@article {pmid41090560,
year = {2025},
author = {Tian, YF and Luo, Y and Li, QM and Zhang, ZQ and Guo, YL and Yang, WC},
title = {CPOP1 is a key enzyme required for nodule microenvironment control and successful symbiotic nitrogen fixation in Lotus japonicus.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70037},
pmid = {41090560},
issn = {1744-7909},
support = {2023YFD1200605//National Key Research and Development Program of China/ ; 2016YFA0500500//National Key Research and Development Program of China/ ; 2023ZD04068//National Key Research and Development Program of China/ ; YSBR-011//CAS Project for Young Scientists in Basic Research/ ; XDA24010205//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA26030105//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {Symbiotic nitrogen fixation in legumes requires the exquisite regulation of the environment within the infected region of the nodule. The microaerobic environment critical for nitrogenase activity is maintained through the physical oxygen diffusion barrier of the cortex and locally the oxygen-binding protein leghemoglobin (Lb). Leghemoglobin binds and releases oxygen with heme moiety to maintain oxygen gradients inside the infected cell (IC) during nitrogen fixation. Heme binds to diverse proteins and plays critical roles in different redox reactions. However, the role and regulation of host-controlled heme production during symbiotic nitrogen fixation are not clear. Here, we identified coproporphyrinogen III oxidase plastid related 1 (CPOP1) as a key regulator of symbiotic heme biosynthesis in Lotus japonicus. CPOP1 is specifically highly expressed in nitrogen-fixing nodules, and knocking out CPOP1 alone causes leaf etiolation and dwarfism which could be recovered by the exogenous application of nitrogen source, indicating nitrogen fixation defect. The IC-specific expression of CPOP1 was directed by the -881 to -740 bp promoter region. The cpop1 mutant shows significantly increased nodule oxygen level and decreased nitrogen fixation activity compared to the wild-type. Intriguingly, bacteria proliferation is inhibited due to the down-regulation of cell division-related gene expression upon CPOP1 knockout. Our data showed that CPOP1 is essential for the microaerobic environment control of ICs and the activation of rhizobial nitrogenase required for symbiotic nitrogen fixation, through host-regulated nodule heme synthesis.},
}

@article {pmid41089933,
year = {2025},
author = {Song, Y and Xu, X and Xie, M and Tao, J and Jin, H and Liu, Y and Liu, L and Song, X and Meng, S and Cheong, IH and Wang, Y and Wei, Q},
title = {The lung microbiome in patients with HIV complicated with community-acquired pneumonia: a cross-sectional pilot study.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100480},
pmid = {41089933},
issn = {2666-5174},
abstract = {BACKGROUND: The composition of lung flora in HIV-combined community-acquired pneumonia (CAP) populations may be associated with the duration and severity of the disease. Additionally, a correlation may exist between lung flora balance and the body's autoimmune status. However, the number of studies in this area is limited. Therefore, we collected alveolar lavage fluid from 110 HIV-positive CAP patients at Beijing Ditan Hospital. We preliminarily explored the lung flora of this population using 16S amplicon analysis, and found some clues about the relationship between flora and immune status by comparing the flora of two groups of people with different immune status.

RESULTS: We found that the lung microbiome of HIV patients with CAP exhibited a "high-level aggregation-low-level dispersion" pattern across taxonomic hierarchies, this was characterised by dominant taxa at higher classification levels and dispersed, low-abundant taxa at lower levels. Microbial diversity in the AIDS group (CD4[+] counts < 200 cells/μL) was marginally lower than in the HIV group, but the difference was not statistically significant. The AIDS group exhibited increased relative abundances of pathogenic taxa (Gammaproteobacteria, Fusobacteriia) and decreased relative abundances of symbiotic taxa (Bacilli, Cyanobacteriia). LEfSe revealed significant enrichment of oral- and gut-associated microbial communities in the HIV group, as opposed to pathogen-enriched communities in the AIDS group. Microbial network analysis showed enhanced modularization in the AIDS group, with reduced clustering coefficients and network density, indicating destabilized microbial communities. Immune collapse appeared to drive a shift from cooperative hub-based to competitive modular microbial structures.

CONCLUSIONS: Immune status profoundly influenced the composition and function of the pulmonary microbiome in HIV infection. AIDS patients exhibited pathogen-dominated, less stable microbial communities. These findings provided foundational insights into interactions among HIV, CAP, and the pulmonary microbiome, and informed the development of microbiome-targeted interventions.},
}

@article {pmid41088742,
year = {2025},
author = {Lyu, X and Liu, K and Guo, T and Wang, X and Gong, Z and Ma, C},
title = {Nitrogen Fertilization Modulates Soybean Nodulation and Nitrogen Fixation via NO-Mediated S-Nitrosylation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11100},
pmid = {41088742},
issn = {1520-5118},
abstract = {Soybean, a symbiotic nitrogen-fixing crop, experiences suppressed nodule nitrogen fixation under excessive nitrogen fertilizer. Nitric oxide (NO) is a key signaling molecule regulating development and stress, primarily via protein S-nitrosylation, although its role in soybeans is unclear. Using a unilateral nodulation system, treatments with nitrogen, an NO scavenger, and an NO donor were applied. Results showed that nitrogen application increased the NO content in the nodules and reduced the nitrogen fixation capacity. Conversely, the NO scavenger lowered the NO levels but enhanced fixation. Exogenous NO inhibited fixation by damaging the nodule structure, reducing leghemoglobin, and disrupting NO homeostasis. Quantitative proteomics with iodoTMT labeling identified 287 S-nitrosylation sites on 238 nodule proteins. Nitrogen-altered proteins were involved in nitrogenase activity, stress response, and ABC transporters. This study establishes the 'nitrogen level-NO signal-S-nitrosylation-nodule function' pathway, offering molecular insights into S-nitrosylation's role in nodule regulation.},
}

@article {pmid41088378,
year = {2025},
author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y},
title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1097},
pmid = {41088378},
issn = {1479-5876},
support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; },
abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."

METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35 mg/kg) for modeling. ZAC rats were orally administered 5 mg/kg Zacopride daily for 7 days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.

RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.

CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Tryptophan/metabolism
Male
*Symbiosis/drug effects
*Benzamides/pharmacology/therapeutic use
*Coronary Vessels/drug effects/physiopathology
*Microvessels/drug effects/physiopathology
Rats
*Microcirculation/drug effects

@article {pmid41086923,
year = {2025},
author = {Liang, Y and Yu, J and Yao, Z and Sun, Y and Feng, J and Shen, R and Luo, J and Zhao, L},
title = {Decoding microbial interactions: Interaction networks and regulatory strategies for medium-chain fatty acid biosynthesis through anaerobic chain elongation.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108735},
doi = {10.1016/j.biotechadv.2025.108735},
pmid = {41086923},
issn = {1873-1899},
abstract = {The anaerobic biosynthesis of medium-chain fatty acids (MCFAs) as valorized bio-based chemicals relies on intricate and dynamic interaction networks within microbial communities. This review systematically summarizes the key mechanisms and regulatory strategies driving MCFA biosynthesis in terms of microbial interactions, with a focus on electron donor-acceptor generation and chain elongation (CE) processes. The functional stability and resilience of anaerobic fermentation systems are collectively sustained by microbial diversity via modular functional partitioning, metabolic complementarity, resilience against perturbations, and environmental adaptation. Notably, substrate competition and syntrophic symbiosis between functional taxa directly govern the directionality and efficiency of the metabolic flux. Carbon source preferences and environmental factors synergistically steer pathway selection, while exogenous interventions such as enhanced electron transfer or niche occupation optimize microbial cooperation. In addition, quorum sensing and electrochemical synergy further balance inter-species competition to achieve a dynamic equilibrium between metabolic branch inhibition and enrichment of CE consortia. These multidimensional interaction mechanisms provide high-purity electron donors and stable metabolic foundations for MCFA synthesis to guide directional microbial engineering strategies to enhance product yields. This study systematically summarized how microbial interaction networks drive efficient MCFA biosynthesis via a multi-scale coordination between various mechanisms, including metabolic flux partitioning control, environmental response feedback, and functional modularization design, providing a theoretical foundation for resolving critical challenges during anaerobic MCFA fermentation.},
}

@article {pmid41086911,
year = {2025},
author = {Tu, C and Fan, R and Wu, Y and Liu, F and Xiao, W and Ziyodillo Ugli, OI and Qiong, Z and Peng, Y and Liu, J and Xu, F and Zhu, Y},
title = {Ultra-low concentrations of a botanical insecticide blend alter microbiota composition and gene expression in the ladybeetle Propylea japonica.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127252},
doi = {10.1016/j.envpol.2025.127252},
pmid = {41086911},
issn = {1873-6424},
abstract = {Botanical pesticides are increasingly promoted as environmentally benign alternatives to synthetic chemicals in integrated pest management. However, the ecological safety of their persistent ultra-low residues remains poorly understood, particularly regarding non-target natural predators. In this study, we investigated the chronic toxicological effects of an ultra-low concentration (ULC; 1/100 of LC30 of 15.106 mg/mL) of a botanical pesticide mixture-composed of commercially available tea saponin and matrine mixed at a ratio of 10:1 (v:v)-on the generalist Propylea japonica. Long-term exposure significantly prolonged larval development, reduced pupal mass, and compromised female fecundity, indicating potential disruptions to population stability and biocontrol efficacy. Gene expression analyses revealed stage-specific alterations in detoxification and hormone-related pathways: fourth-instar larvae exhibited elevated expression of GST and DuoX, downregulation of JHAMT1 and PjIRS1, and upregulation of EcR, whereas adult females showed marked suppression of JHDK, FOXO, PjIRS1, and Vg. These changes point to endocrine disruption and impaired reproductive capacity. Moreover, 16S rRNA sequencing revealed that ULC exposure significantly decreased microbial diversity and altered symbiont composition, particularly in adult beetles. Collectively, our findings demonstrate that even ultra-low residues of botanical pesticides can impose sublethal physiological stress and reshape symbiotic microbial communities in beneficial insects. This work underscores the need for refined ecological risk assessments of green pesticides and advocates for pest management strategies that balance effective control with the conservation of natural enemies.},
}

@article {pmid41086499,
year = {2025},
author = {Li, Y and Zheng, X and He, H and Hu, R and Han, Z and Tao, J and Lin, T and Chen, W},
title = {Microalgal-bacterial granular sludge enhances oxytetracycline removal: Microbial responses, degradation pathways, and adaptive mechanisms.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140103},
doi = {10.1016/j.jhazmat.2025.140103},
pmid = {41086499},
issn = {1873-3336},
abstract = {Oxytetracycline (OTC), an emerging "low-concentration, high-toxicity" contaminant, presents considerable hurdles to wastewater treatment processes. This study systematically evaluated for the first time the impacts of OTC on the operational performance, sludge characteristics, and microbial metabolic activity across three treatment systems: microalgal-bacterial granular sludge (MBGS), aerobic granular sludge (AGS), and activated sludge (AS). Results demonstrated that MBGS exhibited superior treatment efficiency, maintaining stable removal of 500 μg/L OTC at 88.06 ± 1.45 % (p < 0.05). MBGS adapted to OTC exposure by increasing ATP content and reducing lactate dehydrogenase release. Acclimated MBGS primarily removed OTC through biodegradation. Moreover, multiple OTC transformation products with reduced toxic potential were detected, signifying that MBGS systems achieve efficient microbial degradation. Metagenomic analyses revealed that Pseudomonadota in MBGS displayed high adaptability under OTC exposure. Additionally, OTC exposure upregulated carbohydrate and energy metabolism in MBGS, thereby enhancing overall microbial metabolic activity. Alphaproteobacteria contributed most significantly to key functional genes, underscoring their critical role in contaminant removal in the MBGS. Redundancy analysis highlights a robust association between Alphaproteobacteria and the abundance of antibiotic resistance genes. This study confirms the MBGS's resilience to OTC-contaminated wastewater, highlighting its potential for efficient antibiotic wastewater treatment.},
}

@article {pmid41086179,
year = {2025},
author = {Ding, M and Liu, H},
title = {Spatiotemporal coupling and coordinated development of rural revitalization and rural tourism in Jiangsu.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0334241},
doi = {10.1371/journal.pone.0334241},
pmid = {41086179},
issn = {1932-6203},
mesh = {*Rural Population/statistics & numerical data ; China ; Humans ; *Tourism ; Spatio-Temporal Analysis ; },
abstract = {Rural tourism is pivotal in addressing the unidirectional urban-to-rural flow of resources, such as labor migration. However, the interaction between rural tourism and rural revitalization in developed regions remains poorly understood. This study establishes an evaluation index system for rural revitalization and rural tourism, examining their interrelationship. Using the entropy method and coupling coordination degree model, we assess the development levels and coordination degrees of these aspects in Jiangsu Province from 2012 to 2023. Furthermore, the geographical detector model is utilized to pinpoint the primary drivers influencing this coordination. The findings are: (1) Both rural revitalization and tourism exhibit significant growth, with southern Jiangsu outperforming the north; (2) The coupling coordination between these systems has strengthened, indicating a profound symbiotic relationship; (3) Spatial distribution differences are notable, with the coupling coordination degree D value in southern Jiangsu being 26.4% higher than in the north. This disparity is primarily attributable to the wider urban-rural income gap and greater fiscal investment in southern Jiangsu. Notably, the traditional "resource dependence theory" appears ineffective in Jiangsu, as the density of rural tourism resources is relatively low. Accordingly, the study proposes differentiated policy recommendations: northern Jiangsu should focus on talent attraction and the integration of culture and tourism, while southern Jiangsu should explore mechanisms to facilitate the two-way flow of urban-rural elements. This research provides a theoretical framework for coordinating "policy-market" dynamics in the rural transformation of developed regions.},
}

*Rural Population/statistics & numerical data
China
Humans
*Tourism
Spatio-Temporal Analysis

@article {pmid41085894,
year = {2025},
author = {Menaa, B and Ribeiro, I and Oliveira, M and Rahal, S and Carvalho, MF and Chekireb, D},
title = {Isolation and characterization of endophytic actinobacteria associated with Artemisia judaica L. ssp. sahariensis from desert regions in Algeria.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {41085894},
issn = {1678-4405},
abstract = {Endophytic actinobacteria, known for symbiotic relationships with plants and production of bioactive compounds, occur in diverse environments, including deserts. The Sahara's nutrient scarcity, high temperatures, and salinity drive unique microbial adaptations, making it a promising reservoir of novel taxa. This study reports, for the first time, the isolation and characterization of endophytic actinobacteria from Artemisia judaica L. ssp. sahariensis, a medicinal plant of the Algerian desert. Forty-two actinobacterial isolates were obtained from root and leaf tissues and identified through 16 S rRNA gene sequencing, revealing their affiliation with five genera: Micromonospora, Nonomuraea, Nocardiopsis, Gordonia, and predominantly Streptomyces. These isolates were characterized for morphological, physiological, and bioactive traits, including stress tolerance, phosphate solubilization, extracellular enzyme production, and antibacterial activity. More than 93% exhibited antagonistic effects against at least one tested pathogen. The most active strains showed minimum inhibitory concentration values between 4 and 8 µg/mL, highlighting their strong antibacterial potential. All isolates tolerated up to 5% NaCl, and several, including AJR36, AJR38, and AJR16, grew at 15%. Phosphate solubilization was observed in 36% of isolates, while 38% displayed diverse enzymatic activities. Although this study focused on a single plant species, the observed functional diversity underscores the biotechnological potential of these desert-associated endophytes. These findings suggest that unexplored desert ecosystems harbor valuable Actinomycetota resources, supporting further investigations for the discovery of novel species and their potential applications in agriculture and medicine.},
}

@article {pmid41084897,
year = {2025},
author = {Desai, V and Sharma, AK and Chauhan, P},
title = {Endophytes and Plants Interaction: A Hidden Microbial World Inside the Plant.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70112},
doi = {10.1002/jobm.70112},
pmid = {41084897},
issn = {1521-4028},
support = {//The authors received no specific funding for this work./ ; },
abstract = {Endophytes are a diverse group of microbes that colonize internal plant tissues without causing harm to the host. They play a crucial role in plant growth, development, and stress management. The is a complex mechanism involving evasive strategies to bypass host immune response, significant alteration in plant gene expression and establishment of a balance mutualistic relationship. Endophytes enhance plant health through various direct and indirect mechanisms, including the production of phytohormones such as auxin, gibberellins, and cytokinin. Moreover, they also solubilize nutrients, mainly nitrogen and phosphorus. A significant contribution of endophytes is the induction of induced systemic resistance (ISR), a defense response that primes the plant against a broad spectrum of pathogens and environmental stressors. The colonization of endophytes is governed by complex signaling pathways, immune modulation and tissue specificity, influenced by host genotype, age, and environmental conditions. This review highlights the ecological significance, mechanisms of colonization and functional contribution of endophytes to host plants. Furthermore, the review emphasizes that endophytes can recruit or influence other beneficial microbes in the rhizosphere region of host plants. Conclusively, this review synthesizes current understanding of the molecular strategies these microbes employ to survive within plant tissue and modulate plant immune system. We emphasize the immense, yet underexploited, potential of endophytes in enhancing plant resilience and productivity and advocates further research into their mechanisms and applications to meet growing demands of global agriculture.},
}

@article {pmid41083440,
year = {2025},
author = {Prasad, A and Pallujam, AD and Siddaganga, R and Suryanarayanan, A and Mazel, F and Brockmann, A and Yek, SH and Engel, P},
title = {Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9069},
pmid = {41083440},
issn = {2041-1723},
support = {225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Symbiosis ; Phylogeny ; Metagenome/genetics ; *Evolution, Molecular ; Biological Evolution ; },
abstract = {Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as important factors for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes that govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Symbiosis
Phylogeny
Metagenome/genetics
*Evolution, Molecular
Biological Evolution

@article {pmid41083230,
year = {2025},
author = {Caiafa, MV and Kaminsky, L and Healy, R and Sheffer, LP and Willis, CB and Deitz, K and Richter, BS and Lemmond, BR and Borland, D and Roy, BA and Dawson, HA and Delevich, CA and Conery, JS and Warner, D and Caboň, M and Karlsen-Ayala, E and Grupe, AC and Kraisitudomsook, N and Reynolds, NK and Drechsler-Santos, ER and Truong, C and Corrales, A and Mujic, AB and Kennedy, PG and Jusino, MA and Swenie, RA and Noffsinger, CR and Grootmyers, D and Matheny, PB and Wilson, AW and Smith, ME},
title = {Think globally, barcode locally: nine years of macrofungi sampling reveals extensive biodiversity at the ordway-swisher biological station, a subtropical site in Florida.},
journal = {Fungal biology},
volume = {129},
number = {7},
pages = {101643},
doi = {10.1016/j.funbio.2025.101643},
pmid = {41083230},
issn = {1878-6146},
mesh = {Florida ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics/chemistry ; *Fungi/classification/genetics/isolation & purification ; DNA, Ribosomal Spacer/genetics/chemistry ; Phylogeny ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; Molecular Sequence Data ; },
abstract = {The Ordway-Swisher Biological Station (OSBS) is a 38-km[2] reserve owned by the University of Florida and is part of the National Ecological Observatory Network (NEON). The reserve contains several iconic Florida habitats, such as sandhill, mesic hammock, and scrubby flatwoods. While plants and animals have been extensively studied at OSBS, the fungi remain poorly known. Fungal inventories are critical to increase knowledge of both fungal diversity and species ranges, and thus to provide foundational data for a wide array of applications in ecology and resource management. Here, we present the results of a nine-year effort to collect, preserve, and DNA barcode the macrofungi at OSBS. This effort generated >1200 vouchered specimens and 984 ITS rDNA sequences, representing more than 546 species. Our sampling was dominated by Basidiomycota and revealed a high diversity of symbiotic ectomycorrhizal fungi, particularly species of Amanita, Cortinarius, and Russula. Sampling curves and both Chao1 and Jacknife1 richness estimators suggest that our DNA barcoding efforts captured only about half of the macrofungi species and that a more complete inventory would detect 897-1177 macrofungi species at OSBS. Our sampling found more species of macrofungi at OSBS than the known number of vertebrate animal species at the reserve and our estimates also suggest that there are likely more macrofungi species than plant species at OSBS. This study is the first comprehensive macrofungi inventory within a NEON site and highlights the importance of long-term monitoring to provide novel data on fungal diversity, community structure, conservation, biogeography, and taxonomy.},
}

Florida
*Biodiversity
*DNA Barcoding, Taxonomic
DNA, Fungal/genetics/chemistry
*Fungi/classification/genetics/isolation & purification
DNA, Ribosomal Spacer/genetics/chemistry
Phylogeny
Sequence Analysis, DNA
DNA, Ribosomal/genetics/chemistry
Molecular Sequence Data

@article {pmid41082848,
year = {2025},
author = {Chu, W and Li, X and Li, P and Li, J and Wang, Z and Zhou, H and Yang, X and Chen, S and Zhou, M and Wang, S and Zheng, J and Chen, Y and Yu, Y and Tan, Z},
title = {Enhanced treatment of low C/N domestic wastewater in a membrane photobioreactor: Operational control of microalgal-bacterial symbiosis for synergistic pollutant and antibiotic resistance genes removal.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127398},
doi = {10.1016/j.jenvman.2025.127398},
pmid = {41082848},
issn = {1095-8630},
abstract = {Conventional wastewater treatment technologies face significant limitations, including high CO2 emissions, poor resource recovery, and growing challenges from emerging contaminants such as antibiotics and their associated antibiotic resistance genes (ARGs), which pose serious risks to aquatic ecosystems and public health. In response to these challenges and within the framework of China's carbon neutrality goals, this study developed a microalgae-activated sludge membrane photobioreactor (MPBR) to enable synergistic pollutant removal and resource recovery from low carbon-to-nitrogen (C/N) domestic wastewater. Under the optimized internal circulation flow rate of 13.5 m[3]/d, the MPBR system achieved high removal efficiencies for ammonia nitrogen (NH4[+]-N, 99.48 %), total nitrogen (TN, 72.89 %), chemical oxygen demand (COD, 63.20 %), and total phosphorus (TP, 80.37 %). Simultaneously, ARGs and mobile genetic elements (MGEs) were reduced by approximately one log, attributed to two primary mechanisms: (1) suppression of ARGs in the sludge zone through the regulation of drug-resistant bacterial populations, and (2) inhibition of horizontal gene transfer in the microalgal zone via nitrogen-driven suppression of ARGs host bacteria, as well as enhanced microalgae-bacteria co-metabolism and community optimization. Furthermore, the optimization of microalgae photosynthesis and nitrogen cycling, along with microbial cooperation under anoxic conditions, supported efficient nutrient recovery while maintaining low-carbon operation. This study offers a novel, carbon-efficient strategy for integrating wastewater purification with ARGs risk mitigation, contributing to sustainable water management aligned with the circular economy and carbon neutrality objectives.},
}

@article {pmid41082055,
year = {2025},
author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA},
title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {377},
pmid = {41082055},
issn = {1573-0972},
mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.},
}

Animals
Larva/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Gastrointestinal Microbiome/genetics
*Simuliidae/microbiology
*Citrus sinensis/metabolism
*Diptera/microbiology
Nigeria
Metagenome
Metagenomics
Phylogeny

@article {pmid41081965,
year = {2025},
author = {Xu, L and Zhou, Y and Jin, X and Wang, Z and Song, Z and Zhang, X and Ding, H and Li, Y},
title = {Species diversity and drought tolerance of culturable dark septate endophytes in Anemone tomentosa in the Taihang mountain area.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {59},
pmid = {41081965},
issn = {1432-1890},
support = {HBCT2025190206//Innovation Team on Dry Fruits of Hebei Provincial Modern Agricultural Industry Technology System/ ; 2020YFD1000700//National Key R&D Program of China/ ; LC2025-08//Expert Support Team Project for Forest, Fruit and Flower Industry in Hebei Province/ ; 21326802D//Hebei Science and Technology Support Project/ ; },
mesh = {*Endophytes/physiology/classification ; *Droughts ; *Biodiversity ; *Anemone/microbiology/physiology ; China ; Soil Microbiology ; Plant Roots/microbiology ; Symbiosis ; Stress, Physiological ; Drought Resistance ; },
abstract = {Frequent drought events pose escalating threats to global ecosystems, driving vegetation degradation, biodiversity loss, while destabilizing ecosystem functions. Dark septate endophytes (DSE), which exhibit drought stress tolerance in vitro and have the potential to enhance plant drought tolerance in arid environments, represent a key microbial component possibly mitigating drought impacts. Therefore, this study focuses on the dominant drought-tolerant plant Anemone tomentosa (A. tomentosa) and its symbiotic DSE in the drought-prone Taihang Mountain area, aiming to reveal the community composition, spatial distribution and functions of DSE, explore their application potential in arid environments, and provide a basis for fully utilizing DSE resources to promote vegetation restoration and ecological reconstruction in arid regions. Root and soil samples of A. tomentosa were collected from six sampling sites in the Taihang Mountain area to systematically investigate DSE colonization, community composition, species diversity and their correlations with soil environmental factors across different sites. Then six DSE strains with high isolation frequencies were selected for the drought resistance study in pure cultures, and varying polyethylene glycol (PEG-6000) concentrations (0%, 15%, 25%, And 35%) were set to simulate drought stress. The results showed that the roots of A. tomentosa at all six sampling sites in the Taihang Mountain area were highly colonized by DSE, forming typical dark-colored septate hyphae And microsclerotia structures. A total of 20 DSE strains belonging to 14 genera were isolated and identified, and the community composition of DSE at different sampling sites differed significantly (P < 0.05). The results of redundancy analysis (RDA) showed that soil organic carbon and soil total phosphorus were the Main factors influencing the community composition of DSE. The growth of 5 frequently isolated DSE strains under pure culture conditions was not adversely affected by drought stress, except for Exophiala xenobiotica (Ex), and biomass accumulation increased significantly with increasing drought stress, which was related to the content of antioxidant enzymes, osmotic adjustment substances, membrane lipid peroxidases and melanin in the different fungi. In summary, A. tomentosa in Taihang Mountain has rich DSE species diversity, and the two can form a symbiotic relationship, thus enhancing the adaptability of A. tomentosa to the environment. Five DSE strains exhibited drought stress tolerance under in vitro culture conditions, which enriched the understanding of the ecological functions and adaptive mechanisms of DSE in arid environments and provided a basis for the development and application of drought-resistant and water-preserving microbial agents.},
}

*Endophytes/physiology/classification
*Droughts
*Biodiversity
*Anemone/microbiology/physiology
China
Soil Microbiology
Plant Roots/microbiology
Symbiosis
Stress, Physiological
Drought Resistance

@article {pmid41081895,
year = {2025},
author = {Yamaoka, NK and Packard, EE and Jones, MD},
title = {Nitrogen accumulation accompanies ectomycorrhiza formation in pine germinants the first growing season after wildfire or clearcutting.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {58},
pmid = {41081895},
issn = {1432-1890},
support = {RGPIN-2018-03927//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2018-03927//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2018-03927//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Mycorrhizae/growth & development/physiology/metabolism ; *Nitrogen/metabolism ; *Pinus/microbiology/growth & development/metabolism ; Seasons ; Seedlings/microbiology/growth & development ; *Wildfires ; Plant Roots/microbiology ; Symbiosis ; Germination ; Ascomycota ; },
abstract = {Early stages of the ectomycorrhizal symbiosis have rarely been studied on seedlings germinating in the field. By collecting lodgepole and ponderosa pine seedlings during their first growing season in recent clearcuts and burned areas, we were able to identify when colonization of pine roots first began, the rate at which ectomycorrhizal fungi colonized new germinants, and how this related to nitrogen nutrition and growth. Pine seedlings were first colonized in July, a month after germination was first observed. As the first seedlings became mycorrhizal, ectomycorrhizal lodgepole pine seedlings contained approximately 40% more nitrogen and > 60% greater biomass compared to uncolonized seedlings collected at the same time. Nitrogen content was 47% higher in mycorrhizal than nonmycorrhizal naturally-regenerating ponderosa pine seedlings. Ascomycetes, with a Pustularia sp. and Wilcoxina spp. most abundant, formed 80% of the ectomycorrhizae. Because all collected seedlings had ectomycorrhizae present on their roots by the end of the season, we concluded that inoculum of ectomycorrhizal fungi, especially of ruderal ascomycetes, was not limiting colonization of seedlings on these severely burned or recently clearcut sites. Our results are consistent with a role for ectomycorrhizal fungi in nitrogen acquisition, even within the first weeks after mycorrhiza formation; however, it is also possible that larger, more nitrogen-replete seedlings became colonized earlier than smaller seedlings. We saw no evidence of nitrogen loss by mycorrhizal pine seedlings as observed in previous studies.},
}

*Mycorrhizae/growth & development/physiology/metabolism
*Nitrogen/metabolism
*Pinus/microbiology/growth & development/metabolism
Seasons
Seedlings/microbiology/growth & development
*Wildfires
Plant Roots/microbiology
Symbiosis
Germination
Ascomycota

@article {pmid41081502,
year = {2025},
author = {Castro-Camacho, V and Robles-Azor, R and Rodríguez-Burdock, L and Rojas-Jimenez, K and Mendoza-Guido, B},
title = {Draft genome sequence of Methylobacterium aquaticum LEGMi-203a, isolated from root nodules of Pithecellobium hymenaeifolium.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0075425},
doi = {10.1128/mra.00754-25},
pmid = {41081502},
issn = {2576-098X},
abstract = {We report the draft genome of Methylobacterium aquaticum LEGMi-203a, a root nodule isolated from Pithecellobium hymenaeifolium. Genomic analysis supports its classification as M. aquaticum, and annotated nitrogen fixation and nodulation genes underscore its possible functional capabilities as a symbiont in tropical plants.},
}

@article {pmid41081364,
year = {2025},
author = {Barrinha, A and Loyola-Machado, AC and Mariano Dos Santos, MD and Carvalho, PC and de Souza, W and Valente, AP and Galina, A and Motta, MCM},
title = {Endosymbiosis in trypanosomatids: the bacterium regulates the intermediate and oxidative metabolism of the host cell.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0045725},
doi = {10.1128/msphere.00457-25},
pmid = {41081364},
issn = {2379-5042},
abstract = {UNLABELLED: Endosymbiosis in trypanosomatids involves a mutualistic association between a symbiotic bacterium and a host protozoan and represents an excellent model for studying metabolic coevolution and the origin of organelles. This work investigated the influence of the symbiont on the metabolism of Angomonas deanei by comparing wild-type and aposymbiotic strains under different nutritional conditions. The presence of the symbiont enhanced cell proliferation in the medium containing a single carbon source and increased O2 consumption. Wild-type cells utilized oxidative phosphorylation to produce ATP, whereas aposymbiotic cells relied on substrate-level glycolysis, resulting in the excretion of greater amounts of fermentative products, such as acetate, succinate, and ethanol. Proteomic analysis revealed an increased expression of glycolytic and fermentative enzymes by the aposymbiotic strain and oxidative phosphorylation enzymes by symbiont-harboring cells. These findings highlight the role of the symbiotic bacterium in optimizing host metabolism and provide insights into the evolution of parasitism in trypanosomatids when A. deanei is compared with pathogenic species.

IMPORTANCE: This work provides groundbreaking insights into the metabolic and evolutionary dynamics of endosymbiosis, a topic of central importance to cellular evolution. Angomonas deanei, a trypanosomatid species, has become a paradigm for investigating the evolution of eukaryotic cells and the origin of organelles through endosymbiosis. Harbored in the cytoplasm of this protozoan, the symbiont engages in intricate metabolic exchanges, offering a time window to analyze the processes and evolutionary history that underlie the establishment of permanent endosymbiotic relationships. By employing a multidisciplinary approach, we have uncovered how the symbiotic bacterium regulates the oxidative metabolism of the trypanosomatid, integrating glucose catabolism and optimizing energy production. Our discoveries have broad implications for understanding the metabolic integration of organelles, such as mitochondria and glycosomes, with the bacterial endosymbiont. Beyond unravelling the complexities of metabolic adaptations during symbiosis, our work may contribute to the general understanding of the evolutionary dynamics of parasitism within the Trypanosomatidae family.},
}

@article {pmid41080487,
year = {2025},
author = {Boyle, JA and Murphy, B and Teng, F and Babaei Zadeh, P and Ensminger, I and Stinchcombe, JR and Frederickson, ME},
title = {Mutualism Mediates Legume Response to Microbial Climate Legacies.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72271},
pmid = {41080487},
issn = {2045-7758},
abstract = {Climate change is altering both soil microbial communities and the ecological context of plant-microbe interactions. Heat, drought, and their legacies can alter soil microbiomes and potential plant symbionts, but the direct consequences of these microbial changes on plant performance and plant investment in symbiosis remain underexplored. Predicting how soil microbes modulate plant resilience to heat and drought is critical to mitigating the negative effects of climate change on ecosystems and agriculture. In this proof of concept study, we conducted growth chamber experiments to isolate the microbially mediated indirect effects of heat and drought on plant performance and symbiosis. In the first experiment, focused on drought, we found that drought and drought-treated microbes, along with their interaction, significantly decreased the biomass of Medicago lupulina plants compared to well-watered microbiomes and conditions. In a second experiment, we then tested how the addition of a well-known microbial mutualist, Sinorhizobium meliloti, affected heat- and drought-treated microbiomes' impact on M. lupulina. We found that drought-adapted microbiomes negatively impacted legume performance by increasing mortality and reducing branch number, but that adding rhizobia erased differences in plant responses to climate-treated soils. In contrast, heat-adapted microbiomes did not differ significantly from control microbiomes in their effects on a legume. Our results suggest microbial legacy effects, mutualist partners, and their interactions are important in mediating plant responses to drought, with some mutualists equalizing plant responses across microbial legacies.},
}

@article {pmid41080445,
year = {2025},
author = {Burchardt, S and Wojtaczka, P and Kućko, A and Ostrowski, M and Wilmowicz, E},
title = {Advancing 2-DE Techniques: High-Efficiency Protein Extraction From Lupine Roots.},
journal = {Bio-protocol},
volume = {15},
number = {19},
pages = {e5461},
pmid = {41080445},
issn = {2331-8325},
abstract = {Protein isolation combined with two-dimensional electrophoresis (2-DE) is a powerful technique for analyzing complex protein mixtures, enabling the simultaneous separation of thousands of proteins. This method involves two distinct steps: isoelectric focusing (IEF), which separates proteins based on their isoelectric points (pI), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), which separates proteins by their relative molecular weights. However, the success of 2-DE is highly dependent on the quality of the starting material. Isolating proteins from plant mature roots is challenging due to interfering compounds and a thick, lignin-rich cell wall. Bacterial proteins and metabolites further complicate extraction in legumes, which form symbiotic relationships with bacteria. Endogenous proteases can degrade proteins, and microbial contaminants may co-purify with plant proteins. Therefore, comparing extraction methods is essential to minimize contaminants, maximize yield, and preserve protein integrity. In this study, we compare two protein isolation techniques for lupine roots and optimize a protein precipitation protocol to enhance the yield for downstream proteomic analyses. The effectiveness of each method was evaluated based on the quality and resolution of 2-DE gel images. The optimized protocol provides a reliable platform for comparative proteomics and functional studies of lupine root responses to stress, e.g., drought or salinity, and symbiotic interactions with bacteria. Key features • Protocol tailored for isolating proteins from lupine roots, including those involved in symbiotic relationships with bacteria. • Our method is suitable for analyzing complex protein mixtures through IEF and SDS-PAGE for high-resolution separation. • Optimized precipitation method increases protein yield for downstream mass spectrometry and comparative proteomic analyses.},
}

@article {pmid41079636,
year = {2025},
author = {He, W and Wang, M and Zhong, Z and Chen, H and Xi, S and Zhang, H and Li, M and Sun, W and Zhang, Y and Wang, Y and Guo, X and Li, L and Du, Z and Luan, Z and Li, C and Zhang, X},
title = {In situ semi-quantitative imaging of intracellular metabolic interaction by confocal Raman microscopy.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113558},
pmid = {41079636},
issn = {2589-0042},
abstract = {Non-destructive subcellular metabolite quantification can reveal critical insights into biological interactions (e.g., endosymbiont-host crosstalk). Therefore, we developed a multivariate semi-quantitative imaging method using internal standardization to resolve simultaneous subcellular distributions of multiple metabolites, leveraging confocal Raman microscopy's (CRM's) high spatial resolution. The method was applied to the endosymbiotic mussel Gigantidas platifrons, whose symbiotic interaction mechanism has not been elucidated because symbionts cannot be cultivated. The results showed that the aggregated distribution of distinct phenotypes of symbiont strains was characterized by different glycogen abundances, indicating niche-driven metabolic strategies. Our data may provide direct evidence suggesting that symbionts supply intermediates to the host for cholesterol synthesis, potentially via vesicular trafficking. This work demonstrates CRM's capacity for comparative, spatially resolved metabolite quantification across cellular compartments. While semi-quantitative, CRM emerges as a powerful non-invasive tool for probing metabolic network dynamics and compartmentalization in challenging biological systems where traditional methods are limited.},
}

@article {pmid41077848,
year = {2025},
author = {Gao, JP and Kumar, A},
title = {RAM1-WRI Synergy: A GRAS-AP2 Regulatory Axis for Nutrient Exchange in Arbuscular Mycorrhizal Symbiosis.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70237},
pmid = {41077848},
issn = {1365-3040},
support = {//We would like to acknowledge finding support to Jin-Peng Gao by a grant to the University of Cambridge by the Bill & Melinda Gates Foundation and the UK Foreign, Commonwealth and Development Office (grant no. OPP1028264) known as the Enabling Nutrient Symbioses in Agriculture (ENSA) project./ ; },
}

@article {pmid41077805,
year = {2025},
author = {Ma, C and Wu, C and Han, H and Bai, D and Zhang, Z and Li, Y and Wang, H},
title = {Metabolomics Reveals Concentration-Specific Adaptive Mechanisms of Arbuscular Mycorrhizal Fungi in Cadmium Translocation and Detoxification in Arundinoideae (Phragmites australis).},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70230},
pmid = {41077805},
issn = {1365-3040},
support = {//This study was funded by the National Natural Science Foundation of China (52070064, 42330705) and Science Research Project of Hebei Education Department (BJK2024161)./ ; },
abstract = {The symbiosis of arbuscular mycorrhizal fungi (AMF) and Phragmites australis (Pa) is an effective biological strategy for cadmium (Cd) remediation, however, the bioaccumulation and translocation mechanisms underlying this symbiosis remain underexplored. In this study, Cd and nutrient element concentrations in four Pa tissues were analyzed, along with ultrastructure observations and root metabolomics profiling, under different Cd concentrations (1 mg/L, 5 mg/L) and exposure durations (7 days, 30 days). The root metabolomics analysis, in combination with Cd accumulation patterns and ultrastructural observations, provided crucial insights into the biochemical pathways and molecular mechanisms involved in Cd detoxification, nutrient redistribution, and subcellular structural changes in the AMF-Pa symbiotic system. AMF reduced Cd accumulation in all Pa tissues under 1 mg/L Cd for 7 days and in roots under 5 mg/L Cd for 30 days. Conversely, with AMF, Pa accumulated more Cd in the other exposure groups. Under 5 mg/L Cd for 30 days, AMF facilitated Cd translocation from roots to aboveground parts. AMF altered Cu, Zn and P bioaccumulation in old roots and significantly influenced Fe accumulation in roots across all treatments. While 5 mg/L Cd disrupted cellular ultrastructure, AMF inoculation protected intracellular organ integrity and promoted cell wall thickening. This study reveals the dynamic mechanisms by which AMF regulate Cd translocation and accumulation under varying Cd concentrations. Under high Cd concentrations, AMF enhance energy metabolism and chelation, promoting Cd translocation from roots to aerial parts while mitigating Cd toxicity in the endodermis. In contrast, under low Cd concentrations, AMF suppress Cd uptake and promote its immobilization within root tissues by activating amino acid and nucleotide metabolism, reducing Cd translocation to aboveground parts. Additionally, AMF strengthen cell walls through phenylpropanoid biosynthesis, offering protection against Cd toxicity. These findings provide crucial theoretical insights for the application of AMF in phytoremediation of Cd-contaminated soils.},
}

@article {pmid41077488,
year = {2025},
author = {Ding, H and Li, X and Wang, S and Yang, Y and Chen, X and Chen, C and Wang, H},
title = {Trichoderma harzianum for the control of agricultural pests: Potential, progress, applications and future prospects.},
journal = {Revista Argentina de microbiologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ram.2025.09.004},
pmid = {41077488},
issn = {0325-7541},
abstract = {This paper systematically reviews the taxonomic characteristics, pest control mechanisms, and field application cases of Trichoderma harzianum. As a non-toxic and environmentally friendly biocontrol fungus, T. harzianum exerts its pest control effects through various modes of action, including direct actions (such as parasitism, the production of insecticidal metabolites, and the release of antifeedant and repellent compounds) and indirect actions (such as inducing plants to enhance their resistance, attracting natural enemies of pests, and affecting insect symbiotic fungi). It can effectively control various agricultural pests, including nematodes and aphids. Moreover, the paper focuses on analyzing how modern formulation technologies (e.g., microencapsulation), synergistic strategies (in combination with biological and/or chemical agents), and genetic engineering enhance its biocontrol efficiency. This study aims to provide a theoretical basis and technical reference for constructing a sustainable pest management system based on T. harzianum, addressing pest control challenges within the context of increasing global food demand and supporting sustainable agricultural development.},
}

@article {pmid41077112,
year = {2025},
author = {Zonnequin, M and Vallet, M and Delage, L and Pohnert, G and Leblanc, C and Markov, GV},
title = {Differential impact of copper stress in two Ectocarpales: metabolic disruption and defensive signaling in the free-living Ectocarpus sp7 and the endophytic Laminarionema elsbetiae.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2025.10.006},
pmid = {41077112},
issn = {1638-6183},
abstract = {Algae are photosynthetic organisms, responsible for the primary production in oceans and lakes. Brown algae have evolved independently from other major eukaryotic lineages, such as the Opistokonts (animals, fungi) or Archaeplastida (land plants, green and red algae). Within this lineage, there is considerable variation between species, which differ in ecology, diversity, and evolutionary features, suggesting specific adaptations in their changing marine environment. In this context, several questions remain regarding the evolution of brown algal metabolism, particularly in response to oxidative stress. This study explored the consequences of copper stress on two brown algae from the Ectocarpales order: the free-living Ectocarpus sp7 and the endophytic Laminarionema elsbetiae. Using PAM-based fluorescence measurements, we revealed that high copper exposure reduces the photosynthetic capacity and activity of the endophyte. Through a cutting-edge untargeted metabolomic approach using UHPLC-HRMS profiling, we detected metabolic alterations induced by short-term exposure to moderate copper concentration in both free-living and endophytic Ectocarpales. The metabolite-regulated response appears to be substantial in Ectocarpus sp7 compared to L. elsbetiae, as a greater number of up- and down-regulated features were detected. Among the discriminant ions identified by tandem mass spectrometry, our results confirmed that copper exposure triggers the metabolism of algal defense signaling, primarily through the upregulation of oxylipins, but mainly in Ectocarpus sp 7. Altogether, our findings suggest that in Ectocarpales, fine metabolic adaptation may have altered the metabolism linked to defense signaling, such as the oxylipin pathway, particularly in ecological niches like endophytic life.},
}

@article {pmid41074950,
year = {2025},
author = {Zimmermann, F and Bouffaud, ML and Herrmann, S and Göttig, M and Graf, R and Tarkka, M and Opgenoorth, L and Croll, D and Peter, M and Dauphin, B},
title = {An ectomycorrhizal fungus alters developmental progression during endogenous rhythmic growth in pedunculate oak.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {57},
pmid = {41074950},
issn = {1432-1890},
mesh = {*Quercus/microbiology/growth & development ; *Mycorrhizae/physiology ; Symbiosis ; *Basidiomycota/physiology ; Plant Roots/microbiology/growth & development ; *Ascomycota/physiology ; Biomass ; },
abstract = {Pedunculate oak (Quercus robur L.), a long-lived forest tree species, forms symbiotic relationships with ectomycorrhizal (ECM) fungi, which can promote nutrient uptake, stress resilience, and growth. Like other tropical and temperate tree species, pedunculate oak exhibits endogenous rhythmic growth (ERG), a trait conferring the ability to repeatedly alternate root and shoot flushes as well as growth cessation as response to changing environmental conditions. However, the effects of different ECM fungal species on the ERG dynamics remain largely unknown. Here, we investigated the impact of two ECM fungi-Piloderma croceum, a basidiomycete previously shown to promote growth while not found in natural oak stands, and Cenococcum geophilum, an oak-native ascomycete with broad ecological range-on growth performance, biomass partitioning, and ERG patterns in a clonal oak system (clone DF159). By combining in vitro experiments with Bayesian modelling, we show that P. croceum promotes tree growth among treatments, without disrupting the endogenous growth rhythm. In contrast, C. geophilum, while showing high mycorrhization rates, led to reduced biomass accumulation and altered developmental progression through the ERG stages, especially by prolonging the steady state development stage-part of the root flush and characterized by peak net carbon assimilation. Co-inoculation revealed a competitive advantage of C. geophilum in root colonization, yet growth responses resembled those of the control. Our findings demonstrate that ECM species exert species-specific effects on biomass production and temporal development of plants, underscoring the functional importance of ECM fungi in shaping host development. Assessing these interactions provides new insights into the functional diversity of ectomycorrhizal symbiosis and can inform forest management strategies aimed at enhanced resilience in oak-dominated ecosystems under rapidly changing climatic conditions.},
}

*Quercus/microbiology/growth & development
*Mycorrhizae/physiology
Symbiosis
*Basidiomycota/physiology
Plant Roots/microbiology/growth & development
*Ascomycota/physiology
Biomass

@article {pmid41072151,
year = {2025},
author = {Zhou, Y and Man, XY},
title = {The epidermal immune microenvironment plays a central role in the pathogenesis of psoriasis.},
journal = {Current opinion in immunology},
volume = {97},
number = {},
pages = {102674},
doi = {10.1016/j.coi.2025.102674},
pmid = {41072151},
issn = {1879-0372},
abstract = {Psoriasis is a chronic immune-mediated skin disease whose inflammation can affect other systems and lead to various comorbidities. As a model inflammatory skin disease, while advances in mechanistic insights and targeted therapies have improved outcomes, unmet clinical needs persist. Modern technologies like single-cell sequencing and spatial transcriptomics reveal that skin immunity operates as a complex network involving neuroregulation, symbiotic microbial immunity, metabolic abnormalities, and reprogramming. These findings underscore the complexity of the local immune microenvironment in the skin and its central role in disease pathogenesis. In psoriatic inflammation, the epidermal immune microenvironment - driven by keratinocytes, dendritic cells, T cells, and skin microbiota - emerges as a core pathogenic mechanism. Keratinocytes, acting as both inflammatory effectors and disease drivers, interact with immune cells to initiate and amplify responses. Studying this microenvironment offers novel therapeutic targets for psoriasis and related inflammatory skin diseases.},
}

@article {pmid41070750,
year = {2025},
author = {Seah, BKB},
title = {Database Release: PPSDB, a Linked Open Data Knowledge Base for Protist-Prokaryote Symbioses.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {6},
pages = {e70049},
doi = {10.1111/jeu.70049},
pmid = {41070750},
issn = {1550-7408},
mesh = {*Symbiosis ; *Eukaryota/physiology/classification/genetics ; *Knowledge Bases ; *Archaea/physiology/genetics ; *Databases, Factual ; *Prokaryotic Cells/physiology ; *Bacteria/genetics/classification ; Software ; },
abstract = {As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of their diversity and the literature becomes a growing and ongoing challenge. Here I present the Protist-Prokaryote Symbiosis Database (PPSDB), comprising 1146 manually curated interaction statements sourced from 443 publications, where biological taxonomy, anatomical localization, and analytical methods applied have been annotated and mapped to external databases and ontologies, such as Wikidata, NCBI Taxonomy, and Gene Ontology. I describe how its data model deals practically with challenges such as incomplete information and inconsistent taxon concepts, which will be applicable to similar projects. Both the model and underlying Wikibase software platform are highly extensible, so new items and properties can easily be added. Unlike a static table or list of citations, PPSDB is a structured knowledge base that enables programmatic access and powerful, integrated semantic queries. The database is available at https://ppsdb.wikibase.cloud/.},
}

*Symbiosis
*Eukaryota/physiology/classification/genetics
*Knowledge Bases
*Archaea/physiology/genetics
*Databases, Factual
*Prokaryotic Cells/physiology
*Bacteria/genetics/classification
Software

@article {pmid41068596,
year = {2025},
author = {Torrescassana, EC and Del Carmen Montero-Calasanz, M and Knight, M and Stach, J and Howard, TP},
title = {Genomic and functional analyses reveal Pseudomonas granadensis CT364 is a plant growth-promoting endophyte.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {651},
pmid = {41068596},
issn = {1471-2180},
support = {BB/T008695/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RYC2019-028468-I//Ramón y Cajal Research Grant, Spanish Ministry of Economy, Industry and Competitiveness/ ; },
mesh = {*Endophytes/genetics/physiology/isolation & purification ; *Pseudomonas/genetics/physiology/isolation & purification/classification ; Rhizosphere ; Plant Roots/microbiology/growth & development ; Genome, Bacterial ; *Plant Development ; Genomics ; Soil Microbiology ; Olea/microbiology/growth & development ; Arabidopsis/microbiology/growth & development ; Biofilms/growth & development ; },
abstract = {BACKGROUND: Plant-associated endophytes offer promising agricultural, environmental, and biotechnological applications. Despite their potential utility, difficulties in culturing these microorganisms under laboratory conditions have limited both their isolation and a comprehensive understanding of their biology, function, and ecological role. Against this background, Pseudomonas granadensis strain CT364-isolated from the olive tree rhizosphere-emerged as a potential endophyte of interest due to its cultivability and its ability to promote rooting across diverse species, including olive trees, rapeseed, mung bean and cowpea.

RESULTS: Genome Annotation and in silico predictions identified 564 genes linked to rhizosphere competence, plant colonisation and plant growth-promoting traits. Experimental findings confirmed the strain's motility, capacity for biofilm formation, and ability to sense and respond to plant-derived signals. P. granadensis CT364 effectively colonises the rhizosphere, rhizoplane, and internal tissues of Arabidopsis, confirming its endophytic nature without exhibiting any pathogenic traits. Inoculation experiments demonstrated significant effects on root architecture and increases in plant biomass and rosette area. Notably, these benefits were retained under salinity and osmotic stress, underscoring its plant growth-promoting ability. Finally, both genome analysis and experimental tests confirmed its resistance to osmotic stress and heavy metal toxicity, highlighting the strain's ability to survive in difficult environments.

CONCLUSIONS: The integration of genomic insights and experimental validation supports the conclusion that P. granadensis CT364 is a plant growth-promoting endophytic bacterium. Its ability to enhance plant development under both optimal and stressful conditions, combined with its ability to colonise Arabidopsis and non-pathogenic nature, positions this strain as a potential bioinoculant for sustainable agriculture. Furthermore, the identification of specific genes related to plant sensing and colonisation, and its genetic tractability, open avenues for exploring underlying mechanisms of plant-microbe interactions. In summary, P. granadensis CT364 therefore not only holds potential for improving crop performance under challenging environmental conditions but also offers a valuable model for the study of beneficial plant-bacterial symbiosis.},
}

*Endophytes/genetics/physiology/isolation & purification
*Pseudomonas/genetics/physiology/isolation & purification/classification
Rhizosphere
Plant Roots/microbiology/growth & development
Genome, Bacterial
*Plant Development
Genomics
Soil Microbiology
Olea/microbiology/growth & development
Arabidopsis/microbiology/growth & development
Biofilms/growth & development

@article {pmid41068135,
year = {2025},
author = {Cleveland, D and Nayak, R and Joseph, F and Nguyen, TA},
title = {Characterization of sustainable bacterial cellulose from Indigenous Vietnamese biomass for potential textile applications.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35267},
pmid = {41068135},
issn = {2045-2322},
support = {IRG2022/1//RMIT International University/ ; },
mesh = {*Cellulose/chemistry/metabolism ; *Textiles/microbiology ; *Biomass ; Spectroscopy, Fourier Transform Infrared ; Vietnam ; *Bacteria/metabolism ; Microscopy, Electron, Scanning ; Calorimetry, Differential Scanning ; *Acetobacter/metabolism/chemistry ; },
abstract = {This research explored the fabrication and characterization of bacterial cellulose (BC), with a distinct emphasis on leveraging indigenous Vietnamese biomass sources. A diverse sample library consisting of 150 BC samples was prepared, with six samples selected for objective evaluation, based on the standard test methods. These samples were subjected to characterization techniques including Scanning electron microscopy (SEM), Energy dispersive X-ray (EDX), Fourier Transformation Infrared (FTIR) and Differential scanning calorimetry (DSC) to explore potential applications of BC in fashion and textiles. Moreover, the growth medium (or SCOBY- Symbiotic Culture of Bacteria and Yeast), from which the BC was cultivated, was analyzed to identify the constituent bacterial and yeast strains. The EDX analysis showed the major elements of BC were Carbon (C) followed by Oxygen (O), which accounted for 99% of the elemental composition of BC. The cellulosic structure was confirmed by the FTIR results, which indicated the characteristics bonds of BC. The DSC results showed that thermal stability can be achieved for the fashion and textiles produced from BC. Bacterial analysis showed the presence of Acetobacter Indonesiensis, a gram-negative bacterium, in all the BC samples. The outcomes of this study established a deeper comprehension of the morphological, thermal, biological, and chemical attributes of BC, as well as the microbial dynamics within the SCOBY mother. This exploration not only augments the existing knowledge on BC's potential in material design but also paves the way for further research on the influence of local ingredients on biomaterial production, thereby contributing to the burgeoning field of sustainable material innovation within a localized context.},
}

*Cellulose/chemistry/metabolism
*Textiles/microbiology
*Biomass
Spectroscopy, Fourier Transform Infrared
Vietnam
*Bacteria/metabolism
Microscopy, Electron, Scanning
Calorimetry, Differential Scanning
*Acetobacter/metabolism/chemistry

@article {pmid41066987,
year = {2025},
author = {Zhang, C and Zhang, Y and Diao, G and Hou, N and Zhao, X and Li, D},
title = {Decoding pyrene-induced reactive oxygen species production in the rhizosphere and their role in biodegradation: The repair mechanism of symbiotic driving by Fe(II) and microorganisms.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140073},
doi = {10.1016/j.jhazmat.2025.140073},
pmid = {41066987},
issn = {1873-3336},
abstract = {Reactive oxygen species (ROS) are considered key drivers of biogeochemical processes. However, there is limited research on the factors influencing ROS generation in the rhizosphere due to polycyclic aromatic hydrocarbon (PAHs) pollution during plant-microbe joint remediation, as well as their role in biodegradation. This study demonstrated that exposure to pyrene at a concentration of 100 mg/kg significantly enhanced the release of hydrogen peroxide (H2O2), hydroxyl radicals (•OH), and superoxide anions (O2•[-]) in the rhizosphere of ryegrass during root development. The concentrations of these reactive oxygen species were 1.5-7.8 times higher than those in the control group. Additionally, the Fe(II) concentration increased by 37.5 ± 3.2 %, and the pyrene degradation rate reached 26.8 ± 1.4 %. These results indicate that pyrene serves as a major factor stimulating ROS generation in ryegrass. Among these processes, Fe(II) catalyzes the production of •OH, which directly attacks the benzene ring structure of pyrene. High-throughput analysis further revealed that ROS enhanced the diversity, cohesion, and robustness of the rhizosphere microbial community structure. Furthermore, Pseudomonas, Marmoricola, Nocardioides and Dietzia were identified as core microbial genera involved in pyrene degradation and ecological restoration. Metagenomics analysis suggests that rhizosphere microorganisms respond to ROS-induced oxidative stress by enhancing ATP synthesis, which provides energy for antioxidant-related protein production and damage repair, thereby accelerating pyrene degradation. These results elucidate the ROS-mediated driving mechanism behind microbial pyrene degradation in plant-microbe combined remediation systems, thereby providing a theoretical basis for optimizing bioremediation strategies for organically contaminated soils.},
}

@article {pmid41066576,
year = {2025},
author = {Frison, M and Lockey, BS and Nie, Y and Golder, Z and Theiaspra, E and Ryall, CD and Lyons, C and Burr, SP and Prater, M and Bozhilova, LV and Glynos, A and Stewart, JB and Jones, NS and Chiaratti, MR and Chinnery, PF},
title = {Ubiquitin-mediated mitophagy regulates the inheritance of mitochondrial DNA mutations.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6769},
pages = {156-163},
doi = {10.1126/science.adr5438},
pmid = {41066576},
issn = {1095-9203},
mesh = {*Mitophagy/genetics ; Animals ; *DNA, Mitochondrial/genetics ; Mice ; *Mutation ; *Mitochondria/genetics/metabolism ; *Ubiquitin/metabolism ; Heteroplasmy ; Humans ; *Thiolester Hydrolases/metabolism/antagonists & inhibitors/genetics ; Proteasome Endopeptidase Complex/metabolism ; Mitochondrial Diseases/genetics ; Zygote ; Female ; },
abstract = {Mitochondrial synthesis of adenosine triphosphate is essential for eukaryotic life but is dependent on the cooperation of two genomes: nuclear and mitochondrial DNA (mtDNA). mtDNA mutates ~15 times as fast as the nuclear genome, challenging this symbiotic relationship. Mechanisms must have evolved to moderate the impact of mtDNA mutagenesis but are poorly understood. Here, we observed purifying selection of a mouse mtDNA mutation modulated by Ubiquitin-specific peptidase 30 (Usp30) during the maternal-zygotic transition. In vitro, Usp30 inhibition recapitulated these findings by increasing ubiquitin-mediated mitochondrial autophagy (mitophagy). We also found that high mutant burden, or heteroplasmy, impairs the ubiquitin-proteasome system, explaining how mutations can evade quality control to cause disease. Inhibiting USP30 unleashes latent mitophagy, reducing mutant mtDNA in high-heteroplasmy cells. These findings suggest a potential strategy to prevent mitochondrial disorders.},
}

*Mitophagy/genetics
Animals
*DNA, Mitochondrial/genetics
Mice
*Mutation
*Mitochondria/genetics/metabolism
*Ubiquitin/metabolism
Heteroplasmy
Humans
*Thiolester Hydrolases/metabolism/antagonists & inhibitors/genetics
Proteasome Endopeptidase Complex/metabolism
Mitochondrial Diseases/genetics
Zygote
Female

@article {pmid41066235,
year = {2025},
author = {Kaur, R and Kalra, M and Imchen, M and Crowley, BL and McGarry, A and Carpenter, L and Bordenstein, SR},
title = {Histone acetylation modulation by a small molecule inhibitor recapitulates symbiont-induced cytoplasmic incompatibility.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116416},
doi = {10.1016/j.celrep.2025.116416},
pmid = {41066235},
issn = {2211-1247},
abstract = {Symbiotic relationships between arthropod hosts and microorganisms have garnered global attention for their influence on host ecology, evolution, and vector control. A major gap in the field is to mechanistically define and reconstitute symbiotic traits in the absence of microbes. Here, we address this omission by identifying an evolutionarily conserved host mechanism that recapitulates Wolbachia-induced cytoplasmic incompatibility (CI)-a paternal-effect embryonic lethality trait. We first show that Wolbachia alter histone acetylation during sperm development in Drosophila melanogaster. By chemically inhibiting histone acetyltransferase (HAT) activity in aposymbiotic males, we reprogram the chromatin landscape of developing sperm to induce a rescuable CI phenotype. This phenotype is further modulated through transgenic knockdown of HAT and histone deacetylase enzymes, providing tunable control over natural CI intensity. Our findings uncover histone acetylation as a key host-intrinsic pathway, capable of inducing symbiont-independent CI for new avenues of basic and applied studies.},
}

@article {pmid41065807,
year = {2025},
author = {Choi, BJ and Kim, JM and Bayburt, H and Choi, DG and Choi, SH and Jeon, CO},
title = {Description of Tateyamaria algicola sp. nov. and Tateyamaria rhodophyticola sp. nov., Isolated from Marine Algae.},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {545},
pmid = {41065807},
issn = {1432-0991},
support = {20210469//Ministry of Ocean and Fisheries (KR)/ ; NIBR No. 2024-02-001//National Institute of Biological Resources/ ; 2024//Chung-Ang University/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Base Composition ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Nucleic Acid Hybridization ; Ubiquinone ; Phospholipids/analysis ; Seawater/microbiology ; Sequence Analysis, DNA ; Genome, Bacterial ; },
abstract = {Two aerobic, non-motile, Gram-stain-negative strains, designated SN3-11ᵀ and SN6-1ᵀ, were isolated from marine algae. Both strains were oxidase- and catalase-positive, with rod-shaped morphology. Strain SN3-11ᵀ grew optimally at 25 ℃, pH 7.0-8.0, and 2.0-5.0% (w/v) NaCl, while strain SN6-1ᵀ showed optimal growth at 25 ℃, pH 8.0, and 2.0-3.0% NaCl. Both strains contained ubiquinone-10 as the sole respiratory quinone, and their major fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C19:0 cyclo ω8c. Phosphatidylcholine and phosphatidylglycerol were dominant polar lipids, with diphosphatidylglycerol additionally present in SN3-11ᵀ. Strains SN3-11ᵀ and SN6-1ᵀ had genome sizes of 4,762 Kb and 4,157 Kb with G + C contents of 61.3% and 62.0%, respectively. They shared 96.9% 16S rRNA gene sequence similarity, 77.0% average nucleotide identity (ANI), and 20.2% digital DNA-DNA hybridization (dDDH), supporting their classification as distinct species. Their closest relative, Tateyamaria armeniaca KMU-156ᵀ, exhibited 16S rRNA gene sequence similarities of 98.6% to SN3-11ᵀ and 97.7% to SN6-1ᵀ. Phylogenetic trees based on 16S rRNA and whole-genome sequences placed both strains in distinct lineages within Tateyamaria. ANI and dDDH values between the two isolates and other Tateyamaria species were < 78.5% and < 21.0%, respectively. Strains SN3-11ᵀ and SN6-1ᵀ harbored genes encoding diverse carbohydrate-active enzymes and biosynthetic pathways for lycopene, pantothenate, and riboflavin, suggesting potential symbiotic roles with algal hosts. Based on phenotypic, chemotaxonomic, and genomic characteristics, SN3-11ᵀ and SN6-1ᵀ represent two novel species, Tateyamaria algicola sp. nov. (SN3-11ᵀ = KACC 23689ᵀ = JCM 36649ᵀ) and Tateyamaria rhodophyticola sp. nov. (SN6-1ᵀ = KACC 23127ᵀ = JCM 35962ᵀ).},
}

RNA, Ribosomal, 16S/genetics
Phylogeny
Base Composition
Fatty Acids/chemistry/analysis
DNA, Bacterial/genetics
Bacterial Typing Techniques
Nucleic Acid Hybridization
Ubiquinone
Phospholipids/analysis
Seawater/microbiology
Sequence Analysis, DNA
Genome, Bacterial

@article {pmid41065102,
year = {2025},
author = {Pérez-Sepúlveda, M and Jones, AP and Higuita-Aguirre, MI and Holdstock, A and Kafle, A and Cardoso, AA and Vann, R and Mullen, MD and Garcia, K},
title = {Nodulation Is Maintained and Salinity Tolerance Enhanced in Two Soybean Cultivars Inoculated With Sinorhizobium fredii Under Brackish Water.},
journal = {Physiologia plantarum},
volume = {177},
number = {5},
pages = {e70570},
doi = {10.1111/ppl.70570},
pmid = {41065102},
issn = {1399-3054},
support = {2020-67013-31800//USDA National Institute of Food and Agriculture/ ; },
mesh = {*Glycine max/microbiology/physiology/drug effects ; *Salt Tolerance/physiology ; *Sinorhizobium fredii/physiology ; Plant Roots/microbiology/physiology/growth & development ; *Plant Root Nodulation/physiology ; Salinity ; Symbiosis ; Plant Shoots/physiology/microbiology ; Biomass ; Potassium/metabolism ; Phosphorus/metabolism ; Nitrogen/metabolism ; },
abstract = {Salinity is an increasing threat to agriculture, particularly in coastal regions affected by seawater intrusion and sea-level rise. This study evaluated the halotolerance and symbiotic potential of Sinorhizobium fredii USDA 208 in two soybean cultivars (includer and excluder) under three salinity levels-low (freshwater), moderate (brackish water), and high (seawater). The results demonstrated that S. fredii not only tolerates but also exhibits enhanced growth under moderate salinity. Nodulation was successfully established when salinity and inoculation occurred simultaneously. Nodulation was also maintained when salinity occurred after the inoculation, particularly in fresh and brackish water. Root development declined with increasing salinity, but the includer cultivar showed better root system architecture plasticity in brackish water, while the excluder cultivar exhibited higher shoot and root biomass across salinity levels. Bacterial inoculation improved shoot phosphorus uptake, the potassium: sodium ratio, and carotenoid retention, particularly in the includer cultivar, suggesting an enhanced physiological tolerance to moderate salinity. Inoculation also resulted in higher shoot nitrogen and maintained pigment content. Using a seawater recipe provides a better understanding of salinity than traditional NaCl-based studies and highlights the role of S. fredii USDA 208 in supporting soybean performance when salts accumulate in coastal agricultural soils.},
}

*Glycine max/microbiology/physiology/drug effects
*Salt Tolerance/physiology
*Sinorhizobium fredii/physiology
Plant Roots/microbiology/physiology/growth & development
*Plant Root Nodulation/physiology
Salinity
Symbiosis
Plant Shoots/physiology/microbiology
Biomass
Potassium/metabolism
Phosphorus/metabolism
Nitrogen/metabolism

@article {pmid41064789,
year = {2025},
author = {Farias, A and Neves, EG and Johnsson, R},
title = {Kuayguara etymatee sp. nov., a New Genus and Species of Artotrogidae (Copepoda: Siphonostomatoida) with an Uncommonly Atrophied Leg 1.},
journal = {Zoological studies},
volume = {64},
number = {},
pages = {e10},
pmid = {41064789},
issn = {1810-522X},
abstract = {Artotrogidae Brady, 1880 is a cosmopolitan family with 23 valid genera and 131 known species. However, a considerable number of these species were subject of reexaminations and redescriptions recently. With the crescent number of new species discovered, it is becoming possible to better understand their boundaries. This study presents a new genus and species of Artotrogidae, recovered from unidentified hosts in debris of benthonic samples from Todos-os-Santos Bay, northeastern coast of Brazil. Kuayguara etymatee gen. et sp. nov. exhibits an underdeveloped first leg, which possess an unsegmented protopod and 1-segmented exopod, a unique set of morphological characteristics that differentiates it from all other genera of the family.},
}

@article {pmid41064419,
year = {2025},
author = {Corkery, RW and Garvey, CJ and Houston, JE},
title = {In hospite and ex hospite architecture of photosynthetic thylakoid membranes in Symbiodinium spp. using small-angle neutron scattering.},
journal = {Journal of applied crystallography},
volume = {58},
number = {Pt 5},
pages = {1516-1525},
pmid = {41064419},
issn = {0021-8898},
abstract = {We demonstrate that small-angle neutron scattering (SANS) can resolve the architecture of photosynthetic thylakoid membranes in live symbiotic algal cells, both extracted from and living inside their respective hosts (ex hospite and in hospite, respectively). This enables a new non-destructive approach to probing thylakoid organization in coral symbioses, relevant to understanding the mechanisms of coral bleaching. A biologically realistic triple-vesicle model, guided by electron microscopy and established biochemical constraints, was fitted to SANS data from live Symbiodinium associated with both the coral analogue Aiptasia and the reef-building coral Acropora. The resulting compartment scattering length densities, together with established biochemical constraints, define a limited compositional range that supports the plausibility of the structural solution. These fits capture key scattering features and yield dimensional parameters, including inter-thylakoid (IT) gap widths, with uncertainties small enough to test models of stress-related membrane rearrangement. A focused covariance analysis shows that this SANS framework can resolve an IT-gap expansion of ∼2.4 nm with >7σ sensitivity, sufficient to distinguish structural changes proposed in thylakoid stress-response models. This provides a robust baseline for future live-cell studies.},
}

@article {pmid41064255,
year = {2025},
author = {Kong, C and Huang, LB and Yang, MF and Yue, NN and Luo, D and Zhang, Y and Tian, CM and Song, Y and Wei, DR and Shi, RY and Liang, YJ and Yao, J and Wang, LS and Li, DF},
title = {Microbiome engineering: unlocking therapeutic potential in inflammatory bowel disease.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1610029},
pmid = {41064255},
issn = {1664-302X},
abstract = {The human gut microbiome, traditionally linked to infectious diseases, is now recognized as a hub of non-pathogenic microorganisms that play pivotal roles in host communication and homeostasis. Advances in microbiome engineering have enabled the design of "smart" living therapeutics for inflammatory bowel disease (IBD), leveraging engineered symbiotic bacteria, yeasts, and bacteriophages. This review synthesizes recent progress in reprogramming microbes using synthetic biology tools, emphasizing their capacity to sense pathological signals and deliver targeted therapies. We critically evaluate three key approaches: synthetic gene circuits in bacteria for precision drug delivery, phage-mediated modulation of dysbiotic microbiota, and yeast-based systems for metabolic intervention (e.g., butyrate production). Challenges in biocontainment, genetic stability, and clinical translation are discussed, alongside emerging strategies such as outer membrane vesicles (OMVs) for immunomodulation. By distilling these advances, we highlight a roadmap for translating engineered microbes into safe and effective IBD therapies.},
}

@article {pmid41063423,
year = {2025},
author = {Bartz, PM and Grullón-Penkova, IF and Cavaleri, MA and Reed, SC and Shahid, S and Wood, TE and Bachelot, B},
title = {Experimental warming alters free-living nitrogen fixation in a humid tropical forest.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70592},
pmid = {41063423},
issn = {1469-8137},
support = {1754713//Division of Environmental Biology/ ; 2120085//Division of Environmental Biology/ ; 89243018S-SC-000014//Basic Energy Sciences/ ; 89243018S-SC-000017//Basic Energy Sciences/ ; 89243021S-SC-000076//Basic Energy Sciences/ ; DE-SC-0011806//Basic Energy Sciences/ ; DE-SC-0018942//Basic Energy Sciences/ ; DE-SC0012000//Basic Energy Sciences/ ; DE-SC0022095//Basic Energy Sciences/ ; },
abstract = {Microbial nitrogen (N) fixation accounts for c. 97% of natural N inputs to terrestrial ecosystems. These microbes can be free-living in the soil and leaf litter (asymbiotic) or in symbiosis with plants. Warming is expected to increase N-fixation rates because warmer temperatures favor the growth and activity of N-fixing microbes. We investigated the effects of warming on asymbiotic components of N fixation at a field warming experiment in Puerto Rico. We analyzed the function and composition of bacterial communities from surface soil and leaf litter samples. Warming significantly increased asymbiotic N-fixation rates in soil by 55% (to 0.002 kg ha[-1] yr[-1]) and by 525% in leaf litter (to 14.518 kg ha[-1] yr[-1]). This increase in N fixation was associated with changes in the N-fixing bacterial community composition and soil nutrients. Our findings suggest that warming increases the natural N inputs from the atmosphere into this tropical forest due to changes in microbial function and composition, especially in the leaf litter. Given the importance of leaf litter in nutrient cycling, future research should investigate other aspects of N cycles in the leaf litter under warming conditions.},
}

@article {pmid41062940,
year = {2025},
author = {Feng, Y and Zou, Z and Liu, C and Zhang, D and Wang, Y and Ma, Y and Cao, Y and Wu, P},
title = {A LjBAK1-associated E3 ubiquitin ligase, LjPUB7, negatively regulates early symbiosis by targeting NFRs.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1334},
pmid = {41062940},
issn = {1471-2229},
support = {24KJB180002//Jiangsu Higher Education Institutions of China/ ; 32090063//The National Science Fundation of China/ ; AMLKF202510//the State Key Laboratory of Agricultural Microbiology/ ; },
mesh = {*Symbiosis/genetics ; *Ubiquitin-Protein Ligases/metabolism/genetics ; Nicotiana/genetics/microbiology/metabolism ; *Plant Proteins/metabolism/genetics ; *Lotus/genetics/enzymology/microbiology/physiology/metabolism ; Ubiquitination ; Gene Expression Regulation, Plant ; },
abstract = {Nod factor receptors (NFRs) are essential for initiating symbiotic signaling in legumes, mediating rhizobial infection and nodule development. Tight regulation of NFR levels is crucial to prevent inappropriate immune responses and maintain cellular homeostasis. Co-expression of LjNFR1 and LjNFR5 triggers cell death in Nicotiana benthamiana, which is specifically inhibited by LjBAK1-mediated ubiquitination and subsequent degradation, suggesting the existence of a LjBAK1-E3 ligase complex for NFR protein turnover. Further analysis identified LjPUB7, a plant U-box E3 ubiquitin ligase in Lotus japonicus, as a regulator of early symbiotic interactions. LjPUB7 interacts with both LjBAK1 and NFRs, and directly ubiquitinates NFRs. Loss-of-function Ljpub7 mutants display increased infection thread formation, enhanced nodule development, and elevated expression of early nodulation genes. These findings reveal that LjPUB7 negatively regulates early rhizobial infection by targeting NFR1 and NFR5 for ubiquitination and degradation, thereby providing insights into the fine-tuned control of symbiotic signaling in legumes.},
}

*Symbiosis/genetics
*Ubiquitin-Protein Ligases/metabolism/genetics
Nicotiana/genetics/microbiology/metabolism
*Plant Proteins/metabolism/genetics
*Lotus/genetics/enzymology/microbiology/physiology/metabolism
Ubiquitination
Gene Expression Regulation, Plant

@article {pmid41061564,
year = {2025},
author = {Marcos-Torres, FJ and Pérez, J and Torrens-González, D and García-Pedrosa, MÁ and Contreras-Moreno, FJ and Moraleda-Muñoz, A},
title = {Global copper response of the soil bacterial predator Myxococcus xanthus and its contribution to antibiotic cross-resistance.},
journal = {Microbiological research},
volume = {302},
number = {},
pages = {128357},
doi = {10.1016/j.micres.2025.128357},
pmid = {41061564},
issn = {1618-0623},
abstract = {Copper accumulation in agricultural soils poses environmental challenges by selecting copper-resistant bacteria and also contributing to the co-selection of antibiotic-resistant bacteria. In addition, copper influences bacterial predator-prey interactions, potentially altering microbial ecosystems. Myxococcus xanthus, a soil-dwelling bacterium, preys on other microorganisms, including Sinorhizobium meliloti, a symbiotic nitrogen-fixing bacterium associated with leguminous plants. The role of copper in M. xanthus interactions remains poorly understood, although it accumulates at the predator-prey interface. In this study, we explore the transcriptomic response of M. xanthus to copper stress in both monocultures and co-cultures with S. meliloti. Our analysis identified many myxobacterial copper-regulated transcripts, and studies on mutant strains in some copper-induced genes revealed the role of two efflux pumps in cross-resistance to copper and tetracyclines. These findings provide new insights into the adaptive mechanisms of M. xanthus in response to copper, with implications for the co-selection of antibiotic resistance and the broader impact of copper on microbial community dynamics in soil ecosystems.},
}

@article {pmid41061519,
year = {2025},
author = {Liu, J},
title = {How does university-industry collaboration motivate enterprise participation and promote human resource development?.},
journal = {Acta psychologica},
volume = {260},
number = {},
pages = {105686},
doi = {10.1016/j.actpsy.2025.105686},
pmid = {41061519},
issn = {1873-6297},
abstract = {In the knowledge economy era, university-industry collaboration (UIC) has become a vital mechanism for fostering innovation, enhancing enterprise competitiveness, and strengthening human resource development. Yet, enterprise participation in UIC remains uneven and unpredictable, limiting the effectiveness of policies aimed at cultivating talent through academic-industry partnerships. To address this gap, this study integrates Social Cognitive Theory and Symbiosis Theory to develop a cognitive-symbiotic framework that explains the mechanisms driving enterprise willingness to participate in UIC and how such participation facilitates enterprise-level human resource development. Drawing on survey data from 398 Chinese enterprises and structural equation modeling, the findings reveal: (1) Observational learning of successful symbiotic relationships (β = 0.187), symbiotic self-efficacy (β = 0.312), and symbiotic outcome expectations (β = 0.385) significantly enhance enterprise participation willingness, while perceived symbiotic imbalance risk (β = -0.156) inhibits it; (2) Policy support indirectly promotes participation through a dual mediation pathway-enhancing symbiotic self-efficacy (indirect effect = 0.163) and reducing imbalance risk perception (indirect effect = 0.037), with a total indirect effect of 0.232; (3) Innovation capability significantly moderates the effects of cognitive-symbiotic drivers on participation, amplifying their influence in high-innovation enterprises. This study uncovers the cognitive-psychological and relational mechanisms underpinning enterprise engagement in UIC and highlights how such engagement contributes to organizational learning, capability upgrading, and long-term human resource development. It offers actionable insights for policymakers to design dual-pathway interventions that simultaneously build participation confidence and reduce perceived relational risks, and for enterprise leaders to leverage UIC as a strategic channel for developing high-quality talent and innovation capacity.},
}

@article {pmid41060927,
year = {2025},
author = {Ling, H and Xu, F and Shabbir, I and Sulaiman, Z and Shahbaz, M and Al Farraj, DA},
title = {Efficacy of peat-based bioformulation of microbial co-inoculants with silicon for growth promotion of rubber plants.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331899},
doi = {10.1371/journal.pone.0331899},
pmid = {41060927},
issn = {1932-6203},
mesh = {*Silicon/pharmacology ; *Hevea/growth & development/microbiology/drug effects ; *Soil/chemistry ; Soil Microbiology ; *Enterobacter/physiology ; Rhizosphere ; Mycorrhizae/physiology ; *Agricultural Inoculants ; },
abstract = {Recently, microbial consortia of rhizobacteria and arbuscular mycorrhizal fungi (AMF) had demonstrated the potential as plant growth promoting microbes in sustainable agriculture. This study aimed to investigate the effect of a peat moss-based formulation of Enterobacter sp. UPMSSB7, Glomus mosseae, and silicon (Si) on the survival of microbial inoculants under storage conditions for 24 weeks. The study further assessed the potential of this bioformulation to promote the growth of rubber plants in a glasshouse trial. The Enterobacter sp. UPMSSB7 isolated from rubber tree's rhizosphere, can solubilize silicates and has plant growth promoting properties. G. mosseae is an AMF, having symbiotic relationship with majority of cultivated crops. The application of Si has emerged as a sustainable strategy for crop health. It improves soil fertility through nutrient maintenance and also alleviates various biotic and abiotic stresses. Results from laboratory test revealed that bioformulation of co-inoculants with Si sustained a high survivability of Enterobacter sp. (18 × 108 CFU g-1) and G. mosseae (35 spores per 10 g) in formulation for up to 24 weeks of storage. Results from the glasshouse experiment revealed that 24 weeks after treatment with bioformulation of co-inoculants with Si increased the stem height, girth, leaf area, dry weight of shoot and root, chlorophyll content, microbial population of Enterobacter sp. (1.4 × 108 CFU g-1 soil) and G. mosseae (78 spores/10 g soil) in rhizosphere and also increased N, P, K and Si contents in rubber seedlings than bioformulation of single inoculant with Si and control. Our findings indicate that peat moss-based formulation of co-inoculants Enterobacter sp. UPMSSB7 and G. mosseae added with Si proved to be the most effective. This formulation not only maintained good microbial survivability but also significantly enhanced the rubber plants growth compared to the bioformulation of single inoculants. This promising approach using a peat moss-based formulation of microbial co-inoculants with Si, could be further explored for growth enhancement of rubber trees under field conditions.},
}

*Silicon/pharmacology
*Hevea/growth & development/microbiology/drug effects
*Soil/chemistry
Soil Microbiology
*Enterobacter/physiology
Rhizosphere
Mycorrhizae/physiology
*Agricultural Inoculants

@article {pmid41060577,
year = {2025},
author = {Abrham, AB and Degefa, AM and Awlachew, ZT},
title = {Phenotypic diversity, symbiotic effectiveness and plant growth promoting characteristics of rhizobia nodulating chickpea (Cicer arietinum L.) from central and south gondar zones, Ethiopia.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {41060577},
issn = {1678-4405},
}

@article {pmid41060240,
year = {2025},
author = {Toro-Delgado, E and Laetsch, DR and Hayward, A and Talavera, G and Lohse, K and Vila, R},
title = {Wolbachia Host Shifts and Widespread Occurrence of Reproductive Manipulation Loci in European Butterflies.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70125},
doi = {10.1111/mec.70125},
pmid = {41060240},
issn = {1365-294X},
support = {NE/L011522/1//Natural Environment Research Council/ ; BB/N020146/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /ERC_/European Research Council/International ; 2021-SGR-00420//Departament de Recerca i Universitats, Generalitat de Catalunya/ ; 2021-SGR-01334//Departament de Recerca i Universitats, Generalitat de Catalunya/ ; FPU22/02358//Ministerio de Ciencia, Innovación y Universidades/ ; PID2022-139689NB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PID2023-152239NB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {Wolbachia is the most frequent bacterial endosymbiont of arthropods and nematodes. Although it is mostly vertically transmitted, from parent to offspring through the egg cytoplasm, horizontal transfer of Wolbachia is thought to be common over evolutionary timescales. However, the relative frequency of each transmission mechanism has not been studied systematically in closely related species. Additionally, while Wolbachia is generally regarded as a reproductive manipulator, it is unclear how frequently the symbiont induces such effects. In this study, we investigated the presence, phenotypes and phylogenetic relationships among Wolbachia strains in whole genome sequence data for 18 European butterfly sister-species pairs. We find that sister-species share Wolbachia strains more often than random species pairs and that the probability of strain sharing is higher for younger pairs of host species, especially those with greater range overlap. We also find that split times between Wolbachia strains that infect the same sister-species pair generally pre-date host divergence, ruling out co-divergence in favour of horizontal transfer. However, some strains are younger than the mitochondrial split times of their hosts, so introgressive transfer cannot be ruled out in some cases. In addition, all newly assembled Wolbachia genomes contained putative homologues of genes associated with cytoplasmic incompatibility and male killing. This supports the potential for reproductive manipulation in Wolbachia strains infecting European butterflies, which until now was only inferred from mitochondrial diversity patterns. Our results show that horizontal and introgressive transfer of Wolbachia are frequent even between recently speciated host taxa, suggesting the symbiont's turnover rate is higher than had been inferred previously from surveys of distantly related hosts.},
}

@article {pmid41059966,
year = {2025},
author = {Dittmer, J and Mahillon, M and Debonneville, C and Faoro, F and Foissac, X and Schumpp, O and Chouaia, B},
title = {The Endosymbiont Consortia of Two Cixiidae Planthoppers Reveal an Ancient Symbiosis With 'Candidatus Mirabilia Symbiotica'.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70204},
doi = {10.1111/1758-2229.70204},
pmid = {41059966},
issn = {1758-2229},
support = {2020/33/LES-Z II//Swiss Federal Office for Agriculture/ ; 792813//Horizon 2020 Framework Programme/ ; },
mesh = {*Symbiosis ; Animals ; *Hemiptera/microbiology ; Phylogeny ; Genome, Bacterial ; *Gammaproteobacteria/genetics/classification/isolation & purification/physiology ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {Insects of the suborder Auchenorrhyncha harbour multiple ancient endosymbionts that jointly produce essential nutrients lacking from the host's diet. Compared to cicadas, leafhoppers, and spittlebugs, our understanding of the multipartite symbioses among planthoppers, an extremely diverse insect group, is still very limited. Herein, we assembled the genomes of the primary endosymbionts of two planthopper species from the Cixiidae family, Cixius wagneri and Pentastiridius leporinus, both vectors of phytopathogenic Arsenophonus in Europe. Each species harboured a different tripartite endosymbiont consortium: while P. leporinus carried the well-known combination 'Candidatus Karelsulcia muelleri', 'Ca. Vidania fulgoroideae', and 'Ca. Purcelliella pentastirinorum', C. wagneri harboured a yet unknown Gammaproteobacterium in addition to Karelsulcia and Vidania. This new endosymbiont 'Ca. Mirabilia symbiotica' is likely much older than Purcelliella, considering its extremely reduced genome. In both species, Karelsulcia and Vidania jointly produce the 10 essential amino acids, whereas Purcelliella and Mirabilia provide the non-essential amino acid cysteine and slightly different gene sets encoding B vitamins. Our findings confirm the functional stability of multipartite planthopper endosymbiont consortia despite changing partners over evolutionary time. In addition, we describe a new Rickettsia strain from the Meloidae group colonising P. leporinus, highlighting the diversity of bacterial endosymbionts associated with planthoppers.},
}

*Symbiosis
Animals
*Hemiptera/microbiology
Phylogeny
Genome, Bacterial
*Gammaproteobacteria/genetics/classification/isolation & purification/physiology
*Bacteria/genetics/classification/isolation & purification

@article {pmid41059924,
year = {2025},
author = {Priyam, A and Caballero Aguilar, LM and Mahmoudi, N and Barrow, CJ and Nisbet, DR and Williams, RJ},
title = {Staying one step ahead of chronic wounds by designing symbiotic, responsive functionality into dynamic nanohydrogels.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5tb01558h},
pmid = {41059924},
issn = {2050-7518},
abstract = {The dynamic environment of chronic wounds makes them an on-going clinical challenge. Conventional treatments often fail to respond to the pharmacological complexities of the system effectively, which compounded by ineffective pharmacokinetics, means a new multifactorial paradigm is required. Simple hydrogels have long been proposed to be effective wound dressings, as they can provide a highly hydrated and regenerative microenvironment; however, their colloidal instability and inefficient loading parameters may cause burst release of therapeutics and require multiple reapplications, which is both pharmacologically and economically unfavourable. Nanomaterials, on the other hand, facilitate sustained therapeutic release and are generally regarded as stable; however, to avoid off target effects, they need to be spatially defined in a controlled fashion. Here, we discuss the progress made towards engineering the activity of these nanohydrogels through developments in multicomponent materials. The goal is to meet both the wound and clinically relevant demands via the inclusion of symbiotic features across multiple length scales. We introduce critical developments enabled by this approach and discuss their potential application as therapeutic delivery agents to treat various common chronic wounds. We propose future directions to further develop nanohydrogels as function-at-demand topical wound dressings to contain chronic wounds.},
}

@article {pmid41056871,
year = {2025},
author = {Ji, K and Yu, X and Sun, B and Yang, Z and Wang, J and Zhao, Y and Qiu, T and Tang, X and Xiao, H},
title = {The short-term effects of ocean acidification on the epiphytic bacterial community of Sargassum thunbergii via high-throughput sequencing.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107531},
doi = {10.1016/j.marenvres.2025.107531},
pmid = {41056871},
issn = {1879-0291},
abstract = {Marine macroalgae and their epiphytic bacteria have established a symbiotic relationship. Although the effects of ocean acidification (OA) on macroalgae have been extensively studied, its impact on these epiphytic bacteria remains unclear. This study investigated the OA-induced shifts in the epiphytic bacterial community of Sargassum thunbergii from Qingdao's intertidal zone using 16S rDNA sequencing. The results indicated that elevated CO2 altered bacterial community structure and function, reducing diversity while maintaining dominant taxa but significantly changing their relative abundances. The abundances of Proteobacteria, Firmicutes, and Verrucomicrobiota declined, whereas Campylobacterota, Desulfobacterota, and Spirochaetota increased. The specific phyla like Cloacimonadota, Calditrichota and Entotheonellaeota also emerged. Based on the analysis of the characteristics of these altered bacterial taxa, it is speculated that these shifts were linked to the environmental adaptability and stress resistance of epiphytic bacteria as well as the metabolic activities of the host algae. Functional predictions revealed that OA primarily affected nitrogen and sulfur metabolism in the epiphytic bacterial community, with effects intensifying over time. Specifically, nitrogen fixation increased, while dark oxidation of sulfur compounds, dark sulfite oxidation, and dark sulfur oxidation decreased. These results suggest that ocean acidification may influence epiphytic bacterial communities through two potential pathways: it could induce abundance changes in bacterial taxa with varying stress resistance and adaptability, while potentially promoting shifts in bacterial taxa closely associated with host algal metabolic activities, which may ultimately lead to restructuring of the epiphytic bacterial community on S. thunbergii. These findings provided new insights into the macroalgae-epiphytic bacteria interactions under ocean acidification and provided important guidance for macroalgal cultivation.},
}

@article {pmid41056267,
year = {2025},
author = {Sadowski, VA and Sapountzis, P and Kooij, PW and Boomsma, JJ and Adams, RMM},
title = {Bacterial communities of fungus-growing ant queens are species-specific and suggest vertical transmission.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0306011},
doi = {10.1371/journal.pone.0306011},
pmid = {41056267},
issn = {1932-6203},
mesh = {Animals ; *Ants/microbiology ; Symbiosis ; Female ; Species Specificity ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Fungi/growth & development ; *Microbiota ; },
abstract = {Multipartite symbioses are inherently complex, involving dynamic ecological interactions between organisms with intertwined yet distinct evolutionary histories. The fungus-growing (attine) ants facilitate maintenance of a symbiotic species network through maternal vertical transmission of a fungal symbiont. While the gut microbiomes of fungus-growing ant species are remarkably simple, their fungus gardens support diverse microbial communities. Here, we focus on the garden pellet stored in the nest-founding queen's infrabuccal pocket-a food filter in the head that allows ants to expel large particles. The pellet is an inoculate of the new fungal garden but also contains other microbes. We used 16S rRNA gene amplicon sequencing to reconstruct the extent of vertical transmission of bacteria to new gardens via queen pellets in four sympatric fungus-growing ant species from Central Panama (Atta sexdens, Atta cephalotes, Acromyrmex echinatior, and Mycetomoellerius mikromelanos). We also characterized the bacterial communities associated with queen eggs and tissues (mesosomas, guts and ovaries) to assess whether queens are likely to transmit symbiotic bacteria, such as cuticular Actinomycetota and endosymbionts (Wolbachia, Mesoplasma, and Spiroplasma). We made within and between species comparisons, focusing on three hypotheses: (H1) Queens vertically transmit garden-associated bacteria in the garden pellet. (H2) Fungus-growing ant-associated bacteria are maintained through vertical transmission by queens. (H3) Vertically transmitted bacterial communities have host ant species-specificity. While we found mixed evidence for vertical transmission of garden bacteria, our results support maternal transmission as an important route for ant-associated symbionts. The ant species-specificity we see in queen bacterial microbiota mirrors patterns of known symbiont presence in workers from previous studies. Overall, our results suggest that vertical transmission of bacterial associates is mediated by the ant hosts, however the mechanism behind bacterial acquisition before a mating flight and dispersal is not yet understood.},
}

Animals
*Ants/microbiology
Symbiosis
Female
Species Specificity
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
*Fungi/growth & development
*Microbiota

@article {pmid41054315,
year = {2025},
author = {Ayra, L and Jiménez-Nopala, G and de la Rosa, C and Fuentes, SI and Ramírez, M and Leija, A and Hernández, G},
title = {The Common Bean miR172c microRNA, a Relevant Regulator of the N-Fixing Symbiosis, Is Activated by SPL and AGL/MADS-Domain Transcription Factors.},
journal = {Physiologia plantarum},
volume = {177},
number = {5},
pages = {e70566},
doi = {10.1111/ppl.70566},
pmid = {41054315},
issn = {1399-3054},
support = {A1-S-22570//CONAHCYT/ ; IN203722//DGAPA/UNAM/ ; IN204825//DGAPA/UNAM/ ; },
mesh = {*MicroRNAs/genetics/metabolism ; *Symbiosis/genetics ; *Phaseolus/genetics/microbiology/metabolism ; *Transcription Factors/metabolism/genetics ; Gene Expression Regulation, Plant ; *Plant Proteins/metabolism/genetics ; Promoter Regions, Genetic/genetics ; *Nitrogen Fixation/genetics ; Nicotiana/genetics ; Plant Roots/genetics/microbiology ; Plants, Genetically Modified ; },
abstract = {Nitrogen-fixing symbiosis (NFS) between rhizobia and legume plants is a complex and tightly regulated process. Modules of microRNAs (miRNAs) and their targets from different legumes, such as miR156-SPL and miR172-AP2-1, form part of complex cascades relevant for the regulation of NFS. Based on our previous analysis of the regulatory role of the common bean (Phaseolus vulgaris) miR172c-AP2-1 module, as well as in reports from other legumes about the transcriptional regulation of MIR172 in the NFS, in this work, we demonstrated that PvMIR172c is transcriptionally activated by PvSPL9 and PvFUL-like transcription factors from the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE and AGL (AGAMOUS-LIKE/MADS domain) families, respectively. Bioinformatic analysis of the PvMIR172c gene promoter revealed statistically enriched binding sites for both SPL and AGL transcription factors. The PvSPL9 and PvFUL-like genes are highly expressed in roots/nodules from inoculated plants as compared to roots from fertilized plants. Effector/reporter assays in Nicotiana benthamiana leaves transiently transformed with fluorescent reporter constructs confirmed that PvSPL9d and PvFUL-like activate PvMIR172c expression. In addition, we showed an increased level of miR172c in common bean transgenic roots and nodules overexpressing PvSPL9d or PvFUL-like, while the opposite results held in silenced transgenic tissues. These findings provide an additional understanding of the complex regulatory network controlling NFS in common bean plants.},
}

*MicroRNAs/genetics/metabolism
*Symbiosis/genetics
*Phaseolus/genetics/microbiology/metabolism
*Transcription Factors/metabolism/genetics
Gene Expression Regulation, Plant
*Plant Proteins/metabolism/genetics
Promoter Regions, Genetic/genetics
*Nitrogen Fixation/genetics
Nicotiana/genetics
Plant Roots/genetics/microbiology
Plants, Genetically Modified

@article {pmid41054270,
year = {2025},
author = {Six, DL and Hammerbacher, A and Trowbridge, A and Bullington, L},
title = {From beginning to end: the synecology of tree-killing bark beetles, fungi, and trees.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.70084},
pmid = {41054270},
issn = {1469-185X},
abstract = {Over a century of research has revealed an amazing complexity of behaviours and physiological adaptations that allow tiny bark beetles to overcome large trees, sometimes resulting in outbreaks that kill millions of trees. Turning a tree into a home and successfully raising offspring involves constant interactions among the beetles, the tree, its microbiome, and the beetles' associated microbes, all influenced by abiotic factors that can determine success or failure. While we have learned much about these systems, substantial knowledge gaps remain. This synthesis aims to clarify and integrate current understanding, identify gaps, challenge long-held assumptions, and address interpretative issues that impede progress toward a holistic understanding of these systems. We advocate for expanding perspectives using synecological approaches to understand these complex systems better. We encourage expanding research into how colonization by the bark beetle-fungi complex influences subsequent tree decay and forest carbon dynamics. An explicit goal is to provide a comprehensive resource for new researchers while encouraging them to question established hypotheses and to explore new avenues of enquiry.},
}

@article {pmid41053782,
year = {2025},
author = {Giannetti, D and Giovannini, I and Massa, E and Schifani, E and Rebecchi, L and Guidetti, R and Grasso, DA},
title = {Dispersion and new shelters offered by ants: myrmecophoresy of tardigrades.},
journal = {Frontiers in zoology},
volume = {22},
number = {1},
pages = {30},
pmid = {41053782},
issn = {1742-9994},
support = {E93C22001090001//Italian Ministry of University and Research funded by the European Union - NextGenerationEU/ ; },
abstract = {The present study investigates the potential role of ants as dispersal hosts for tardigrades and for the first time provides evidence of ant-mediated tardigrade phoresy. Tardigrades are microscopic cosmopolitan animals which have limited autonomous dispersal abilities but can withstand extreme conditions in a desiccated state. Being dominant terrestrial organisms, ants interact with many components of ecosystems, yet their role in dispersing meiofaunal organisms is unknown. In a field survey, four arboreal ant species were first analyzed to test the presence of tardigrades in their nests (i.e. tree galls), and on their bodies. In another experiment, galls were maintained isolated, then exposed to ant colonization to evaluate any transport of tardigrades by ants. Finally, the behavior of the ant Colobopsis truncata was tested by crafting an experimental apparatus to verify the actual phoresy of tardigrades. The field survey and gall colonization experiments show an association of tardigrades, especially with C. truncata. Gall colonization and laboratory experiments reveal that the ants transport tardigrades and other meiofaunal organisms, such as nematodes and rotifers. This phoresy can be direct (transporting animals) or indirect (transporting substrates with animals), over significant distances, thereby suggesting an unknown ecological interaction. Thanks to the widespread presence and abundance of ant species, this myrmecophoretic dispersion could play a crucial role in the spreading of meiofaunal organisms in terrestrial environments. These findings may represent just the 'tip of the iceberg' of an unexplored passive dispersal modality for terrestrial meiofauna micrometazoans, expanding our knowledge of phoretic relationships.},
}

@article {pmid41053368,
year = {2025},
author = {An, J and Fang, L and Cremers, W and Aleksejeva, K and Wang, Y and Li, G and Zhang, M and Huang, J and Ma, X and Cao, Q and Bisseling, T and Limpens, E},
title = {A mobile DELLA controls Medicago truncatula root cortex patterning to host arbuscular mycorrhizal fungi.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {41053368},
issn = {2055-0278},
abstract = {Cell division and specification are crucial for plant development and coping with diverse environmental cues. Most land plants rely on symbiosis with arbuscular mycorrhizal (AM) fungi to cope with soil nutrient limitations by forming arbuscules in root inner cortex cells. What determines the AM susceptibility of these inner cortex cells is currently unknown. Here we show that DELLA transcriptional regulators control the number of inner cortex cells with an AM-susceptible identity at the root stem cell niche of Medicago truncatula in a dose-dependent manner. Genetic analyses suggest that this activity converges with the well-known mobile SHORT-ROOT transcription factor regulating ground tissue development. Furthermore, we show that MtDELLA1 protein moves from the stele/endodermis to the cortex in the mature part of the root to facilitate arbuscule formation. We propose that the formation of a root inner cortex cell identity controlled by mobile DELLA and SHORT-ROOT is a fundamental basis for AM symbiosis.},
}

@article {pmid41051678,
year = {2026},
author = {Kumar, A and Li, F and Li, Q},
title = {Quantifying Arbuscular Mycorrhizal Fungal Colonization via Anthocyanin Pigmentation in Medicago truncatula Roots.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2988},
number = {},
pages = {195-205},
pmid = {41051678},
issn = {1940-6029},
mesh = {*Medicago truncatula/microbiology/metabolism/genetics ; *Mycorrhizae/physiology/growth & development ; *Anthocyanins/metabolism ; *Plant Roots/microbiology/metabolism ; Symbiosis ; Pigmentation ; Plant Proteins/genetics/metabolism ; },
abstract = {Plant responses to environmental stimuli are often shaped by a history of previous interactions, forming the foundation for stress memory and adaptive plasticity. Arbuscular mycorrhizal (AM) fungi establish a mutualistic relationship with most land plants, enhancing nutrient uptake and stress resilience, and are increasingly recognized as biological agents contributing to plant stress memory. However, quantifying AM colonization, especially in large-scale or time-course experiments investigating priming or memory effects, remains a technical bottleneck. Conventional staining methods are time-consuming, destructive, and incompatible with live imaging. This chapter presents a robust, nondestructive, and quantitative protocol to assess AM colonization in Medicago truncatula roots using a visible anthocyanin pigmentation marker. The method employs a synthetic construct expressing the R2R3 MYB transcription factor MtLAP1, driven by the AM-inducible Kunitz Protease Inhibitor 106 (KPI106) promoter, enabling visualization of arbuscule-containing root cells through purple/red pigmentation. The protocol encompasses Agrobacterium rhizogenes-mediated hairy root transformation, standardized mycorrhization assays, and anthocyanin pigment extraction and quantification. Anthocyanin accumulation correlates strongly with conventional staining-based colonization estimates, and the system enables early detection, live imaging, and high-throughput screening of mutants with altered AM phenotypes. This method offers a powerful tool for dissecting the functional role of mycorrhizal symbiosis in plant stress memory and is especially suited for forward genetic screens, stress priming experiments, and live-tracking of root-fungus interactions over time.},
}

*Medicago truncatula/microbiology/metabolism/genetics
*Mycorrhizae/physiology/growth & development
*Anthocyanins/metabolism
*Plant Roots/microbiology/metabolism
Symbiosis
Pigmentation
Plant Proteins/genetics/metabolism

@article {pmid41051369,
year = {2025},
author = {Zhou, C and Xing, S and Ma, J and Sui, M},
title = {Synergistic Piezoelectric-Nanoscale Zero-Valent Iron Catalyst for Peroxyacetic Acid Activation: A Self-Driven Advanced Oxidation Process.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08828},
pmid = {41051369},
issn = {1520-5851},
abstract = {Conventional advanced oxidation processes (AOPs) that utilize iron-based catalysts encounter several limitations, including rapid deactivation and low electron transfer efficiency. Although piezoelectric materials have shown potential for mechanochemical energy conversion, their practical application is often hindered by the need for substantial external energy inputs. This requirement results in considerable energy consumption and waste. Herein, we innovatively designed a symbiotic self-driven nZVI@BTO catalyst through dual incorporation of nZVI within the barium titanate (BTO) lattice and its surface, achieving breakthrough synergy between piezoelectric activation and peracetic acid (PAA)-mediated oxidation. The nZVI@BTO/PAA system completely degraded sulfamethoxazole (SMX) within 10 min, exhibiting 12-fold enhancement in kobs compared to the nZVI/PAA system. The hydraulic vortex-induced piezoelectric polarization of nZVI@BTO generated a surface-enhanced built-in electric field (BIEF), creating a localized reducing microenvironment. This enhanced charge carrier separation and promoted the efficient regeneration of Fe[2+], ensuring a sustained abundance of active Fe[2+] sites on the catalyst surface. Surface Fe[2+] sites enabled rapid PAA activation, generating hydroxyl radical ([•]OH), singlet oxygen ([1]O2), and acetylperoxy radical (CH3C(O)OO[•]). Our findings demonstrated the efficiency, stability (maintaining >80% SMX removal after 5 cycles), and practicality of the nZVI@BTO/PAA system for real-world applications. The nZVI@BTO/PAA system represented a sustainable strategy for AOPs, advancing the development of environmentally resilient water treatment technologies.},
}

@article {pmid41050163,
year = {2025},
author = {Ando, M and Kito, I and Rachi, T and Matsuda, T and Oshima, K},
title = {Formation of the intestinal microbiota during mouse weaning promotes maturation of the IgA repertoire after growth.},
journal = {Bioscience of microbiota, food and health},
volume = {44},
number = {4},
pages = {261-271},
pmid = {41050163},
issn = {2186-6953},
abstract = {Secretory IgA (sIgA) is a class of antibodies that plays a pivotal role in mucosal immunity. The sIgA secreted into the intestinal tract acts to prevent luminal pathogens and food antigens from penetrating across the intestinal epithelial barrier, thereby contributing to the suppression of infections and food allergies. Furthermore, it binds extensively to symbiotic bacteria, exerting a significant impact on the gut microbiota. The antigen recognition specificity of antibodies is determined by the amino acid sequence of the variable region. Therefore, the type of IgA repertoire influences the formation and maintenance of the gut microbiota and susceptibility to infection and food allergy. The initial repertoire of IgA is induced by the extensive colonization of intestinal bacteria during the weaning period and is maintained for an extended period. However, the relationship between the initial gut microbiota and IgA repertoire development has yet to be fully analyzed. In the present study, the weaning gut microbiota was disrupted with antibiotics, and the IgA repertoire was subsequently analyzed in young adulthood. The administration of antibiotics during the weaning period resulted in the suppression of somatic hypermutation in the variable regions of IgA expressed in the small intestine, as well as an impact on multivalent reactivity in IgA during early childhood. Additionally, disturbances in the weaning gut microbiota led to alterations in the microbiota structure of adolescent mice. These findings suggest that the weaning gut microbiota plays a role in promoting the maturation of IgA function.},
}

@article {pmid41049555,
year = {2025},
author = {Lee, MH and Morris, RA and Phillips, R and Rio, RVM},
title = {mir-31 mediated control of bacteriome size in tsetse flies.},
journal = {Current research in insect science},
volume = {8},
number = {},
pages = {100117},
pmid = {41049555},
issn = {2666-5158},
abstract = {Tsetse flies are the primary vectors of African trypanosomes, which are transmitted through blood feeding. To supplement this nutritionally limited diet, tsetse evolved an obligate mutualism with the bacterium Wigglesworthia glossinidia, housed within a specialized organ called the bacteriome. While the functional contributions of this symbiosis towards tsetse fitness have been studied, host morphological changes that accommodate this relationship remain less understood. In pregnant flies, variable expression of microRNAs (miRNAs) regulates protein expression, but the specific impacts are unknown. During pregnancy, high expression of fatty acyl-CoA reductase (far) within the bacteriome is indirectly correlated with miR-31 abundance and coincides with bacteriome size increase. We explored the roles of far and miR-31 towards this morphological change. Although RNAi effectively reduced far expression, bacteriome size still increased, suggesting its expansion is independent of far. In contrast, disrupting miR-31 activity resulted in significantly enlarged bacteriomes in virgin flies, resembling those of mated females. These results suggest that gene(s) other than far are regulated by miR-31 and may contribute to bacteriome remodeling during pregnancy, potentially to meet increased symbiosis demands. Ultimately, disrupting this obligate mutualism may present a promising target for future vector control strategies.},
}

@article {pmid41049204,
year = {2025},
author = {Wang, L and Du, X and Liu, J and Zhang, J and Lv, S},
title = {Effects of grazing on plant functional groups across spatial scales in Stipa breviflora desert steppe.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1643655},
pmid = {41049204},
issn = {1664-462X},
abstract = {This study investigated the Stipa breviflora desert steppe through multi-scale (50m×50m, 25m×25m, 2.5m×2.5m) and grazing intensity (no grazing vs. heavy grazing) comparative analyses, revealing the response mechanisms of plant functional group diversity, interspecific associations, and stability. Key findings include: (1) Heavy grazing significantly reduced functional group diversity and evenness, while the Margalef richness index increased at the 25m×25m scale due to patchy invasion of grazing-tolerant species. (2) Interspecific associations exhibited scale-dependent patterns: Large-scale (50m×50m) associations were driven by environmental heterogeneity (e.g., resource competition and complementarity), whereas small-scale (2.5m×2.5m) interactions were dominated by direct species interactions (mutualism or exclusion). (3) Grazing-induced structural simplification through "environmental filtering", heavy grazing reduced functional group quantity, forming simplified symbiotic networks (PC≥0.6) between perennial grasses and annual/biennial plants, while significantly suppressing woody plants and forbs (Perennial forbs, Shrubs and semi-shrubs). (4) Stability analysis demonstrated higher stability of perennial grasses and forbs in ungrazed areas, though the overall system remained unstable. Annual/biennial plants and shrubs/semi-shrubs generally exhibited low disturbance resistance. The study proposes a multi-scale grassland restoration strategy: optimizing resource allocation at large scales while enhancing key species interactions at small scales. These findings provide theoretical foundations for the ecological restoration of degraded desert steppes and adaptive grazing regimes. Future research should integrate climate change and socioeconomic factors to develop more resilient grassland ecosystem management frameworks.},
}

@article {pmid41047046,
year = {2025},
author = {Cho, M and Choi, E and Lee, SJ and Choi, S and Kim, I and Shin, D and Kim, W and Hur, JS and Kim, JH and Rhee, JS and Park, H},
title = {Whole-genome sequence of the lichen-forming fungus Cetrariella delisei reveals an expanded repertoire of biosynthetic gene clusters.},
journal = {Genomics},
volume = {},
number = {},
pages = {111131},
doi = {10.1016/j.ygeno.2025.111131},
pmid = {41047046},
issn = {1089-8646},
abstract = {Lichens represent a distinctive symbiotic relationship between fungi and photosynthetic algae, allowing them to persist in harsh and extreme habitats. While known for their adaptability, the genomic features of lichen-forming fungi remain relatively understudied. In this study, the genome of the lichen-forming fungus Cetrariella delisei was assembled into 40 contigs, spanning 45.8 Mbp, with a BUSCO completeness of 96.7 %. Repetitive sequences comprised 18.14 % of the genome. A total of 11,716 genes were annotated, including 401 putative carbohydrate-active enzymes (CAZymes), though polysaccharide lyases were absent. Comparative analysis with five additional Parmeliaceae species showed that C. delisei contains a markedly higher number of auxiliary activity genes. Notably, C. delisei harbors 79 biosynthetic gene clusters (BGCs), exceeding the 50 to 65 clusters typically observed in related species, reflecting an expanded biosynthetic repertoire potentially underlying enhanced natural product diversity. These results improve our understanding of lichen symbiosis and provide a valuable genomic resource for future research.},
}

@article {pmid41046273,
year = {2025},
author = {Ding, Q and Tian, XY and Wu, WS and Yu, FJ and Shao, ZQ and Zeng, Z},
title = {The metabolic landscape of tomato roots during arbuscular mycorrhizal symbiosis reveals lipid-related metabolic rewiring.},
journal = {Plant cell reports},
volume = {44},
number = {10},
pages = {230},
pmid = {41046273},
issn = {1432-203X},
support = {32400186//National Natural Science Foundation of China/ ; 32270241//National Natural Science Foundation of China/ ; GZB20230303//Postdoctoral Fellowship Program of CPSF/ ; 2023ZB796//Jiangsu Excellent Postdoctoral Funding/ ; },
mesh = {*Mycorrhizae/physiology ; *Symbiosis/physiology ; *Solanum lycopersicum/metabolism/microbiology/genetics ; *Plant Roots/metabolism/microbiology ; *Lipid Metabolism ; Gene Expression Regulation, Plant ; },
abstract = {This study reveals lipid-related metabolic rewiring in tomato roots during arbuscular mycorrhizal symbiosis, identifying potential candidate lipids for fungal carbon transfer and signaling. Arbuscular mycorrhizal (AM) symbiosis induces substantial metabolic rearrangement in host plants to facilitate nutrient exchange and symbiotic efficiency. While previous metabolomic studies have characterized metabolite shifts in AM symbiosis, the lipid-related metabolic rewiring underlying nutrient exchange in host plant roots remains poorly resolved. Here, we investigated the metabolic response in tomato roots colonized by AM fungi. A total of 219 differentially accumulated metabolites (DAMs) were identified by the ultra-high-performance liquid chromatography-tandem mass spectrometry analysis, with lipids and lipid-like molecules representing the predominant classes. The most significantly upregulated metabolite was 2-(14,15-epoxyeicosatrienoyl) glycerol, a 2-monoacylglycerols (2-MAGs) mapped to arachidonic acid metabolism. This compound represents a C20-based epoxy fatty acid-derived 2-MAG, distinct from the C16:0 2-MAG induced by AM symbiosis in legumes, thereby implying the possibility of transferring diverse lipid substrates from different host plants to AM fungi. Concurrently, enhanced accumulation of dihomo-γ-linolenic acid (DGLA) and arachidonic acid (ARA) in AM fungi colonized roots underscored alterations of arachidonic acid metabolism and unsaturated fatty acid pathway. Gene set enrichment analysis based on the transcriptome data revealed significant transition of the glycerophospholipid metabolism pathway, primarily driven by multiple lysophosphatidylcholine (LPC) species that showed significant upregulation. Integrated transcriptomic and metabolomic analysis identified 31 overlapping KEGG pathways, emphasizing the importance of lipid and amino acid metabolism. In summary, our integrated analysis demonstrates that lipid-related metabolic reprogramming, represented by the induction of 2-MAGs and LPCs, is a feature of AM symbiosis that enables cross-kingdom nutrient exchange and host metabolic adaptation.},
}

*Mycorrhizae/physiology
*Symbiosis/physiology
*Solanum lycopersicum/metabolism/microbiology/genetics
*Plant Roots/metabolism/microbiology
*Lipid Metabolism
Gene Expression Regulation, Plant

@article {pmid41045972,
year = {2025},
author = {Song, X and Meng, H and Yang, T and Li, Y and Zheng, F and Yan, X},
title = {Female accessory reproductive glands of Paederus fuscipes serve as a reservoir of symbiotic pederin-producing bacteria.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104408},
doi = {10.1016/j.ibmb.2025.104408},
pmid = {41045972},
issn = {1879-0240},
abstract = {Paederus fuscipes, an ecologically and medically important species, is known for its blistering toxin pederin in hemolymph. Evidence demonstrates that the toxin is synthesized by the uncultured symbiotic pederin-producing bacteria (PPB) in P. fuscipes, but the biological characteristics of PPB within the beetle host remain poorly characterized. Here, we investigated PPB abundance variations in P. fuscipes across different factors (sexes, life stages, habitats, and organs), along with their colonization sites and metabolic potentials. The findings revealed that the PPB abundance in female P. fuscipes at the level of individuals and tissues exhibited stable colonization patterns, independent of habitat and time changes. Notably, PPB dominated the bacterial community in females (relative abundance ≥ 66.08%) and nearly occupied reproductive organs (relative abundance ≥ 96.31%). Moreover, our results indicated that PPB were predominantly enriched in the accessory glands of female reproductive organs, which could serve as a reservoir for PPB proliferation. Although PPB were not cultured in this study, metagenomic binning yielded the draft genome of PPB (CheckM completeness = 85.14%, contamination = 0), in which genes related to pederin biosynthesis were identified. Phylogenetic analyses revealed that PPB formed a sister clade to Pseudomonas aeruginosa rather than nesting within the P. aeruginosa lineage. Metabolic module prediction analysis revealed specific deficiencies in PPB's energy metabolism and amino acid biosynthesis pathways, suggesting limited free-living potential for PPB. Collectively, this study provides insights into PPB biological characteristics within their beetle host and paves the way for biotechnological exploitation related to pederin production.},
}

@article {pmid41045963,
year = {2025},
author = {Lu, S and Miao, Y and Wang, D and Xu, D and Liu, R and Liu, X and Zhang, Y and Zhang, X and Qin, H},
title = {Engineered tumor-symbiotic bacterial membrane nanovesicles enable precise immuno-chemotherapy of colorectal cancer.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114291},
doi = {10.1016/j.jconrel.2025.114291},
pmid = {41045963},
issn = {1873-4995},
abstract = {Gut microorganisms show promising therapeutic effects and drug delivery potential for colorectal cancer (CRC) treatment, but are limited by their insufficient targeting ability and side effects. Fusobacterium nucleatum (Fn) is a key symbiotic bacterium in CRC, which can preferentially accumulate in tumor tissues and invade tumor cells, while its tumorigenicity restricts the application in drug delivery. Herein, we engineered Fn with anchored PD-L1 antibody (αPD-L1), and then isolated the Fn membranes to construct bacterial membrane nanovesicles (ab-FMNVs) for precise delivery of chemotherapeutic drugs. The ab-FMNVs exploited Fn's inherent tumor colonization capabilities to achieve tumor-targeted delivery through the specific membrane protein FadA-mediated pathway, and modulated the PD-L1 immune checkpoint pathway for tumor immunotherapy. Simultaneously, ab-FMNVs were internalized into CT26 cells to release the chemotherapeutic agent doxorubicin, synergistically inhibiting tumor cell proliferation and metastasis. In a CRC-bearing mouse model, doxorubicin-loaded ab-FMNVs increased tumor accumulation and demonstrated superior antitumor efficacy against both primary and recurrent CRC progression without inducing any side effects. This innovative approach holds promise for precision cancer therapies by harnessing the symbiotic relationship between bacteria and CRC.},
}

@article {pmid41045882,
year = {2025},
author = {Hao, J and Shah, NS and Zhou, B},
title = {S[2]CAC: Semi-supervised coronary artery calcium segmentation via scoring-driven consistency and negative sample boosting.},
journal = {Medical image analysis},
volume = {107},
number = {Pt A},
pages = {103823},
doi = {10.1016/j.media.2025.103823},
pmid = {41045882},
issn = {1361-8423},
abstract = {Coronary artery calcium (CAC) scoring plays a pivotal role in assessing the risk for cardiovascular disease events to guide the intensity of cardiovascular disease preventive efforts. Accurate CAC scoring from gated cardiac Computed Tomography (CT) relies on precise segmentation of calcification. However, the small size, irregular shape, and sparse distribution of calcification in 3D volumes present significant challenges for automated CAC assessment. Training reliable automatic segmentation models typically requires large-scale annotated datasets, yet the annotation process is resource-intensive, requiring highly trained specialists. To address this limitation, we propose S[2]CAC, a semi-supervised learning framework for CAC segmentation that achieves robust performance with minimal labeled data. First, we design a dual-path hybrid transformer architecture that jointly optimizes pixel-level segmentation and volume-level scoring through feature symbiosis, minimizing the information loss caused by down-sampling operations and enhancing the model's ability to preserve fine-grained calcification details. Second, we introduce a scoring-driven consistency mechanism that aligns pixel-level segmentation with volume-level CAC scores through differentiable score estimation, effectively leveraging unlabeled data. Third, we address the challenge of incorporating negative samples (cases without CAC) into training. Directly using these samples risks model collapse, as the sparse nature of CAC regions may lead the model to predict all-zero maps. To mitigate this, we design a dynamic weighted loss function that integrates negative samples into the training process while preserving the model's sensitivity to calcification. This approach effectively reduces over-segmentation and enhances overall model performance. We validate our framework on two public non-contrast gated CT datasets, achieving state-of-the-art performance over previous baseline methods. Additionally, the Agatston scores derived from our segmentation maps demonstrate strong concordance with manual annotations. These results highlight the potential of our approach to reduce dependence on annotated data while maintaining high accuracy in CAC scoring. Code and trained model weights are available at: https://github.com/JinkuiH/S2CAC.},
}

@article {pmid41045547,
year = {2025},
author = {Yang, X and Li, Y and Wang, T and Li, Z and Zhuang, Q and Liang, C and Wang, X and Tian, J},
title = {GmSPX5 regulates arbuscular mycorrhizal colonization and phosphate acquisition through modifying transcription profile and microbiome in soybean.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {1},
pages = {e70511},
doi = {10.1111/tpj.70511},
pmid = {41045547},
issn = {1365-313X},
support = {2021YFF1000500//National Key Research and Development Program of China/ ; 2024A1515013054//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZD04072//STI 2030-Major Project/ ; 2022B0202060005//Key Areas Research and Development Programs of Guangdong Province/ ; 2022SDZG07//the Open Competition Program of Ten Major Directions of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province/ ; 32172658//National Natural Science Foundation of China/ ; 32172659//National Natural Science Foundation of China/ ; 32302662//National Natural Science Foundation of China/ ; },
mesh = {*Glycine max/microbiology/genetics/metabolism ; *Mycorrhizae/physiology ; *Phosphates/metabolism ; Symbiosis ; *Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Gene Expression Regulation, Plant ; Plant Roots/microbiology/metabolism ; *Microbiota/genetics ; },
abstract = {Symbiosis with arbuscular mycorrhizal (AM) fungi is a crucial strategy for plant adaptation to low phosphorus (P) stress. However, the mechanisms underlying how phosphate (Pi) signaling regulators participate in AM colonization remain largely unknown in soybean (Glycine max). In this study, the expression of GmSPX5, one member of the SPX (SYG1/Pho81/XPR1) family, was induced by AM fungal inoculation in soybean roots. Furthermore, the expression of GmSPX5 seems to overlap with AM infection structures through analyzing GUS activity of transgenic soybean plants harboring ProGmSPX5:GUS. Four transgenic lines with GmSPX5 overexpression (OX8 and OX12) and suppression (Ri9 and Ri11) were subsequently used to examine the functions of GmSPX5 on AM symbiosis and Pi acquisition. Despite no difference between Ri and wild-type (WT), the overexpression of GmSPX5 significantly increased AM colonization as reflected by 8.4% in OX8 and 8.7% in OX12, respectively. Consistently, the dry weight and total P content of OX8 and OX12 were higher than WT. Furthermore, a total of 3483 genes were found to exhibit differential expression patterns in roots between OX12 and WT, including genes related to linolenic acid metabolism and flavonoid metabolism. Meanwhile, the composition of the bacterial community in the roots of OX12 was distinct from that in WT through β-diversity analysis. Particularly, an ASV19 (Sphingomonadales) was enriched in OX12 roots, which was positively related to total P content and AM fungi colonization. Taken together, these results highlight that GmSPX5 can regulate AM symbiosis, as well as Pi acquisition in soybean. Our findings advance the understanding of SPX functions in plant-microbe interaction.},
}

*Glycine max/microbiology/genetics/metabolism
*Mycorrhizae/physiology
*Phosphates/metabolism
Symbiosis
*Plant Proteins/genetics/metabolism
Plants, Genetically Modified
Gene Expression Regulation, Plant
Plant Roots/microbiology/metabolism
*Microbiota/genetics

@article {pmid41044905,
year = {2025},
author = {Zhang, W and Cheng, H and Yan, X and Suo, B and Wen, S and Liu, W and Wei, G and Chen, J},
title = {H2S-Mediated GH3.1 Persulfidation Regulates IAA Homeostasis to Enhance Nodulation Formation and Nitrogen Fixation in Robinia pseudoacacia.},
journal = {Molecular plant pathology},
volume = {26},
number = {10},
pages = {e70145},
doi = {10.1111/mpp.70145},
pmid = {41044905},
issn = {1364-3703},
support = {42477370//National Natural Science Foundation of China (NSFC)/ ; 2023yfd1900502//National Key Research and Development Program of China/ ; },
mesh = {*Nitrogen Fixation/drug effects/physiology ; *Indoleacetic Acids/metabolism ; Homeostasis/drug effects ; *Robinia/metabolism/drug effects/microbiology/genetics ; *Hydrogen Sulfide/pharmacology/metabolism ; *Plant Proteins/metabolism/genetics ; *Plant Root Nodulation/drug effects/physiology ; Gene Expression Regulation, Plant/drug effects ; },
abstract = {Hydrogen sulphide (H2S), a gaseous signalling molecule, plays a multifaceted role in plant physiology by enhancing adaptability to environmental stresses. However, the regulatory mechanism of symbiotic nitrogen (N) fixation by H2S in indeterminate nodules of woody legumes remains unclear. In this study, we investigated the mechanism by which H2S promotes nodulation and N fixation in the woody legume Robinia pseudoacacia. Exogenous H2S significantly enhanced rhizobium infection, nodule formation and nitrogenase activity, demonstrating its positive role in the symbiotic process. Transcriptomic analysis of roots and nodules revealed that H2S signalling modulates auxin metabolism, particularly through the regulation of indole-3-acetic acid (IAA) homeostasis. H2S was found to promote free IAA accumulation and reduce IAA conjugation (IAA-Asp and IAA-Glu). Further investigation revealed that H2S directly targets GH3.1, a key IAA-amido synthetase responsible for IAA conjugation. Specifically, H2S mediated persulfidation at Cys304 of GH3.1, inhibiting its enzymatic activity and preventing IAA inactivation. This modification was confirmed by LC-MS/MS, UPLC-ESI-MS/MS and site-directed mutagenesis. This post-translational modification maintained active IAA levels, facilitating early nodule development. These findings highlight the active role of H2S in regulating IAA homeostasis, thereby enhancing indeterminate nodule formation and N fixation through persulfidation of the Cys304 residue of GH3.1 in R. pseudoacacia.},
}

*Nitrogen Fixation/drug effects/physiology
*Indoleacetic Acids/metabolism
Homeostasis/drug effects
*Robinia/metabolism/drug effects/microbiology/genetics
*Hydrogen Sulfide/pharmacology/metabolism
*Plant Proteins/metabolism/genetics
*Plant Root Nodulation/drug effects/physiology
Gene Expression Regulation, Plant/drug effects

@article {pmid41044678,
year = {2025},
author = {Ren, C and Meng, Y and Liu, Y and Wang, Y and Wang, H and Liu, Y and Liu, C and Fan, X and Zhang, S},
title = {Probiotic Bacillus subtilis enhances silkworm (Bombyx mori) growth performance and silk production via modulating gut microbiota and amino acid metabolism.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {103},
pmid = {41044678},
issn = {2524-4671},
support = {No. SDAIT-18//Modern Agricultural Technology System of Shandong Province/ ; No. CARS-18//China Agriculture Research System of MOF and MARA/ ; },
abstract = {BACKGROUND: Artificial diet-reared silkworms (Bombyx mori) exhibit reduced gut microbial diversity and impaired growth performance compared to mulberry-fed counterparts. While Bacillus subtilis is widely used as a probiotic in livestock and aquaculture, its impact on silkworms remains unexplored. This study investigates whether dietary supplementation with B. subtilis enhances larval development and elucidates the underlying mechanisms involving gut microbiota and metabolic pathways.

RESULTS: Supplementing artificial diets with B. subtilis (6 × 10[5] CFU/g) significantly increased larval body weight by 9.1-22.1% during instar stages and improved feed utilization efficiency (FUE) by 4.09%-6.80% compared to controls. Cocoon quality metrics, including cocoon shell weight (+ 9.77% in females) and cocoon shell ratio (+ 6.56%), also improved. Mechanistically, B. subtilis did not colonize the midgut but transiently modulated gut physiology: it elevated midgut fluid pH and enhanced α-amylase, trypsin, and lipase activities. 16 S rRNA sequencing revealed reduced gut microbial diversity (Shannon index, P < 0.01) and shifts in community structure, with decreased abundances of potential pathogens (e.g., Pseudomonas) and commensals (e.g., Lactobacillus). Targeted metabolomics identified a 3.1-fold increase in phenylalanine levels in hemolymph, linked to upregulated aromatic amino acid metabolism pathways (KEGG). Dietary phenylalanine supplementation (0.4%) replicated B. subtilis-induced growth promotion, confirming its pivotal role in host-microbe interactions.

CONCLUSIONS: B. subtilis enhances silkworm growth and silk production through multi-faceted mechanisms: reshaping gut microbiota composition, improving digestive enzyme activity, and elevating phenylalanine biosynthesis. These findings establish B. subtilis as a promising probiotic for optimizing artificial diet systems in Lepidoptera and highlight the central role of amino acid metabolism in insect-microbiome symbiosis.},
}

@article {pmid41042365,
year = {2025},
author = {Bernal-Castro, C and Camargo-Herrera, Á and Gutiérrez-Cortés, C and Díaz-Moreno, C},
title = {Probiotic and Technological Potential of Native Lactic Acid Bacteria Strains from High Andean Forest Bee Bread: In Vitro Study.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {80},
number = {4},
pages = {163},
pmid = {41042365},
issn = {1573-9104},
mesh = {*Probiotics ; *Bread/microbiology ; Animals ; Bees ; *Lactobacillales/isolation & purification/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Pollen ; *Pediococcus pentosaceus/isolation & purification/growth & development/genetics ; *Pediococcus/isolation & purification/genetics/growth & development ; Functional Food ; Hydrogen-Ion Concentration ; Bile Acids and Salts ; },
abstract = {Bioprospecting of lactic acid bacteria with probiotic potential from apicultural products is an important key for the research in functional foods. The in vitro evaluation of the probiotic and technological potential of commercial HOWARU strains and native strains isolated from bee bread was conducted in this study. The strains were molecularly identified (16S rRNA sequencing), revealing differences between molecular characterization and the microorganisms described in the technical datasheet. Most native strains belong to the genus Pediococcus. The ability to resist simulated gastrointestinal conditions (acidic pH and bile salts), as well as tolerance to extreme conditions (high temperature and osmotic pressure), was determined. VEGE 092 culture showed survival levels above 80%, and Pediococcus pentosaceus exceeded 95%. Finally, growth on alternative substrates (by-product of supercritical fluid extraction of bee pollen, car-rot waste flour, and turmeric flour) was evaluate by the quantitative prebiotic index. This study demonstrated that the best symbiotic combination was VEGE 092 and turmeric (prebiotic index = 0.96), and P. pentosaceus with the pollen extraction by-product, demonstrating a strain-substrate relationship. This study highlights the potential use of these strains in functional food applications, emphasizing their resilience and ability to thrive in various substrates.},
}

*Probiotics
*Bread/microbiology
Animals
Bees
*Lactobacillales/isolation & purification/genetics/physiology
RNA, Ribosomal, 16S/genetics
Pollen
*Pediococcus pentosaceus/isolation & purification/growth & development/genetics
*Pediococcus/isolation & purification/genetics/growth & development
Functional Food
Hydrogen-Ion Concentration
Bile Acids and Salts

@article {pmid41042234,
year = {2025},
author = {Sathe, S and Becks, L},
title = {Reciprocal effects of programmed cell death on fitness in unicellular endosymbiotic Chlorella and its ciliate host.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf119},
pmid = {41042234},
issn = {1420-9101},
abstract = {Programmed cell death (PCD), the genetically controlled active cellular suicide mechanism in multicellular organisms, also exists in unicellular organisms. However, explaining the evolution of PCD by natural selection in these organisms remains a challenge. PCD likely emerged during early endosymbiotic events as an initial antagonistic adaptation, enabling unicellular parasitic proto-endosymbionts to exploit their hosts, for example, by triggering host death in response to nutrient depletion or releasing offspring. Over time, during endosymbiont domestication and, as proposed, through horizontal gene transfer from endosymbionts to the host, PCD evolved in the host, providing benefits to both the host and the endosymbionts. However, the underlying assumption of this hypothesis, that PCD benefits and non-PCD (necrosis) harms the endosymbionts and/or the host, remains untested. Here, we investigated the fitness consequences of heat-shock-induced PCD in the endosymbiotic chlorophyte Chlorella variabilis and its facultative symbiotic ciliate host Paramecium bursaria, the non-symbiotic C. sorokiniana, and the predatory host P. duboscqui. Heat-shock triggered PCD in C. variabilis and the two ciliate species, causing significant fitness consequences. The supernatant from C. variabilis PCD enhanced the growth of its own clones and endosymbiotic host while inhibiting the growth of the predatory host. The supernatants from necrotic C. variabilis reduced growth of both Chlorella and Paramecium. Similarly, PCD in the symbiotic Paramecium host benefited Chlorella, whereas PCD and necrosis in the predatory Paramecium host were detrimental. These results expand the understanding of unicellular PCD, highlighting its dual role in benefiting clonal populations and their specific endosymbiotic partners, thereby affecting endosymbiosis evolution.},
}

@article {pmid41041976,
year = {2025},
author = {Breusing, C and Hauer, MA and Hughes, IV and Becker, JS and Casagrande, D and Phillips, BT and Girguis, PR and Beinart, RA},
title = {Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70126},
doi = {10.1111/mec.70126},
pmid = {41041976},
issn = {1365-294X},
support = {//Schmidt Ocean Institute/ ; EPSCoR Cooperative Agreement OIA-#1655221//National Science Foundation/ ; OCE-0732369//Division of Ocean Sciences/ ; OCE-1536331//Division of Ocean Sciences/ ; OCE-1736932//Division of Ocean Sciences/ ; 1747454//National Science Foundation Graduate Research Fellowship Program/ ; //Argonne National Laboratory/ ; },
abstract = {Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.},
}

@article {pmid41040871,
year = {2025},
author = {Zeng, L and Qian, Y and Cui, X and Zhao, J and Ning, Z and Cha, J and Wang, K and Ge, C and Jia, J and Dou, T and Chen, H and Liu, L and Bao, Z and Jian, Z},
title = {Immunomodulatory role of gut microbial metabolites: mechanistic insights and therapeutic frontiers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675065},
pmid = {41040871},
issn = {1664-302X},
abstract = {The gut microbiota modulates host immunity through a wide array of metabolic products that function as signaling molecules, thereby linking microbial activity with both mucosal and systemic immune responses. Notably, short-chain fatty acids, secondary bile acids, tryptophan-derived indoles, polyamines, and lipid derivatives play pivotal roles in regulating innate and adaptive immune functions via G protein-coupled receptors, nuclear receptors, and epigenetic pathways. These metabolites modulate immune cell differentiation, epithelial barrier integrity, and the resolution of inflammation in a dose- and site-specific manner. Recent advancements in spatial metabolomics, synthetic biology, and nanomedicine have facilitated the spatiotemporal delivery of these immunomodulatory compounds, revealing novel therapeutic avenues for the treatment of inflammatory and autoimmune disorders. This review summarizes the biosynthesis and immunoregulatory functions of key microbial metabolites, highlights the compartmentalized and systemic mechanisms of action, and discusses emerging therapeutic approaches, including postbiotics, engineered probiotics, and receptor-targeting drugs. We also explore the challenges in achieving personalized microbiome-immune modulation and propose future directions integrating multiomics and AI-driven predictive modeling. Understanding the metabolite-immune axis paves the way for novel interventions targeting host-microbe symbiosis.},
}

@article {pmid41040407,
year = {2025},
author = {Tan, CH and Schwartz, HT and Rodak, NY and Sternberg, PW},
title = {Evolution of parasitism-related traits in nematodes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.26.678730},
pmid = {41040407},
issn = {2692-8205},
abstract = {UNLABELLED: The abundant resources provided by the host provide an evolutionary rationale for parasitism and drive the metabolic and developmental divergence of parasitic and free-living animals. Two evolutionally distant nematode genera, Steinernema and Heterorhabditis , independently evolved an entomopathogenic lifestyle, in which they invade insects and kill them with the assistance of specifically associated symbiotic pathogenic bacteria. It had been generally assumed that the worm, being a bacterivore, feeds on its symbiotic bacteria, which rapidly reproduce while consuming the insect host. The evolutionary adaptations of entomopathogenic nematodes to a parasitic lifestyle developmentally, and the symbiotic relationships of entomopathogenicity, remain largely unknown. We developed an axenic culture medium that allows for robust and sustained growth of Steinernema hermaphroditum , allowing finite control of nutrients available to the nematodes. We found that, uniquely among nematodes tested, the hatchlings of S. hermaphroditum cannot endure in a nutrient-poor environment; this ability is impaired but still present in Heterorhabditis bacteriophora . Similarly, the ability to forage for food is completely lost in H. bacteriophora hatchlings and severely compromised in S. hermaphroditum . We reasoned that these traits were lost because they are unnecessary to obligate parasites that always hatch in a resource-rich host. We further found that Steinernema and, to a limited extent, Heterorhabditis nematodes can successfully invade, develop, and reproduce inside a living insect host independent of their symbiotic bacteria, apparently feeding on the hemolymph, and emerge carrying bacteria found within, explaining the evolutionary origins of entomopathogenic nematodes.

HIGHLIGHTS: A simple but robust axenic culturing method for the emerging model nematode Steinernema hermaphroditum and other invertebrate parasitic nematodes. Convergent evolution led to the loss of hatchling survival traits in entomopathogenic nematodes.Nematode adaptation to parasitism is associated with changes in modes of feeding.Entomopathogenic nematodes evolved from parasitoid ancestors.},
}

@article {pmid41040397,
year = {2025},
author = {Sankari, S and Arnold, MF and Babu, VMP and Deutsch, M and Walker, GC},
title = {Exploiting Peptide Chirality and Transport to Dissect the Complex Mechanism of Action of Host Peptides on Bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.24.678446},
pmid = {41040397},
issn = {2692-8205},
abstract = {UNLABELLED: Elucidation of the complex mechanisms of action of antimicrobial peptides (AMPs) is critical for improving their efficacy. A major challenge in AMP research is distinguishing AMP effects resulting from various protein interactions from those caused by membrane disruption. Moreover, since AMPs often act in multiple cellular compartments, it is challenging to pinpoint where their distinct activities occur. Nodule-specific cysteine-rich (NCR) peptides secreted by legumes, including NCR247, have evolved from AMPs to regulate differentiation of their nitrogen-fixing bacterial partner during symbiosis as well as to exert antimicrobial actions. At sub-lethal concentrations, NCR247 exhibits strikingly pleiotropic effects on Sinorhizobium meliloti . We used the L- and D-enantiomeric forms of NCR247 to distinguish between phenotypes resulting from stereospecific, protein-targeted interactions and those caused by achiral interactions such as membrane disruption. In addition, we utilized an S. meliloti strain lacking BacA, the transporter that imports NCR peptides into the cytoplasm. BacA plays critical symbiotic roles by reducing periplasmic peptide accumulation and fine-tuning symbiotic signaling. Use of the BacA-deficient strain made it possible to distinguish between phenotypes resulting from peptide interactions in the periplasm and those occurring in the cytoplasm. At high concentrations, both L- and D-NCR247 permeabilize bacterial membranes, consistent with nonspecific cationic AMP activity. In the cytoplasm, both NCR247 enantiomers sequester heme and trigger iron starvation in an achiral but BacA-dependent manner. However, only L-NCR247 activates bacterial two-component systems via stereospecific periplasmic interactions. By combining stereochemistry and genetics, this work disentangles the spatial and molecular complexity of NCR247 action. This approach provides critical mechanistic insights into how host peptides with pleiotropic functions modulate bacterial physiology.

AUTHOR SUMMARY: Many organisms produce antimicrobial peptides (AMPs) to fight infections, but legumes have uniquely co-opted these molecules to control their symbiotic partners. During symbiosis between Medicago truncatula and Sinorhizobium meliloti , the plant secreted Nodule-specific Cysteine-Rich (NCR) peptides, transforms free-living bacteria into differentiated bacteroids that fix nitrogen but cannot reproduce outside the host. One such peptide, NCR247, exerts pleiotropic effects on the bacteria, acting on different subcellular locations, including membrane, heme, and proteins. Using a mirror-image (D-form) peptide, we disentangled peptide effects arising from generic physiochemical interactions versus stereospecific binding. The inner membrane protein BacA is known to play a protective role by importing NCR peptides into the cytoplasm. Using a bacterium lacking BacA, we were able to distinguish the effects of the peptide within and outside the cytoplasm. It was thought that BacA safeguards symbiotic bacteria by internalizing NCR peptides, thereby limiting their toxic membrane lytic effects, yet this has not been demonstrated. We show that BacA prevents lethal overstimulation of signaling pathways in the periplasm by internalizing the peptides. Our methods provide a framework for testing mechanism of action of new peptide-based antibiotics to combat multidrug-resistant bacteria.},
}

@article {pmid41040118,
year = {2025},
author = {Bonnette, H and Savitt, LR},
title = {Optimizing Colorectal Surgery Outcomes: The Role of the Advanced Practice Provider (APP) in Developing a Center for Pelvic Floor Disorders and Maximizing Scope of Practice for APPs.},
journal = {Clinics in colon and rectal surgery},
volume = {38},
number = {6},
pages = {411-416},
pmid = {41040118},
issn = {1531-0043},
abstract = {Many patients with pelvic floor disorders who are referred to colorectal surgery do not actually need surgery. The Massachusetts General Hospital (MGH) Center for Pelvic Floor Disorders (PFDC) was established in 2008 out of a recognition of the need for a specialized comprehensive treatment for patients living with a pelvic floor disorder. To describe the model that we have created utilizing advanced practice providers (APPs) within the PFDC at the MGH as an example of a model of care for patients who historically may have been managed by colorectal surgeons. The utilization of APPs in surgery has increased, which in turn has had positive effects on patient care and can help reduce the demands put on surgeons to see patients who ultimately do not end up having surgery. There is also a potential for both direct and indirect revenue production through the utilization of APPs at the top of their scope of practice as well as increased access to care for these patients. Training APPs to work at the top of their scope within a surgical practice increases patient's access to care, allows surgeons to focus on those who ultimately require surgery, and can lead to better patient outcomes at a reduced healthcare cost. In order for this symbiotic relationship between APPs and surgeons to be successful, it is essential that there is mutual collaboration and trust between providers. It requires commitment from surgeons to appropriately train their APPs.},
}

@article {pmid41039684,
year = {2025},
author = {Xu, N and Yang, X and Li, C and Zhang, C and Guo, M},
title = {Identification and functional characterization of chemoreceptors for phenolic acids in Agrobacterium tumefaciens.},
journal = {Microbiological research},
volume = {302},
number = {},
pages = {128348},
doi = {10.1016/j.micres.2025.128348},
pmid = {41039684},
issn = {1618-0623},
abstract = {Phenolic acids influence host-pathogen interactions and function as key signals in Agrobacterium-mediated transformation or plant-microbe symbiosis. Agrobacterium tumefaciens uses chemotaxis to detect plant-secreted phenolic compounds and migrates to infection sites, though the chemotactic mechanism remains unclear. In this study, starting with structurally simple phenolic acids, the chemotactic response of A. tumefaciens C58 was investigated. The chemotaxis of A. tumefaciens toward 4-hydroxybenzoate and protocatechuate is not impacted by the methyl-accepting chemotaxis proteins (MCPs) Atu0387 and Atu0738, which share a four-helix bundle domain with previously discovered phenolic-sensing MCPs. To identify chemoreceptors for phenolic acids, a heterologous expression and functional screening system was constructed in Escherichia coli. Among the 13 MCPs, Atu0872 could respond to both 4-hydroxybenzoate and protocatechuate. Furthermore, atu0872 deletion weakened chemotaxis toward vanillin, acetosyringone, guaiacol, caffeic, vanillic, salicylic, gallic, p-coumaric, syringic, and sinapinic acids. Although the ligand-binding domain of Atu0872 was predicted to be a nitrate- and nitrite-sensing domain, the A. tumefaciens deletion mutant Δatu0872 did not affect chemotaxis toward nitrate and nitrite. In addition to chemotaxis, atu0872 deletion decreased the tumor weight on Daucus carota roots, Kalanchoe daigremontiana leaves, and the number of bacterial colonies per 0.1 g of tumor, implying that atu0872 affects bacterial colonization on the host by regulating chemotactic behavior. To our knowledge, this is for the first study identifying Atu0872 as a core chemoreceptor in A. tumefaciens for phenolic compounds, providing a theoretical foundation for elucidating the chemotaxis-pathogenicity relationship in A. tumefaciens and optimizing its use in genetic transformations.},
}

@article {pmid41039422,
year = {2025},
author = {Wong, ELY and Calchera, A and Otte, J and Schmitt, I},
title = {Temperature variability and other climatic attributes linked to genomic features in the lichen-forming fungal genus Umbilicaria.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {293},
pmid = {41039422},
issn = {1741-7007},
support = {LOEWE/1/10/519/03/03.001(0014)/52//Hessisches Ministerium für Wissenschaft und Kunst/ ; },
mesh = {*Genome, Fungal ; *Temperature ; *Lichens/genetics ; *Climate ; *Ascomycota/genetics ; },
abstract = {BACKGROUND: Many species of lichen-forming fungi exhibit large geographical ranges and broad thermal niches, making them excellent models for investigating the genomics of climate adaptation. In this study, we examined the impacts of climatic variables on genomic features in 11 Umbilicaria species. We compared PacBio genomes of individuals from the same species collected in different climate zones: alpine, cold temperate, or Mediterranean.

RESULTS: Our findings revealed several links between climatic and genomic features: (1) Selection pressure: in each climate zone, specific genes are under strong selection. (2) Genomic feature correlations: certain temperature variables (BIO2: mean diurnal range, BIO4: seasonality, BIO6: minimum in coldest month, BIO7: annual range) are correlated with GC content and the usage of the amino acids arginine and valine, suggesting these variables may drive convergent evolution of these genomic features. (3) Temperature variability: bioclimatic variables representing temperature variability, e.g. BIO2,4,7 are more influential in shaping genomic features than temperature means or extrema, with BIO6 also playing a significant role. (4) Epigenetic modifications: the rate of 5-methylcytosine (5mc) methylation within species is generally higher in samples from the colder habitat, suggesting that epigenetic modifications may contribute to climate adaptation.

CONCLUSIONS: Overall, our study shows that genome evolution is partially shaped by climate and, particularly, temperature variability. This aligns with numerous ecological and climate modelling studies, which show that climate variability has a stronger impact on species behaviour and evolution than climate means and extrema. Further genomics studies are required to provide additional evidence on this topic.},
}

*Genome, Fungal
*Temperature
*Lichens/genetics
*Climate
*Ascomycota/genetics

@article {pmid41038270,
year = {2025},
author = {Liu, T and Lin, H and Tian, Z},
title = {Genetic innovations underlying the evolution of root nodule symbiosis in Leguminosae.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2025.09.008},
pmid = {41038270},
issn = {1673-8527},
abstract = {Root nodule symbiosis (RNS) is a mutualistic association formed between nitrogen-fixing rhizobia or Frankia and host plants limited to four orders within Rosid I-Fabales, Fagales, Cucurbitales and Rosales-which comprise the so-called 'Nitrogen Fixing Nodulation Clade' (NFNC). The majority of nodulation studies have focused on Leguminosae, given their agricultural and environmental importance, as well as the widespread occurrence of nodulation among members of this family. Endowing cereal crops with nitrogen fixation, like Leguminosae, presents a strategy to reduce the detrimental effects of synthetic fertilizer overuse. Different hypotheses on the origin of RNS have been proposed, however key genetic innovations underlying the evolution of RNS, even in Leguminsoae, have been rarely reported. In this review, we begin by examining current knowledge of genetic innovations-including gene gain, gene loss, and the acquisition or loss of conserved noncoding sequences (CNS) in preexisting genes. We explore the available evidence supporting these genetic innovations underlying the evolution of RNS in Leguminosae and offer the phylogenomics approach that could be applied to uncover these genetic innovations. Finally, we conclude by proposing a model of genetic innovations underlying the evolution of RNS in Leguminsoae and consider the potential implications for the development of nitrogen-fixing crops.},
}

@article {pmid41038028,
year = {2025},
author = {Almeida, AC and Reid, M and Lillicrap, A},
title = {Specific toxicity of octinoxate and octocrylene on Symbiodinium sp., a symbiotic microalga with corals.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119151},
doi = {10.1016/j.ecoenv.2025.119151},
pmid = {41038028},
issn = {1090-2414},
abstract = {The widespread use of UV filters in sunscreens and personal care products has raised concerns about their detrimental effects to the aquatic environment. This study examined the specific toxicity of two UV filters, octinoxate and octocrylene to Symbiodinium sp., a photosynthetic dinoflagellate essential for coral symbiosis, nutrient acquisition, and reef structure. The study employed a comprehensive set of sub-lethal endpoints analyzed through flow cytometry, including cell viability, pigment fluorescence, cell size, complexity, metabolic activity, production of reactive oxygen species and membrane potential. The exposure of exponentially proliferating Symbiodinium sp. to octinoxate and octocrylene demonstrated pronounced toxicity, with octinoxate exhibiting toxicity levels significantly greater than those of octocrylene. This disparity underscores the different ecological impacts of these UV filters. Even at lower concentrations, octinoxate significantly influenced cellular parameters, including cell size, complexity, viability, and metabolic activity, as evidenced by increased lipid peroxidation (LPO) and neutral lipid accumulation, alongside a reduction in cellulose levels, suggesting potential structural alterations in cellular components. In contrast, octocrylene's sub-lethal effects are manifested as enhanced cell complexity and LPO, with elevated neutral lipids and cellulose levels. However, at elevated concentrations, octocrylene adversely affected cell viability and metabolic activity, indicative of severe membrane depolarization. These findings highlight the importance of an early warning system to protect Symbiodinium sp. and consequently corals. Flow cytometry proved to be a valuable diagnostic tool for detecting sub-lethal effects, providing insights into Symbiodinium sp. health status and, consequently, the resiliency of coral reef ecosystems.},
}

@article {pmid41037855,
year = {2025},
author = {Reynoso, MA},
title = {Update on translational control modes in plant cell signaling.},
journal = {Current opinion in plant biology},
volume = {88},
number = {},
pages = {102799},
doi = {10.1016/j.pbi.2025.102799},
pmid = {41037855},
issn = {1879-0356},
abstract = {Protein synthesis can contribute to plant cell signaling at multiple regulatory levels. Recent studies have expanded the conditions that are directly impacted by translational regulation. This control can balance responses to developmental, environmental, and diverse stress stimuli. Processes with evidence of translational regulation include: immunity to bacterial pathogens, symbiotic interactions, abiotic responses, hormonal perception, light-dependent metabolism, and developmental programs for lateral root initiation, root hair growth, and sepal initiation. Translational control modes rely on the sequence and secondary structure of mRNAs due to the presence of upstream open reading frames (uORFs) and/or internal ribosome entry sites (IRES), protein-binding regions or structures, and the decoding of the epitranscriptomic mRNA modifications such as N[6]-methyladenosine, N[4]-acetylcytidine or pseudouridine. In addition, the post-translational modification of ribosomal proteins and eukaryotic initiation factors such as eIF4G, eIFiso4G, eIF2, as well as changes in ribosome protein composition contribute to translational control. These factors, mRNAs, regulatory proteins and other RNAs can be confined by the formation of biomolecular condensates such as stress granules, processing bodies and others, resulting in paths that modulate translation both globally and specifically. The covered topics place translation as a hub for cell responses during development and within the environmental context. Current understanding of translation has allowed the development of applications in crops, reinforcing the relevance of the study of translational control in plants.},
}

@article {pmid41037509,
year = {2025},
author = {Pardo-De la Hoz, CJ and Haughland, DL and Thauvette, D and Toni, S and Goyette, S and White, W and Medeiros, ID and Cornet, L and Dvořák, P and Garfias-Gallegos, D and Miadlikowska, J and Magain, N and Lutzoni, F},
title = {Rapid radiations outweigh reticulations during the evolution of a 750-million-year-old lineage of cyanobacteria.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf244},
pmid = {41037509},
issn = {1537-1719},
abstract = {Species are a fundamental unit of biodiversity. Yet, the existence of clear species boundaries among bacteria has long been a subject of debate. Here, we studied species boundaries in the context of the phylogenetic history of Nostoc, a widespread genus of photoautotrophic and nitrogen-fixing cyanobacteria that includes many lineages that form symbiotic associations with plants (e.g., cycads and bryophytes) and fungi (e.g., cyanolichens). We found that the evolution of Nostoc was characterized by eight rapid radiations, many of which were associated with major events in the evolution of plants. In addition, incomplete lineage sorting associated with these rapid radiations outweighed reticulations during Nostoc evolution. We then show that the pattern of diversification of Nostoc shapes the distribution of average nucleotide identities (ANIs) into a complex mosaic, wherein some closely related clades are clearly isolated from each other by gaps in genomic similarity, while others form a continuum where genomic species boundaries are expected. Nevertheless, recently diverged Nostoc lineages often form cohesive clades that are maintained by within-clade gene flow. Boundaries to homologous recombination between these cohesive clades persist even when the potential for gene flow is high, i.e., when closely related clades of Nostoc cooccur or are locally found in symbiotic associations with the same lichen-forming fungal species. Our results demonstrate that rapid radiations are major contributors to the complex speciation history of Nostoc. This underscores the need to consider evolutionary information beyond thresholds of genomic similarity to delimit biologically meaningful units of biodiversity for bacteria.},
}

@article {pmid41036755,
year = {2025},
author = {Rahman, A and Borah, P and Hussain, S and Sen, A and Bharalee, R and Chabukdhara, M and Upadhyaya, H and Verma, AK},
title = {Chemical Diversity of Carotenoids Derived from Aquatic Animals and their Therapeutic, Biomedical, and Natural Colorant Applications.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113862073377688250903053348},
pmid = {41036755},
issn = {1875-5402},
abstract = {Carotenoids, prevalent in a diverse range of aquatic animals, perform critical and multifaceted roles essential for marine and freshwater ecosystems. This review examines the distribution, biological functions, and potential biomedical applications of carotenoids sourced from various aquatic animals. Carotenoids are acquired through food consumption or metabolic pathways, playing vital roles such as photoprotection, antioxidant defense, and nutritional enhancement, particularly provitamin A. Marine sponges and cnidarians display a diverse spectrum of carotenoids, crucial for symbiosis and photoprotection. Molluscs and crustaceans exhibit varied carotenoid profiles corresponding to their trophic strategies, whereas fish and echinoderms utilize carotenoids in reproductive and developmental processes. In biomedical contexts, carotenoids act as potential anti-cancer agents and antioxidants. Lycopene, β-carotene, and astaxanthin demonstrate anti-proliferative and antioxidant effects, pivotal in cancer prevention and therapeutic interventions. Their applications extend to biomedical technologies like Raman spectroscopy and drug delivery systems, underscoring their diagnostic and therapeutic potential. Carotenoids, as powerful antioxidants, neutralize free radicals and diminish oxidative stress, which is linked to chronic diseases like cardiovascular diseases, neurodegenerative disorders, and cancer. Some carotenoids, such as beta-carotene, are precursors to vitamin A, vital for vision, immune response, and cell communication. Furthermore, carotenoids have anti-inflammatory properties that modulate inflammatory pathways and provide therapeutic potential in diseases like inflammatory bowel disease and arthritis, which are marked by chronic inflammation. Furthermore, carotenoids provide photoprotection, safeguarding the skin and other tissues from damage caused by ultraviolet radiation. This paper highlights the integral role of carotenoids in biomedical advancements, emphasizing their significance in human health research.},
}

@article {pmid41035639,
year = {2025},
author = {Li, Y and Wang, S and Yao, D and Zhang, K and Yin, Y and Kong, X and Li, J and Zeng, L and Zhang, R and Zhang, Z},
title = {A taste of one's own medicine: Bacillus velezensis isolated from adult housefly intestines demonstrates effective fly control.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1575292},
pmid = {41035639},
issn = {1664-3224},
mesh = {Animals ; *Bacillus/physiology/isolation & purification/immunology ; *Gastrointestinal Microbiome ; *Houseflies/microbiology/immunology ; Larva/microbiology/immunology ; *Intestines/microbiology/immunology ; Transcriptome ; *Pest Control, Biological/methods ; Symbiosis ; Immunity, Humoral ; },
abstract = {INTRODUCTION: Bacillus spp. are widely used as biological agents for managing diseases in crops, livestock, poultry, and aquatic animals. Bacillus velezensis, a novel species within the Bacillus genus, is extensively used in the biological control of animal and plant diseases. However, the association between B. velezensis and insect hosts remains a complex and poorly understood process.

METHODS: In this study, we utilized a housefly larvae model to investigate the relationship between B. velezensis and houseflies by examining the changes in intestinal microbiota, transcriptomics, and humoral immunity following symbiotic B. velezensis treatment.

RESULTS: The results revealed striking dynamic changes in the bacterial community composition of larvae in the treatment group at the genus level. Notably, Providencia and Morganella content increased, while Enterobacter content decreased, leading to inhibited larval growth. Moreover, the bacterial association with the larva significantly impacted the larval transcriptome, modulating the expression of genes involved in various biological pathways, including host growth and development, macronutrient metabolism, and energy production, which are essential for insect development and survival. Oral feeding of B. velezensis also caused significant morphological changes in the larval gut, resulting in notable larval mortality, cell degeneration, shrinkage, and the formation of various vacuoles. Additionally, we observed a significant decrease in immune response in housefly larvae, with a reduction in phenoloxidase activity and melanization ability in treated larvae compared to controls.

DISCUSSION: Therefore, B. velezensis can damage the vital functions of housefly larvae and may be utilized as a microecological regulator for the green prevention and control of housefly populations.},
}

Animals
*Bacillus/physiology/isolation & purification/immunology
*Gastrointestinal Microbiome
*Houseflies/microbiology/immunology
Larva/microbiology/immunology
*Intestines/microbiology/immunology
Transcriptome
*Pest Control, Biological/methods
Symbiosis
Immunity, Humoral

@article {pmid41035504,
year = {2025},
author = {Olaguez-Gonzalez, JM and Chairez, I and Breton-Deval, L and Alfaro-Ponce, M},
title = {In-silico assessment of dynamic symbiotic microbial interactions in a reduced microbiota related to the autism spectrum disorder symptoms.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {4078-4088},
pmid = {41035504},
issn = {2001-0370},
abstract = {The gut microbiota plays a crucial role in human health, with growing evidence linking its composition to the development of Autism Spectrum Disorder. However, inconsistencies in previous studies have hindered the identification of a definitive microbial signature associated with Autism Spectrum Disorder. Machine learning models have emerged as powerful tools for analyzing microbiome data, yet their interpretability remains limited. In this study, we integrate in silico simulations with machine learning predictions to explore microbial interactions under different dietary conditions and provide biological context to features of the intestinal microbiota that are linked to Autism Spectrum Disorder. This study employs constraint-based modeling to simulate metabolic exchanges among key bacterial taxa in order to assess their ecological relationships. Findings reveal that high-fiber diets foster mutualistic and balanced interactions, whereas Western-style diets promote competitive and parasitic dynamics, potentially contributing to gut dysbiosis in Autism Spectrum Disorder. In addition, the presence of oxygen (a factor associated with colonocyte permeability, a pathological condition of the colon) significantly alters microbial interactions, influencing metabolic dependencies and the overall structure of the community. This integrative approach enhances the interpretability of machine learning-based Autism Spectrum Disorder classifiers, bridging computational predictions with mechanistic insights. By identifying diet-dependent microbial interactions, our study highlights potential dietary interventions to modulate the composition of the gut microbiota in Autism Spectrum Disorder. These findings underscore the value of combining in silico modeling and machine learning for unraveling complex microbiome-host relationships and improving Autism Spectrum Disorder biomarker identification.},
}

@article {pmid41034188,
year = {2025},
author = {Li, S and Wang, Y and Zhang, Z and Xu, H and Wu, S and Jin, H and Han, X and Liu, Y and Wen, X and Wu, Y and Zhang, Z and Hu, L and Hu, L and Zhang, C and Wang, J and Yan, R and Chen, M and Xiao, G and Sun, G and Zhang, D and Wang, S},
title = {Sodium nitrate protects against metabolic syndrome by sialin-mediated macrophage rebalance.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {323},
pmid = {41034188},
issn = {2059-3635},
support = {82201054//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030031, L2224038//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Mice ; *Metabolic Syndrome/drug therapy/genetics/pathology/metabolism ; *Macrophages/drug effects/metabolism/pathology ; Humans ; *Nitrates/pharmacology/administration & dosage ; *Diabetes Mellitus, Type 2/drug therapy/genetics/pathology/metabolism ; Male ; Disease Models, Animal ; },
abstract = {Metabolic syndrome, characterized by metabolic dysfunction-associated steatotic liver disease (MASLD) and type 2 diabetes mellitus (T2DM), poses a significant threat to patients' health worldwide; however, efficient treatment is currently unavailable. Here, we show that oral administration of sodium nitrate (NaNO3) greatly attenuates the development and advancement of MASLD-like and T2DM-like phenotypes in mice induced by choline-deficient high-fat, western, or methionine/choline-deficient diet. NaNO3 attenuates metabolic turbulence by rebalancing CD206[+]/CD11C[+] polarization (anti-inflammatory/pro-inflammatory) and the function of bone marrow-derived macrophages (MoMFs). Using metabolic disorder animal models and bone marrow-reconstituted mice with mutated gene function in Slc17a5, which encodes sialin, we demonstrate that NaNO3 protects against metabolic disorders through the actions of sialin in MoMFs. NaNO3 can directly regulate MoMFs polarization and function in vitro and in mice, in which nitric oxide production from oral and enteral symbiotic bacteria is essentially abolished. At the molecular level, sialin, via the inhibition of the key transcription factor Rel, inhibits cathepsin L (CtsL) expression and thereby activates the Nrf2 pathway to modulate macrophage homeostasis and ameliorate metabolic abnormalities. Interestingly, the sialin-CtsL-Nrf2 pathway is downregulated in human macrophages from metabolic dysfunction-associated steatohepatitis (MASH) patients. Overall, we demonstrate the prophylactic and therapeutic effects of NaNO3 on metabolic syndrome and reveal a new macrophage rebalancing strategy involving NaNO3 through a novel sialin pathway. Our research indicates that NaNO3 may be a pharmaceutical agent for managing and alleviating metabolic turbulence in humans.},
}

Animals
Mice
*Metabolic Syndrome/drug therapy/genetics/pathology/metabolism
*Macrophages/drug effects/metabolism/pathology
Humans
*Nitrates/pharmacology/administration & dosage
*Diabetes Mellitus, Type 2/drug therapy/genetics/pathology/metabolism
Male
Disease Models, Animal

@article {pmid41033381,
year = {2025},
author = {Avgousti, K and Dushku, E and Spyropoulou, A and Kotzamanidis, C and Staikou, A and Yiangou, M},
title = {Revealing probiotic properties of Lactiplantibacillus plantarum and Enterococcus faecalis in Cornu aspersum animal model.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105481},
doi = {10.1016/j.dci.2025.105481},
pmid = {41033381},
issn = {1879-0089},
abstract = {This study explores the probiotic potential, immunomodulatory capacity, and safety of Lactiplantibacillus plantarum and Enterococcus faecalis strains isolated from the intestinal tract of the edible terrestrial snail Cornu aspersum maxima. Although host-microbe interactions are well studied in vertebrates, such research remains limited in invertebrates, particularly snails. To address this gap, 12 lactic acid bacteria strains were isolated and screened for tolerance to the defense mechanisms of snails and probiotic-associated traits, followed by machine learning (ML) predictions of immunomodulatory potential. According to results, 10 strains exhibited high tolerance to the external and internal defense mechanisms of snails (pedal and gastric mucus, gastric juices, low gut pH) in association with increased autoaggregation and hydrophobicity values and were predicted to have 100% probability of eliciting immunomodulatory activity in vivo. Five strains, the L. plantarum Spp1 and Spp11 and E. faecalis Spp3, Spp8, Spp19, were selected for in vivo evaluation. Strain-specific immune responses were observed, with some strains mainly induced cellular immune responses, such as chemotaxis and phagocytic activity of hemocytes, while others also induced humoral responses. However, safety evaluations revealed that certain E. faecalis strains exhibited antimicrobial resistance or induced inflammatory reactions. Only two strains, the L. plantarum Spp11 and E. faecalis Spp19, were validated as safe and effective immunomodulatory probiotics in vivo. Overall, this study provides a comprehensive comparative analysis of the functionality of probiotic Lactiplantibacillus and Enterococcus strains in snails. These findings advance our understanding of snail-microbe symbiosis, particularly in the context of host-probiotic interactions, and support the use of C. aspersum as a valuable invertebrate model for probiotic research.},
}

@article {pmid41032286,
year = {2025},
author = {Krall, E and Benza, K and Kannenberg, R and Medina-Jimenez, K and Mukhia, S and Vanyo, V and Bravo, A},
title = {Conservation of Genes Required for Arbuscular Mycorrhizal Symbiosis.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-05-25-0065-CR},
pmid = {41032286},
issn = {0894-0282},
abstract = {Arbuscular mycorrhizal (AM) symbiosis is an ancient association that played a key role in the adaptation of plants to terrestrial environments. Originating over 400 million years ago at the dawn of land plants, this interaction depends on a core set of conserved genes that enable hosts to establish and maintain symbiotic relationships with AM fungi. The AM symbiotic program includes distinct genetic components for each stage of development, from signal perception to nutrient exchange. While AM-host plants have retained key genes dedicated to symbiosis, non-host lineages have independently lost these genes multiple times over evolutionary history. Recent studies in the liverwort Marchantia paleacea demonstrate that core mechanisms underlying AM symbiosis are conserved from bryophytes to angiosperms. Comparative genomic studies continue to uncover how symbiosis-specific genes are integrated with broadly conserved cellular machinery to sustain this interaction. Understanding these deeply conserved genetic modules is essential for uncovering the evolutionary foundations of plant-microbe associations and for harnessing their potential in sustainable agriculture.},
}

@article {pmid41031293,
year = {2025},
author = {Rui, J and Long, X and Wang, X and Xiong, X and Zhu, J},
title = {Soil microclimate and vegetation dynamics shape elevational and seasonal variations of diazotrophic communities in alpine grasslands.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1587343},
pmid = {41031293},
issn = {1664-462X},
abstract = {INTRODUCTION: Diazotrophs play critical roles in maintaining ecosystem nitrogen (N) cycling in alpine grasslands. However, the elevational and seasonal variations of diazotrophic communities in these ecosystems remain poorly understood. This gap in knowledge limits our ability to predict how N fixation will respond to environmental change. Here, we investigated the seasonal dynamics of soil diazotrophic communities across a 3200-4000 m elevational gradient in Qinghai-Tibetan alpine grasslands during the growing season.

METHODS: Soil samples were collected across an elevational gradient (3200-4000 m) throughout the growing season. The diazotrophic community composition was assessed by sequencing the nifH gene, which was also quantified using quantitative PCR. Soil nitrogenase activity was measured to assess N fixation potential. Key environmental variables, such as soil temperature, moisture, and plant biomass (particularly legume biomass), were monitored.

RESULTS AND DISCUSSION: Our results revealed that diazotrophic alpha-diversity followed an inverted V-shaped pattern along the elevational gradient, primarily driven by soil temperature and moisture. Beta-diversity analyses demonstrated that diazotrophic communities generally exhibited similar elevational distribution patterns throughout the growing season, also primarily influenced by temperature and moisture. Seasonal variations in diazotrophic communities were more pronounced at lower elevations, primarily associated with plant biomass dynamics, including delayed legume emergence at 3200 m in June and their subsequent biomass accumulation after July. In contrast, soil microclimate (particularly temperature) dominated community shifts at higher elevations. Notably, nifH gene abundance and soil nitrogenase activity were higher in the early growing season, suggesting free-living diazotrophs may play a crucial role in N fixation. Abundant species were key contributors to diazotrophic beta-diversity. Symbiotic Mesorhizobium was more abundant at low elevations, while free-living Geobacter at high elevations. Conversely, associative diazotrophs peaked later in the growing season, in contrast to Geobacter. Rare species played a key role in shaping alpha diversity, particularly at mid-elevations, where soil moisture was the highest. Our study underscores the complex interactions between soil microclimate change and plant dynamics in regulating diazotrophic communities. Furthermore, it highlights the essential roles of both abundant and rare species in sustaining ecosystem functions in alpine grasslands. These findings provide new insights into the biogeochemical processes supporting N cycling in alpine grasslands and highlight the potential impacts of vegetation and climate change on these fragile ecosystems.},
}

@article {pmid41030555,
year = {2025},
author = {Worku, AT and Sciarretta, A and Guarnieri, A and Falcone, M and Brancazio, N and Minwuyelet, A and Cutuli, MA and Atenafu, G and Nicolosi, D and Colacci, M and Yewhalaw, D and Di Marco, R and Petronio Petronio, G},
title = {Microbial gatekeepers: midgut bacteria in Aedes mosquitoes as modulators of arboviral transmission and targets for sustainable vector control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656709},
pmid = {41030555},
issn = {1664-302X},
abstract = {Arboviral diseases such as Dengue virus, Zika virus, Chikungunya virus, and West Nile virus pose significant global public health and economic challenges, particularly in tropical and subtropical regions. The absence of effective vaccines and sustainable vector control strategies continues to drive high morbidity and mortality rates. Symbiotic bacteria residing in the mosquito midgut can produce antimicrobial compound, stimulate the host immune response, disrupt nutrient pathways critical for pathogen development, and interfere with the pathogen's lifecycle and dissemination. Additionally, these microbes may reduce vector reproduction and shorten the lifespan of both immature and adult stages. Genetically modified symbiotic bacteria can release effector molecules that target pathogens without harming mosquitoes. Advances in genomic and metagenomic tools have deepened our understanding of the mosquito gut microbiome. This review highlights current knowledge of gut bacteria and arbovirus interactions and explores strategies to reduce arboviral transmission. Comprehensive literature searches were conducted using global databases, including PubMed, Web of Science, and Scopus, with a focus on English-language publications.},
}

@article {pmid41030195,
year = {2025},
author = {Vancaester, E and Oldrieve, GR and Reid, A and Koutsovoulos, G and Laetsch, DR and Makepeace, BL and Tanya, V and Poppert, S and Krücken, J and Wolstenholme, A and Blaxter, M},
title = {Ghosts of symbionts past: The hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf226},
pmid = {41030195},
issn = {2160-1836},
abstract = {Many, but not all, parasitic filarial nematodes (Onchocercidae) carry intracellular, maternally-transmitted, alphaproteobacterial Wolbachia symbionts. The association between filarial nematodes and Wolbachia is often portrayed as mutualist, where the nematode is reliant on Wolbachia for an essential but unknown service. Wolbachia are targets for anti-filarial chemotherapeutic interventions for human disease. Wolbachia of Onchocercidae derive from four of the major supergroups (C, D, F and J) defined within the genus. We explored the evolutionary history of the filarial nematode-Wolbachia symbiosis in twenty-two nematode species, sixteen of which have current Wolbachia infections, by screening the nematode nuclear genome sequences for nuclear Wolbachia transfers, fragments of the Wolbachia genome that have been inserted into the nuclear genome. We identified Wolbachia insertions in five of the six species that have no current Wolbachia infection, showing they have previously had and have now lost Wolbachia infections. In currently-infected species we found a diversity of origins of the insertions, including many cases where they derived from a different supergroup to the current live infection. Mapping the origins of the insertions onto the filarial nematode phylogeny we derive a complex model of evolution of Wolbachia symbiosis. The history of association between Wolbachia and onchocercid nematodes includes not only cospeciation, as would be expected from a mutualist symbiosis, but also loss (in the five Wolbachia-free species), frequent symbiont replacement, and dual infection. This dynamic pattern is challenging to models that assume host-symbiont mutualism.},
}

@article {pmid41029997,
year = {2025},
author = {Ferreras-Garrucho, G and Chancellor, T and Paszkowski, U},
title = {Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf404},
pmid = {41029997},
issn = {1460-2431},
abstract = {Arbuscular mycorrhizal symbiosis (AMS) is a ubiquitous and ancient interaction between plant root systems and fungi of the Glomeromycotina subphylum. The resulting relationship is mutually beneficial and deeply intimate where the fungus intracellularly colonises root cortex cells to receive organic carbon and deliver minerals and water to the plant. Fungal colonisation of plant roots and cells is extremely dynamic and asynchronous across the root system. Symbiosis development must therefore result from spatio-temporally fine-tuned molecular control mechanisms of plant and fungus. Although the plant genetic program underpinning AMS has been extensively studied, little is known about its dynamic regulation across root cell layers and developmental stages of the association. Thus, many questions remain outstanding: how do different cell-types transcriptionally respond to AMS, how are distinct cell-type specific regulatory states coordinated, and what are the transcriptional activities in the fungus associated with discrete stages of root colonisation? The advent of single cell-based techniques now enables the high-resolution analysis to address these questions. In this review, we recapitulate the current knowledge on the spatio-temporal control of AMS, we evaluate the relevance of existing spatial datasets to AMS research and provide new perspectives for future study.},
}

@article {pmid41029519,
year = {2025},
author = {Modara, B and Rahimi, MM and Abdipour, M and Hosseinifarahi, M},
title = {Physiological and antioxidant responses of marjoram (Origanum Majorana L.) under drought stress mediated by Salicylic acid and mycorrhizal symbiosis.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1248},
pmid = {41029519},
issn = {1471-2229},
mesh = {*Mycorrhizae/physiology ; *Salicylic Acid/metabolism/pharmacology ; *Droughts ; *Antioxidants/metabolism ; *Symbiosis ; Stress, Physiological ; },
abstract = {Drought stress, exacerbated by climate change, is a major limiting factor for herbs cultivation. This study aimed to evaluate the combined effects of salicylic acid (SA) and mycorrhizal fungi (MF) on marjoram under drought stress conditions. The experiment was conducted over two years (2022-2023) using a split factorial design within a randomized complete block with three replications. The study's primary factor was drought stress at three levels: 90% (D0), 70% (D1), and 35% (D2) of field capacity (FC). The secondary factor included two sub-factors: SA concentrations (0, 100, and 300 mg L[-1]) and MF inoculation (non-inoculated (M0) and inoculated with Glomus hoi (M1)). Results demonstrated that drought stress decreased relative water content (RWC) (46.8%), chlorophyll content (35%), carotenoids (25.7%), and dry weight (49.3%), while increasing proline (38.6%), soluble sugars (29.4%), electrolyte leakage (44.8%), superoxide dismutase (35.2%), peroxidase (43.1%), and catalase activities (29.3%). Additionally, the combined treatment of SA and MF enhanced water status by 44%, proline content by 12%, and soluble sugar content by 6% under severe drought conditions. Antioxidant enzyme activities (Catalase) were also significantly increased by up to 91% with the combined treatments, supporting the hypothesis that the synergy of SA and MF can effectively mitigate the adverse effects of drought stress on marjoram. Overall, this study demonstrated that the combined application of SA and MF could be a promising strategy for enhancing drought tolerance in marjoram, especially in drought-prone areas. TRIAL REGISTRATION: This study does not involve clinical trials or human participants and, as such, does not require clinical trial registration.},
}

*Mycorrhizae/physiology
*Salicylic Acid/metabolism/pharmacology
*Droughts
*Antioxidants/metabolism
*Symbiosis
Stress, Physiological

@article {pmid41028587,
year = {2026},
author = {Anandakumar, S and Senthamilselvi, D and Kalaiselvi, T},
title = {Estimation of Foliar Volatiles Emitted by Mycorrhizal Colonized Blackgram (Vigna mungo L) Infested with Spodoptera litura.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2966},
number = {},
pages = {233-243},
pmid = {41028587},
issn = {1940-6029},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Animals ; *Spodoptera/physiology ; Gas Chromatography-Mass Spectrometry/methods ; *Mycorrhizae/physiology ; *Plant Leaves/metabolism/chemistry/parasitology ; *Vigna/metabolism/parasitology/microbiology/chemistry ; Symbiosis ; },
abstract = {Plant-emitted volatile organic compounds (VOCs) play a significant role in signaling and tolerance to biotic stressors, including insect pest infestation. Mycorrhizae, a symbiotic fungus, improves the tolerance of blackgram plants to Spodoptera litura by altering the profiling of foliage VOCs. Recently, gas chromatography-mass spectrometry (GC-MS) coupled with headspace (HS) trapping of VOCs is the most frequently used analytical technique to understand the metabolic process and responses of plants to biotic stresses. This method performs four steps such as (i) trapping of HS-VOCs, (ii) concentration and enrichment of VOCs, (iii) transfer of VOCs from air sample to analytical device, and (iv) detection and identification of compounds. HS volatiles is trapped using fiber polymers like Tenax TA and desorbed thermally in GC-MS with TD autosampler and thermal desorption (TD). The identification of VOCs compounds is performed by searching mass spectral peaks against NIST mass spectral library. This chapter provides the detailed procedure for the estimation of plant-produced VOCs using HS sapling coupled with gas chromatography-mass spectrometry (TD-GC/MS) with TD autosampler and thermal desorption method.},
}

*Volatile Organic Compounds/analysis/metabolism
Animals
*Spodoptera/physiology
Gas Chromatography-Mass Spectrometry/methods
*Mycorrhizae/physiology
*Plant Leaves/metabolism/chemistry/parasitology
*Vigna/metabolism/parasitology/microbiology/chemistry
Symbiosis

@article {pmid41027965,
year = {2025},
author = {Cao, J and Wang, J and Yang, Q and Guo, B and Colombi, T and Valverde-Barrantes, OJ and Ding, J and Zhang, Y and Wu, H and Feng, Z and Yang, X and Kong, D},
title = {Root anatomy governs bi-directional resource transfer in mycorrhizal symbiosis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8731},
pmid = {41027965},
issn = {2041-1723},
support = {32471824, 32171746, 31870522, and 31670550//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Mycorrhizae/physiology/metabolism ; *Symbiosis/physiology ; *Plant Roots/anatomy & histology/microbiology/metabolism ; Carbon/metabolism ; Models, Biological ; },
abstract = {Plants form mycorrhizal symbioses to enhance nutrient acquisition, yet the biophysical principles governing carbon and nutrient exchange remain unclear. Here, we develop a theory of bi-directional carbon-nutrient transfer that integrates root anatomy, energetic costs, and mycorrhizal positioning. We show that nutrient uptake per unit carbon or energy investment declines with increasing root diameter due to higher carbon demands across thicker cortical tissues. Mycorrhizal fungi mitigate this constraint by enabling more carbon-efficient nutrient uptake, particularly when arbuscules are positioned in inner cortical layers. This spatial optimization minimizes the carbon cost of transporting nutrients to the stele. Our framework reconciles anatomical variation, symbiotic structure, and functional efficiency across root types and mycorrhizal strategies and offers a new lens for understanding the coevolution between roots and mycorrhizal fungi.},
}

*Mycorrhizae/physiology/metabolism
*Symbiosis/physiology
*Plant Roots/anatomy & histology/microbiology/metabolism
Carbon/metabolism
Models, Biological

@article {pmid41027223,
year = {2025},
author = {Jing, X and Zhang, X and Wang, X and Chen, H and Xing, S and Jin, Z and Yang, D and Li, J and Wu, S and Hao, Z and Song, F and Chen, B},
title = {Bidirectional interference between nanoplastics and arsenic in arbuscular mycorrhizal symbiosis: Reciprocal modulation of uptake, transformation and translocation.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139983},
doi = {10.1016/j.jhazmat.2025.139983},
pmid = {41027223},
issn = {1873-3336},
abstract = {Nanoplastics, which persist in the environment with high specific surface areas, interact with the well-documented pollutant arsenic, thereby exacerbating its phytotoxicity. Arbuscular mycorrhizal fungi, forming symbiotic relationships with most plants and enhancing their arsenic tolerance, possess hyphae capable of capturing nanoplastics. However, no studies have investigated either how arbuscular mycorrhizal fungi absorb and transfer arsenic during nanoplastics co-exposure, or whether nanoplastics are internalized by arbuscular mycorrhizal fungi hyphae and translocated to mycorrhizal tissues under arsenic stress. In this study, a two-compartment in vitro monoxenic cultivation system was used to investigate the synergistic translocation and transformation of arsenic-nanoplastic co-contaminants at the plant-microbe interface. The results indicated that nanoplastics hindered the arsenic absorption by arbuscular mycorrhizal fungi hyphae and promoted the transformation of inorganic arsenic to organic arsenic via upregulating the relative expression of the RiMT-11 gene in the hyphae. Scanning electron microscopy and confocal laser scanning microscopy imaging confirmed nanoplastics internalization by hyphae and subsequent translocation to mycorrhizae under arsenic exposure. This study deciphers nanoplastic-arsenic-arbuscular mycorrhizal fungi interaction mechanisms and validates arbuscular mycorrhizal fungi's potential role in the bioremediation of arsenic-nanoplastic co-contaminated soils.},
}

@article {pmid41026427,
year = {2025},
author = {Kumar, SC and Kumar, M and Singh, R and Saxena, AK},
title = {Selection of competitive and effective rhizobial strain for enhanced chickpea production under Indo-Gangetic plains of India.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {41026427},
issn = {1678-4405},
support = {Application of Microorganisms in Agriculture and Allied Sectors (AMAAS).//Application of Microorganisms in Agriculture and Allied Sectors (AMAAS)./ ; },
abstract = {Chickpea (Cicer arietinum L.) is a vital legume crop, but its productivity is often limited by poor soil fertility. This study aimed to assess the nodulation efficacy and plant growth-enhancing activities of six Mesorhizobium spp. strains in the chickpea cultivar Pusa 362 through the Leonard jar experiment and field trial. The strains, including two strains from ICRISAT (reference strains), were tested for solubilization of phosphate, potassium, and zinc, and production of Indole-3-Acetic Acid (IAA). Strain C5 excelled in phosphate solubilization (61.40 µg/ml), while C7 was superior in potassium (26.10 µg/ml) and zinc phosphate (69.15 µg/ml) solubilization; C17 showed the highest IAA production (25.75 µg/ml). In the Leonard jar experiment, inoculation of strains M. ciceri C5 and M. helmanticense C17 exhibited the highest nodule number and root dry weight, while treatments with M. ciceri C5 and M. helmanticense C7 inoculation recorded the maximum nodule dry weight and shoot dry weight. Field trials indicated significant improvements in nodulation, biomass, and nitrogen content in chickpeas inoculated with these strains. Treatment with strain C7 led to the highest increase in nodule number and root dry weight over the control, while strain C5 inoculation recorded maximum grain yield. Correlation analysis showed positive relationships between yield and several growth parameters. Nodule occupancy tests revealed that strain C7 had the highest occupancy (32.98%), followed by C5 (31.92%), indicating superior nodulation competitiveness under field conditions. These results suggest that inoculation with specific Mesorhizobium strains can significantly enhance chickpea productivity through improved nodulation and nitrogen fixation.},
}

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

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

@article {pmid41025674,
year = {2025},
author = {Ste-Croix, DT and Gagnon, AÈ and Mimee, B},
title = {The genome and stage-specific transcriptomes of the carrot weevil, Listronotus oregonensis, reveal adaptive mechanisms for host specialisation and symbiotic interactions.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70012},
pmid = {41025674},
issn = {1365-2583},
support = {J-002846//Alternative Pest Management Solutions initiative/ ; //Agriculture and Agri-Food Canada/ ; },
abstract = {Throughout their evolution, insects have become specialised to occupy diverse ecological niches. The carrot weevil, Listronotus oregonensis, is an important agricultural pest that exhibits a very specific host range. In this study, we characterised the genome and transcriptomes of each developmental stage of L. oregonensis and its Wolbachia endosymbiont to gain deeper knowledge of the genetic determinants controlling its biology. We annotated 14,637 genes and showed expression profiles across the developmental stages. We also compared orthologous genes between L. oregonensis and nine other species, with particular focus on chemoreceptors and detoxification genes. We identified 24 distinct odorant-binding protein genes and 41 genes for receptors involved in stimulus perception, relatively low numbers compared with other species, which would be consistent with a narrow host range. In contrast, we found a high number of detoxification genes, with significant expansion of certain gene families. Among the annotated genes, 46 were putatively acquired through horizontal gene transfer, with 17 showing strong evidence for this, including several cell-wall degrading enzymes. The phylogeny of a cytolethal distending toxin gene also suggests an initial transfer from a prokaryotic source and vertical dissemination in members of Curculionidae through recent evolution. The presence of the endosymbiotic bacterium Wolbachia (supergroup A) was confirmed in all tested L. oregonensis individuals from several regions in northeastern North America and showed very little diversity. This study enhances our understanding of the genomic, functional, and evolutionary aspects of a significant agricultural pest and makes important and useful databases available to the scientific community.},
}

@article {pmid41025407,
year = {2025},
author = {Esquinas-Ariza, RM and Villar, I and Minguillón, S and Zamarreño, Á and Pérez-Rontomé, C and Reeder, BJ and Sandal, N and Yan, D and García-Mina, JM and Duanmu, D and Martínez-Júlvez, M and Becana, M},
title = {Structural and functional comparison of hemoglobin Glb2-1 of Lotus japonicus with Glb1-1 and leghemoglobins.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf434},
pmid = {41025407},
issn = {1460-2431},
abstract = {The legume Lotus japonicus expresses nine hemoglobins, including leghemoglobins (Lbs), class 1 phytoglobin (Glb1-1), and an unusual phytoglobin (Glb2-1). Quantitative PCR, proteomics, and plant mutant analyses indicate that Glb2-1 is mainly present in nodules without replacing Lb function, but is also in roots and photosynthetic tissues. Comparison of hormonal profiles of the knock-out mutants glb1-1, glb2-1, and glb1-1/2-1 reveals that Glb1-1 and Glb2-1 have distinct functions. The increase of salicylic acid in the leaves of glb1-1 reveals a role of Glb1-1 in the defense response, which was corroborated by accumulation of pipecolic acid, a metabolite involved in plant immunity. In contrast, the decrease of bioactive jasmonoyl-isoleucine in glb2-1 is consistent with a role of Glb2-1 in the plant's reproductive stage. The mutants also showed changes in cytokinins, gibberellins, and polyamines, but without clear distinctive patterns. The crystal structure of Glb2-1 was determined to 1.6 Å resolution and compared with those of soybean Lba and Arabidopsis Glb1. In combination with mutant versions of Glb2-1, residues Tyr31, His64, and Cys65 were identified as critical for O2-binding stability. Spectral changes in heme coordination when Tyr31 is substituted for Phe highlights the importance of the residue at the B10 position for Lb and Glb function.},
}

@article {pmid41025248,
year = {2025},
author = {Park, YJ and Lim, JK and Lee, YJ and Kwon, KK},
title = {Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {9},
pages = {e2507003},
doi = {10.71150/jm.2507003},
pmid = {41025248},
issn = {1976-3794},
support = {EA0311//Ministry of Oceans and Fisheries/ ; KIMST 20210469//Ministry of Oceans and Fisheries/ ; },
mesh = {Animals ; *Microbiota/genetics ; *DNA, Bacterial/isolation & purification/genetics ; *Aquatic Organisms/microbiology ; *Bacteria/genetics/isolation & purification/classification ; *Porifera/microbiology ; Symbiosis ; Republic of Korea ; *Invertebrates/microbiology ; Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; },
abstract = {Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts' immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.},
}

Animals
*Microbiota/genetics
*DNA, Bacterial/isolation & purification/genetics
*Aquatic Organisms/microbiology
*Bacteria/genetics/isolation & purification/classification
*Porifera/microbiology
Symbiosis
Republic of Korea
*Invertebrates/microbiology
Anthozoa/microbiology
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
Polymerase Chain Reaction

@article {pmid41024490,
year = {2025},
author = {Speijer, D},
title = {Eukaryogenesis From FECA to LECA: Radical Steps Along the Way.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70063},
doi = {10.1002/bies.70063},
pmid = {41024490},
issn = {1521-1878},
abstract = {The characteristics of the last eukaryotic common ancestor (LECA) population and the root of the eukaryotic tree have been coming into focus lately. However, the trajectory taking the host, related to present-day Asgard archaea and the endosymbiont, related to present-day alphaproteobacteria, toward such fully integrated and complex organisms is still unclear. Here I marshal recent evidence supporting the early arrival of the "mitochondrion-to-be", setting up the evolutionary dynamic for a series of mutual adaptations leading to eukaryotes. Upon critical analysis of some presuppositions in phylogenomic reconstructions of eukaryogenesis, I again propose that pre-symbiosis, efficient ATP generation, internal reactive oxygen species (ROS) formation and enhanced retention of genes supplied by horizontal gene transfer (HGT) interdependently allowed this unique transformation to occur.},
}

@article {pmid41024329,
year = {2025},
author = {Manjili, MH},
title = {The Invisible Lens: Why Theoretical Models Are Essential for Interpreting Immune Phenomena.},
journal = {Scandinavian journal of immunology},
volume = {102},
number = {4},
pages = {e70057},
pmid = {41024329},
issn = {1365-3083},
support = {W81XWH2210793//U.S. Department of Defense/ ; P30 CA 016059/NH/NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Models, Theoretical ; *Models, Immunological ; *Immune System/immunology ; *Allergy and Immunology ; },
abstract = {Immunology progresses not merely by accumulating data but by evolving the conceptual lenses through which those data are interpreted; yet for six decades the self-non-self/infectious-non-self (SNS/INS) paradigm-casting allogeneity as activating signal and 'self' as intrinsically tolerogenic-has dominated research design, peer review and curriculum. This, in turn, systematically amplifies concordant findings while attenuating evidence for tissue integrity, metabolic, symbiotic and network-centric cues. This conceptual monoculture appears as a hidden dogma that impedes breakthroughs in our understanding of the immune system and the development of curative therapies. By institutionalising theoretical immunology as a formal discipline and treating models as explicit, testable tools rather than hidden assumptions, immunologists can sharpen hypothesis generation and achieve a better understanding of existing data. This essay provides an overview of empirically grounded theoretical models to counter monoculture, clarify how frames shape interpretation, and expand the field's conceptual toolkit.},
}

Humans
Animals
*Models, Theoretical
*Models, Immunological
*Immune System/immunology
*Allergy and Immunology