; Symbiosis ; Ecosystem ; Dinoflagellida/physiology ; },
abstract = {Coral bleaching is a widespread stress response of reef-building corals to elevated sea temperatures, resulting in the loss of symbiotic algae and often leading to coral death and reef degradation. Although coral bleaching occurs globally, not all reefs, species, colonies, or polyps bleach equally. Understanding intra-colony bleaching heterogeneity is crucial to anticipate the extent of coral loss at 2°C warming and harness variability to inform restorative interventions. Partially bleached coral colonies are commonly documented yet rarely tracked to determine whether they reflect ecologically distinct heterogeneity (e.g., in thermal tolerance) or eventually bleach completely. Focusing on bleaching that appears restricted to certain areas within a coral colony, we examine its putative basis in the spatial variability of the holobiont. A coral's three-dimensional structure creates mosaics of microenvironments. Adaptations to these microenvironments are underpinned by intra-colony differences in Symbiodiniaceae association, microbiome assemblage, and nutritional status, giving rise to microhabitats. Genetic mosaicism and epigenetic changes further contribue to intra-colony phenotypic heterogeneity. We pinpoint methodologies to align spatially restricted bleaching to different forms of coral surface heterogeneity, examine the common assumption that coral fragments represent entire colonies, and illuminate implications for coral biology and restoration.},
}

Animals
*Anthozoa/physiology/microbiology
Coral Reefs
*Coral Bleaching
Symbiosis
Ecosystem
Dinoflagellida/physiology

@article {pmid40359357,
year = {2025},
author = {Zhao, X and Hou, X and Zhou, W and Yan, H and Wen, H and Jiang, H and Tan, L},
title = {Variation of [239,240]Pu in Coral and Its Response to the Climate System in South China Sea.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c02025},
pmid = {40359357},
issn = {1520-5851},
abstract = {With the acceleration of climate change, understanding the behavior of the anthropogenic radioactive substances─particularly their responses to the climate system─has become critical for assessing their transport, transfer, and impact on the ecosystems. However, this remains underexplored, particularly in the South China Sea (SCS), where radioactivity is derived from both the close-in fallout of the Pacific Proving Ground (PPG) and the global fallout. Additionally, this region is quite sensitive to climate change. A coral core collected from Xisha Island, SCS, was initially analyzed for high-radiotoxicity [239,240]Pu. Approximately 72-84% of plutonium in coral originated from the close-in fallout of PPG through ocean current compared to the direct global fallout. However, the [239,240]Pu concentration still remains in background levels and does not show a significant radiation risk. After 1980, a distinct pattern emerged characterized by a "higher" concentration but a "lower" [240]Pu/[239]Pu atom ratio compared to the levels in the open west Pacific. This is primarily attributed to the seasonal upwelling of subsurface seawater on the continental shelf of SCS, driven by the prevailing southwest monsoon. Significantly elevated [239,240]Pu concentrations were observed during typical ENSO years 1983, 1988, and 1997. This is due to the elevated temperature, coral bleaching, and expulsion of symbiotic zooxanthellae. After expulsion, zooxanthellae containing higher [239,240]Pu compared to skeleton rapidly die, and their debris directly deposit onto the coral skeleton, in contrast to the metabolic way of [239,240]Pu during normal years. This finding offers critical insights into ecosystem protection in SCS amid global changes and the potential threat of nuclear contamination.},
}

@article {pmid40358997,
year = {2025},
author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and , and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R},
title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e64894},
doi = {10.2196/64894},
pmid = {40358997},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; },
abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.

OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote français" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.

METHODS: "Le French Gut - Le microbiote français" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Système National des Données de Santé). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.

RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.

CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.

DERR1-10.2196/64894.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
France
*Life Style
Feces/microbiology
*Diet
Adult
Prospective Studies
*Health Status
Female
Male
Metagenomics/methods

@article {pmid40358698,
year = {2025},
author = {Hasali, NHM and Shahbaz, M and Seelan, JSS and Ibrahim, NA and Wiart, C and Arumugam, N and Salam, MA and Musthafa, MM and Appalasamy, S},
title = {Endophytes of Zingiberaceae: distribution and bioactivity of their bioactive metabolites.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {145},
pmid = {40358698},
issn = {1432-072X},
mesh = {*Endophytes/metabolism/chemistry ; *Zingiberaceae/microbiology ; Anti-Bacterial Agents/pharmacology ; Plant Growth Regulators/metabolism ; Bacteria/metabolism ; Anti-Infective Agents/pharmacology ; },
abstract = {The endophytes associated with the Zingiberaceae family have demonstrated remarkable potential in various biological activities through their bioactive compounds that are useful for both medical and agricultural purposes. Additionally, isolated secondary metabolites from symbiotic microbes associated with this family of plants have shown promising results in various biological activities such as antifungal, anticancer, antidiabetic, anti-inflammatory, and antibacterial. This review focuses on the bioactive metabolites of Zingiberaceae endophytes with their potential biological activities against different pathogens as well as the production of phytohormones that promote plant growth. Furthermore, bibliometric analysis revealed the current key trends and collaborative works in this field. Additionally, the bibliometric analysis also explored a total of 75 relevant publications from the Scopus database that India is the most contributing country in this field with 38.7% of the total reported research work. The bibliometric approach helps uncover new research gaps by identifying emerging trends, underexplored topics, and collaborative networks, providing insights into areas that require further investigation and development. Notably, Streptomyces spp. have been commonly reported as potent endophytes, generating bioactive substances such as Vanillin and Resacetophenone with strong antibacterial activities. Significant knowledge gaps still exist, and with evolving therapeutic potential, this could offer a wide opportunity for new studies to emerge.},
}

*Endophytes/metabolism/chemistry
*Zingiberaceae/microbiology
Anti-Bacterial Agents/pharmacology
Plant Growth Regulators/metabolism
Bacteria/metabolism
Anti-Infective Agents/pharmacology

@article {pmid40357979,
year = {2025},
author = {Ntiri, ES and Chun Nin Wong, A},
title = {Microbial metabolites as engines of behavioral variation across animals.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2501191},
doi = {10.1080/19490976.2025.2501191},
pmid = {40357979},
issn = {1949-0984},
mesh = {Animals ; *Behavior, Animal/physiology ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism/genetics/classification ; Vertebrates/physiology/microbiology ; Invertebrates/physiology/microbiology ; Humans ; Circadian Rhythm ; Signal Transduction ; },
abstract = {The microbiome, especially that present in the gut, has emerged as a key modulator of animal behavior. However, the extent of its influence across species and behavioral repertoires, as well as the underlying mechanisms, remains poorly understood. Increasing evidence suggests that microbial metabolites play an important role in driving behavioral variation. In this review, we synthesize findings from vertebrates to invertebrates, spanning both model and non-model organisms, to define key groups of microbial-derived metabolites involved in modulating seven distinct behaviors: nutrition, olfaction, circadian rhythms, reproduction, locomotion, aggression, and social interactions. We discuss how these microbial metabolites interact with host chemosensory systems, neurotransmitter signaling, and epigenetic modifications to shape behavior. Additionally, we highlight critical gaps in mechanistic understanding, including the need to map additional host receptors and signaling pathways, as well as the untapped potential of microbial biosynthetic gene clusters as sources for novel bioactive compounds. Advancing these areas will enhance understanding of the microbiome's role in behavioral modulation and open new avenues for microbiome-based interventions for behavioral disorders.},
}

Animals
*Behavior, Animal/physiology
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism/genetics/classification
Vertebrates/physiology/microbiology
Invertebrates/physiology/microbiology
Humans
Circadian Rhythm
Signal Transduction

@article {pmid40357892,
year = {2025},
author = {Neubauer, A and Iniesta-Pallarés, M and Álvarez, C and Bailly, A and Szövényi, P and Mariscal, V},
title = {Quantitative Assessment of Hormogonia Induction in Nostoc punctiforme by a Fluorescent Reporter Strain.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf197},
pmid = {40357892},
issn = {1460-2431},
abstract = {While symbiotic plant-cyanobacteria interactions hold significant potential for revolutionizing agricultural practices by reducing the application of artificial nitrogen fertilizers, the genetic underpinnings of the symbiotic interaction between the plant host and the cyanobiont remain poorly understood. In particular, the molecular mechanisms through which host plants induce the formation of motile cyanobacterial filaments (hormogonia), essential for colonization and initiation of symbiosis, are not well characterized. In this study, we present a novel yet objective method for quantifying hormogonia induction, addressing limitations of traditional qualitative approaches. We have developed a reporter strain of Nostoc punctiforme PCC 73102 capable of quantifying hormogonia induction in response to diverse biotic and abiotic stimuli. This reporter strain, generated via triparental mating conjugation transformation, contains the promoter sequence of prepilin pilA fused to a green fluorescent protein (GFP) and enables quantitative and high throughput monitoring of hormogonia induction using a microplate reader. Our innovative approach, using a cyanobacterial hormogonia reporter strain, allows high-throughput screening of the hormogonia-inducing effect of a wide array of environmental and plant signals. This method is expected to greatly advance our understanding of the genetic determinants underpinning plant-cyanobacteria symbioses.},
}

@article {pmid40357891,
year = {2025},
author = {Salem, MA and Jamil, M and Wang, JY and Berqdar, L and Liew, KX and Paramita, A and Ablazov, A and Balakrishna, A and Al-Babili, S},
title = {Disruption of the Karrikin Receptor DWARF 14 LIKE (D14L) Gene Leads to Distinct Effects on Root and Shoot Growth, and Reprogramming of Central Metabolism in Rice.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf201},
pmid = {40357891},
issn = {1460-2431},
abstract = {The rice (Oryza sativa L.) α/β hydrolase D14 LIKE (D14L), a paralog of the strigolactone receptor D14, is essential for the establishment of arbuscular mycorrhizal (AM) symbiosis and responses to karrikins, smoke-derived compounds that regulate several developmental processes. It is supposed that D14L is the receptor for a yet unidentified endogenous growth regulator. Herein, we determined the effects of disrupting the D14L on rice growth and metabolism. Our results revealed that the D14L loss of function altered rice architecture, leading to a significant increase in root growth and mesocotyl elongation, while hindering shoot growth, and a notable decrease in the number of tillers, especially under phosphate limiting conditions. Furthermore, d14l mutants exhibited significant reduction in the total grain yield. Metabolomics analysis revealed a notable shift of key metabolites, such as carbohydrates and amino acids involved in energy production and growth, from shoots to roots. This redistribution likely reflects an adaptive strategy to enhance nutrient acquisition and increase root biomass, albeit at the cost of shoot growth and productivity. Our findings highlight the pivotal role of D14L in regulating the root-to-shoot growth ratio and in coordinating the metabolism and allocation of resources across the rice plant.},
}

@article {pmid40357403,
year = {2025},
author = {Mejías, S and Jiménez, NE and Conca, C and Salgado, JC and Gerdtzen, ZP},
title = {Unveiling Wolbachia transcriptomic signature in the arboviral vector Aedes aegypti.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1538459},
pmid = {40357403},
issn = {2235-2988},
mesh = {Animals ; *Wolbachia/genetics/physiology ; *Aedes/microbiology/genetics/virology ; *Mosquito Vectors/microbiology/genetics/virology ; Symbiosis/genetics ; *Transcriptome ; Gene Expression Profiling ; Female ; },
abstract = {INTRODUCTION: The mosquito Aedes aegypti is the main vector of arboviral diseases such as dengue and imposes a global health burden. A promising control strategy is to infect A. aegypti populations with Wolbachia, a genus of intracellular bacteria capable of blocking arboviral infections. Enhancing and preserving the efficacy of this method will depend on a solid mechanistic knowledge of the A. aegypti-Wolbachia symbiosis. By identifying differences between Wolbachia-infected and uninfected A. aegypti, previous transcriptomic studies proposed a wide range of symbiotic interactions, but a systematic identification of consistent effects across datasets is still missing.

METHODS: To identify A. aegypti genes and functions consistently affected by Wolbachia, we performed differential expression and functional enrichment analysis on published transcriptomic datasets, followed by a meta-analysis of the obtained p-values using the maxP method. Six datasets were retrieved from Gene Expression Omnibus, Sequence Read Archive and ArrayExpress (last searched in July 2024, considering lack of replication as the exclusion criteria). After discarding one dataset from wAlbB-infected cell line due to poor mapping to the A. aegypti genome, the data comprised adult female A. aegypti heads, muscles, carcasses, midguts and bodies, and Wolbachia strains wMel and wMelPop.

RESULTS AND DISCUSSION: Meta-analysis revealed 10 and 21 consistently down- and upregulated host genes, some of which have escaped the focus of previous research, including the consistently downregulated exonuclease AAEL009650 which has a pro-dengue virus homolog in Drosophila. At the function level, we found consistent upregulation of electron transport chain (ETC), carbohydrate transport and serine-type peptidase activity and inhibition, and downregulation of DNA replication. ETC upregulation suggests an alternative mechanism for Wolbachia's induction of antiviral oxidative stress, previously attributed to dual- and NADPH-oxidases which here showed downregulation or no regulation. Through analysis of previously published datasets, this work identifies promising molecular and functional targets for future studies aimed at elucidating the most fundamental mechanisms of the A. aegypti-Wolbachia symbiosis.},
}

Animals
*Wolbachia/genetics/physiology
*Aedes/microbiology/genetics/virology
*Mosquito Vectors/microbiology/genetics/virology
Symbiosis/genetics
*Transcriptome
Gene Expression Profiling
Female

@article {pmid40356659,
year = {2025},
author = {Zheng, X and Liu, R and Li, K and Sun, J and Wang, K and Shao, Y and Hu, Z and Zhu, J and Pan, Z and Nakhla, G},
title = {Microalgae-bacteria symbiosis enhanced nitrogen removal from wastewater in an inversed fluidized bed bioreactor: performance and microflora.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1591974},
pmid = {40356659},
issn = {1664-302X},
abstract = {Conventional wastewater biological nitrogen removal (BNR) processes require a large amount of air and external organic carbon, causing a significant increase in operating costs and potential secondary pollution. Herein, this study investigated the nitrogen removal performance and the underlying mechanisms of a novel simultaneous nitrification and denitrification (SND) coupled with photoautotrophic assimilation system in an inversed fluidized bed bioreactor (IFBBR). Nitrogen removal was achieved through the synergistic interaction of microalgae and bacteria, with microalgae providing O2 for nitrification and microbial biomass decay supplying organic carbon for denitrification. The IFBBR was continuously operated for more than 240 days without aeration and external organic carbon, the total nitrogen (TN) removal efficiency reached over 95%. A novel C-N-O dynamic balance model was constructed, revealing that nitrification and denitrification were the primary pathways for nitrogen removal. The model further quantified the microbial contributions, showing that microalgae generated O2 at a rate of 81.82 mg/L·d, while microbial biomass decay released organic carbon at a rate of 148.66 mg/L·d. Microbial diversity analysis confirmed the majority presence of microalgae (Trebouxiophyceae), nitrifying bacteria (Gordonia and Nitrosomonas) and denitrifying bacteria (Ignavibacterium and Limnobacter). This study successfully achieved enhanced nitrogen removal without the need for aeration or external organic carbon. These advancements provide valuable insights into efficient wastewater nitrogen removal, offering significant benefits in terms of reduced energy consumption, lower operational costs, and decreased CO2 emissions.},
}

@article {pmid40355047,
year = {2025},
author = {Yu, J and Wang, D and Zhao, T and Yu, X and Liu, S and Wang, Y and Wang, K and Zhao, M and Chen, P and Wang, Y and Zhang, M},
title = {Potential Participants and Regulatory Factors in Ginsenoside Biosynthesis of Panax Ginseng C.A. Meyer: The Role of Endophytic Fungus PBF-08.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {112553},
doi = {10.1016/j.plantsci.2025.112553},
pmid = {40355047},
issn = {1873-2259},
abstract = {Panax ginseng C.A. Meyer was recognized as a precious traditional Chinese medicine with a long history of application. It is widely used due to its high medicinal value. Ginsenosides were identified as a group of triterpenoid secondary metabolites in ginseng and were considered the main active ingredients of ginseng. Plant endophytes were recognized as microorganisms that resided within plant tissues, coexisting with the host plant for part or all of their life cycle and interacting with the external environment together. Ginseng endophytes, as symbiotic microorganisms with ginseng, possess various functions such as enhancing yield, increasing resistance, and improving quality, making them an important microbial resource for potential utilization. In this study, we screened and identified an endophytic fungus PBF-08, which has the ability to produce ginsenosides Rg2, Rg3, and Re. By optimizing its fermentation conditions using the response surface methodology, the total ginsenoside yield was significantly increased. Additionally, ginseng adventitious roots were treated with strain PBF-08 as an elicitor, which significantly increased the ginsenoside content by regulating the expression of key enzyme genes in the ginsenoside biosynthesis pathway under optimal treatment concentration and time. Widely targeted metabolomic analysis revealed that strain PBF-08 not only possesses a complete and active terpenoid biosynthesis pathway but also synthesizes various metabolites that influence plant growth and metabolism. In summary, the strain PBF-08 was found to have potential application value in exploring new methods for obtaining ginsenosides and in developing microbial elicitors for regulating ginsenoside biosynthesis.},
}

@article {pmid40351789,
year = {2025},
author = {Bourgeois, D and Orsini, G and Carrouel, F},
title = {Editorial: Exploring oral microbiota dysbiosis as a risk factor for oral and non-communicable diseases.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1611120},
pmid = {40351789},
issn = {2673-4842},
}

@article {pmid40349586,
year = {2025},
author = {Wang, X and Du, C and Li, Y and Liu, S and Zeng, X and Li, Y and Wang, S and Jia, Y},
title = {Metal pollution-induced alterations in soil fungal community structure and functional adaptations across regional scales.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138553},
doi = {10.1016/j.jhazmat.2025.138553},
pmid = {40349586},
issn = {1873-3336},
abstract = {Soil contamination with heavy metal(loid)s (HMs) threatens soil ecosystem health and function. However, how cross-regional HM contamination influences the structure and function of soil fungal communities remains understudied. We conducted a large-scale soil survey in southern China, using the Nemerow synthetic Pollution Index to assess contamination levels of seven metals (copper, lead, cadmium, arsenic, nickel, zinc and chromium). Soils were classified as low, medium, and high contamination (LC/MC/HC) to examine HM biogeographic patterns and their ecological impacts on soil fungi along the gradient. Cd was the most prevalent contaminant, followed by As in all the studied soils. The combined soil pollution significantly altered fungal community structure, with Cd and Pb identified as key drivers of structural and evenness changes, respectively. Fungal diversity and evenness declined with pollution, accompanied by reduced Staphylotrichum (-0.45 %) and Saitozyma (-1.5 %). Homogeneous selection dominated the assembly processes of soil fungal communities across all contamination levels (contributing 55.8-64.9 %). The most enriched characteristic species included Eurotiomycetes (LC), Sordariales (MC), and Coniochaeta (HC). Pollution-induced habitat heterogeneity enhanced the complexity and stability of fungal symbiotic networks, with 10.0 % more synergistic interactions in highly contaminated soils. The abundance of potential pathogenic fungi increased by 3.0-5.8 % in highly polluted soils compared to low- and moderately polluted soils, indicating possible negative implications for ecosystem health. Our findings provide novel and comprehensive insights into the ecological response of soil fungal communities to HM contamination.},
}

@article {pmid40349544,
year = {2025},
author = {Guo, X and Huang, L and Miao, H and Mi, L and Han, Z},
title = {Exploring carbon reduction pathways in the steel industry from the perspective of emerging technologies for achieving carbon neutrality.},
journal = {Journal of environmental management},
volume = {385},
number = {},
pages = {125768},
doi = {10.1016/j.jenvman.2025.125768},
pmid = {40349544},
issn = {1095-8630},
abstract = {The iron and steel industry (ISI) plays a pivotal role in global decarbonization efforts, yet achieving carbon neutrality remains a significant challenge due to the sector's high emissions and technological complexity. Strategically identifying emerging technologies is critical for aligning industrial transformation with climate goals, optimizing resource allocation, and mitigating transition risks in a rapidly evolving technological landscape. This study bridges this gap by developing a multi-source data analytical framework that integrates Topmine phrase mining, K-means clustering, and Text2vec similarity analysis. The framework enhances the identification of emerging technologies through a reverse verification mechanism, ensuring the robustness of clustering results. By systematically classifying technologies into hot, growing, mature, and weak-signal categories, this study uncovers key technological pathways shaping the future of ISI decarbonization. Additionally, topic phrase burst analysis is employed to forecast technology evolution trends, revealing key shifts such as multi-technology integration for synergistic effects, intelligent process optimization, and industrial symbiosis. These methodological advancements not only provide a replicable toolkit for strategic decision-making but also empower stakeholders to prioritize investments, foster cross-sector collaboration, and accelerate the ISI's transition to carbon neutrality. The findings offer a transformative roadmap for policymakers and enterprises to navigate technological uncertainties while balancing economic competitiveness and environmental imperatives.},
}

@article {pmid40348264,
year = {2025},
author = {Hu, Z and Li, Z and Xu, Y and He, F and Zhang, J and Li, T},
title = {MgFe-LDHs/Vallisneria natans combined system for simultaneous elimination of endogenous N and P pollution in eutrophic water: Performance, synergetic mechanism, and metagenomics analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121798},
doi = {10.1016/j.envres.2025.121798},
pmid = {40348264},
issn = {1096-0953},
abstract = {Eutrophication is the main factor for the degradation of lake ecosystems. More than exogenous input, endogenous N and P nutrients are responsible for it. Although the P passivation technology with functional materials is common for alleviating endogenous P pollution, will it have the same effect for endogenous N removal? In this study, a novel MgFe-LDHs/Vallisneria natans (V. natans) combined system was established for effective eliminating endogenous N and P simultaneously. During remediation periods, MgFe-LDHs/V. natans combined system with the most obvious improvement for overlying water quality that was reflected by DO, ORP, and SS, and TP, TN, and NH4[+]-N removal efficiency were up to 99%. In sediments, TP and TN removal rate was approximately 68% and 63%, where the reduction of Org-P and NH4[+]-N accounted for the majority of it, respectively. Under stimulation of MgFe-LDHs, NH4[+]-N assimilation in V. natans could be promoted through improving the metabolizing enzymes activity. In turn, V. natans contributed to Org-P mineralization by secreting organic acid, further facilitating IP enrichment on MgFe-LDHs. Additionally, owing to the synergism between V. natans allelopathy and MgFe-LDHs, the symbiotic relationship between microbial communities was much closer and more stable, the expression of functional genes that relate to denitrification, assimilatory nitrate reduction, phosphorylation and organophosphorus mineralization processes were up-regulated prominently. That is, microorganisms acted synergistically were important for endogenous N and P elimination performance. This study proposed a high-efficiency and environmentally friendly materials/plants combined remediation technology for eutrophication, especially those where with much high endogenous N and P loading.},
}

@article {pmid40347990,
year = {2025},
author = {Wang, Y and Ekblom, C and Kruangkum, T and Uribeondo, JD and Söderhäll, K and Söderhäll, I},
title = {Specific host factors determine resistance in a North American crayfish to the crayfish plague, Aphanomyces astaci.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {110392},
doi = {10.1016/j.fsi.2025.110392},
pmid = {40347990},
issn = {1095-9947},
abstract = {The crayfish plague is caused by the oomycete Aphanomyces astaci with North American crayfish (for example Pacifastacus leniusculus and Procambarus clarkii) serving as carriers and vectors for this pathogen. This poses a constant threat to native crayfish in Europe, Asia, South America and Australia, which all are highly susceptible to this pathogen. In this study we now show how the symbiotic balance between the pathogen and its host are maintained at the molecular level. The host factors involved in this balance between the pathogen, A. astaci and the host, P. leniusculus, are one glycine-rich antimicrobial peptide (GRP) that is specifically active against A. astaci, but not to other microorganisms and two Kazal proteinase inhibitors (KPI2 and KPILA) inhibit secreted A. astaci proteases by binding to subtilisin enzymes from the pathogen. Accordingly, the expression of GRP, KPI2, KPILA, as well as proPO mRNAs increases following A. astaci infection. Silencing GRP, or KPI2 + KPILA mRNAs results in death of the crayfish from infection. Over time, this host-pathogen relationship has evolved to allow resistant crayfish to coexist with A. astaci in their cuticle for life, provided critical components remain unaltered by environmental changes or other pathogens. It is unclear whether a similar relationship could develop between currently susceptible crayfish and A. astaci.},
}

@article {pmid40346478,
year = {2025},
author = {de Oliveira, BR and Zuffo, AM and Dos Santos Silva, FC and Steiner, F and AlGarawi, AM and Okla, MK and Nhs, M and Alhaj Hamoud, Y and Josko, I and Sheteiwy, MS and Alyafei, MS and Sulieman, S},
title = {Random forest algorithms: a tool to identify the impact of arbuscular mycorrhizal fungi inoculation, seed maturation stage and geographic diversity of Pimpinella anisum L. accessions on the physicochemical composition of seeds.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {608},
pmid = {40346478},
issn = {1471-2229},
support = {RSPD2024R931//King Saud University/ ; RSPD2024R931//King Saud University/ ; },
mesh = {*Mycorrhizae/physiology ; *Seeds/growth & development/microbiology/chemistry ; *Algorithms ; *Pimpinella/microbiology/growth & development/chemistry ; Symbiosis ; Principal Component Analysis ; Random Forest ; },
abstract = {BACKGROUND: A study using random forest (RF) algorithms and principal component analysis (PCA) was proposed to identify the effects of arbuscular mycorrhizal fungal inoculation, the seed maturation stage and the geographic diversity of Pimpinella anisum L. accessions on the physicochemical composition of seeds. Seeds of six anise varieties from North African and Middle Eastern accessions were inoculated or not inoculated with AMF (an arbuscular mycorrhizal fungus) and then grown under controlled conditions. Seeds were harvested at three different maturity stages: mature seeds (157 d after sowing), premature seeds (147 d after sowing), and immature seeds (137 d after sowing). Forty-nine variables related to physical properties, total nutrients, metabolic compounds, essential oils, and biological activity were measured in P. anisum seeds.

RESULTS: The RF algorithm allows the differentiation of P. anisum varieties inoculated with AMF from different countries in North Africa and the Middle East. This evidence proves that the geographic origin of P. anisum seeds significantly influences the efficiency of the symbiotic association between anise roots and AMF. In turn, no significant effects of the seed maturation stage on the symbiotic interaction of plants with mycorrhizae were observed. The chemical compounds related to the biological activity of seeds are not influenced by AMF, followed by chemical compounds related to metabolism, total nutrients, and oil components.

CONCLUSIONS: The performance of classification models using RF is driven primarily by independent variables related to the chemical composition of anise seeds, overshadowing the effects of geographic diversity and the seed maturation stage. Among the chemical constituents of the seed, the variables belonging to the biological activity category best contain information (patterns) on the impacts of AMF inoculation.},
}

*Mycorrhizae/physiology
*Seeds/growth & development/microbiology/chemistry
*Algorithms
*Pimpinella/microbiology/growth & development/chemistry
Symbiosis
Principal Component Analysis
Random Forest

@article {pmid40345999,
year = {2025},
author = {Bačić, A and Abboud, KY and Zhang, Y and Rajilić-Stojanović, M},
title = {Yarrow (Achillea millefolium) Extract Modulates the Gut Microbiota Composition and Activity in the TIM-2 In Vitro Model of the Colon.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70074},
doi = {10.1002/mnfr.70074},
pmid = {40345999},
issn = {1613-4133},
support = {451-03-68/2022-14/200135//Science and Technological Development of the Republic of Serbia/ ; 101060130//Horizon Europe 2021-2027 research and innovation program, TwinPrebioEnz/ ; },
abstract = {Phenolic compounds, abundantly found in medicinal herbs, may promote health by modulating the gut microbiota. Yarrow is a traditional remedy for digestive and non-gastrointestinal diseases with unexplored interaction with gut microbes. This study aimed to evaluate the effects of yarrow extract and a phenolic mixture comprising apigenin, caffeic, and chlorogenic acids on the gut microbiota using the TIM-2 in vitro system. The TIM-2 units were inoculated with fecal samples from healthy individuals and supplemented with test substrates for 72 h. Microbiota composition was assessed by V3-V4 16S rRNA gene sequencing, while organic acid production was evaluated by GC-MS. The yarrow extract stimulated probiotic bacteria Lactiplantibacillus, and other abundant and symbiotic gut inhabitants, including Eggerthellaceae, Christensenellaceae, Butyricicoccaceae, and the Eubacterium coprostanoligenes group. The phenolic mixture exerted milder effects on gut microbiota by enhancing the growth of Eggerthellaceae and Collinsella. Looking at the microbial activity, the production of SCFAs, specifically acetic and propionic acids, was increased in the yarrow group. The obtained results highlight the importance of yarrow phenolics in maintaining microbiota balance. The yarrow extract and specific phenolics may modulate the gut microbiota by promoting the growth of SCFA producers and stimulating SCFA synthesis.},
}

@article {pmid40343785,
year = {2025},
author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ},
title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf070},
pmid = {40343785},
issn = {1472-765X},
abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.},
}

@article {pmid40342598,
year = {2025},
author = {Meng, XX and Jia, X and Zhao, YH},
title = {Effects of arbuscular mycorrhizal fungi on flavonoid content in Astragali Radix cultivated in cadmium-contaminated soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1576236},
pmid = {40342598},
issn = {1664-302X},
abstract = {INTRODUCTION: As bioactive components in Astragali Radix (AR), flavonoids can promote hematopoiesis and have hypolipidemic properties, among others, and they are easily affected by environmental factors. Arbuscular mycorrhizal fungi (AMF) can influence flavonoid synthesis in plants exposed to heavy metals by expanding the root absorption area to establish a reciprocal symbiotic relationship with most plants.

METHODS: We investigated the effects of Funneliformis mosseae and time on the total flavonoids and key monomers (calycosin, calycosin-7-glucoside, formononetin, and ononin) in AR exposed to cadmium (Cd) using a pot experiment. The treatments consisted of non-inoculation and F. mosseae inoculation. A two-way analysis of variance and Duncan's test were conducted.

RESULTS: Shoot total flavonoids decreased (p < 0.05) at 60 (20.5%) and 90 d (18.3%), while formononetin decreased (83.4%) by 120 d; conversely, calycosin-7-glucoside increased (p < 0.05) with inoculation, although calycosin-7-glucoside decreased (p < 0.05) over time from 60 to 120 d regardless of inoculation. Shoot calycosin increased (p < 0.05) over time regardless of inoculation. Root total flavonoids decreased (p < 0.05) by 15.2% at 60 d, then increased (p < 0.05) by 23.5% at 90 d, along with increases in formononetin (117.1%) and ononin (59.6%) at 60 d, and calycosin-7-glucoside (21.2%) at 120 d, which increased (p < 0.05) under inoculation. The colonization rate, along with shoot Cd, C, P, H, and C/N ratio, significantly affected shoot flavonoids, while Cd accounted for 90.0% of flavonoid variation, which may be associated with its impact on flavonoid synthase. The variation in root flavonoids was significantly influenced by root S, biomass, and N, suggesting that AMF regulation may vary between AR organs. Calycosin-7-glucoside was significantly affected by phenylalanine ammonia-lyase (a key gene in flavonoid synthesis). Overall, F. mosseae led to significant increases in shoot total flavonoids and calycosin-7-glucoside. The total flavonoids were higher in shoots than in roots, indicating that annual AR shoots exposed to Cd may be utilized for medicinal purposes under inoculation.

DISCUSSION: These results provide insights into the enhancement of AMF on the quality of medicinal plants grown in Cd-contaminated soils, and the long-term effects of AMF on flavonoids at varying Cd levels should be further investigated.},
}

@article {pmid40339063,
year = {2025},
author = {Zavala-Mazariegos, FJ and Cruz-Esteban, S and Álvarez-Solís, JD and Rojas, JC},
title = {Mycorrhizal fungus colonization on maize seedlings diminishes oviposition of fall armyworm females and affect larval performance.},
journal = {Environmental entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ee/nvaf045},
pmid = {40339063},
issn = {1938-2936},
abstract = {Arbuscular mycorrhizal fungi are key components of the soil microbiota and are characterized by their symbiosis with terrestrial plants. In addition to providing nutrients to plants during symbiosis, arbuscular mycorrhizal fungi can enhance plant defenses against herbivorous insects and pathogens, including induced systemic resistance. Previous studies have demonstrated that Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) larvae perform better in maize plants colonized by arbuscular mycorrhizal fungi, which generally exhibit greater growth and higher nitrogen and phosphorus contents. However, these studies were limited to a small number of maize varieties. Additionally, prior research has not considered the host preference of S. frugiperda females for noncolonized versus arbuscular mycorrhizal fungi-colonized maize plants, although female choice can significantly influence progeny performance. In this study, we evaluated the effects of Rhizophagus irregularis (Blaszk, Wubet, Renker, & Buscot) C. Walker & A. Schüßler (Glomerales: Glomeraceae) inoculation on 4 maize inbred lines (CML 124, CML 343, CML 122, and CML 126) susceptible to S. frugiperda on female oviposition preference and larval performance of S. frugiperda. Overall, females preferred ovipositing on uncolonized seedlings to arbuscular mycorrhizal fungi-colonized seedlings, independent of the inbred lines. Larval performance was affected by inbred lines and arbuscular mycorrhizal fungi colonization. Larvae feeding on noncolonized maize seedlings exhibited significantly higher weights than those feeding on arbuscular mycorrhizal fungi-colonized seedlings. Among the inbred lines, larvae fed CML 122 performed better than those fed CML 126 and CML 343 seedlings. The weight of the larvae fed on CML 124 seedlings was similar to that of the larvae fed on CML 122, CML 126, and CML 343 seedlings.},
}

@article {pmid40338463,
year = {2025},
author = {Yang, G and Li, M and Zhang, J and Zhou, J and Cheah, WY and Abdullah, R and Ling, TC},
title = {Evaluation of cultivation conditions in hydrogel systems to enhance Chlorella vulgaris growth.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40338463},
issn = {1618-1905},
support = {MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; },
abstract = {Microalgae have gained significant attention as sustainable alternatives to traditional agriculture and energy resources. The cultivation efficiency of microalgae within hydrogel systems presents a promising avenue for spatially efficient bio-production. However, the optimum cultivation conditions of hydrogel cultivation systems have not been elucidated. This study focused on evaluating the hydrogel-based cultivation of Chlorella vulgaris in symbiosis with Bacillus Strain Salmah Ismail (SI) 139SI. It investigated the impact of hydrogel concentration, pH, light exposure, and system thickness on the growth and chlorophyll production of the algae. Our findings highlighted that, in coculture, a 7% (w/v) hydrogel concentration, pH of 7.4, a 12-h light/dark cycle at a hydrogel concentration of 7% but continuous light exposure under 5% hydrogel concentration, and a system thickness of 10 mm have provided the most favorable environmental conditions for the proliferation and chlorophyll production of C. vulgaris. These conditions significantly enhanced the biomass yields, suggesting that tailored hydrogel environments can substantially improve microalgae productivity.},
}

@article {pmid40338334,
year = {2025},
author = {Diao, F and Liu, K and Wu, W and Xu, J},
title = {Leaf transcriptomic responses to arbuscular mycorrhizal symbioses exerting growth depressions in tomato.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {139},
pmid = {40338334},
issn = {1432-072X},
support = {2021BQ132//Program of Doctoral Research Foundation of Shanxi Agricultural University/ ; 2022ZDYF115//Shanxi Provincial Key Research and Development Project/ ; 2021YFD1901105//National Key Research and Development Program of China/ ; },
mesh = {*Mycorrhizae/physiology ; *Solanum lycopersicum/microbiology/growth & development/genetics/metabolism ; *Symbiosis ; *Transcriptome ; *Plant Leaves/microbiology/genetics/growth & development/metabolism ; *Glomeromycota/physiology ; Plant Roots/microbiology/growth & development ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; Seedlings/microbiology/growth & development ; Carbon/metabolism ; Fungi ; },
abstract = {Arbuscular mycorrhizal (AM) fungi play important roles in sustainable agriculture, given that they provide multiple benefits for numerous crops. Conversely, negative plant growth effects induced by AM fungi are also occasionally observed. However, little information is available regarding the responses of symbiosis. In this study, compared with an absence of AM fungus inoculation, tomato seedlings inoculated with Funneliformis mosseae or Rhizophagus intraradices were characterized by reduced shoot and root growth. The two AM fungi decreased the carbon contents and the carbon-nitrogen ratios in shoots. To gain further insights into the underlying mechanisms, transcriptomic analyses were performed in the study. A total of 190 and 870 differentially expressed genes (DEGs) were identified in the F. mosseae vs. control and R. intraradices vs. control comparisons, respectively. KEGG enrichment analysis of the former 190 DEGs revealed significant enrichment of the "Protein processing in endoplasmic reticulum," "Flavonoid biosynthesis," "Flavone and flavonol biosynthesis," and "Stilbenoid, diarylheptanoid, and gingerol biosynthesis" pathways, whereas "DNA replication," "Photosynthesis - antenna proteins," "Cutin, suberine, and wax biosynthesis," "Protein processing in endoplasmic reticulum," and "Glycerophospholipid metabolism" were identified as pathways significantly enriched with the latter 870 DEGs. GO functional analysis revealed that among both groups of DEGs, large numbers of genes were assigned the "Response to stimulus" term. Moreover, many of the enriched terms were associated with stimulus and stress response processes, including response to salt stress, heat, and reactive oxygen species. Therefore, the findings indicated that AM fungi may trigger defense-related responses in hosts, even though the symbioses performed growth depressions. These findings will contribute to advancing our current understanding of AM fungi.},
}

*Mycorrhizae/physiology
*Solanum lycopersicum/microbiology/growth & development/genetics/metabolism
*Symbiosis
*Transcriptome
*Plant Leaves/microbiology/genetics/growth & development/metabolism
*Glomeromycota/physiology
Plant Roots/microbiology/growth & development
Gene Expression Regulation, Plant
Gene Expression Profiling
Plant Proteins/genetics/metabolism
Seedlings/microbiology/growth & development
Carbon/metabolism
Fungi

@article {pmid40338317,
year = {2025},
author = {Graziosi, S and Deloche, L and Januario, M and Selosse, MA and Deveau, A and Bach, C and Chen, Z and Murat, C and Iotti, M and Rech, P and Zambonelli, A},
title = {Newly Designed Fluorescence In Situ Hybridization Probes Reveal Previously Unknown Endophytic Abilities of Tuber magnatum in Herbaceous Plants.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {42},
pmid = {40338317},
issn = {1432-184X},
support = {K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; },
mesh = {*Endophytes/genetics/isolation & purification/physiology ; *In Situ Hybridization, Fluorescence/methods ; Plant Roots/microbiology ; *Mycorrhizae/genetics/isolation & purification/physiology ; *Ascomycota/genetics/isolation & purification/physiology ; Symbiosis ; Italy ; Polymerase Chain Reaction ; Hyphae/genetics ; },
abstract = {Tuber magnatum Picco (the Italian white truffle) is the most valuable and widely appreciated truffle. It is an ectomycorrhizal fungus known to associate with many broadleaf tree species. However, its mycorrhizae are rarely observed in the field, suggesting possible alternative symbiotic strategies, such as endophytism with non-ectomycorrhizal plants. In order to test potential endophytic interactions of T. magnatum with wild plants, a combination of polymerase chain reaction (PCR) and Fluorescence In Situ Hybridization (FISH) approaches were used. Specific FISH probes for T. magnatum were designed, tested in vitro on hyphae and/or ectomycorrhizae, and selected for their specificity. These probes were then used on a wide variety root samples of wild plants collected from three T. magnatum production areas in Italy and previously tested for the presence of T. magnatum mycelium using PCR-specific primers. Molecular analyses detected the presence of T. magnatum in 21 of 100 plant samples analyzed. FISH analysis confirmed the extracellular presence of active T. magnatum hyphae inside the root system of Carex pendula Huds plant. This study provides the first evidence of T. magnatum acting as an endophyte in an herbaceous plant. The newly designed, highly specific T. magnatum FISH probes can be used for further investigations to confirm the endophytic tendencies of T. magnatum and to understand their influence on the life cycle and biology of this fungus.},
}

*Endophytes/genetics/isolation & purification/physiology
*In Situ Hybridization, Fluorescence/methods
Plant Roots/microbiology
*Mycorrhizae/genetics/isolation & purification/physiology
*Ascomycota/genetics/isolation & purification/physiology
Symbiosis
Italy
Polymerase Chain Reaction
Hyphae/genetics

@article {pmid40337257,
year = {2025},
author = {Zemeitat, DS and Coquilleau, M and Pierce, NE and Elgar, MA},
title = {Ant responses in a lycaenid-ant symbiosis are not facilitated by cuticular compounds alone.},
journal = {Royal Society open science},
volume = {12},
number = {5},
pages = {241320},
pmid = {40337257},
issn = {2054-5703},
abstract = {Initiating partnerships in protective symbioses can be asymmetrical if there is a risk of attack from their symbionts. Myrmecophiles may encounter chemically mediated recognition systems that allow the host ants to distinguish nestmates from natural enemies, including non-nestmate conspecifics. The immature stages of the lycaenid butterfly Jalmenus evagoras form an obligate symbiosis with workers of Iridomyrmex mayri that protect them against natural enemies. However, the first instar larvae cannot anticipate this colony-specific chemical recognition system, since they are unlikely to encounter workers from the same colony that tended their mother. We show experimentally that workers of I. mayri can use chemical signals alone to distinguish between conspecifics and the larvae of J. evagoras; between nestmate and non-nestmate conspecifics and between larvae tended by nestmate and non-nestmate conspecifics. Nevertheless, we also show experimentally that while workers paid more attention to fourth than second instar larvae, they did not respond more aggressively to larvae that had been tended by non-nestmate versus nestmate workers. These data suggest that workers pay attention to other signals, perhaps via tactile, visual or vibratory sensory modalities, thereby allowing the butterfly myrmecophiles to mitigate the risks associated with the chemically mediated colony-specific recognition systems of their ant hosts.},
}

@article {pmid40336531,
year = {2025},
author = {Ma, P and Li, Y and Hao, J and Lu, H and He, Y and Wei, L and Ai, L and Wang, S},
title = {Co-Culture of Lactobacillus bulgaricus With Streptococcus thermophilus and Bifidobacterium Impact the Metabolism and Flavor of Fermented Milk.},
journal = {Food science & nutrition},
volume = {13},
number = {5},
pages = {e70182},
pmid = {40336531},
issn = {2048-7177},
abstract = {Incorporating Bifidobacterium into fermented milk alters the balance between Lactobacillus bulgaricus and Streptococcus thermophilus. We investigated the bacterial interaction and metabolism post-fermentation and during 21-day storage. Utilizing non-targeted metabolomics and electronic nose technology, we assessed impacts on product quality and flavor. Bifidobacterium significantly increased the viability of the other two species, with AI-2 levels rising in the mixed culture. Metabonomic analysis revealed distinct metabolic profiles, with Bifidobacterium-fermented milk showing enriched key metabolites. Volatile compounds like ketones, aldehydes, esters, alcohols, and acids were identified, with 2-heptanone and 2-pentanone as initial discriminators and 2-pentanone and acetaldehyde as key flavor compounds after storage. This study advances understanding of symbiotic interactions and metabolite profiles in fermented dairy ecosystems.},
}

@article {pmid40335917,
year = {2025},
author = {Lan, M and Gao, K and Qin, Z and Li, Z and Meng, R and Wei, L and Chen, B and Yu, X and Xu, L and Wang, Y and Yu, K},
title = {Coral microbiome in estuary coral community of Pearl River Estuary: insights into variation in coral holobiont adaptability to low-salinity conditions.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {278},
pmid = {40335917},
issn = {1471-2180},
support = {42206157//National Natural Science Foundation of China/ ; 42030502//National Natural Science Foundation of China/ ; GXLSCRSCS2022103//Self-Topic Project of Guangxi Laboratory on the Study of Coral Reefs in the South China Sea/ ; 2022GXNSFBA035449//Natural Science Foundation of Guangxi Province/ ; PM-zx703-202004-143//Central Public-Interest Scientific Institution Basal Research Fund/ ; },
mesh = {Animals ; *Anthozoa/microbiology/physiology ; Estuaries ; *Microbiota ; Salinity ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Rivers ; Biodiversity ; Phylogeny ; Adaptation, Physiological ; RNA, Ribosomal, 16S/genetics ; Dinoflagellida/genetics/classification/physiology ; Ecosystem ; China ; },
abstract = {BACKGROUND: Low salinity is a crucial environmental stressor that affects estuarine coral ecosystems considerably. However, few studies have focused on the effects of low-salinity conditions on coral-associated microorganisms and the adaptability of coral holobionts.

METHODS: We explored the community structure of coral symbiotic Symbiodiniaceae and associated bacteria in low-salinity conditions using samples of six coral species from the Pearl River Estuary and analyzed the adaptability of coral holobionts in estuaries.

RESULTS: The symbiotic Symbiodiniaceae of all six studied coral species were dominated by Cladocopium, but, the Symbiodiniaceae subclades differed among these coral species. Some coral species (e.g., Acropora solitaryensis) had a high diversity of symbiotic Symbiodiniaceae but low Symbiodiniaceae density, with different adaptability to low-salinity stress in the Pearl River Estuary. Other coral species (e.g., Plesiastrea versipora) potentially increased their resistance by associating with specific Symbiodiniaceae subclades and with high Symbiodiniaceae density under low-salinity stress. The microbiome associated with the coral species were dominated by Proteobacteria, Chloroflexi, and Bacteroidetes; however, its diversity and composition varied among coral species. Some coral species (e.g., Acropora solitaryensis) had a high diversity of associated bacteria, with different adaptability owing to low-salinity stress. Other coral species (e.g., Plesiastrea versipora) potentially increased their resistance by having minority bacterial dominance under low-salinity stress.

CONCLUSIONS: High Symbiodiniaceae density and high bacterial diversity may be conducive to increase the tolerance of coral holobiont to low-salinity environments. Different coral species have distinct ways of adapting to low-salinity stress, and this difference is mainly through the dynamic regulation of the coral microbiome by corals.},
}

Animals
*Anthozoa/microbiology/physiology
Estuaries
*Microbiota
Salinity
*Bacteria/classification/genetics/isolation & purification
Symbiosis
Rivers
Biodiversity
Phylogeny
Adaptation, Physiological
RNA, Ribosomal, 16S/genetics
Dinoflagellida/genetics/classification/physiology
Ecosystem
China

@article {pmid40335854,
year = {2025},
author = {Dolgikh, AV and Salnikova, EA and Dymo, AM and Kantsurova, ES and Aksenova, TS and Yuzikhin, OS and Kurchak, ON and Onishchuk, OP and Dolgikh, EA},
title = {Characterization and De Novo Genome Assembly for New Rhizobium Ruizarguesonis Rhizobial Strain Vst36-3 Involved in Symbiosis with Pisum and Vicia Plants.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {284},
pmid = {40335854},
issn = {1432-0991},
support = {24-16-00180//Russian Science Foundation/ ; },
mesh = {*Symbiosis ; *Genome, Bacterial ; Phylogeny ; *Rhizobium/genetics/classification/isolation & purification/physiology ; *Pisum sativum/microbiology ; *Vicia/microbiology ; Root Nodules, Plant/microbiology ; Whole Genome Sequencing ; },
abstract = {Pea and vetch are the important legume crops used as food, forage, and green manure in agriculture. Several new rhizobial isolates were obtained from vetch Vicia sativa root nodules. For one of them, Vst36-3, the nodulation test showed various specificity in relation to plant hosts from the Fabeae tribe, such as pea and vetch. It is in contrast to typical strains of the Rhizobium leguminosarum species complex (Rlc), which formed effective nodules as in pea and vetch. Here, whole genome sequencing was performed followed by de novo genome assembly for Vst36-3 strain. As a result of de novo genome assembly, seven contigs were generated using Oxford Nanopore Technology long reads and subsequently Illumina short reads. Phylogenetic analysis allowed us to identify this strain as Rhizobium ruizarguesonis Vst36-3. Analysis of the Sym plasmid containing the nod and nif genes revealed that R. ruizarguesonis Vst36-3 has a complete suite of essential genes for the development of symbiosis. Nevertheless, this new strain forms ineffective nodules in pea. This makes Rhizobium ruizarguesonis Vst36-3 attractive for the search and investigation of new factors of host specificity in future.},
}

*Symbiosis
*Genome, Bacterial
Phylogeny
*Rhizobium/genetics/classification/isolation & purification/physiology
*Pisum sativum/microbiology
*Vicia/microbiology
Root Nodules, Plant/microbiology
Whole Genome Sequencing

@article {pmid40335388,
year = {2025},
author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R},
title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.004},
pmid = {40335388},
issn = {1878-4372},
abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.},
}

@article {pmid40334379,
year = {2025},
author = {Zhang, J and Wang, X and Chen, Z and Yu, Q and Zhang, Y},
title = {Microbial advanced oxidation aroused by bacteria-algae symbiosis induced abiotic methane production in anaerobic digestion.},
journal = {Water research},
volume = {282},
number = {},
pages = {123776},
doi = {10.1016/j.watres.2025.123776},
pmid = {40334379},
issn = {1879-2448},
abstract = {The slow decomposition of recalcitrant substrate limits the conversion efficiency of anaerobic digestion. Microbial advanced oxidation, capable of in-situ generating reactive oxygen species (ROS) with the microbial aerobic/anaerobic respiration, provided a potential way to strengthen the substrate-methane conversion in anaerobic digestion. In this study, microalgae were inoculated in anaerobic system and formed redox oscillation under the intermittent illumination, which ultimately increased the methane production by 27.4 %. With the redox oscillation, •OH, the typical ROS, showed a 6.27-fold increase in production (72.95 ± 9.06 μM vs. 10.03 ± 1.49 μM), facilitating the decomposition of lignocelluloses. Notably, abiotic methanation was observed in anaerobic digestion with the occurrence of microbial advanced oxidation. ROS quenching experiments revealed that abiotic methanation roughly accounted for 17.5 % of the total methane production. Microbial advanced oxidation formed by redox oscillation showed the potential to strengthen anaerobic digestion. Notably, for the first time, it was confirmed that abiotic methanation could be established in anaerobic digestion with the ROS generated by microbial advanced oxidation, which offered a new perspective to understand and improve the performances of natural and engineered ecosystems.},
}

@article {pmid40333244,
year = {2025},
author = {Schaub, GA},
title = {Trypanosoma cruzi/Triatomine Interactions-A Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40333244},
issn = {2076-0817},
mesh = {*Trypanosoma cruzi/physiology ; Animals ; *Chagas Disease/parasitology/transmission ; *Insect Vectors/parasitology/microbiology ; *Host-Parasite Interactions ; *Triatominae/parasitology/microbiology ; Humans ; Gastrointestinal Microbiome ; Symbiosis ; },
abstract = {This review summarizes the interactions between Trypanosoma cruzi, the etiologic agent of Chagas disease, and its vectors, the triatomines, and highlights open questions. Four important facts should be emphasized at the outset: (1) The development of T. cruzi strains and their interactions with the mammalian host and the insect vector vary greatly. (2) Only about 10 of over 150 triatomine species have been studied for their interactions with the protozoan parasite. (3) The use of laboratory strains of triatomines makes generalizations difficult, as maintenance conditions influence the interactions. (4) The intestinal microbiota is involved in the interactions, but the mutualistic symbionts, Actinomycetales, have so far only been identified in four species of triatomines. The effects of the vector on T. cruzi are reflected in a different colonization ability of T. cruzi in different triatomine species. In addition, the conditions in the intestine lead to strong multiplication in the posterior midgut and rectum, with infectious metacyclic trypomastigotes developing almost exclusively in the latter. Starvation and feeding of the vector induce the development of certain stages of T. cruzi. The negative effects of T. cruzi on the triatomines depend on the T. cruzi strain and are particularly evident when the triatomines are stressed. The intestinal immunity of the triatomines responds to ingested blood-stage trypomastigotes of some T. cruzi strains and affects many intestinal bacteria, but not all and not the mutualistic symbionts. The specific interaction between T. cruzi and the bacteria is evident after the knockdown of antimicrobial peptides: the number of non-symbiotic bacteria increases and the number of T. cruzi decreases. In long-term infections, the suppression of intestinal immunity is indicated by the growth of specific microbiota.},
}

*Trypanosoma cruzi/physiology
Animals
*Chagas Disease/parasitology/transmission
*Insect Vectors/parasitology/microbiology
*Host-Parasite Interactions
*Triatominae/parasitology/microbiology
Humans
Gastrointestinal Microbiome
Symbiosis

@article {pmid40332819,
year = {2025},
author = {Ali, S and Tahir, S and Hassan, SS and Lu, M and Wang, X and Quyen, LTQ and Zhang, W and Chen, S},
title = {The Role of Phytohormones in Mediating Drought Stress Responses in Populus Species.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
pmid = {40332819},
issn = {1422-0067},
support = {2022YED2200800//National Key Research and Development Program of China/ ; 2572022CG06//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Populus/physiology/metabolism/microbiology ; *Plant Growth Regulators/metabolism ; *Droughts ; *Stress, Physiological ; Plant Roots/metabolism/microbiology ; Mycorrhizae/physiology ; },
abstract = {Drought stress substantially impacts the development and viability of Populus spp., which are essential for forestry and bioenergy production. This review summarizes and describes the functions of phytohormones, such as abscisic acid, auxins, and ethylene, in modulating physiological and molecular responses to water scarcity. Drought-induced ABA-mediated stomatal closure and root extension are essential adaptation processes. Furthermore, auxin-ABA (abscisic acid) interactions augment root flexibility, whereas ethylene regulates antioxidant defenses to alleviate oxidative stress. The advantageous function of endophytic bacteria, specifically plant growth-promoting rhizobacteria (PGPR), can augment drought resistance in spruce trees by enhancing nutrient absorption and stimulating root development. Structural adaptations encompass modifications in root architecture, including enhanced root length and density, which augment water uptake efficiency. Similarly, Arbuscular Mycorrhizal Fungi (AMF) significantly enhance stress resilience in forest trees. AMF establishes symbiotic relationships with plant roots, improving water and nutrient uptake, particularly phosphorus, during drought conditions. Furthermore, morphological alterations at the root-soil interface enhance interaction with soil moisture reserves. This review examines the complex mechanisms by which these hormones influence plant responses to water shortage, aiming to offer insights into prospective techniques for improving drought tolerance in common tree species and highlights the importance of hormone control in influencing the adaptive responses of prominent trees to drought stress, providing significant implications for research and practical applications in sustainable forestry and agriculture. These findings lay the groundwork for improving drought tolerance in Populus spp. by biotechnological means and by illuminating the complex hormonal networks that confer drought resistance.},
}

*Populus/physiology/metabolism/microbiology
*Plant Growth Regulators/metabolism
*Droughts
*Stress, Physiological
Plant Roots/metabolism/microbiology
Mycorrhizae/physiology

@article {pmid40332799,
year = {2025},
author = {Bai, C and Duan, Y and Zhao, C and Yan, L and Suthisut, D and Lü, J and Bai, Y and Zeng, F and Zhang, M},
title = {Abundance of the Dominant Endosymbiont Rickettsia and Fitness of the Stored-Product Pest Liposcelis bostrychophila (Psocoptera: Liposcelididae).},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
pmid = {40332799},
issn = {2075-4450},
support = {32172260//National Natural Science Foundation of China/ ; },
abstract = {Endosymbiotic bacteria are key factors that regulate the biological traits of Liposcelis bostrychophila. This study employed metagenomic methods to analyze the dominant species of symbiotic microorganisms associated with L. bostrychophila. By controlling the environmental temperature, we were able to manipulate the abundance of endosymbionts and establish populations with high, medium, and low levels of these bacteria. This allowed us to examine the fitness parameters of L. bostrychophila under different levels of endosymbiont abundance. The experimental results revealed that L. bostrychophila hosts 51 genera of symbiotic microorganisms, with Rickettsia being the dominant genus, accounting for 84.11% to 98.16% of the total share. Environmental temperature significantly affected the abundance of Rickettsia, with notable differences observed during the adult stage of L. bostrychophila. A temperature gradient of 28 °C, 35 °C, and 37 °C was established, allowing for the classification of populations based on Rickettsia abundance into three categories: high-abundance populations (LBhp), medium-abundance populations (LBmp), and low-abundance populations (LBlp). The abundance of Rickettsia had a significant impact on the fitness of L. bostrychophila. Specifically, a high abundance of Rickettsia contributed positively to population fitness by increasing egg production, prolonging egg hatching time, enhancing lifespan, and improving both survival and reproductive rates. Therefore, the endosymbiont Rickettsia plays a crucial role in the growth and development of L. bostrychophila. In the future, our research will help further uncover the interactions between Rickettsia and its host, providing new perspectives for pest control and offering a better understanding of insect biology and ecology.},
}

@article {pmid40332327,
year = {2025},
author = {Kaddouri, K and Lamrabet, M and Alami, S and Chaddad, Z and Abdelmoumen, H and Badaoui, B and Missbah El Idrissi, M},
title = {Draft genome sequence of Bradyrhizobium sp. strain RDM4, a microsymbiont bacterium isolated from the root nodules of Retama dasycarpa in soils of Maâmora forest, Morocco.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0006525},
doi = {10.1128/mra.00065-25},
pmid = {40332327},
issn = {2576-098X},
abstract = {Bradyrhizobium sp. RDM4 is a symbiotic nitrogen-fixing bacterium, isolated from root nodules of the Moroccan endemic shrub Retama dasycarpa grown in Moroccan forest soils. In this work, we present the 8.4 Mb draft genome of this strain, characterized by a GC content of 63% and the presence of 8,141 total genes, with 7,032 protein-coding.},
}

@article {pmid40331988,
year = {2025},
author = {Gan, CM and Tang, T and Zhang, ZY and Li, M and Zhao, XQ and Li, SY and Yan, YW and Chen, MX and Zhou, X},
title = {Unraveling the Intricacies of Powdery Mildew: Insights into Colonization, Plant Defense Mechanisms, and Future Strategies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
pmid = {40331988},
issn = {1422-0067},
support = {2022YFD1700200//Moxian-Chen/ ; ZK[2023]-099//Moxian-Chen/ ; },
mesh = {*Plant Diseases/microbiology/immunology ; Disease Resistance/genetics ; Host-Pathogen Interactions ; *Ascomycota/pathogenicity ; Plant Immunity ; Gene Expression Regulation, Plant ; *Plants/microbiology/immunology ; *Erysiphe/pathogenicity ; },
abstract = {Powdery mildew, a debilitating phytopathogen caused by biotrophic fungi within the order Erysiphales, endangers crop yields and global food security. Although traditional approaches have largely emphasized resistant cultivar development and chemical control, novel strategies are necessary to counter the advent of challenges, such as pathogen adaptation and climate change. This review fully discusses three principal areas of pathogen effector functions, e.g., the reactive oxygen species (ROS)-suppressive activity of CSEP087, and host susceptibility factors, like vesicle trafficking regulated by Mildew Locus O (MLO). It also briefly mentions the transcriptional regulation of resistance genes mediated by factors, like WRKY75 and NAC transcription factors, and post-transcriptional regulation via alternative splicing (As). In addition, this discussion discusses the intricate interactions among powdery mildew, host plants, and symbiotic microbiomes thereof, highlighting the mechanism through which powdery mildew infections disrupt the foliar microbiota balance. Lastly, we present a new biocontrol approach that entails synergistic microbial consortia, such as combinations of Bacillus and Trichoderma, to induce plant immunity while minimizing fungicide dependency. Through the study of combining knowledge of molecular pathogenesis with ecological resilience, this research offers useful insights towards climate-smart crop development and sustainable disease-management strategies in the context of microbiome engineering.},
}

*Plant Diseases/microbiology/immunology
Disease Resistance/genetics
Host-Pathogen Interactions
*Ascomycota/pathogenicity
Plant Immunity
Gene Expression Regulation, Plant
*Plants/microbiology/immunology
*Erysiphe/pathogenicity

@article {pmid40331181,
year = {2025},
author = {Melby, MK and Watanabe, K and Haraoui, LP},
title = {Addressing Antimicrobial Resistance by Changing Our Relationships with Microbes: Lessons from Japan.},
journal = {Delaware journal of public health},
volume = {11},
number = {1},
pages = {28-31},
pmid = {40331181},
issn = {2639-6378},
abstract = {Antimicrobial resistance (AMR) is a global health problem, but it is only the 'tip of the iceberg' of microbial disruption caused by antibiotics. Under the surface, cultural factors such as understandings of and attitudes toward microbes may play a significant role influencing relationships between humans and microbes. Western strategies to address pathogenic microbes and AMR often overlook the symbiotic relationship humans share with beneficial microbes (our microbiota), viewing humans as separate from nature and focusing on control. Given the increasing prevalence of novel pathogens, antimicrobial resistance, and chronic illnesses associated with disturbed microbiota (dysbiosis), alternative approaches are needed. Cross-cultural studies may provide ways forward. An exploration of Japanese perspectives on microbes through the lens of food and health reveals practices where microbes are often regarded as partners and friends rather than foes.},
}

@article {pmid40330728,
year = {2025},
author = {Ren, CG and Kong, CC and Li, SM and Wang, XJ and Yu, X and Wang, YC and Qin, S and Cui, HL},
title = {Symbiotic microalgae and microbes: a new frontier in saline agriculture.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1540274},
pmid = {40330728},
issn = {1664-302X},
abstract = {With the growing human population worldwide, innovative agricultural development is needed to meet food security needs. However, this has inadvertently led to problematic irrigation practices and overuse of agrochemicals. Such practices can exacerbate soil salinization, which prevents plant growth. As a progressively widespread and escalating problem, soil salinization poses a major threat to global food security. Compared with the traditional use of microalgae or microorganisms that act on plant growth, microalgae-microorganism symbiosis has significant advantages in promoting plant growth. Microalgae and microorganisms can work together to provide a wide range of nutrients required by plants, and they exhibit nutrient complementarity, which supports plant growth. Here, the development potential of microalgae-microbial symbiosis for enhancing plant salt tolerance was investigated. Our review demonstrated that the metabolic complementarity between microalgae and microorganisms can enhance plant salt tolerance. The diversity of a microalgae-microorganism symbiotic system can improve ecosystem stability and resistance and reduce the incidence of plant disease under salt stress. These systems produce bioactive substances (e.g., phytohormones) that promote plant growth, which can improve crop yield, and they can improve soil structure by increasing organic matter and improving water storage capacity and soil fertility. Exploiting the synergistic effects between microalgae and beneficial microorganisms has biotechnological applications that offer novel solutions for saline agriculture to mitigate the deleterious effects of soil salinity on plant health and yield. However, there are several implementation challenges, such as allelopathic interactions and autotoxicity. To make microalgae-bacteria consortia economically viable for agricultural applications, optimal strains and species need to be identified and strategies need to be employed to obtain sufficient biomass in a cost-effective manner. By elucidating the synergistic mechanisms, ecological stability, and resource utilization potential of microalgae-microbial symbiotic systems, this review clarifies salt stress responses and promotes the shift of saline-alkali agriculture from single bioremediation to systematic ecological engineering.},
}

@article {pmid40330701,
year = {2025},
author = {Teraishi, M and Sakaguchi, K and Yoshikawa, T},
title = {Identification of Novel Candidate Genes Associated With the Symbiotic Compatibility of Soybean With Rhizobia Under Natural Conditions.},
journal = {Plant direct},
volume = {9},
number = {5},
pages = {e70069},
pmid = {40330701},
issn = {2475-4455},
abstract = {A robust symbiotic relationship between soybean and rhizobia can enhance the yield and quality of soybeans by reducing nitrogen fertilizer input, thereby contributing to sustainable agriculture. However, the genetic interplay between soybean cultivars and the rhizobial species colonizing their roots under natural conditions is yet to be sufficiently assessed. In this study, we build on previous observations that have revealed a significant variation in the prevalence of rhizobial species associated with the soybean cultivars "Peking" and "Tamahomare." Using recombinant inbred lines derived from a cross between Peking and Tamahomare, we performed quantitative trait loci (QTL) analysis of the proportion of Rhizobium species present in the root nodules of these cultivars and accordingly identified a major QTL on chromosome 18, accounting for 42% of the phenotypic variation, which was subsequently localized to a 240-kb region. RNA-seq analysis indicated that a single gene harboring nucleotide binding site-leucine-rich repeat domains exhibited markedly different expression within the QTL region in the parent cultivars. As this locus is distinct from the chromosomal regions containing known nodule-related genes, such as Rj and rj, we speculate that it represents a novel gene involved in the symbiosis between rhizobia and soybeans. Further research on the function and role of this new gene could potentially contribute to enhancing soybean yield, and hence sustainable agriculture, under low-nitrogen fertilization conditions.},
}

@article {pmid40328455,
year = {2025},
author = {Akpodiete, NO and Carlos, B and Voges, K and Nunes, BT and Souza-Neto, JA and Noulin, F and Tonge, D and Zuharah, WF and Tripet, F},
title = {Improvement of water quality for mass anopheline rearing: Dynamics of larval tray bacterial communities under different water treatments revealed by 16S ribosomal RNA amplicon sequencing.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf110},
pmid = {40328455},
issn = {1365-2672},
abstract = {BACKGROUND: Immature anophelines inhabit aquatic environments with diverse physicochemical properties and microorganisms. In insectary settings, ammonia accumulation in larval rearing trays can lead to high larval mortality. Bacterial communities in these trays may influence ammonia levels through nitrification and denitrification. While symbiotic bacteria are known to be crucial for nutrition, digestion, reproduction, and immune responses in anophelines, the microbial communities specifically associated with Anopheles coluzzii larvae have not been characterised.

METHODS AND RESULTS: Building on a study examining ammonia-capturing zeolite and water changes for rearing Anopheles coluzzii, this research characterised the bacterial communities using 16S rRNA gene sequencing to identify species linked to larval survival and phenotypic quality. Functional filters were applied to identify bacteria related to ammonia nitrification and their impact on larval development. qPCR was used to validate the sequencing data for the ten most significant bacteria. Water changes significantly reduced bacterial diversity and abundance, improving adult mosquito development and quality. In contrast, untreated trays showed a higher abundance of potentially harmful bacteria, adversely affecting development. Applying zeolite increased nitrifying bacteria presence, benefiting mosquito growth while lowering toxic bacteria levels-trends confirmed by qPCR.

CONCLUSIONS: This study offers insights into the bacterial communities in mosquito larval-rearing water, highlighting species that could enhance ammonia nitrification and overall rearing success.},
}

@article {pmid40328341,
year = {2025},
author = {Abd-El-Aziz, A and Elnagdy, SM and Han, J and Mihelič, R and Wang, X and Agathos, SN and Li, J},
title = {Bacteria-microalgae interactions from an evolutionary perspective and their biotechnological significance.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108591},
doi = {10.1016/j.biotechadv.2025.108591},
pmid = {40328341},
issn = {1873-1899},
abstract = {Interactions between bacteria and microalgae have been studied in natural environments and in industrial consortia. As results of co-evolution for millions of years in nature, they have developed complex symbiotic relationships, including mutualism, commensalism and parasitism, the nature of which is decided by mechanisms of the interaction. There are two main types of molecular interactions between microalgae and bacteria: exchange of nutrients and release of signalling molecules. Nutrient exchange includes transport of organic carbon from microalgae to bacteria and nutrient nitrogen released from nitrogen-fixing bacteria to microalgae, as well as reciprocal supply of micronutrients such as B vitamins and iron. Signalling molecules such as phytohormones secreted by microalgae and quorum sensing molecules secreted by bacteria have been shown to positively affect growth and metabolism of the symbiotic partner. However, there are still a number of potential microalgae-bacteria interactions that have not been well explored, including cyclic peptides, other quorum signalling molecules, and extracellular vesicles involved in exchange of genetic materials. A more thorough understanding of these interactions may not only result in a deeper understanding of the relationships between these symbiotic organisms but also have potential biotechnological applications. Upon new mechanisms of interaction being identified and characterized, novel bioprocesses of synthetic ecology might be developed especially for wastewater treatment and production of biofertilizers and biofuels.},
}

@article {pmid40328313,
year = {2025},
author = {Wang, D and Jin, R and Shi, X and Guo, H and Tan, X and Zhao, A and Lian, X and Dai, H and Li, S and Xin, K and Tian, C and Yang, J and Chen, W and Macho, AP and Wang, E},
title = {A kinase mediator of rhizobial symbiosis and immunity in Medicago.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-025-09057-0},
pmid = {40328313},
issn = {1476-4687},
abstract = {Legume roots secure nitrogen by forming a symbiosis with soil rhizobia but remain resistant to pathogenic bacteria[1-4]. How this tolerance to rhizobia is achieved without compromising plant immunity is largely unknown. Here, we identify the cytoplasmic kinase MtLICK1/2, which interacts with nodulation factor receptor MtLYK3 to drive symbiotic signaling and suppress plant immunity. Rhizobial infection and nodule development are defective in Mtlick1/2, phenocopying the Mtlyk3-1 mutant. MtLICK1/2 and MtLYK3 undergo reciprocal trans-phosphorylation during rhizobial symbiosis. Phosphorylated MtLYK3 activates the receptor-like kinase MtDMI2 to stimulate symbiotic signaling. MtLICK1/2 is activated in the rhizobia infection area to suppress plant immunity. Thus, MtLICK1/2 and MtLYK3 together amplify symbiotic signaling and dampen host immunity to enable legume-rhizobium symbiosis.},
}

@article {pmid40328220,
year = {2025},
author = {Doremus, MR and Hunter, MS},
title = {Symbiosis: An escalating arms race between a butterfly and bacterium.},
journal = {Current biology : CB},
volume = {35},
number = {9},
pages = {R339-R341},
doi = {10.1016/j.cub.2025.03.061},
pmid = {40328220},
issn = {1879-0445},
mesh = {*Symbiosis ; Animals ; *Butterflies/microbiology/physiology ; *Wolbachia/physiology/genetics ; Male ; Gene Transfer, Horizontal ; },
abstract = {Symbiotic bacteria such as Wolbachia can dramatically affect the reproduction of their arthropod hosts, in some instances causing male progeny to die as embryos. A recent paper describes an escalating arms race over Wolbachia-mediated male-killing in a tropical butterfly, with butterfly suppression of male-killing being overcome by acquisition of an additional male-killing gene via phage-mediated horizontal gene transfer.},
}

*Symbiosis
Animals
*Butterflies/microbiology/physiology
*Wolbachia/physiology/genetics
Male
Gene Transfer, Horizontal

@article {pmid40328215,
year = {2025},
author = {Hughes, C and Ringelberg, JJ and Bruneau, A},
title = {Legumes.},
journal = {Current biology : CB},
volume = {35},
number = {9},
pages = {R323-R328},
doi = {10.1016/j.cub.2025.03.049},
pmid = {40328215},
issn = {1879-0445},
mesh = {*Fabaceae/physiology/microbiology/genetics ; Symbiosis ; Crops, Agricultural ; Nitrogen Fixation ; Ecosystem ; },
abstract = {Whatever continent you are on (besides Antarctica), whatever type of vegetation you are in, and however that vegetation has been disturbed and modified by humans, there will very likely be a legume growing nearby. Leguminosae or Fabaceae, commonly known as legumes, with ∼22,500 species is the third largest family of flowering plants, after the daisies (Asteraceae) and orchids (Orchidaceae). A central question in legume biology is understanding why the family is so diverse, geographically widespread and abundant, and how legumes came to form significant components of almost all terrestrial ecosystems across the globe. Economically, legumes are also important as major world food crops, and have been so since the dawn of agriculture. The ability to fix atmospheric nitrogen through root nodule symbiosis with bacteria - the hallmark of many legumes - is important in both ecosystem functioning and agriculture, and current research even aims to engineer nodulation in non-legume crops. This combined eco-evolutionary and societal importance means that legumes have occupied a central position in botanical and wider biological research ever since the late 19[th] century, when Gregor Mendel used the garden pea in his experiments, which famously provided early insights into genetics. In this Primer, we present an overview of the diversity, evolution and ecological and economic importance of legumes across the globe, and discuss the evolution of nodulation, one of the key traits of the family.},
}

*Fabaceae/physiology/microbiology/genetics
Symbiosis
Crops, Agricultural
Nitrogen Fixation
Ecosystem

@article {pmid40328120,
year = {2025},
author = {Wang, X and Xia, X and Riaz, M and Babar, S and El-Desouki, Z and Qasim, M and Wang, J and Jiang, C},
title = {Biochar amendment modulate microbial community assembly to mitigate saline-alkaline stress across soil depths.},
journal = {Journal of environmental management},
volume = {385},
number = {},
pages = {125574},
doi = {10.1016/j.jenvman.2025.125574},
pmid = {40328120},
issn = {1095-8630},
abstract = {While microbial community assembly in saline-alkali topsoils is well-documented, distribution patterns across biochar application depths and soil layers remain unclear. This incubation study evaluated five treatment: no biochar (CK), homogeneous application (EB), and concentrated applications in upper (FB: 0-10 cm), middle (MB: 10-20 cm), or bottom layers (DB: 20-30 cm). Biochar application significantly accelerated vertical salt migration, with FB inducing 45.55 % and 61.01 % increases in water-soluble Na[+] and Cl[-] accumulation in the bottom layer. Microbial network complexity and interspecies interactions were highest in the upper layer (edges: 926), contrasting sharply with simplified communities in deeper layer (edges ≤552). Community assembly across layers was primarily driven by salt gradients, with deep-layer communities dominated by salt-tolerant taxa (such as Halomonas and Desulfobacterota). Among treatments, FB led to the highest biomarker abundance and α-diversity. Mechanistically, FB mitigated microbial diversity loss in mid-deep layers by establishing a symbiotic consortium of salt-tolerant keystone taxa (Bacillus-Pseudomonas-Ascomycota), which enhanced stress resilience via cross-feeding. These findings demonstrate that stratified biochar application (FB) optimizes salt redistribution while fostering stress-adapted microbial consortia across soil profiles, offering a targeted strategy for saline-alkali soil remediation.},
}

@article {pmid40327715,
year = {2025},
author = {Radzikowska-Kujawska, D and Piechota, T and Jarzyniak, K and Kowalczewski, PŁ and Wojewódzki, P},
title = {Effects of biopreparations based on Bacillus and Trichoderma, combined with mineral and organic fertilization and a Pisum sativum L. forecrop on improving the tolerance of Maize plants to drought stress.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0322718},
pmid = {40327715},
issn = {1932-6203},
mesh = {*Zea mays/physiology/microbiology/growth & development ; *Droughts ; *Fertilizers ; *Trichoderma/physiology ; Photosynthesis ; *Bacillus/physiology ; *Pisum sativum/growth & development/physiology ; Minerals/pharmacology ; *Stress, Physiological ; Symbiosis ; Chlorophyll/metabolism ; Soil/chemistry ; },
abstract = {The increased frequency of extreme weather phenomena, such as heat waves and drought, adversely affects the condition of plants. The need to strive for more sustainable methods of growing plants requires undertaking researches that focus on strengthening the immunity of plants using methods that have a positive impact on both crops and the natural environment. The aim of the study was to assess the effectiveness and compare the effects of selected microbiological preparations based on Bacillus bacteria and Trichoderma symbiotic fungi, combined with mineral (NPK) and organic fertilization (manure) and a Pisum sativum L. forecrop on improving the tolerance of maize plants to drought stress. The pot experiment was carried in 2023 as a two-factor experiment in three replicates. Physiological parameters were assessed based on measurements of photosynthetic efficiency (A - CO2 assimilation rate, E - Transpiration Rate, Gs - Stomatal Conductance) and chlorophyll content (CCI) and fluorescence (F0 - initial fluorescence, Fm - maximum fluorescence, Fv/Fm - maximum photochemical efficiency of PSII, Yield - quantum yield of the photochemical reaction in PSII, ETR - electron transport rate, NPQ - Non - Photo-chemical Quenching), as well as soil respiration (NCER- Net CO2 Exchange Rate, W flux- Net H2O Exchange Rate, Ce- Soil Respiration) and biometric measurements (dry mass of shoots and roots).The measurement of photosynthesis efficiency under drought stress clearly indicated the highest, significant effect caused by Trichoderma preparation with both fertilizers. In the control, CO2 assimilation was practically inhibited due to drought (98% drop), while in the plants in which the Trichoderma preparation was used together with half dose of NPK and manure, there was only a slight decrease (1% and 13% respectively). A greatest, significant improvement in the DM of roots under drought was noted in plants in which the Pisum forecrop was applied together with NPK and manure (230% and 168% respectively). Pisum forecrop and treatments with microbiological preparation containing Trichoderma, make it possible to reduce the fertilization dose by at least half. This is particularly important in view of the global trend of increasing drought stress and efforts to improve soil quality.},
}

*Zea mays/physiology/microbiology/growth & development
*Droughts
*Fertilizers
*Trichoderma/physiology
Photosynthesis
*Bacillus/physiology
*Pisum sativum/growth & development/physiology
Minerals/pharmacology
*Stress, Physiological
Symbiosis
Chlorophyll/metabolism
Soil/chemistry

@article {pmid40327507,
year = {2025},
author = {Chen, CY and Naqvi, NI},
title = {Endophytic mycobiont provides growth benefits via a phenylpropanoid-auxin axis in host plants.},
journal = {Cell reports},
volume = {44},
number = {5},
pages = {115648},
doi = {10.1016/j.celrep.2025.115648},
pmid = {40327507},
issn = {2211-1247},
abstract = {Beneficial association with symbiotic fungi helps improve growth and fitness in most land plants and shows great potential as biofertilizers in precision agriculture. Here, we demonstrated that a root fungal endophyte, Tinctoporellus species isolate AR8, enabled yield improvement in Brassicaceae leafy green choy sum (Brassica rapa var. parachinensis). Mechanistically, AR8 colonized the root cortex/endosphere and channeled the metabolic flux to phenylpropanoids and requisite secondary metabolites to promote plant growth. AR8-assisted biosynthesis of auxin improved root growth and provided an intrinsic source for long-distance signaling that enhanced shoot biomass. Chemical complementation with exogenous p-coumaric acid restored auxin signaling and enhanced growth in AR8-inoculated pal1 mutant plants, thus implicating such a phenylpropanoid-auxin nexus as a pivotal regulator of symbiotic plant growth. Comparative metabolomics established hydroxycinnamic acid and p-coumaric acid as major plant-growth-promoting hubs that bridge the phenylpropanoid pathway and auxin signaling in the cross-kingdom AR8 symbiotic interaction model.},
}

@article {pmid40327084,
year = {2025},
author = {Zhang, M and Hu, Y and Ma, Y and Hou, T and Wang, J and Che, Q and Chen, B and Wang, Q and Feng, G},
title = {Soil Bacterial Diversity and Community Structure of Cotton Rhizosphere under Mulched Drip-Irrigation in Arid and Semi-arid Regions of Northwest China.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {39},
pmid = {40327084},
issn = {1432-184X},
mesh = {*Gossypium/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; China ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; *Agricultural Irrigation/methods ; Biodiversity ; Desert Climate ; Microbiota ; Alkaline Phosphatase/genetics ; },
abstract = {Xinjiang is situated in an arid and semi-arid region, where abundant heat and sunlight create highly favorable conditions for cotton cultivation. Xinjiang's cotton output accounts for nearly one-quarter of global production. Moreover, the implementation of advanced planting techniques, such as 'dwarfing, high-density, early-maturing' strategies combined with mulched drip irrigation, ensures stable and high yields in this region. Despite these advancements, limited research has focused on the microbial mechanisms in cotton fields employing these advanced planting methods. In this study, high-throughput sequencing technology was utilized to investigate the diversity and composition of bacterial and phoD (Alkaline phosphatases encoding gene) communities in the rhizosphere of cotton grown under different yield levels in Xinjiang Province, China. The Mantel test, redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were employed to explore the interactions between soil bacterial and phoD communities, their network structures, and environmental factors. The bacterial and phoD communities in the cotton rhizosphere were predominantly composed of nine bacterial phyla (i.e., Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes, Rokubacteria, Firmicutes, and Nitrospirae) and five phoD phyla (i.e., Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, and Firmicutes), respectively. Alpha diversity analysis indicated that the medium yield cotton field (MYF) exhibited higher bacterial richness and diversity indices compared to low yield (LYF) and high yield (HYF) fields. The symbiotic network analysis of LYF revealed greater values of average degree, number of edges, and modularity, suggesting a more complex network structure in both bacterial and phoD communities. The Mantel test, RDA, and PLS-PM model identified soil pH, electrical conductivity (EC), organic phosphorus (OP), available phosphorus (AP), total nitrogen (TN), microbial biomass carbon (MBC), and clay content as the main driving factors influencing changes in the rhizosphere bacterial community diversity and network structure. These findings provide a theoretical basis for future research aimed at improving soil quality and cotton yield.},
}

*Gossypium/microbiology/growth & development
*Rhizosphere
*Soil Microbiology
China
*Bacteria/classification/genetics/isolation & purification
Soil/chemistry
*Agricultural Irrigation/methods
Biodiversity
Desert Climate
Microbiota
Alkaline Phosphatase/genetics

@article {pmid40324680,
year = {2025},
author = {Jones, JE and Court, R and Kageyama, D and Obbard, DJ and Hurst, GDD},
title = {Variable prevalence of protective Spiroplasma infection over time in two natural populations of Drosophila hydei.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108349},
doi = {10.1016/j.jip.2025.108349},
pmid = {40324680},
issn = {1096-0805},
abstract = {The temporal dynamics of protective symbionts have rarely been characterized outside of aphid hosts. Here, we determine the prevalence of Spiroplasma in two populations of Drosophila hydei where Spiroplasma infection had been previously recorded (UK and Japan). We observe that infection in both populations is variable over time and confirm the persistence of Spiroplasma in the UK population for 9 years. Thus, variable prevalence over time appears to be a common feature of these symbioses.},
}

@article {pmid40324391,
year = {2025},
author = {Schatz, D and Le Blevenec, A and Moratti, FG and Chung, KP and Mercier, P and Iqbal, RK and Vallet, E and Dietrich, A and Bock, R and Weber-Lotfi, F and Gualberto, JM},
title = {R-loop control and mitochondrial genome stability require the 5'-3' exonuclease/flap endonuclease OEX1.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf104},
pmid = {40324391},
issn = {1532-298X},
abstract = {Maintenance of the plant organelle genomes involves factors mostly inherited from their symbiotic ancestors. In bacteria, DNA Polymerase I (Pol I) performs multiple replication and repair functions through its 5'-3'-exonuclease/flap-endonuclease domain. Plant organelles possess two DNA polymerases that are evolutionarily derived from Pol I but lack this key domain. ORGANELLAR EXONUCLEASES 1 and 2 (OEX1 and OEX2) compensate for this missing function and are targeted to mitochondria and chloroplasts, respectively, in Arabidopsis (Arabidopsis thaliana). Loss of OEX1 causes developmental and fertility defects that increase with increasing differential segregation of mitochondrial DNA (mtDNA) subgenomes generated by recombination. OEX1 activity is modulated by alternative splicing, which generates two isoforms that variably affect mtDNA stability and repair. OEX1 has 5'-3'-exonuclease and flap endonuclease activities, with a high affinity for RNA-DNA hybrids. It rapidly degrades RNA in Okazaki-like structures and R-loops. Consistent with a role in suppressing R-loops, oex1 mutant plants accumulate RNA-DNA hybrids in highly transcribed mtDNA regions. Taken together, our results identify OEX1 as an important factor that compensates for the missing activity of plant organellar polymerases, playing multiple important roles in the processing of replication and recombination intermediates, such as replication primers and R-loops, whose accumulation can lead to genome instability.},
}

@article {pmid40324302,
year = {2025},
author = {Tleuken, A and Rogetzer, P and Fraccascia, L and Yazan, DM},
title = {Designing a stakeholder engagement framework with critical success factors for Hubs for Circularity.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125324},
doi = {10.1016/j.jenvman.2025.125324},
pmid = {40324302},
issn = {1095-8630},
abstract = {This paper introduces a framework aimed at evaluating stakeholder involvement within Hubs for Circularity (H4C), which play a critical role in advancing the circular economy. It demonstrates the significance of collaboration among stakeholders and the need for a structured approach to assess the effectiveness of H4C initiatives. As a result of the literature review synthesis, the paper proposes a novel and actionable framework for stakeholder engagement. It is composed of several key elements: it begins with the identification and analysis of the different stakeholder groups participating in H4C projects. Next, it advocates for a comprehensive review of the factors influencing H4C implementation through an analysis of drivers, barriers, and enablers. It also emphasizes the development of success criteria aligned with the Sustainable Development Goals to measure the outcomes of H4C initiatives. The paper concludes by proposing future research directions, such as integrating the Societal Readiness Level and utilizing social network analysis and regional input-output modeling to assess the socio-economic impacts of H4C projects. Overall, the paper highlights the critical role of stakeholder engagement and effective evaluation frameworks in the success of H4C initiatives and the advancement of sustainability goals.},
}

@article {pmid40323933,
year = {2025},
author = {Pacheco, R and Juárez-Verdayes, MA and Chávez-Martínez, AI and Palacios-Martínez, J and Leija, A and Nava, N and Cárdenas, L and Quinto, C},
title = {The non-specific phospholipase C of common bean PvNPC4 modulates roots and nodule development.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0306505},
pmid = {40323933},
issn = {1932-6203},
mesh = {*Phaseolus/enzymology/microbiology/genetics/growth & development ; Symbiosis ; *Root Nodules, Plant/growth & development/microbiology ; *Plant Roots/growth & development/microbiology/genetics/enzymology ; Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; *Type C Phospholipases/metabolism/genetics ; Rhizobium tropici/physiology ; Indoleacetic Acids/metabolism ; RNA Interference ; },
abstract = {Plant phospholipase C (PLC) proteins are phospholipid-degrading enzymes classified into two subfamilies: phosphoinositide-specific PLCs (PI-PLCs) and non-specific PLCs (NPCs). PI-PLCs have been widely studied in various biological contexts, including responses to abiotic and biotic stresses and plant development; NPCs have been less thoroughly studied. No PLC subfamily has been characterized in relation to the symbiotic interaction between Fabaceae (legume) species and the nitrogen-fixing bacteria called rhizobia. However, lipids are reported to be crucial to this interaction, and PLCs may therefore contribute to regulating legume-rhizobia symbiosis. In this work, we functionally characterized NPC4 from common bean (Phaseolus vulgaris L.) during rhizobial symbiosis, findings evidence that NPC4 plays an important role in bean root development. The knockdown of PvNPC4 by RNA interference (RNAi) resulted in fewer and shorter primary roots and fewer lateral roots than were seen in control plants. Importantly, this phenotype seems to be related to altered auxin signaling. In the bean-rhizobia symbiosis, PvNPC4 transcript abundance increased 3 days after inoculation with Rhizobium tropici. Moreover, the number of infection threads and nodules, as well as the transcript abundance of PvEnod40, a regulatory gene of early stages of symbiosis, decreased in PvNPC4-RNAi roots. Additionally, transcript abundance of genes involved in autoregulation of nodulation (AON) was altered by PvNPC4 silencing. These results indicate that PvNPC4 is a key regulator of root and nodule development, underscoring the participation of PLC in rhizobial symbiosis.},
}

*Phaseolus/enzymology/microbiology/genetics/growth & development
Symbiosis
*Root Nodules, Plant/growth & development/microbiology
*Plant Roots/growth & development/microbiology/genetics/enzymology
Gene Expression Regulation, Plant
*Plant Proteins/genetics/metabolism
*Type C Phospholipases/metabolism/genetics
Rhizobium tropici/physiology
Indoleacetic Acids/metabolism
RNA Interference

@article {pmid40323127,
year = {2025},
author = {Almahal, ZH and Hasan, A and Razzak, SA and Nzila, A and Uddin, S},
title = {Molecular Perspective of Dietary Influences on the Gut Microbiome alongside Neurological Health: Exploring the Gut-Brain Axis.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00058},
pmid = {40323127},
issn = {1948-7193},
abstract = {Gut-brain axis, an intricate, two-way communication network between gut microorganisms and the central nervous system, plays a critical role in controlling brain function and thereby influencing mental health. Changes to this axis, frequently due to shifts in gut microbiota, can greatly affect brain function by hindering the creation of essential metabolites. This review examines new nutritional trends, including fermented foods and diets rich in prebiotics, that demonstrate the potential to improve microbial diversity and metabolic well-being. Although current studies emphasize possible advantages, most concentrate mainly on older populations, leaving research in younger groups limited. The field of nutritional psychiatry encounters difficulties due to the diversity in research methodologies and the intricacies of nutrient balance, potentially hindering prompt interventions. This review highlights the necessity for prolonged research to evaluate the effects of eating habits, especially regarding Western dietary patterns. Promising fields include the influence of the Mediterranean diet, the role of symbiotic and short-chain fatty acids (SCFAs), and the importance of high-fiber foods, polyphenols, and fruits and vegetables in enhancing mental health through gut-derived metabolites. We promote interdisciplinary methods that combine nutrition science, microbiology, and neurology to create tailored dietary recommendations focused on enhancing brain health.},
}

@article {pmid40323071,
year = {2025},
author = {Zhao, Z and Yuan, Z and Li, Y and Huang, X},
title = {The Balance and Imbalance of Microbial Communities: Oral-Gut Microbiota and Colorectal Cancer.},
journal = {American journal of clinical oncology},
volume = {},
number = {},
pages = {},
doi = {10.1097/COC.0000000000001213},
pmid = {40323071},
issn = {1537-453X},
abstract = {The microbiome is a significant multimicrobial community that coexists with the human body in a symbiotic relationship. These microbial communities participate in mechanisms, such as defense against infections, absorption of nutrients, and maintenance of internal homeostasis. Although the microbiome is involved in physiological processes that are beneficial to host health, it can also lead to serious problems. Despite being far apart, the oral cavity and colon are both highly colonized by different microbial communities. Studies have shown that oral bacteria can migrate to and colonize the colon, which is most evident in diseases such as periodontitis. These oral pathogenic bacteria, which contain a large number of carcinogenic factors such as Fusobacterium nucleatum and Porphyromonas gingivalis, can penetrate the large intestine and cause intestinal microbial imbalance and dysfunction, thereby stimulating carcinogenesis. Increasing evidence suggests that oral microbiota, especially certain periodontal pathogens, may be used as biomarkers for colorectal cancer (CRC). Understanding the exact mechanisms of microbiome interactions and their impact on CRC will provide future opportunities for the prevention and treatment of colorectal cancer, and is an important prerequisite for its use as a precise noninvasive biomarker, which is crucial for the early detection of CRC. This review aims to summarize the current research status of oral microbiota, gut microbiota, and their association with CRC, and to evaluate the effectiveness of oral microbiome-derived biomarkers.},
}

@article {pmid40320570,
year = {2025},
author = {Torres Ascurra, YC and Müller, LM},
title = {Signaling peptides control beneficial and pathogenic plant-microbe interactions.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf180},
pmid = {40320570},
issn = {1460-2431},
abstract = {Interactions between organisms, such as those between plants and microbes, require extensive signaling between and within each organism to detect and recognize the partner and elicit an appropriate response. Multiple families of small signaling peptides regulate plant interactions with beneficial or pathogenic microbes, and sometimes both. Some of these signaling peptides transmit information between different cells or organs of the host and allow plants to orchestrate a coordinated response towards microbial mutualists or pathogens. However, not only plants produce signaling peptides required for the interactions. Microbes themselves also secrete peptide signals, which are detected by host receptors and required for infection. Among these are microbial peptides mimicking those of plants, allowing mutualistic or pathogenic microbes to hijack endogenous plant signaling pathways and evade the host immune system. In this review, we provide a comprehensive summary of current knowledge on host- and microbe-derived signaling peptides and their cognate receptors regulating mutualistic and parasitic plant-microbe interactions. Furthermore, we describe how microbes hijack endogenous host signaling pathways, and discuss possible crosstalk between the plant signaling pathways controlling mutualism with those modulating immune responses to pathogens.},
}

@article {pmid40320362,
year = {2025},
author = {Johansson, A and Sarrette, B and Boscari, A and Prudent, M and Gruber, V and Brouquisse, R and Jacquet, C and Gough, C and Pauly, N},
title = {The role of reactive oxygen, nitrogen and sulphur species in the integration of (a)biotic stress signals in legumes.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf175},
pmid = {40320362},
issn = {1460-2431},
abstract = {Legumes are crops of considerable economic and ecological significance. They are suitable for cultivation in a variety of environments and temperatures. They are able to form a symbiotic relationship with nitrogen-fixing soil bacteria called rhizobia contributing to the enrichment of marginal soils with this essential nutrient, and reduces artificial fertilizer use. Similarly, legumes establish a widespread mutualistic association with soil fungi, involving a reciprocal transfer of nutrients. Global warming is reshaping plant interactions with its environment, exerting profound effects on global agricultural systems. Plants have evolved sensing, signaling, and adaptive molecular mechanisms to respond to (a)biotic stimuli. Reactive oxygen, nitrogen, and sulphur species (RONSS) are key players in stress tolerance mechanisms, and their homeostasis, mainly accomplished by antioxidant enzymes and metabolites, is essential to allow redox signaling while preventing oxidative damage. Here, we review recent findings, highlighting metabolic pathways of RONSS and antioxidants, with emphasis on their functions in signaling and protection in response to (a)biotic constraints in legumes. Special attention is paid to the molecular crosstalk between RONSS in response to multiple stimuli and notably how redox homeostasis adjustment can increase (a)biotic stress tolerance and potentially be exploited to mitigate the negative effects of climate change.},
}

@article {pmid40320312,
year = {2025},
author = {Thia, JA and Dorai, APS and Hoffmann, AA},
title = {Symbiotic bacteria and pest control: plant toxins, chemical pesticides, and fungal entomopathogens.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.007},
pmid = {40320312},
issn = {1878-4380},
abstract = {Bacterial symbionts in pests are being increasingly investigated to assess their potential uses for sustainable control approaches. We undertook a review and analysis of the impacts of endosymbionts and gut symbionts on responses to toxins from plants and pesticides, and to attack by fungal entomopathogens. Despite methodological issues affecting estimates of effect sizes, there is evidence for symbionts increasing resistance to all three agents. However, impacts can be small, and for pesticides, these may not reach levels required for resistance at field rates. Negative or neutral effects may be underreported. Further complications arise because host genotype and the environment impact symbiont effects. We anticipate rapid progress in this area over coming years that should clarify practical implications of these effects.},
}

@article {pmid40319919,
year = {2025},
author = {Liu, Y and Yang, M and Li, N and Huang, Y and Yang, C},
title = {Black ink staining protocol: A cost-effective substitute in quantifying arbuscular mycorrhizal colonization in plant roots.},
journal = {Journal of microbiological methods},
volume = {232-234},
number = {},
pages = {107141},
doi = {10.1016/j.mimet.2025.107141},
pmid = {40319919},
issn = {1872-8359},
abstract = {Arbuscular mycorrhizal (AM) fungi, ubiquitously distributed across diverse terrestrial ecosystems, establish symbiotic associations with the majority of vascular plants, fulfilling essential physiological and ecological functions. Mycorrhizal development represents the initiation of host-fungus interactions and serves as a metric for assessing mutualistic efficacy. However, mycorrhizal detection underscores the urgent need to develop cost-effective, efficient, and environmentally benign dyestuff. Therefore, wild-collected and laboratory-grown roots of Medicago sativa were selected. Six reagents including black ink, red ink, acid fuchsin, trypan blue, Sudan IV, and aniline blue were evaluated in conjunction with computer vision techniques to identify optimal one. Concurrently, root characteristics were quantified, and interrelationships among root traits, image quality, and colonization indices were analyzed to unravel the mechanism of their interactions. The findings demonstrated that wild roots exhibited pronounced lignification, achieving a mycorrhizal colonization rate of 100 %, which was better than the two laboratory groups. And the fungal community displayed a markedly greater colonization intensity compared to the Claroideoglomus etunicatum. Evaluation of the six reagents revealed distinct staining efficacy, with significant variations in image clarity, gray-level co-occurrence matrix (GLCM) indices, and colonization parameters across treatments. Specifically, aniline blue proved ineffective, while Sudan IV showed selective binding. Notably, black ink in glacial acetic acid achieved optimal mycorrhizal detection efficacy. Moreover, correlation matrix identified microscopic image quality as critical determinant of quantification accuracy, influenced by both reagent types and root properties, and AvgDiam exerted the most substantial impact (|R| > 0.75).},
}

@article {pmid40319781,
year = {2025},
author = {Liu, Z and Zeng, T and Wang, J and Wang, Z and Zhao, D and Wei, J and Peng, Y and Miao, L},
title = {AHL-mediated quorum sensing drives microbial community succession and metabolic pathway in algal-bacterial biofilm system.},
journal = {Water research},
volume = {282},
number = {},
pages = {123702},
doi = {10.1016/j.watres.2025.123702},
pmid = {40319781},
issn = {1879-2448},
abstract = {Microalgae, ammonia-oxidizing bacteria (AOB), and anaerobic ammonium-oxidizing bacteria (AnAOB) have been proven to form an integrated algal-bacterial biofilm system with over 93 % of total nitrogen removal. Compared to conventional nitrification-denitrification process, this system operated without additional organic carbon or aeration. In order to understand the interaction mechanisms between bacteria and algae, this study investigated microbial community succession, the changes in metabolic pathways and the potential role of acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) during the formation of the algae/partial nitrification/anammox biofilm system. Within this algal-bacterial symbiotic biofilm, the dominant genera identified were Candidatus_Brocadia (AnAOB), Nitrosomonas (AOB), and Geitlerinema (microalgae), with relative abundances of 13.86 %, 6.37 %, and 2.88 %, respectively. Compared with the first two stages, the abundance of genes related to nitrogen metabolism pathways (anaerobic ammonium oxidation, denitrification, and ammonia assimilation) increased, indicating enhanced nitrogen transformation capacity in the algal-bacterial symbiotic stage. Co-occurrence network analysis also revealed enhanced microbial interactions, with increased negative correlations (from 36.07 % to 39.38 %), high average standard betweenness centrality (from 0.193 to 0.304), and reduced community vulnerability (from 0.037 to 0.028), contributing to biofilm stability and resilience. The variations in AHLs provided direct evidence for more frequent interspecies communication, facilitating the ecological reconfiguration in the biofilm. Overall, the close synergistic relationship between microalgae and bacteria supports stable biofilm development and high nitrogen removal efficiency.},
}

@article {pmid40319203,
year = {2025},
author = {Li, JF and Yang, LY and Zhang, Z and Huang, XR and Li, H and Li, S and Yang, XR},
title = {Asymbiotic Nitrogen Fixation in the Phyllosphere of Urban Green Spaces.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {276},
pmid = {40319203},
issn = {1432-0991},
support = {42277110//National Natural Science Foundation of China/ ; 42177097//National Natural Science Foundation of China/ ; },
mesh = {*Nitrogen Fixation ; *Plant Leaves/microbiology/chemistry ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Cities ; Nitrogen/metabolism ; Symbiosis ; Biodiversity ; Ecosystem ; },
abstract = {Biological nitrogen fixation (BNF) is an important source of nitrogen in ecosystems. Compared to symbiotic nitrogen-fixing microorganisms, free-living diazotrophic bacteria have a broader distribution and greater diversity, demonstrating greater potential for application. Leaf surfaces constitute one of the largest microbial reservoirs on Earth, harboring a variety of free-living diazotrophic bacteria, contributing significantly to plant N acquisition and growth. The distribution patterns, abundance, diversity, and the environmental variables affecting the asymbiotic nitrogen fixation (ANF) rates of free-living diazotrophic bacteria of non-leguminous plants in urban green spaces were investigated using high-throughput sequencing of nifH gene amplicons and the acetylene reduction method. Both green space type and plant species significantly impact ANF rates and nifH gene abundance in the phyllosphere, with green space type having a more pronounced effect. Leaf metal elements iron (Fe), molybdenum (Mo), and the free-living diazotrophic bacteria of the genus Skermanella collectively influence the ANF rates in the phyllosphere of urban green spaces. Linear regression analysis revealed that metal elements Fe, Mo, and potassium (K) in the leaves were significantly positive correlated with the diversity of the free-living diazotrophic bacteria and the abundance of the N-fixing gene nifH. The alpha diversity and symbiotic network structure of the free-living diazotrophic bacterial community in the phyllosphere indicated a significant negative correlation between human disturbance and environmental perturbation and the biodiversity and network complexity of these bacteria. This study provides a crucial foundation for understanding the nitrogen-fixing functions of microbes in urban ecosystems and their contributions to the nitrogen cycle.},
}

*Nitrogen Fixation
*Plant Leaves/microbiology/chemistry
*Bacteria/genetics/metabolism/classification/isolation & purification
Cities
Nitrogen/metabolism
Symbiosis
Biodiversity
Ecosystem

@article {pmid40318826,
year = {2025},
author = {Campos-Herrera, R and Georgis, R and Londoño, DK and Malan, A and Molina, C and Shapiro-Ilan, D and Soler, R and Patricia Stock, S and Vandenbossche, B},
title = {Connecting academia and industry: Advancing the use of entomopathogenic nematodes to tackle emerging challenges and opportunities in modern agriculture.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108350},
doi = {10.1016/j.jip.2025.108350},
pmid = {40318826},
issn = {1096-0805},
abstract = {The collaboration among academia, industry, and government is crucial for scientific progress and innovation. Academia generates fundamental knowledge, which industry translates into sound applications, considering government policies. This partnership is vital to feed progress and constant development and address global challenges like climate change and food security. Sustainable crop protection is a topical theme, with efforts to reduce pesticide reliance and promote alternatives to chemical pest management, and it continues to grow and be accepted worldwide. In this respect, biopesticides such as entomopathogenic nematodes (EPNs) offer a promising solution for pest and disease management as an eco-friendly alternative. However, EPN continue to face adoption barriers due to regulatory, commercialization and basic and applied knowledge gaps. Thus, stronger collaborations are needed to unlock their full potential, as highlighted in the 2024 congress organized in La Rioja (Spain) to commemorate the 100 years since the discovery of the first EPN. This review examines the gap between academia and industry, suggesting strategies to bridge it, thereby promoting the advancement of EPN in 21st-century agriculture. Despite decades of research demonstrating their efficacy, EPN commercialization remains limited by production, formulation, and application challenges. Universities and government research agencies have driven fundamental innovation through the discovery of new EPN-bacteria partnerships in new regions of the world, which are helping us understand their distribution and habitant adaptations which are required for their registration and in establishing global regulations. Research conducted both in academia and the private sector (both big and small start-up companies) has and continues to play a key role in the characterization of EPN and in assessing their performance for their subsequent formulation, product optimization, and commercialization. These are fundamental steps to reach the ultimate goal, which is to provide growers with reliable products that are cost-effective and sustainable. In this review, we summarize key findings that have led to the commercialization and application of EPN, spanning from the characterization of EPN and their symbiotic bacteria to production, formulation, and the requirements for their registration. We also highlight critical knowledge gaps and opportunities for collaboration between academia, government agencies, and industry. Strengthening these partnerships will drive EPN adoption in agriculture, establishing them as a desirable biocontrol solution.},
}

@article {pmid40318822,
year = {2025},
author = {Uthra, C and Shunmugam, S and Nagaraj, K and Muralitharan, G and Albeshr, MF and Velmurugan, G},
title = {Ultra-fast liquid chromatography detection of β-N-methylamine-L-alanine and its isomers in cycad seeds and cyanobacterial symbionts for neurotoxic risk assessment.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115503},
doi = {10.1016/j.fct.2025.115503},
pmid = {40318822},
issn = {1873-6351},
abstract = {The cyanobacterial neurotoxin has been implicated in various neurological disorders, posing a potential global health risk. Initial studies revealed alarming levels of β-N-methylamine-L-alanine (BMAA) in cyanobacteria, particularly in symbiotic species, suggesting widespread exposure. This study aimed to validate the efficacy of ultra-fast liquid chromatography (UFLC) technique for the detection and quantification of BMAA in various samples. Derivatizing agents, including 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) and N-(2-aminoethyl) glycine (AEG), were synthesized and confirmed via nuclear magnetic resonance (NMR) spectroscopy to enhance the detection of isomeric neurotoxic compounds. Among the samples analyzed cycad seeds, leaves, male cones, cyanobacterial symbionts, coralloid roots, and processed cycad seed flour BMAA and its isomers (2,4-diaminobutyric acid (2,4-DAB) and AEG) were detected in cycad seeds, cyanobacterial symbionts, and coralloid roots. The retention times for L-BMAA, AEG, and 2,4-DAB were 5.4, 5.6, and 6.1 minutes, respectively. Quantification revealed lower levels of these toxic isomers in seeds compared to high levels in cyanobacterial symbionts. Furthermore, UFLC methods effectively reduced the levels of neurotoxic compounds in cycad seeds to below detectable limits (6 × 10[3] ng/mL). This study underscores the utility of UFLC method combined with derivatization for the efficient detection and separation of L-BMAA and its isomers, providing a reliable approach for neurotoxin analysis.},
}

@article {pmid40318807,
year = {2025},
author = {Liu, R and Guo, L and Shi, D and Sun, X and Shang, M and Zhao, Y and Wang, X and Yang, Y and Xiao, S and Li, J},
title = {Multilayer cascade-response nanoplatforms as metabolic symbiotic disruptors to reprogram the immunosuppressive microenvironment.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {383},
number = {},
pages = {113797},
doi = {10.1016/j.jconrel.2025.113797},
pmid = {40318807},
issn = {1873-4995},
abstract = {Nanomedicine is extensively utilized in tumor treatment, however, the restricted permeability of nanomaterials within tumor tissues, along with the inherent metabolic complexity of these tissues, have hindered effective control of tumor progression. Hypoxic and normoxic tumor cells utilize monocarboxylic acid transporters (MCTs) for the rapid reutilization of lactate, facilitating accelerated tumor growth. Here, cascade-response nanoplatforms (NPs) with contrast-enhanced ultrasound imaging (CEUI) capability had been established, incorporating basigin siRNA internally and featuring hyaluronidase (HAase) and γ-glutamyltranspeptidase (GGT)-responsive lipid coatings externally (GHB NPs). The GHB NPs took advantage of GGT-responsive HAase release to facilitate deep tumor penetration. Furthermore, ultrasound (US) irradiation decreased the expression of glycolysis-related proteins through the modulation of the β-catenin/c-Myc pathway, and US irradiation induced mitochondrial damage, leading to a low-energy state in tumor cells. On this basis, GHB NPs was paired with US stimulation to provide a combination therapy that disturbed tumor cell metabolic symbiosis and remodeled the immunosuppressive tumor microenvironment. This study formulates an effective therapeutic approach for metabolic-immunotherapy, potentially offering a viable candidate for tumor treatment.},
}

@article {pmid40318614,
year = {2025},
author = {Ma, Q and Xu, B and Bititci, U},
title = {Unpacking financial aspects of circular economy: A systematic literature review.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125507},
doi = {10.1016/j.jenvman.2025.125507},
pmid = {40318614},
issn = {1095-8630},
abstract = {The integration of circular economy (CE) principles into practical applications is accelerating, driving rapid growth in research within this field. However, critical financial aspects that could facilitate the wider adoption of CE practices remain underexplored. This study aims to address this gap through a systematic literature review to analyse the key financial topics related to CE. Specifically, we categorise financial themes in CE research into three distinct areas: the financial performance of CE practices, diverse financing approaches and their impact on CE adoption, and strategies for de-risking CE projects. By synthesising the existing literature, identifying research gaps, and presenting a case study of a UK-based SME that exemplifies both the challenges and opportunities within the industrial symbiosis concept, our review provides deeper insights into the financial implications of CE practices. Additionally, we propose a conceptual framework to highlight current knowledge and gaps, offering a guide for future investigations in this area.},
}

@article {pmid40317738,
year = {2025},
author = {Li, J and Shao, Z and Cheng, K and Yang, Q and Ju, H and Tang, X and Zhang, S and Li, J},
title = {Coral-associated Symbiodiniaceae exhibit host specificity but lack phylosymbiosis, with Cladocopium and Durusdinium showing different cophylogenetic patterns.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70184},
pmid = {40317738},
issn = {1469-8137},
support = {42122045//National Natural Science Foundation of China/ ; U23A2036//National Natural Science Foundation of China/ ; },
abstract = {Altering the composition of the Symbiodiniaceae community to adapt to anomalous sea water warming represents a potential survival mechanism for scleractinian corals. However, the processes of Symbiodiniaceae assembly and long-standing evolution of coral-Symbiodiniaceae interactions remain unclear. Here, we utilized ITS2 (internal transcribed spacer 2) amplicon sequencing and the SymPortal framework to investigate the diversity and specificity of Symbiodiniaceae across 39 scleractinian coral species. Furthermore, we tested phylosymbiosis and cophylogeny between coral hosts and their Symbiodiniaceae. In our study, environmental samples exhibited the highest Symbiodiniaceae diversity. Cladocopium and Durusdinium dominated the Symbiodiniaceae communities, with significant β-diversity differences among coral species. Additionally, host specificity was widespread in Symbiodiniaceae, especially Durusdinium spp., yet lacked a phylosymbiotic pattern. Moreover, Cladocopium spp. showed cophylogenetic congruence with their hosts, while there was no evidence for Durusdinium spp. Furthermore, host switching was the predominant evolutionary event, implying its contribution to Cladocopium diversification. These findings suggest that Symbiodiniaceae assembly does not recapitulate host phylogeny, and host specificity alone does not drive phylosymbiosis or cophylogeny. As environmental reservoirs, free-living Symbiodiniaceae may influence symbiotic communities. Additionally, Durusdinium-coral associations lack cophylogenetic signals, indicating more flexible partnerships than Cladocopium. Overall, our results enhance understanding of Symbiodiniaceae assembly and coral-Symbiodiniaceae evolutionary interactions.},
}

@article {pmid40317021,
year = {2025},
author = {Pasinato, A and Singh, G},
title = {Bioinformatic exploration of RiPP biosynthetic gene clusters in lichens.},
journal = {Fungal biology and biotechnology},
volume = {12},
number = {1},
pages = {6},
pmid = {40317021},
issn = {2054-3085},
abstract = {BACKGROUND: Ribosomally synthesized and posttranslationally modified peptides (RiPPs) represent a relatively recent addition to the biosynthetic gene cluster (BGC) repertoire of fungi. These BGCs are primarily involved in toxins production and defense-related functions and resulting metabolites also have a significant therapeutic potential. While only a limited number of fungal RiPPs, primarily from a few model fungi, have been characterized, genome mining approaches show that RiPP BGCs are nearly ubiquitous across the fungal kingdom. However, the RiPP biosynthetic landscape of fungi involved in intricate relationship as symbiosis, such as lichen-forming fungi (LFF), remains unexplored.

RESULTS: This study presents the first comprehensive survey of RiPP BGCs across 111 LFF genomes employing an integrative framework that combines genome mining, phylogenetic inference, and gene network reconstruction. We identified 987 RiPP BGCs, constituting approximately 17% of the total biosynthetic diversity in LFF, a proportion significantly higher than previously estimated. Most lichen RiPP BGCs are unique and do not cluster with any known RiPP gene cluster. We found two RiPP BGCs that were shared among the members of the family Parmeliaceae (Lecanoromycetes), with the signature gene homologous to ustiloxin signature enzyme, indicating a putative similarity to fungal mycotoxin-related BGCs. While one of these BGCs, members of Clan R1, contains the accessory genes for dikaritin synthesis (tyrosinase and methyltransferase), the accessory genes of other BGCs, members of Clan R2, have not yet been reported from any characterized fungal RiPP BGC but only from bacteria. Additionally, for lichen RiPP BGCs that do not cluster with any known BGCs in the RiPP network, we unraveled the presence of the conserved HXXHC motif in the signature gene and, based on this we report the widespread distribution of putative dikaritin homologs across Lecanoromycetes.

CONCLUSIONS: This study highlights the presence and distribution of RiPP BGCs in Lecanoromycetes and identifies two conserved RiPP clusters putatively homologous to dikaritins (involved in mycotoxin production) within the Lecanoromycete family Parmeliaceae and a general prevalence of putative signature dikaritin genes (not the cluster) in Lecanoromycetes. Our study highlights the widespread presence of putative mycotoxin-related BGCs in lichenized fungi.},
}

@article {pmid40315931,
year = {2025},
author = {Yang, L and Sun, X and Li, H and Hao, R and Liu, F},
title = {New insights into microalgal-bacterial immobilization systems for wastewater treatment: mechanisms, enhancement strategies, and application prospects.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132609},
doi = {10.1016/j.biortech.2025.132609},
pmid = {40315931},
issn = {1873-2976},
abstract = {The wastewater treatment based on the symbiosis of microalgae and bacteria has attracted increasing attention for its excellent pollutant removal efficiency, energy savings, and resource recovery. Among them, the microalgae-bacteria immobilization (MABI) system stands out by enhancing the electron transfer efficiency through carrier domain confinement, thereby overcoming bottlenecks of low light energy utilization and challenging biomass recycling. MABI is considered a key breakthrough for advancing engineering applications. However, a comprehensive exploration of MABI systems remains lacking. This review systematically summarizes the latest advancements, covering major immobilization techniques and the intrinsic mechanisms underlying microalgae-bacteria interactions and electron transport. Additionally, it explores enhancement strategies aimed at balancing microbial light energy allocation, optimizing nutrient supply, and constructing complementary ecological niches. The advantages and application prospects of MABI systems are highlighted. The review contributes to structuring the knowledge framework of MABI research and identifies critical gaps for future investigation.},
}

@article {pmid40315358,
year = {2025},
author = {Wang, L and Tian, T and Deng, Y and Ji, J and Liang, J and Guan, Y and Li, R and Huang, X and Wang, Y and Ning, G and Fan, Q and Becana, M and Duanmu, D},
title = {Plant glutamyl-tRNA reductases coordinate plant and rhizobial heme biosynthesis in nitrogen-fixing nodules.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf095},
pmid = {40315358},
issn = {1532-298X},
abstract = {Heme is biosynthesized in legume root nodules to meet the demand for leghemoglobins (Lbs) and other heme-binding proteins. However, the main source of nodule heme remains unknown. Both the plant host and rhizobia possess a complete heme biosynthetic pathway, differing slightly in the production of 5-aminolevulinic acid (ALA), a key regulatory step catalyzed by glutamyl-tRNA reductase (GluTR) in the plant and by HemA in the rhizobia. Transcriptomic analysis revealed that many plant heme biosynthetic genes, including GluTR2 but not GluTR1, are upregulated in nodules compared to roots, whereas expression of related rhizobial genes, including both HemA1 and HemA2, is generally inhibited under symbiotic conditions compared to free-living conditions. Knockout of Lotus japonicus GluTR2, but not of HemA1 and HemA2, led to a significant decrease (∼50%) in nodule heme content. The stable heterozygous mutant of GluTR1 or transient knockdown of GluTR1 exhibited a ∼20% reduction in nodule heme content. Overexpression of Fluorescent in blue light (FLU), a feedback inhibitor of GluTR activity, caused a much greater reduction in nodule heme content (∼75%) and an increased level of apo-Lb and, in combination with the hemA1 hemA2 mutant, a drastic inhibition of nitrogenase activity (>90%). This study provides genetic evidence supporting a major role of plant GluTRs in coordinating heme biosynthesis between the two symbionts by supplying heme to assemble with cytoplasmic apo-Lbs and by providing ALA for heme synthesis in the bacteroids.},
}

@article {pmid40315234,
year = {2025},
author = {Abeysingha, DN and Dinesh, S and Kottage, SM and Chen, L and Roopesh, MS and Thilakarathna, MS},
title = {Effects of cold plasma seed treatment on pea (Pisum sativum L.) plant performance under drought and well-watered conditions.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0322108},
pmid = {40315234},
issn = {1932-6203},
mesh = {*Pisum sativum/growth & development/drug effects/physiology ; *Droughts ; *Seeds/drug effects/growth & development ; *Plasma Gases/pharmacology ; Water/metabolism ; Nitrogen Fixation/drug effects ; Plant Roots/growth & development/drug effects ; Stress, Physiological ; Plant Shoots/growth & development/drug effects ; },
abstract = {Cold plasma (CP) technology is an emerging technology with the potential to enhance agricultural productivity and sustainability. Although its application in crop production is still in the early stages, CP seed treatment has demonstrated promise in improving various growth parameters, especially in legumes. We hypothesized that CP seed treatment can improve nodulation, symbiotic nitrogen fixation (SNF), root and shoot growth, overall productivity, and drought stress resistance in field pea. A controlled environmental study was conducted to investigate the effects of dielectric barrier discharge-generated CP seed treatment for 6 min on yellow field pea under different moisture regimes [30%, 45%, 60%, and 75% field capacity (FC)], focusing on nodulation, and root and shoot growth parameters at the flowering stage. Based on experiment-1 findings, 30% and 75% FC were selected as drought and well-watered conditions, respectively, to study the effect of CP seed treatments on SNF parameters at the flowering stage and nitrogen fixation, yield, and seed quality parameters at maturity. CP seed treatment improved root growth parameters at the flowering stage and an increasing trend was observed for shoot and nodulation parameters across different moisture levels. As an independent factor, moisture stress negatively affected nodulation and shoot growth parameters at the flowering stage. CP seed treatment improved nitrogen fixation and yield parameters under well-watered conditions compared to drought conditions at seed maturity. However, the seed protein content or the quality was not improved by the CP seed treatment. Grain yield, yield parameters, grain nitrogen, and nitrogen fixation were reduced under drought stress compared to the well-watered condition. Therefore, these findings underscore the potential of CP to enhance crop performance in well-watered conditions. The underperformance of the CP-treated seeds at drought conditions is not well understood and warrants further investigation.},
}

*Pisum sativum/growth & development/drug effects/physiology
*Droughts
*Seeds/drug effects/growth & development
*Plasma Gases/pharmacology
Water/metabolism
Nitrogen Fixation/drug effects
Plant Roots/growth & development/drug effects
Stress, Physiological
Plant Shoots/growth & development/drug effects

@article {pmid40315204,
year = {2025},
author = {Ayra, L and Jiménez-Nopala, G and Guerrero, G and Fuentes, SI and Leija, A and Ramírez, M and Hernández, G},
title = {Expression profiling and transcriptional regulation of the SRS transcription factor gene family of common bean (Phaseolus vulgaris) in symbiosis with Rhizobium etli.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321784},
pmid = {40315204},
issn = {1932-6203},
mesh = {*Symbiosis/genetics ; *Phaseolus/genetics/microbiology/metabolism ; *Transcription Factors/genetics/metabolism ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; Phylogeny ; *Rhizobium etli/physiology ; Gene Expression Profiling ; Root Nodules, Plant/genetics/microbiology ; Multigene Family ; },
abstract = {The SRS/STY transcription factors from the model legumes: Lotus japonicus and Medicago truncatula, are part of regulatory networks that play relevant roles for nodule development during the N-fixing symbiosis with rhizobia. In this work we analyzed the participation of the PvSRS transcription factors from common bean (Phaseolus vulgaris), a most important legume crop, in the symbiosis with Rhizobium etli. Our phylogenetic analysis of SRS TFs across five plant species, including four legumes and Arabidopsis thaliana, identified clades that group SRS proteins that are highly expressed in legume nodules and in Arabidopsis roots. A qRT-PCR expression analysis of the 10 PvSRS in root/nodule of inoculated plants, revealed that all the PvSRS genes are expressed at different stages of the symbiosis, albeit at different levels. Based on what is known for L. japonicus, we demonstrated that the PvSRS10 gene -with highest expression during symbiosis- is transcriptionally activated by NF-Y transcription factor, thus indicating its participation in the NIN-NF-Y regulatory cascade. Based on our previous work about the relevant role of members from the MADS-domain/AGL transcription factors as regulators of the N-fixing symbiosis, in this work we demonstrated the transcriptional regulation of PvSRS10 by the MADS-TF PvFUL-like. Analysis of protein-protein interaction networks predicted thatPvSRS5 and PvSRS6 interact with proteins involved in transcriptional regulation and the auxin-activated signaling pathway. The regulatory mechanisms of PvSRS TF in common bean symbiosis may be related to auxin biosynthesis regulation, that is essential for determinate nodules development. Our study highlights the role of PvSRS TF in the N-/fixing symbiosis, a relevant process for sustainable agriculture.},
}

*Symbiosis/genetics
*Phaseolus/genetics/microbiology/metabolism
*Transcription Factors/genetics/metabolism
*Gene Expression Regulation, Plant
*Plant Proteins/genetics/metabolism
Phylogeny
*Rhizobium etli/physiology
Gene Expression Profiling
Root Nodules, Plant/genetics/microbiology
Multigene Family

@article {pmid40314411,
year = {2025},
author = {Meilhoc, E and Boscari, A and Pauly, N and Lepetit, M and Frendo, P and Bruand, C and Puppo, A and Brouquisse, R},
title = {"Oxygen and derived reactive species in Legume - Rhizobia interactions: paradoxes and dual roles".},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf160},
pmid = {40314411},
issn = {1460-2431},
abstract = {Biological nitrogen fixation (BNF) between legumes and Rhizobia is the result of a symbiosis characterized by the formation of a new organ, the nodule, in which the plants house and feed the bacteria. Oxygen (O2) concentration inside the nodule is very low (on the order of a few tens of nanomolar). The nitrogenase which is responsible for the reduction of atmospheric nitrogen (N2) to ammonia (NH3) is irreversibly inhibited by traces of O2, while O2 is required for the overall process of N2 fixation which consumes high amounts of energy and reducing power. How is this paradox solved? The set-up of a physical and chemical O2 diffusion barrier, including the synthesis of numerous leghemoglobins, a class of hemoproteins with a very high O2 absorption capacity, was evidenced. However, why are so many leghemoglobin genes present while they appear to be mainly expressed in the same nodule zone? Furthermore, why do the bacterial symbionts contain multiple O2 sensors despite the existence of a very low O2 tension inside the nodule? On the other hand, the O2 derived reactive species, such as superoxide radical, hydrogen peroxide and nitric oxide, which play important metabolic and signalling roles in the symbiotic process, appear to act as Janus molecules. They exhibit opposite effects throughout symbiosis establishment and nodule life. The aim of this review is to provide possible answers to the questions asked and to highlight the dual roles of O2 reactive species in nodule development, functioning and senescence.},
}

@article {pmid40314323,
year = {2025},
author = {Webster, SS},
title = {From the archives: Nitrogen matters in crop domestication, rice nitrogen nutrition, and symbiotic nitrogen fixation.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf099},
pmid = {40314323},
issn = {1532-298X},
}

@article {pmid40313410,
year = {2025},
author = {Liu, J and Zhou, Y and Feng, J and Cai, C and Zhang, S},
title = {Comparative metagenomic analysis reveals the adaptive evolutionary traits of siboglinid tubeworm symbionts.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533506},
pmid = {40313410},
issn = {1664-302X},
abstract = {Tubeworms flourish in marine cold seeps and hydrothermal vents through the establishment of symbiotic relationships with chemosynthetic bacteria. However, the environmental adaptations and evolutionary relationships of tubeworm symbionts across diverse habitats and hosts remain largely unknown. In this study, we characterized the genomes of 26 siboglinid tubeworm symbionts collected from deep-sea hydrothermal vents, cold seeps, and deep-sea mud, including two sequenced in this study and 24 previously published. Phylogenetic analysis classified the 26 symbiont genomes into five distinct clusters at the genus level. The findings highlight the remarkable diversity in symbiont classification, influenced by the habitat and species of tubeworm, with the symbiont genome characteristics of various genera revealing unique evolutionary strategies. Siboglinid symbionts exhibit functional metabolic diversity, encompassing chemical autotrophic capabilities for carbon, nitrogen, and sulfur metabolism, hydrogen oxidation, and a chemoorganotrophic ability to utilize various amino acids, cofactors, and vitamins. Furthermore, the symbiont's homeostatic mechanisms and CRISPR-Cas system are vital adaptations for survival. Overall, this study highlights the metabolic traits of siboglinid symbionts across different genera and enhances our understanding of how different habitats and hosts influence symbiont evolution, offering valuable insights into the strategies that symbionts use to adapt and thrive in extreme environments.},
}

@article {pmid40311709,
year = {2025},
author = {Bai, B and Wang, L and Guan, F and Pi, H and Wang, A and Zhai, L},
title = {Maturity phase is crucial for removing antibiotic resistance genes during composting: novel insights into dissolved organic matter-microbial symbiosis system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132607},
doi = {10.1016/j.biortech.2025.132607},
pmid = {40311709},
issn = {1873-2976},
abstract = {Composting is widely regarded as an effective method for reducing antibiotic resistance genes (ARGs) in livestock and poultry manure. However, the critical mechanism of ARGs in different composting phase is still unclear. In this study, normal compost and two various rapid composting (without mature phase) were used to analyze the removal of ARGs and the succession of dissolve organic matter (DOM). Compared to normal composting, rapid composting reactivated tetracyclines, sulfonamide, and quinolones resistance genes during the maturation phase and reduced the total ARGs removal rates by 45.58 %-57.87 %. Humus-like components could inhibit the proliferation of ARGs, and the enrichment of protein-like components increased abundances of Pusillimonas, Persicitalea, and Pseudomonas, indirectly reducing the removal. This study is the first to demonstrate that contribution of DOM and microbial community to ARGs removal, emphasizing the importance of the maturation phase for ARGs elimination. This research provides guidance for producing safe compost products.},
}

@article {pmid40311530,
year = {2025},
author = {Wang, HM and Zhou, J and Ma, CY and Wu, XH and Ullah, Y and Zhang, ZH and Li, Y and Wang, XX and Dai, CC},
title = {Identification of a small secreted protein, PlSSP, that contributes to the symbiotic association of Phomopsis liquidambaris with rice under nitrogen starvation.},
journal = {Plant physiology and biochemistry : PPB},
volume = {224},
number = {},
pages = {109969},
doi = {10.1016/j.plaphy.2025.109969},
pmid = {40311530},
issn = {1873-2690},
abstract = {Endophytic fungi are crucial for enhancing plant growth and stress tolerance. Phomopsis liquidambaris B3, a broad-spectrum endophytic fungus, significantly improves plant nitrogen uptake and growth under nitrogen-limited conditions. In this study, we identified a small secreted protein, PlSSP, which localizes to the cytoplasmic matrix of host cells and modulates plant immune responses. Using proteomic and transcriptomic approaches, we found that PlSSP upregulates key defense-related genes, including members of the PR and WRKY families, as well as genes involved in reactive oxygen species scavenging and nitrogen assimilation. Structural analysis revealed PlSSP's secondary and thermal stability features, which likely contribute to its functional interaction with host cellular components. Functional analyses demonstrated that PlSSP expression correlates with increased fungal colonization and rice biomass accumulation under nitrogen-starved conditions. These results advance our understanding of how P. liquidambaris promotes plant resilience and nutrient uptake, providing insights with potential applications in sustainable agriculture.},
}

@article {pmid40310917,
year = {2025},
author = {Zhou, S and Li, M and Wang, P and Guo, C and Zhang, J and Luo, X and Fan, YC and Chen, EQ and Qi, X and Chen, J and Ye, L and Yuan, HY and Yin, WB and Wang, K and Zheng, MH and Pang, Y and Qiao, J and Jiang, C},
title = {A symbiotic filamentous gut fungus ameliorates MASH via a secondary metabolite-CerS6-ceramide axis.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6746},
pages = {eadp5540},
doi = {10.1126/science.adp5540},
pmid = {40310917},
issn = {1095-9203},
mesh = {Animals ; Male ; Mice ; *Ceramides/metabolism ; Disease Models, Animal ; *Fusarium/metabolism/isolation & purification/physiology ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Secondary Metabolism ; *Sphingosine N-Acyltransferase/metabolism/antagonists & inhibitors ; *Symbiosis ; *Fatty Liver/metabolism/microbiology/therapy ; *Cell Culture Techniques ; },
abstract = {The gut microbiota is known to be associated with a variety of human metabolic diseases, including metabolic dysfunction-associated steatohepatitis (MASH). Fungi are increasingly recognized as important members of this community; however, the role of fungal symbionts in metabolic diseases is unknown. We have systematically isolated and characterized gut fungi, identifying Fusarium foetens as an intestinal symbiotic filamentous fungus in mice. F. foetens reverses MASH progression in mouse models through an intestinal ceramide synthetase 6 (CerS6)-ceramide axis. Moreover, we identified FF-C1, a secondary metabolite from F. foetens, as a CerS6 inhibitor that has an endogenous protective effect on MASH progression.},
}

Animals
Male
Mice
*Ceramides/metabolism
Disease Models, Animal
*Fusarium/metabolism/isolation & purification/physiology
*Gastrointestinal Microbiome
Mice, Inbred C57BL
Secondary Metabolism
*Sphingosine N-Acyltransferase/metabolism/antagonists & inhibitors
*Symbiosis
*Fatty Liver/metabolism/microbiology/therapy
*Cell Culture Techniques

@article {pmid40310603,
year = {2025},
author = {Hutmacher, F and Conrad, B and Appel, M and Schwan, S},
title = {Mediated autobiographical remembering in the digital age: insights from an experimental think-aloud study.},
journal = {Cognitive research: principles and implications},
volume = {10},
number = {1},
pages = {18},
pmid = {40310603},
issn = {2365-7464},
mesh = {Humans ; *Memory, Episodic ; Female ; Male ; Adult ; Young Adult ; *Mental Recall/physiology ; *Thinking/physiology ; },
abstract = {Autobiographical remembering may undergo significant transformations in the digital age, in which the omnipresence of digital tools has led to an increased density of recorded life episodes. To gain deeper insights into these processes, we conducted an experimental think-aloud study in which participants (N = 41) had to remember an important day and a random day that happened about one year ago. As the results demonstrate, participants repeatedly switched between information stored in their minds and information stored in external resources when remembering these events, with digital resources playing a particularly prominent role. The number of changes between internal memories and external resources as well as the number of digital resources that individuals used were higher when remembering the random day. In sum, this suggests that the iterative combination of information stored in one's mind and information stored in external resources can be considered a potentially symbiotic process.},
}

Humans
*Memory, Episodic
Female
Male
Adult
Young Adult
*Mental Recall/physiology
*Thinking/physiology

@article {pmid40308943,
year = {2025},
author = {Sharp, V and Pfeil, K and Kitch, K and Medina, M},
title = {Cassiopea xamachana polyp feeding under husbandry conditions.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40308943},
issn = {2578-9430},
abstract = {Research on the upside-down jellyfish Cassiopea xamachana has increased in the past few decades, hence the need for more efficient husbandry protocols. We tested the effect of weekly feeding frequencies, light cycles, and nutrient supplements on symbiotic and aposymbiotic polyp asexual reproduction and mortality. C. xamachana polyps have better survivorship and reproduction when kept in a day/night cycle and given additional food beyond Artemia nauplii.},
}

@article {pmid40308709,
year = {2025},
author = {Zhao, Y and Xiong, C and Wang, B and Li, D and Liu, J and Wei, S and Hou, Y and Zhou, Y and Zheng, R},
title = {The Discovery of Phages in the Substantia Nigra and Its Implication for Parkinson's Disease.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0657},
pmid = {40308709},
issn = {2639-5274},
abstract = {Background: A century ago, a mystery between a virus and Parkinson's disease (PD) was described. Owing to the limitation of human brain biopsy and the challenge of electron microscopy in observing virions in human brain tissue, it has been difficult to study the viral etiology of PD. Recent discovery of virobiota reveals that viruses coexist with humans as symbionts. Newly developed transcriptomic sequencing and novel bioinformatic approaches for mining the encrypted virome in human transcriptome make it possible to study the relationship between symbiotic viruses and PD. Nevertheless, whether viruses exist in the human substantia nigra (SN) and whether symbiotic viruses underlie PD pathogenesis remain unknown. Methods: We collected current worldwide human SN transcriptomic datasets from the United States, the United Kingdom, the Netherlands, and Switzerland. We used bioinformatic approaches including viruSITE and the Viral-Track to identify the existence of viruses in the SN of patients. The comprehensive RNA sequencing-based virome analysis pipeline was used to characterize the virobiota in the SN. The Pearson's correlation analysis was used to examine the association between the viral RNA fragment counts (VRFCs) and PD-related human gene sequencing reads in the SN. The differentially expressed genes (DEGs) in the SN between PD patients and non-PD individuals were used to examine the molecular signatures of PD and also evaluate the impact of symbiotic viruses on the SN. Findings: We observed the existence of viruses in the human SN. A dysbiosis of virobiota was found in the SN of PD patients. A marked correlation between VRFC and PD-related human gene expression was detected in the SN of PD patients. These PD-related human genes correlated to VRFC were named as the virus-correlated PD-related genes (VPGs). We identified 3 bacteriophages (phages), including the Proteus phage VB_PmiS-Isfahan, the Escherichia phage phiX174, and the Lactobacillus phage Sha1, that might impair the gene expression of neural cells in the SN of PD patients. The Proteus phage VB_PmiS-Isfahan was a common virus in the SN of patients from the United Kingdom, the Netherlands, and Switzerland. VPGs and DEGs together highlighted that the phages might dampen dopamine biosynthesis and weaken the cGAS-STING function. Interpretation: This is the first study to discover the involvement of phages in PD pathogenesis. A lifelong low symbiotic viral load in the SN may be a contributor to PD pathogenesis. Our findings unlocked the black box between brain virobiota and PD, providing a novel insight into PD etiology from the perspective of phage-human symbiosis.},
}

@article {pmid40308308,
year = {2025},
author = {Sujkowska-Rybkowska, M and Rusaczonek, A},
title = {Editorial: Plant-microbes interactions and resistance against abiotic stress.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1599870},
pmid = {40308308},
issn = {1664-462X},
}

@article {pmid40308299,
year = {2025},
author = {Lei, M and Wang, X and Chen, K and Wei, Q and Zhou, M and Chen, G and Su, S and Tai, Y and Zhuang, K and Li, D and Liu, M and Zhang, S and Wang, Y},
title = {Sugar transporters: mediators of carbon flow between plants and microbes.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1536969},
pmid = {40308299},
issn = {1664-462X},
abstract = {Pathogens and symbiotic microorganisms significantly influence plant growth and crop productivity. Enhancing crop disease resistance and maximizing the beneficial role of symbiotic microorganisms in agriculture constitute critical areas of scientific investigation. A fundamental aspect of plant-microorganisms interactions revolves around nutritional dynamics, characterized by either "food shortage" or "food supply" scenarios. Notably, pathogenic and symbiotic microorganisms predominantly utilize photosynthetic sugars as their primary carbon source during host colonization. This phenomenon has generated substantial interest in the regulatory mechanisms governing sugar transport and redistribution at the plant-microorganism interface. Sugar transporters, which primarily mediate the allocation of sugars to various sink organs, have emerged as crucial players in plant-pathogen interactions and the establishment of beneficial symbiotic associations. This review systematically categorized plant sugar transporters and highlighted their functional significance in mediating plant interactions with pathogenic and beneficial microorganisms. Furthermore, we synthesized recent advancements in understanding the molecular regulatory mechanisms of these transporters and identified key scientific questions warranting further investigation. Elucidating the roles of sugar transporters offers novel strategies for enhancing crop health and productivity, thereby contributing to agricultural sustainability and global food security.},
}

@article {pmid40307010,
year = {2025},
author = {Fujiwara, A and Hagiwara, H and Tsuchimoto, M and Tsuchida, T},
title = {Prevalence, Symbiosis with Rickettsia, and Transmission of Tomato yellow leaf curl virus of Invasive Bemisia tabaci MED Q2 in Japan.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME24095},
pmid = {40307010},
issn = {1347-4405},
mesh = {Animals ; *Hemiptera/virology/microbiology ; *Begomovirus/physiology/isolation & purification ; Japan ; *Plant Diseases/virology ; *Symbiosis ; *Rickettsia/physiology/isolation & purification/genetics ; *Insect Vectors/virology/microbiology ; Introduced Species ; Prevalence ; Solanum lycopersicum/virology ; },
abstract = {The whitefly, Bemisia tabaci, is a notorious insect pest that transmits plant pathogenic viruses to a wide range of economically important crops. An invasive genetic group of B. tabaci, Mediterranean Q2 (MED Q2), has recently spread to Europe, USA, and Asia. In the present study, we investigated the prevalence of MED Q2 in Japanese agricultural sites and found that its distribution has expanded since it was initially detected in 2013. A polymerase chain reaction ana-lysis revealed that all MED Q2 individuals were infected with Rickettsia. Rickettsia titers increased during nymphal development, presumably in response to the nutritional needs of the host. A fluorescence in situ hybridization ana-lysis revealed that Rickettsia was densely located near Portiera-containing bacteriocytes at all growth stages. Therefore, Rickettsia may play an important role, such as supplying nutrients to the host, in cooperation with Portiera. Transfer experiments indicated that MED Q2 was as effective a vector for Tomato yellow leaf curl virus as MED Q1 and, thus, is a high-risk agricultural pest. These results provide important insights into the biology and ecology of invasive MED Q2 to effectively control its spread and minimize its impact on crops.},
}

Animals
*Hemiptera/virology/microbiology
*Begomovirus/physiology/isolation & purification
Japan
*Plant Diseases/virology
*Symbiosis
*Rickettsia/physiology/isolation & purification/genetics
*Insect Vectors/virology/microbiology
Introduced Species
Prevalence
Solanum lycopersicum/virology

@article {pmid40307009,
year = {2025},
author = {Moriuchi, M and Kuzunuki, K and Ikenishi, F and Sameshima, R and Nakagiri, A and Toyoda, S and Katsuyama, C and Kakizaki, K and Itakura, M and Yoshida, N and Suwa, Y and Minamisawa, K},
title = {Fusarium Fungi Produce Nitrous Oxide (N2O) from Nitrite (NO2[-]) in a Model Pot System Simulating the Soybean Rhizosphere.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME24092},
pmid = {40307009},
issn = {1347-4405},
mesh = {*Nitrous Oxide/metabolism ; *Rhizosphere ; *Glycine max/microbiology ; Soil Microbiology ; *Nitrites/metabolism ; Phylogeny ; *Fusarium/metabolism/isolation & purification/genetics/classification ; Plant Roots/microbiology ; Denitrification ; },
abstract = {Nitrous oxide (N2O) is a key atmospheric greenhouse gas that contributes to global warming, with anthropogenic N2O emissions from agriculture being a particular concern. Among agricultural sources, unknown soil organisms in the legume rhizosphere emit N2O from degraded root nodules. To discriminate between fungal and bacterial N2O emissions, we adopted an isotopomer ana-lysis, which provides site preference values (the difference in [15]N abundance of the central and terminal N atoms in the N2O molecule). The addition of nitrite instead of nitrate to soybean nodulated roots significantly increased SPN2O from -3.5‰ to 4.2‰ in a pot system. Moreover, a mutation of the nirK gene (encoding dissimilatory nitrite reductase) in symbiotic bradyrhizobia significantly increased SPN2O from 4.2‰ to 13.9‰ with nitrite. These results suggest that nitrite-utilizing N2O emissions via fungal denitrification occurred in the model pot system of the soybean rhizosphere. Microscopic observations showed fungal hyphae and crescent spores around N2O-emitting nodules. Therefore, we isolated single spores from soybean nodules under a microscope. A phylogenetic ana-lysis revealed that all 12 fungal isolates were Fusarium species, which exist in soybean field soil. When these isolates were cultivated in glycerol-peptone medium supplemented with nitrate or nitrite (1‍ ‍mM), 11 of the 12 isolates strongly converted nitrite to N2O; however, no N2O emissions were noted in the presence of nitrate. A [15]N-nitrite tracer experiment revealed that one N2O molecule was derived exclusively from two molecules of nitrite (NO2[-]) in the fungal culture. These results suggest that nitrite-utilizing Fusarium fungi mediate N2O emissions in the soybean rhizosphere.},
}

*Nitrous Oxide/metabolism
*Rhizosphere
*Glycine max/microbiology
Soil Microbiology
*Nitrites/metabolism
Phylogeny
*Fusarium/metabolism/isolation & purification/genetics/classification
Plant Roots/microbiology
Denitrification

@article {pmid40306340,
year = {2025},
author = {Yan, R and Ji, H and Liu, ZC and Ren, MQ and Wang, S and Yang, LM and Cui, D},
title = {Construction and optimization of low carbon-to-nitrogen ratio-adapted Chlorococcum-Bacteria symbiosis for energy-efficient wastewater remediation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132601},
doi = {10.1016/j.biortech.2025.132601},
pmid = {40306340},
issn = {1873-2976},
abstract = {This study developed a microalgae-bacteria symbiosis (MBS) system using Chlorococcum robustum AY122332.1 isolated from rare earth tailings wastewater to treat synthetic municipal wastewater. Systematic optimization identified a 1:1 bacteria-microalgae ratio (MBS 1) as optimal, achieving nearly 100 % removal of ammonia and 92.2 ± 0.6 % of chemical oxygen demand. Microbial community analysis identified significant enrichment of nitrogen-transforming consortia in MBS 1, particularly Thauera (7.43 % relative abundance), whose nitrite reductase activity and polyhydroxyalkanoate biosynthesis capacity enhanced simultaneous nitrification-denitrification. The optimized system showed superior stability with an elevated zeta potential (+17.72 mV) driven by protein-rich extracellular polymeric substances production and humic acid accumulation. These biopolymers facilitated microaggregate formation through ligand bridging and hydrophobic interactions, creating redox-stratified microenvironments that supported functional microbial niches. The synergistic interactions in the MBS system enabled efficient nutrient recovery while maintaining ecological resilience under carbon-limited conditions, providing new insights into sustainable wastewater bioremediation processes.},
}

@article {pmid40304278,
year = {2025},
author = {Lentendu, G and Singer, D and Agatha, S and Bahram, M and Hannula, SE and Helder, J and Tedersoo, L and Traunspurger, W and Geisen, S and Lara, E},
title = {EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14118},
doi = {10.1111/1755-0998.14118},
pmid = {40304278},
issn = {1755-0998},
support = {PID2021-128499NB-I00 10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades/ ; 182531//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes-a prerequisite to better understanding soil systems.},
}

@article {pmid40303862,
year = {2025},
author = {Munene, R and Mustafa, O and Loftus, S and Banfield, CC and Rötter, RP and Bore, EK and Mweu, B and Mganga, KZ and Otieno, DO and Ahmed, MA and Dippold, MA},
title = {Contribution of arbuscular mycorrhiza and exoenzymes to nitrogen acquisition of sorghum under drought.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1514416},
pmid = {40303862},
issn = {1664-462X},
abstract = {INTRODUCTION: For low-fertile and degraded soils of sub-Saharan Africa, nitrogen (N) is often the most growth-limiting factor restricting crop yields. The often-suggested exploitation of advantageous rhizosphere traits such as enzyme secretion and/or the symbiosis with arbuscular mycorrhizal fungi (AMF) remains to be validated as a potential strategy to overcome N limitation, especially when N deficiency co-occurs with further abiotic stresses such as water scarcity.

METHODS: Three sorghum genotypes were cultivated in soil mesocosms with a root-exclusion compartment, where only AMF could scavenge for nutrients under drought and optimal conditions. Plant carbon (C) investment into the rhizosphere and N uptake were tracked by [15]N application coupled with [13]CO2 labeling.

RESULTS: Under drought, uptake of mineral [15]N by AMF from the root-exclusion compartment increased 4-12 times compared to well-watered conditions. In addition, water stress enhanced below-ground allocation of recently assimilated C into microbial biomass. Drought reduced the enzymatic potential (Vmax) of chitinase while increasing leucine aminopeptidase (LAP) activity. This suggests that N acquisition via protein mineralization in soil was relatively enhanced compared to that of chitin following moisture limitation. LAP substrate affinity (Km) was reduced by drought compared to that of chitinase with genotype-specific shifts in the rhizosphere enzyme systems observed.

CONCLUSION: Our findings suggest that below-ground C allocation activated AMF symbiosis and its associated microbiome. This not only led to a shift in enzyme-driven exploitation of distinct organic N sources but also induced a strong increase in AMF-based mineral N acquisition from the mycosphere. This trait plasticity in response to drought may be harnessed to stabilize food production from low-fertile soil under the increasingly negative impacts of droughts due to climate change.},
}

@article {pmid40303176,
year = {2024},
author = {Li, Z and Wu, X and Zhang, Y and Li, Q and Gao, J and Hu, Y and Yuan, J and Hu, H and Jin, X and Wei, Z},
title = {Isolation and Pathogenicity of a Chinese Porcine Astrovirus Type 5 Strain HNPDS-01 and Its Influence on Cecum Microbiota in Piglets.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {5777097},
pmid = {40303176},
issn = {1865-1682},
mesh = {Animals ; *Astroviridae/pathogenicity ; *Astroviridae Infections/veterinary/virology/microbiology ; *Cecum/microbiology/virology ; China/epidemiology ; *Gastrointestinal Microbiome ; Genome, Viral ; Phylogeny ; Swine ; *Swine Diseases/virology/microbiology ; Virulence ; },
abstract = {Astroviruses have frequently been found in mammals and poultry, but only a few have been successfully isolated for extensive research. Here, we isolated a strain of porcine astrovirus type 5 (PAstV 5) on LLC-porcine kidney (LLC-PK) cells, from the intestinal contents of diarrhea piglets, namely PAstV 5-HNPDS-01. The complete genome sequence length of this strain was 6,419 nt, which has 77.2%-91.1% nucleotide homology with other PAstV 5 strains and 45.0%-50.0% nucleotide homology with other mammalian astroviruses. The recombination analysis indicated that the recombination events were occurred in ORF 2 region (4,444-5,323 nt) in PAstV 5-HNPDS-01 strain. Subsequently, the pathogenicity of PAstV 5-HNPDS-01 was evaluated in 5-day-old piglets. It showed that the PAstV 5-HNPDS-01 could cause mild diarrhea, growth retardation, minor damage to intestinal villi clinically. Meanwhile, PAstV 5-HNPDS-01 infection could affect the microbiota diversity and composition of cecum in piglet from phylum to genus level. After infected with PAstV 5, there was a significant downregulation of beneficial bacteria, including Faecalibacterium, Bacteroides, Lactobacillus, and Prevotella, while harmful bacteria such as Subdoligranulun showed a significant upregulation. These results provided a research basis for pathogenic mechanisms, vaccine development, and beneficial symbiotic bacteria development for PAstV 5 infection.},
}

Animals
*Astroviridae/pathogenicity
*Astroviridae Infections/veterinary/virology/microbiology
*Cecum/microbiology/virology
China/epidemiology
*Gastrointestinal Microbiome
Genome, Viral
Phylogeny
Swine
*Swine Diseases/virology/microbiology
Virulence

@article {pmid40302384,
year = {2025},
author = {Sharma, V and Sheershwal, A and Bisht, S},
title = {Rhizobacteria Revolution: Amplifying Crop Resilience and Yield in a Changing Climate Through Plant Growth Promotion.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e039},
doi = {10.1002/jobm.70039},
pmid = {40302384},
issn = {1521-4028},
abstract = {The rapid progression of climate change poses significant challenges to global agriculture, necessitating innovative solutions to ensure food security for an expanding population. Plant growth-promoting rhizobacteria (PGPR) offer a promising avenue for sustainable agriculture by enhancing crop resilience and productivity under environmental constraints. These beneficial microbes regulate key physiological processes in plants, such as phytohormone synthesis and nutrient solubilization. This enhances root architecture, improves soil fertility, and enables crops to adapt to resource-limited conditions. Moreover, PGPR strengthen plant defenses against abiotic stressors such as salinity, drought, and nutrient deficiencies, as well as biotic threats like pathogens. Empirical evidence demonstrates that PGPR inoculation can significantly enhance crop yields across diverse agroecosystems by increasing nutrient use efficiency and stress tolerance. Despite their proven potential, the effective deployment of PGPR in farming systems requires addressing critical issues related to scalability, formulation, and integration with existing practices. This review underscores the role of PGPR in mitigating climate-induced agricultural challenges, highlighting the need for interdisciplinary collaborations and robust knowledge-sharing networks to drive the adoption of PGPR-based interventions. By leveraging these microbial allies, we can pave the way for climate-resilient farming systems and safeguard global food security amidst an uncertain future.},
}

@article {pmid40302234,
year = {2025},
author = {Dallstream, C and Milder, L and Powers, JS and Soper, FM},
title = {Strong scale-dependent relationships between fine-root function and soil properties uncovered with spatially coupled sampling.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70143},
pmid = {40302234},
issn = {1469-8137},
support = {2020-04556//Natural Sciences and Engineering Research Council of Canada/ ; //Association for Tropical Biology and Conservation/ ; 40533//Canadian Foundation for Innovation John F. Evans Leadership Fund/ ; 333545//Fonds de recherche du Québec - Nature et technologies/ ; },
abstract = {Substantial fine-root trait variation is found at fine spatial scales but rarely linked to edaphic variation. We assessed the spatial scales of variation in fine-root traits and adjacent soils using a spatially coupled, nested sampling scheme along a fertility gradient in a seasonally dry tropical forest tree, Handroanthus ochraceus. We examined relationships among fine-root traits and identified edaphic drivers of fine-root function. We collected fine-root samples at three scales: multiple samples within individual trees (separated by > 1 m), among trees in a site (3-60 m) and across three sites (15-60 km). We quantified physiological, symbiotic, morphological, chemical and architectural traits, and paired soil physical and chemical properties. Fine-root traits and soils often varied most at fine spatial scales. Root arbuscular mycorrhizal colonization and phosphomonoesterase activity were coordinated and driven by coarse-scale heterogeneity in bulk density, magnesium and phosphate. The trade-off between large diameter and high specific root length, respiration rate and nitrogen concentration was driven by fine-scale heterogeneity in ammonium. The role of base cations was notable, with nitrogen and phosphorus being less influential than expected. Intraspecific fine-root responses to edaphic properties can occur at multiple spatial scales simultaneously and be detected when variation in both is properly captured and spatially matched.},
}

@article {pmid40302032,
year = {2025},
author = {Li, Y and Rui, W and Sheng, X and Deng, X and Li, X and Meng, L and Huang, H and Yang, J},
title = {Bifidobacterium breve synergizes with Akkermansia muciniphila and Bacteroides ovatus to antagonize Clostridioides difficile.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf086},
pmid = {40302032},
issn = {1751-7370},
abstract = {The development of ecologically based in vivo microecological formulations for treating Clostridioides difficile infection (CDI) is a current research focus. Here, we selected three microorganisms-Akkermansia muciniphila (AM), Bacteroides ovatus (BO), and Bifidobacterium breve (BB)-to formulate a mixed bacterial formulation (ABB). Subsequently, we evaluated the ecological interactions among these three microorganisms and investigated their therapeutic efficacy in a CDI murine model. Our investigation revealed the presence of a commensalism relationship among AM, BO, and BB. These microorganisms collectively formed a robust and densely packed symbiotic biofilm, with BB being the predominant member in terms of numerical abundance. This phenomenon was concomitant with a marked elevation in the levels of AI-2 and c-di-GMP. ABB exhibits the capability to inhibit crucial biological indicators of C. difficile (CD), such as toxin production, through the secretion of substantial quantities of lactic acid. Additionally, ABB indirectly suppresses CD by activating the NF-κB signaling pathway in Raw 264.7 cells, which stimulates the secretion of significant quantities of IL-6, IL-8, TNF-α, and IL-1β. ABB demonstrated exceptional efficacy in a CDI murine model, as evidenced by a substantial enhancement in survival rates and intestinal short-chain fatty acid (SCFAs) level, the down-regulation of inflammation-associated cytokine secretion, a notable reduction in fecal CD toxin levels, and CD viable bacterial counts. Concurrently, there was an augmentation in the level of gut microbial diversity, accompanied by a rapid reduction in Enterococcus abundance. This ABB formulation holds promise for further development into a novel microecological formulation for the treatment of CDI.},
}

@article {pmid40301729,
year = {2025},
author = {Hariprasath, K and Dhanvarsha, M and Mohankumar, S and Sudha, M and Saranya, N and Saminathan, VR and Subramanian, S},
title = {Characterization of gut microbiota in Apis cerana Across different altitudes in the Peninsular India.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {39},
pmid = {40301729},
issn = {2730-7182},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; India ; RNA, Ribosomal, 16S/genetics/analysis ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Honey bees are vital to global ecosystems and agriculture due to their role as key pollinators. The gut microbiota of honey bees is essential for their health, providing nutrition and protection against pathogens. While extensive research has been conducted on Western honey bees, Less is understood about the gut microbiota of Apis cerana, an economically important species in South Asia. This study aimed to identify and describe the gut microbiota of Apis cerana across different elevations in the Indian peninsula to understand how these bacterial communities adapt to various ecological niches.

RESULTS: High-throughput metagenome sequencing of the 16S rRNA gene (V1-V9 region) showed that the core microbiota genera in Apis cerana guts across elevations were Gilliamella, Lactobacillus, Snodgrassella, and Frischella. Gilliamella apicola and Lactobacillus kunkeei were identified as the most abundant species. Alpha diversity analysis showed a trend of decreasing species diversity as altitude increased from 200 to 1200 m, with a slight increase observed above 1400 m. Culturable bacterial species identified through 16S rRNA amplification belonged to the Proteobacteria, Firmicutes, and Actinobacteria phyla. Different elevations harboured distinct bacterial communities, with some species being unique to certain altitudes.

CONCLUSIONS: This study provides valuable insights into the diversity and adaptations of Apis cerana gut microbiota across various ecological niches in the Indian peninsula. The observed variations in microbial communities at different elevations suggest that environmental factors play a significant role in shaping the gut microbiota of honey bees. Understanding these microbial dynamics could help in developing strategies to improve bee health and address critical questions in host-microbe symbiosis. Furthermore, this research lays the groundwork for future studies on the functional roles of these bacterial communities in Apis cerana and their potential applications in beekeeping practices.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome
India
RNA, Ribosomal, 16S/genetics/analysis
*Altitude
*Bacteria/classification/genetics/isolation & purification

@article {pmid40301151,
year = {2025},
author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C},
title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {36},
pmid = {40301151},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation & purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; },
abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.},
}

*Geologic Sediments/microbiology
*Vibrionaceae/genetics/classification/isolation & purification
*Genome, Bacterial
Phylogeny
Japan
*Seawater/microbiology
Genetic Variation

@article {pmid40301143,
year = {2025},
author = {Weitzman, CL and Day, K and Brown, GP and Gibb, K and Christian, K},
title = {Differential Temporal Shifts in Skin Bacteria on Wild and Captive Toads.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {35},
pmid = {40301143},
issn = {1432-184X},
support = {DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; },
mesh = {Animals ; *Skin/microbiology ; Seasons ; *Bacteria/classification/isolation & purification/genetics ; *Bufo marinus/microbiology ; *Microbiota ; Ecosystem ; Australia ; Animals, Wild/microbiology ; Animals, Zoo/microbiology ; },
abstract = {Skin bacteria on amphibian hosts play an important role in host health, but those communities are also constantly shifting based on environmental and host-related feedback. On some hosts, stability of skin communities depends on relatively abundant taxa, with less abundant taxa more readily entering and exiting the system. Cane toads (Rhinella marina) have invaded widespread, diverse tropical ecosystems, with varying ecology, physiology, and behaviour in different environments. In this study, we described temporal patterns of skin bacterial communities on cane toads at a site in northern Australia through the wet and dry seasons over two years. Toads in the wild population were paired with a captive-held population, housed in a semi-natural environment, to detect effects of time and season on wild toads, explore bacterial transience and volatility in skin taxa, and determine the extent to which skin communities on captive toads represent those on the wild population. We found community differences by captivity status, sampling timepoint, and season, with increased richness in the wet season on wild toads. Bacterial communities also became more similar among individuals (lower dispersion) in the wet season. Captive toads harboured more stable communities over time, likely owing to the reduced bacterial reservoirs experienced while in captivity. We propose that cane toads, with varied movement patterns among their diverse invaded habitats, provide an interesting direction for future work understanding the influences of habitat and movement on skin microbes, and the flexibility of microbial symbiotic interactions in invasive hosts.},
}

Animals
*Skin/microbiology
Seasons
*Bacteria/classification/isolation & purification/genetics
*Bufo marinus/microbiology
*Microbiota
Ecosystem
Australia
Animals, Wild/microbiology
Animals, Zoo/microbiology

@article {pmid40300365,
year = {2025},
author = {Fan, X and Wang, C and Kong, L and Wang, J and Tan, Y and Yu, Z and Xu, X and Zhu, L},
title = {Spatial heterogeneity of EPS-mediated microplastic aggregation in phycosphere shapes polymer-specific Trojan horse effects.},
journal = {Water research},
volume = {281},
number = {},
pages = {123686},
doi = {10.1016/j.watres.2025.123686},
pmid = {40300365},
issn = {1879-2448},
abstract = {The pervasive contamination of aquatic ecosystems by microplastics represented a critical environmental challenge. While algal-bacterial symbiosis systems demonstrated potential for microplastic aggregation via extracellular polymeric substances (EPS), prior studies have focused on temporal dynamics rather than spatial heterogeneity in phycosphere. This study systematically investigated the adsorption mechanisms of Polyvinyl chloride (PVC), polyethylene terephthalate (PET), polyethylene (PE) and polystyrene (PS) across stratified EPS fractions, tightly bound (TB-EPS), loosely bound (LB-EPS), and soluble (S-EPS), in phycosphere. Combining controlled aggregation assays with multimodal characterization, we revealed a hierarchical spatial framework governing EPS-microplastic interactions. Adsorption efficiency governed by polymer-specific interfacial energies and EPS organic composition. EPS at distinct hierarchical levels exhibited material-specific adsorption preferences for microplastics. PVC and PET demonstrated higher affinities for hydrocarbon components, while PE and PS were preferentially captured through interactions with polysaccharides and amide I groups, respectively. The adsorption and aggregation behaviors between EPS and microplastics in the phycosphere promoted eco-corona formation and induced the Trojan horse effect. However, the energy barrier of interaction forces and EPS spatial configurations jointly governed the hierarchical stabilization of polymer-specific microplastics. PVC and PET primarily colonized the outermost S-EPS layer, PS preferentially accumulated in the intermediate LB-EPS layer, and PE penetrated into the innermost TB-EPS layer. These findings addressed a key knowledge gap by delineating the ecological niche-specific distribution of EPS-microplastic binding, offering novel insights for optimizing bioremediation strategies and informing regulatory measures targeting particulate plastic pollution in hydrologic systems.},
}

@article {pmid40299131,
year = {2025},
author = {Liu, Y and Liu, Y and Liang, W},
title = {Breeding barn swallows recognize householders from strangers.},
journal = {Animal cognition},
volume = {28},
number = {1},
pages = {33},
pmid = {40299131},
issn = {1435-9456},
support = {2023YFF1304600//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Swallows/physiology ; Female ; Humans ; *Recognition, Psychology ; China ; },
abstract = {The aim of this study was to investigate the ability of barn swallows (Hirundo rustica) to recognize humans. A field study was conducted in Caoyang Village, Zhanjiang City, Guangdong Province, South China. We assessed the responses of female barn swallows to the recognition of different types of human individuals by measuring their flight initiation distance (FID) when they incubated eggs in the nests. Our results demonstrated that barn swallows can identify the householder where their nest is located, displaying lower FID when the householder approaches, compared to an unfamiliar experimenter. Furthermore, there was no significant difference in FID between swallows reacting to householders who were rarely at home versus those who were frequently present, suggesting that barn swallows may possess the capability to recognize and retain memory of individual humans over time. Our findings provide evidence that barn swallows exhibit remarkable cognitive abilities. The long-standing symbiotic relationship between barn swallows and humans provides a unique model for studying the adaptation of species to environments with close human interactions. Research on their behavior and survival strategies can offer insights into the influence of symbiotic relationships on species adaptability and evolution.},
}

Animals
*Swallows/physiology
Female
Humans
*Recognition, Psychology
China

@article {pmid40299062,
year = {2025},
author = {Harumoto, T and Moriyama, M and Fukatsu, T},
title = {Peculiar structural features of midgut symbiotic organ in the early development of the stinkbug Plautia stali Scott, 1874 (Hemiptera: Pentatomidae).},
journal = {Die Naturwissenschaften},
volume = {112},
number = {3},
pages = {34},
pmid = {40299062},
issn = {1432-1904},
support = {JPMJER1902//JST ERATO/ ; JPMJER1902//JST ERATO/ ; JPMJER1902//JST ERATO/ ; JP24H02294//JSPS KAKENHI/ ; },
mesh = {Animals ; *Symbiosis/physiology ; *Heteroptera/microbiology/growth & development/ultrastructure/anatomy & histology ; Pantoea/physiology ; Nymph/microbiology/ultrastructure/growth & development ; Gastrointestinal Tract/microbiology/ultrastructure ; Digestive System/microbiology/ultrastructure ; *Hemiptera/microbiology/growth & development/ultrastructure ; },
abstract = {Many insects have symbiotic microorganisms within their body. Such microbial symbiosis underpins the survival and prosperity of insects through multiple means. The brown-winged green stinkbug Plautia stali, which is notorious as an agricultural pest and utilized as an experimental model insect, harbors a bacterial symbiont Pantoea in a posterior part of the midgut, which is essential for the host's development and reproduction. From both basic and applied research perspectives, it is important to investigate the mechanistic bases underpinning the insect-microbe symbiotic association. Here, we performed detailed electron and optical microscopic analyses of the early nymphal midguts to reveal the type of cellular structure and property that orchestrates the symbiont colonization in the restricted part of the midgut. We identified two peculiar structural features of the nymphal midgut that develop in a region-restricted manner: long and heterogenous cellular protrusions (microvilli) solely emerged in the midgut symbiotic region and highly developed circular muscle cell layers specifically observed in the junction of non-symbiotic and symbiotic regions of the midgut. We discuss the potential roles of these unique structures in the midgut bacterial symbiosis.},
}

Animals
*Symbiosis/physiology
*Heteroptera/microbiology/growth & development/ultrastructure/anatomy & histology
Pantoea/physiology
Nymph/microbiology/ultrastructure/growth & development
Gastrointestinal Tract/microbiology/ultrastructure
Digestive System/microbiology/ultrastructure
*Hemiptera/microbiology/growth & development/ultrastructure

@article {pmid40299055,
year = {2025},
author = {Belechheb, T and Yemalahi, A and Bouhnik, O and Hassani, MZ and El Galiou, O and Laglaoui, A and Bakkali, M and El Idrissi, MM and Arakrak, A},
title = {Plant Growth of the Wild Forage Legume Genista monspessulana is Improved by Bradyrhizobium sp. sv. Genistearum in the Acidic Soils of Northern Morocco.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {267},
pmid = {40299055},
issn = {1432-0991},
mesh = {Morocco ; *Bradyrhizobium/genetics/classification/isolation & purification/physiology ; Phylogeny ; Symbiosis ; *Soil Microbiology ; Root Nodules, Plant/microbiology ; RNA, Ribosomal, 16S/genetics ; *Genista/microbiology/growth & development ; Nitrogen Fixation ; Soil/chemistry ; DNA, Bacterial/genetics/chemistry ; Bacterial Proteins/genetics ; },
abstract = {Genista monspessulana is a wild legume of high fodder value in northern Morocco, where it contributes to livestock feeding, particularly during the lean season. The plant fixes nitrogen in symbiosis with soil bacteria known as rhizobia. To identify and characterize its symbiotic partners, we isolated twenty-two bacteria inhabiting the plant nodules and assessed their phenotypic and genetic diversity as well as their symbiotic efficiency. The 16S rRNA sequences analysis proved that 7 isolates were affiliated with the genus Bradyrhizobium, which significantly improve plant growth under nitrogen deficiency. Based on multi-locus sequence analysis using five different housekeeping genes, three representative strains were selected for further analyses. The phylogenetic analysis of the concatenated sequences of the five genes showed that the closest type strain is Bradyrhizobium canariense LMG 2122265T. The strains nodulate also other Genisteae such as Cytisus villosus and Lupinus luteus besides their host plant. The phylogenetic analysis of the symbiotic nodC gene allowed the assignment of the strains to the symbiovar genistearum. The three strains proved to be very efficient in the fixation of N2 as revealed by their relative and absolute efficiency indexes and may be used as effective individual or mixed inocula, to improve the plant growth in its natural habitat and contribute to soil restoration, and revegetation in Northern Morocco.},
}

Morocco
*Bradyrhizobium/genetics/classification/isolation & purification/physiology
Phylogeny
Symbiosis
*Soil Microbiology
Root Nodules, Plant/microbiology
RNA, Ribosomal, 16S/genetics
*Genista/microbiology/growth & development
Nitrogen Fixation
Soil/chemistry
DNA, Bacterial/genetics/chemistry
Bacterial Proteins/genetics

@article {pmid40298621,
year = {2025},
author = {Antache, A and Simionov, IA and Petrea, ȘM and Nica, A and Georgescu, PL and Oprică, L and Grigore, MN and Oroian, M and Jitaru, D and Liteanu, A and Ciobîcă, AS and Poroch, V},
title = {Insect-Antioxidants Symbiotic Nexus-Pathway for Sustainable and Resilient Aquaculture: A Case Study for Evaluating Koi Carp Growth and Oxidative Stress Status.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298621},
issn = {2076-3921},
abstract = {Various innovative fish feeds were tested for the production of koi carp in a recirculating aquaculture system, considering insect meal (Acheta domestica) as the main protein source and phytogenic additives (Curcuma longa-turmeric and Beta vulgaris-beetroot) as antioxidants, in the spirit of sustainable aquaculture practice. The growth performance, metabolic rate (respirometry), hematological profile, blood biochemical indicators, and oxidative stress of koi carp were determined, using feeds according to the following experimental design: CF-commercial feed, IF-innovative feed based on cricket meal, BIF-innovative feed (IF) with beetroot, and TIF-innovative feed (IF) with turmeric. The TIF recorded the best growth rate. The lowest values of lipid peroxidation (MDA), standard metabolic rate (SMR), and routine metabolic rate (RMR) were registered for the IF and TIF variants. A reduction in MDA was noted, correlated to the decrease in the metabolic rate regarding SMR and RMR for the IF and TIF. An intensification in amylase was recorded in the TIF and BIF. Compared with the CF, it seems that the IF, TIF, and BIF had a beneficial effect on the koi carp by reducing cholesterol, HDL cholesterol, alanine aminotransferase, triglycerides, and urea and by increasing the concentration of calcium and growth hormone in the blood plasma.},
}

@article {pmid40298441,
year = {2025},
author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N},
title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.},
journal = {mBio},
volume = {},
number = {},
pages = {e0070525},
doi = {10.1128/mbio.00705-25},
pmid = {40298441},
issn = {2150-7511},
abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.},
}

@article {pmid40298336,
year = {2025},
author = {Kumar, RN and Scolarici, MJ and Gorsline, C and Danziger-Isakov, L and Baddley, J and Harris, CE},
title = {Research Advice for Early Career Transplant Infectious Disease Clinicians.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70041},
doi = {10.1111/tid.70041},
pmid = {40298336},
issn = {1399-3062},
abstract = {As part of an ongoing series of social media discussions, the Transplant Infectious Diseases Early Career Network hosted an open forum for the transplant infectious disease community to discuss the development of research careers for junior faculty. Topics discussed included opportunities for research, identifying potential research questions, institutional support, grant funding, common barriers to research, and trainee involvement. The forum highlighted symbiotic relationships between junior faculty and trainees. The insights from the forum provide a valuable resource for early-career transplant infectious diseases (TID) researchers.},
}

@article {pmid40298200,
year = {2025},
author = {Thapa, A and Hasan, MR and Kabir, AH},
title = {Trichoderma afroharzianum T22 Induces Rhizobia and Flavonoid-Driven Symbiosis to Promote Tolerance to Alkaline Stress in Garden Pea.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15581},
pmid = {40298200},
issn = {1365-3040},
support = {//This study was supported by Louisiana Biomedical Research Network (grant ID: KAB004) and a startup grant (grant ID: 5SFAES-293007) from the University of Louisiana at Monroe./ ; },
abstract = {Soil alkalinity is a limiting factor for crops, yet the role of beneficial fungi in mitigating this abiotic stress in garden pea is understudied. In this study, Trichoderma afroharzianum T22 colonised the roots of garden pea cultivars exposed to soil alkalinity in a host-specific manner. In alkaline-exposed Sugar Snap, T22 improved growth parameters, consistent with increased tissue mineral content, particularly Fe and Mn, as well as enhanced rhizosphere siderophore levels. The split-root assay demonstrated that the beneficial effects of T22 on alkaline stress mitigation are the result of a whole-plant association rather than localised root-specific effects. RNA-seq analysis showed 575 and 818 differentially expressed genes upregulated and downregulated in the roots inoculated with T22 under alkaline conditions. The upregulated genes were mostly involved in the flavonoid biosynthetic pathway (monooxygenase activity, ammonia-lyase activity, 4-coumarate-CoA ligase), along with genes related to mineral transport and redox homoeostasis. Further, a flavonoid precursor restored plant health even in the absence of T22, confirming the role of microbial symbiosis in mitigating alkaline stress. Interestingly, T22 restored the abundance of rhizobia, particularly Rhizobium leguminosarum and Rhizobium indicum, along with the induction of NifA, NifD, and NifH in nodules, suggesting a connection between T22 and rhizobia under soil alkalinity. Further, the elevated rhizosphere siderophore, root flavonoid, expression of PsCoA (4-coumarate-CoA ligase) as well as the relative abundance of TaAOX1 and R. leguminosarum diminished when T22 was substituted with exogenous Fe. This suggests that exogenous Fe eliminates the need for microbiome-driven mineral mobilisation, while T22-mediated alkaline stress mitigation depends on flavonoid-driven symbiosis and R. leguminosarum abundance. It was further supported by the positive interaction of T22 on R. leguminosarum growth in alkaline media. Thus, the beneficial effect of T22 on rhizobia likely stems from their interactions, not solely from the improved mineral status, particularly Fe, in plants. This study provides the first mechanistic insights into T22 interactions with host and rhizobia, advancing microbiome strategies to alleviate soil alkalinity in peas and other legumes.},
}