The ISME Journal最新文献_第5页

Viroid-like “obelisk” agents are widespread in the ocean and exceed the abundance of RNA viruses in the prokaryotic fraction 类病毒“方尖碑”病原体在海洋中广泛存在，其丰度超过了原核部分RNA病毒的丰度

The ISME Journal Pub Date : 2025-02-25 DOI: 10.1093/ismejo/wraf033

Javier López-Simón, Marcos de la Peña, Manuel Martínez-García

{"title":"Viroid-like “obelisk” agents are widespread in the ocean and exceed the abundance of RNA viruses in the prokaryotic fraction","authors":"Javier López-Simón, Marcos de la Peña, Manuel Martínez-García","doi":"10.1093/ismejo/wraf033","DOIUrl":"https://doi.org/10.1093/ismejo/wraf033","url":null,"abstract":"“Obelisks” are recently discovered RNA viroid-like elements present in diverse environments with no phylogenetic similarity to any known biological agent. Obelisks were first identified in the human gut and in a commensal bacterium acting as a replicative host. They have a circular ∼1 kb RNA genome, rod-like secondary structures, and the encoding of a protein superfamily called “Oblins”. We performed a large-scale search of Obelisks in the ocean using the Pebblescout program and the transcriptomic Sequence Archive Read databases, revealing the biogeography and abundance of these viroid-like RNA elements. We detected 45 Obelisk genomes resulting in 35 marine clusters at the species level. These Obelisks were detected in the prokaryotic fraction and to a lesser extent in the eukaryotic fraction, and distributed across all the oceans from surface to mesopelagic including the Arctic, and even in the coldest seawater of Earth beneath the Antarctic Ross Ice Shelf. The Obelisk hallmark protein Oblin-1 confirmed by 3D models was found in various marine samples. Some of the detected marine Obelisks harbour hammerhead self-cleaving ribozymes in both polarities. In the prokaryotic, but not the eukaryotic, fraction of the Tara Ocean dataset, relative abundance of Obelisks calculated by transcriptomic fragment recruitment indicated that they are abundant in marine samples, reaching or even exceeding the relative abundance of the previously discovered uncultured RNA viruses. In conclusion, Obelisks are abundant and widespread viroid-like elements that should be included in ocean biogeochemical models.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"129 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Halophilic archaea produce wax esters and use an alternative fatty acyl-CoA reductase for precursor synthesis 嗜盐古细菌产生蜡酯，并使用一种替代的脂肪酰基辅酶a还原酶进行前体合成

The ISME Journal Pub Date : 2025-02-24 DOI: 10.1093/ismejo/wraf035

Vincent Grossi, Philippe Cuny, Cécile Militon, Jerzy Witwinowski, Balkis Eddhif, Léa Sylvi, Mireille Nowakowski, Artemis Kosta, Ingrid Antheaume, Johan Cornil, Sarah Dubrac, Julia Kende, Simonetta Gribaldo, Guillaume Borrel

{"title":"Halophilic archaea produce wax esters and use an alternative fatty acyl-CoA reductase for precursor synthesis","authors":"Vincent Grossi, Philippe Cuny, Cécile Militon, Jerzy Witwinowski, Balkis Eddhif, Léa Sylvi, Mireille Nowakowski, Artemis Kosta, Ingrid Antheaume, Johan Cornil, Sarah Dubrac, Julia Kende, Simonetta Gribaldo, Guillaume Borrel","doi":"10.1093/ismejo/wraf035","DOIUrl":"https://doi.org/10.1093/ismejo/wraf035","url":null,"abstract":"Wax esters are fatty acid-based neutral lipids thought to be restricted to bacteria and eukaryotes that play a key role in the functioning and maintenance of cells, especially under adverse conditions. Here we show that several halophilic archaea (Halobacteriales) carry a homologue of the bacterial wax synthase gene. Wax ester synthesis and accumulation is demonstrated in one of these (poly)extremophilic archaea, Natronomonas pharaonis, during growth on long-chain fatty acids. Our bioinformatic analysis also shows that the synthesis of fatty alcohols required for wax ester synthesis could be performed by an enzyme evolutionarily related to class I 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR, classically involved in isoprenoid biosynthesis). Using heterologous expression and enzymatic assays, we show that this HMGR homolog, which we named FcrA (for fatty acyl-CoA reductase), reduces fatty acyl-CoA to fatty alcohol, but cannot reduce 3-hydroxy-3-methylglutaryl-CoA to mevalonate. The conservation of HMGR catalytic residues in FcrA suggests that the two enzymes have a similar catalytic mechanism, whereas an elongated substrate-binding pocket and distinct residues may explain FcrA’s selectivity for long chain fatty acyl-CoA. In addition to archaea, FcrA is present in a wide range of bacteria, including ~25% of those predicted to produce wax esters, and accounts for a large proportion of the fatty acyl-CoA reductases found in various environments. Challenging the long-held paradigm that archaea cannot biosynthesize fatty acid-based neutral lipids de novo, this study lays the foundations for further physiological, ecological, and biotechnological investigation of neutral lipid production by systems markedly different from those of eukaryotes and bacteria.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"110 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143486071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Carbon dioxide enhances Akkermansia muciniphila fitness and anti-obesity efficacy in high-fat diet mice 二氧化碳增强高脂饮食小鼠嗜粘阿克曼氏菌的健康和抗肥胖功效

The ISME Journal Pub Date : 2025-02-23 DOI: 10.1093/ismejo/wraf034

Xiangfeng Wang, Qianqian Yang, Changping Shi, Yuyang Wang, Dingming Guo, Xuchun Wan, Pengyuan Dong, Qianyao Zhang, Yueyan Hu, Ruilin Zhang, Hongju Yang, Weihua Chen, Zhi Liu

{"title":"Carbon dioxide enhances Akkermansia muciniphila fitness and anti-obesity efficacy in high-fat diet mice","authors":"Xiangfeng Wang, Qianqian Yang, Changping Shi, Yuyang Wang, Dingming Guo, Xuchun Wan, Pengyuan Dong, Qianyao Zhang, Yueyan Hu, Ruilin Zhang, Hongju Yang, Weihua Chen, Zhi Liu","doi":"10.1093/ismejo/wraf034","DOIUrl":"https://doi.org/10.1093/ismejo/wraf034","url":null,"abstract":"Numerous studies and clinical applications have underscored the therapeutic potential of the indigenous gut bacterium Akkermansia muciniphila in various diseases. However, our understanding of how A. muciniphila senses and responds to host gastrointestinal signals remains limited. Here, we demonstrate that A. muciniphila exhibits rapid growth, facilitated by its self-produced carbon dioxide, with key enzymes such as glutamate decarboxylase, carbonic anhydrase, and pyruvate ferredoxin oxidoreductase playing pivotal roles. Additionally, we design a novel delivery system, comprising calcium carbonate, inulin, A. muciniphila, and sodium alginate, which enhances A. muciniphila growth and facilitates the expression of part probiotic genes in mice intestinal milieu. Notably, the administration of this delivery system induces weight loss in mice fed high-fat diets. Furthermore, we elucidate the significant impact of carbon dioxide on the composition and functional genes of the human gut microbiota, with genes encoding carbonic anhydrase and amino acid metabolism enzymes exhibiting heightened responsiveness. These findings reveal a novel mechanism by which gut commensal bacteria sense and respond to gaseous molecules, thereby promoting growth. Moreover, they suggest the potential for designing rational therapeutic strategies utilizing live bacterial delivery systems to enhance probiotic growth and ameliorate gut microbiota-related diseases.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"61 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Wide-ranging organic nitrogen diets of freshwater Picocyanobacteria 淡水Picocyanobacteria的广泛有机氮饮食

The ISME Journal Pub Date : 2025-02-23 DOI: 10.1093/ismejo/wrae236

Elliot Druce, Stephen C Maberly, Patricia Sánchez-Baracaldo

{"title":"Wide-ranging organic nitrogen diets of freshwater Picocyanobacteria","authors":"Elliot Druce, Stephen C Maberly, Patricia Sánchez-Baracaldo","doi":"10.1093/ismejo/wrae236","DOIUrl":"https://doi.org/10.1093/ismejo/wrae236","url":null,"abstract":"Freshwater picocyanobacteria (Syn/Pro clade) contribute substantially to the primary production of inland waters, especially when nitrogen is limiting or co-limiting. Nevertheless, they remain poorly understood ecologically and genomically, with research on their nitrogen acquisition mainly focused on inorganic sources. However, dissolved organic nitrogen is often a major component of the freshwater nitrogen pool and it is increasingly evident that many forms are bioavailable. Comparative genomic analyses, axenic growth assays, and proteomic analyses were used here to investigate organic nitrogen acquisition mechanisms in the Syn/Pro clade. Comparative analysis of the genomes of 295 freshwater and marine strains of picocyanobacteria identified a large diversity of amino acid transporters, the absence of degradation pathways for five amino acids (asparagine, phenylalanine, serine, tryptophan, and tyrosine), and alternative mechanisms for chitin assimilation (direct chitin catabolise vs initial acetylation to chitosan and subsequent degradation). Growth assays demonstrated the widespread bioavailability of amino acids, including basic amino acids though the known basic amino acid transporter is not encoded. This suggests further genetic components are involved, either through extracellular catabolism or the presence of novel transporters. Proteomic analysis demonstrates the dual utilisation of nitrogen and carbon from the amino acid substrate and provides evidence for a mild stress response through the up-regulation of lysine biosynthesis and FtsH1, potentially caused by accumulation of secondary metabolites. Our results are relevant to understanding how picocyanobacteria have come to thrive in dissolved organic nitrogen-rich oligotrophic environments and explores how their different molecular capabilities may influence communities between habitats.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Murine gut microbial interactions exert anti-hyperglycemic effects 小鼠肠道微生物相互作用具有抗高血糖作用

The ISME Journal Pub Date : 2025-02-17 DOI: 10.1093/ismejo/wraf028

Liying Guo, Libing Xu, Yanhong Nie, Lu Liu, Zongping Liu, Yunpeng Yang

{"title":"Murine gut microbial interactions exert anti-hyperglycemic effects","authors":"Liying Guo, Libing Xu, Yanhong Nie, Lu Liu, Zongping Liu, Yunpeng Yang","doi":"10.1093/ismejo/wraf028","DOIUrl":"https://doi.org/10.1093/ismejo/wraf028","url":null,"abstract":"The correlations between gut microbiota and host metabolism had been studied extensively, whereas little relevant work had been done to investigate the impact of gut microbial interactions on host metabolism. Assisted with bacteriocin-targeting strategy, we aimed to identify the glucose and lipid metabolism-associated gut microbes by adjusting the gut microbial composition of high-fat diet-fed mice. To fulfill this goal, the Listeria monocytogenes-derived bacteriocin Lmo2776 secretion module was constructed and integrated into the genome of Escherichia coli Nissle 1917, yielding the Lmo2776-secreting strain EcN-2776. EcN-2776 administration decreased the blood glucose and increased the serum triglyceride of high-fat diet-fed mice. 16S rRNA gene amplicon sequencing indicated that intestinal secretion of Lmo2776 adjusted the gut microbial composition of high-fat diet-fed mice. Specifically, Lmo2776 restricted the growth of Ligilactobacillus murinus, thus alleviating its inhibitory impact towards Faecalibaculum rodentium. Further analyses indicated that Faecalibaculum rodentium administration decreased the fasting blood glucose of high-fat diet-fed mice, which might be achieved by the intestinal consumption of glucose by Faecalibaculum rodentium. Our study identified the glucose metabolism-associated gut microbes, uncovered their interactions, deciphered the impact of gut microbial interaction on host glucose metabolism, and paved the way for treating hyperglycemia from the perspective of gut microbial interactions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143435496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correlating phylogenetic and functional diversity of the nod-free but nodulating Bradyrhizobium phylogroup 无结瘤但结瘤的慢生根瘤菌系统群的系统发育和功能多样性的相关性研究

The ISME Journal Pub Date : 2025-02-17 DOI: 10.1093/ismejo/wraf030

Lu Ling, Alicia Camuel, Sishuo Wang, Xiaojun Wang, Tianhua Liao, Jinjin Tao, Xingqin Lin, Nico Nouwen, Eric Giraud, Haiwei Luo

{"title":"Correlating phylogenetic and functional diversity of the nod-free but nodulating Bradyrhizobium phylogroup","authors":"Lu Ling, Alicia Camuel, Sishuo Wang, Xiaojun Wang, Tianhua Liao, Jinjin Tao, Xingqin Lin, Nico Nouwen, Eric Giraud, Haiwei Luo","doi":"10.1093/ismejo/wraf030","DOIUrl":"https://doi.org/10.1093/ismejo/wraf030","url":null,"abstract":"Bradyrhizobium is a main rhizobial lineage of which most members nodulate legume plants using Nod factors synthetized by the nod genes. However, members of the Photosynthetic supergroup (phylogroup) within Bradyrhizobium are nod-free, but still capable of establishing nitrogen-fixing nodules with some tropical legumes of the Aeschynomene genus. These unusual findings are based on the genomic sequences of only 13 Photosynthetic Bradyrhizobium strains, and almost all were isolated from Aeschynomene nodules. Here, we report that Photosynthetic Bradyrhizobium supergroup members are more abundantly associated with rice root (endosphere and rhizosphere) compared to grassland, forest, and maize samples based on rpoB amplicon sequence analyses. We sequenced 263 new isolates of this supergroup mostly from two main subspecies of cultivated rice (Oryza sativa L. spp. indica and japonica). The extended supergroup comprises three major clades with their diversity broadly covering the natural community of this supergroup: a basal clade with significant expansion of its diversity, a clade composed by two phylogenetically diverse strains including one newly isolated, and a new clade exclusively represented by our new strains. Although this supergroup members universally lack the canonical nod genes, all 28 assayed strains covering the broad diversity induced nodules on Aeschynomene indica. The three clades displayed important differences in the efficiency of symbiosis, aligning well with their phylogenetic divergence. With this expanded ecological, phylogenetic, and functional diversity, we conclude that the nod factor-independent nodulation of Aeschynomene is a common trait of this supergroup, in contrast to the photosynthetic trait originally thought of as its unifying feature.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143435214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial ecology of Serpentinite-hosted ecosystems 蛇纹石生态系统的微生物生态学

The ISME Journal Pub Date : 2025-02-16 DOI: 10.1093/ismejo/wraf029

Daniel R Colman, Alexis S Templeton, John R Spear, Eric S Boyd

{"title":"Microbial ecology of Serpentinite-hosted ecosystems","authors":"Daniel R Colman, Alexis S Templeton, John R Spear, Eric S Boyd","doi":"10.1093/ismejo/wraf029","DOIUrl":"https://doi.org/10.1093/ismejo/wraf029","url":null,"abstract":"Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143435212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Strain identity effects contribute more to Pseudomonas community functioning than strain interactions 菌株同一性效应比菌株相互作用对假单胞菌群落功能的影响更大

The ISME Journal Pub Date : 2025-02-08 DOI: 10.1093/ismejo/wraf025

Jos Kramer, Simon Maréchal, Alexandre R T Figueiredo, Rolf Kümmerli

{"title":"Strain identity effects contribute more to Pseudomonas community functioning than strain interactions","authors":"Jos Kramer, Simon Maréchal, Alexandre R T Figueiredo, Rolf Kümmerli","doi":"10.1093/ismejo/wraf025","DOIUrl":"https://doi.org/10.1093/ismejo/wraf025","url":null,"abstract":"Microbial communities can shape key ecological services, but the determinants of their functioning often remain little understood. While traditional research predominantly focuses on effects related to species identity (community composition and species richness), recent work increasingly explores the impact of species interactions on community functioning. Here, we conducted experiments with replicated small communities of Pseudomonas bacteria to quantify the relative importance of strain identity versus interaction effects on two important functions, community productivity and siderophore production. By combining supernatant and competition assays with an established linear model method, we show that both factors have significant effects on functioning, but identity effects generally outweigh strain interaction effects. These results hold irrespective of whether strain interactions are inferred statistically or approximated experimentally. Our results have implications for microbiome engineering, as the success of approaches aiming to induce beneficial (probiotic) strain interactions will be sensitive to strain identity effects in many communities.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143367262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Occurrence of “under-the-radar” antibiotic resistance in anthropogenically affected produce 在人为影响的农产品中发生“不为人知的”抗生素耐药性

The ISME Journal Pub Date : 2025-02-06 DOI: 10.1093/ismejo/wrae261

Chagai Davidovich, Kseniia Erokhina, Chhedi Lal Gupta, Yong-Guan Zhu, Jian-Qiang Su, Steven P Djordjevic, Ethan R Wyrsch, Shlomo E Blum, Eddie Cytryn

{"title":"Occurrence of “under-the-radar” antibiotic resistance in anthropogenically affected produce","authors":"Chagai Davidovich, Kseniia Erokhina, Chhedi Lal Gupta, Yong-Guan Zhu, Jian-Qiang Su, Steven P Djordjevic, Ethan R Wyrsch, Shlomo E Blum, Eddie Cytryn","doi":"10.1093/ismejo/wrae261","DOIUrl":"https://doi.org/10.1093/ismejo/wrae261","url":null,"abstract":"With global climate change, treated-wastewater irrigation and manure amendment are becoming increasingly important in sustainable agriculture in water- and nutrient-stressed regions. Yet, these practices can potentially disseminate pathogens and antimicrobial resistance determinants to crops, resulting in serious health risks to humans through the food chain. Previous studies demonstrated that pathogen and antimicrobial resistance indicators from wastewater and manure survive poorly in the environment, suggesting that ecological barriers prevent their dissemination. However, we recently found that these elements can persist below detection levels in low quality treated wastewater-irrigated soil, and potentially proliferate under favorable conditions. This “under-the-radar” phenomenon was further investigated here, in treated wastewater-irrigated and poultry litter-amended lettuce plants, using an enrichment platform that resembles gut conditions, and an analytical approach that combined molecular and cultivation-based techniques. Enrichment uncovered clinically relevant multidrug-resistant pathogen indicators and a myriad of antibiotic resistance genes in the litter amended and treated wastewater-irrigated lettuce that were not detected by direct analyses, or in the enriched freshwater irrigated samples. Selected resistant E. coli isolates were capable of horizontally transferring plasmids carrying multiple resistance genes to a susceptible strain. Overall, our study underlines the hidden risks of under-the-radar pathogen and antimicrobial resistance determinants in anthropogenically affected agroenvironments, providing a platform to improve quantitative microbial risk assessment models in the future.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum 植物-丛枝菌根真菌-细菌连续体的合作机制

The ISME Journal Pub Date : 2025-02-06 DOI: 10.1093/ismejo/wraf023

Shilong Duan, Zexing Jin, Lin Zhang, Stéphane Declerck

{"title":"Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum","authors":"Shilong Duan, Zexing Jin, Lin Zhang, Stéphane Declerck","doi":"10.1093/ismejo/wraf023","DOIUrl":"https://doi.org/10.1093/ismejo/wraf023","url":null,"abstract":"In nature, cooperation is an essential way for species, whether they belong to the same kingdom or to different kingdoms, to overcome the scarcity of resources and improve their fitness. Arbuscular mycorrhizal fungi are symbiotic microorganisms whose origin date back 400 million years. They form symbiotic associations with the vast majority of terrestrial plants, helping them to obtain nutrients from the soil in exchange for carbon. At the more complex level, soil bacteria participate in the symbiosis between arbuscular mycorrhizal fungi and plants: they obtain carbon from the exudation of hyphae connected to the roots and compensate for the limited saprophytic capacity of arbuscular mycorrhizal fungi by mineralizing organic compounds. Therefore, plants, arbuscular mycorrhizal fungi and soil bacteria constitute a continuum that may be accompanied by multiple forms of cooperation. In this review, we first analyzed the functional complementarities and differences between plants and arbuscular mycorrhizal fungi in arbuscular mycorrhizal symbiosis. Secondly, we discussed the resource exchange relationship between plants and arbuscular mycorrhizal fungi from the perspective of biological market theory and “surplus carbon” hypothesis. Finally, on the basis of mechanisms for maintaining cooperation, direct and indirect reciprocity in the hyphosphere, induced by the availability of external resource and species fitness, were examined. Exploring these reciprocal cooperations will provide a better understanding of the intricate ecological relationships between plants, arbuscular mycorrhizal fungi and soil bacteria as well as their evolutionary implications.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143367263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0