The ISME Journal最新文献

{"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}

{"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}

{"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}

{"title":"Active bacteria driving N2O mitigation and dissimilatory nitrate reduction to ammonium in ammonia recovery bioreactors","authors":"Hop V Phan, Shohei Yasuda, Kohei Oba, Hiroki Tsukamoto, Tomoyuki Hori, Megumi Kuroiwa, Akihiko Terada","doi":"10.1093/ismejo/wraf021","DOIUrl":"https://doi.org/10.1093/ismejo/wraf021","url":null,"abstract":"Shifting from ammonia removal to recovery is the current strategy in wastewater treatment management. We recently developed a microaerophilic activated sludge system for retaining ammonia whereas removing organic carbon with minimal N2O emissions. A comprehensive understanding of nitrogen metabolisms in the system is essential to optimize system performance. Here, we employed metagenomics and metatranscriptomics analyses to characterize the microbial community structure and activity during the transition from a microoxic to an oxic condition. A hybrid approach combining high-quality short reads and Nanopore long reads reconstructed 98 medium- to high-quality non-redundant metagenome-assembled genomes from the communities. The suppressed bacterial ammonia monooxygenase (amoA) expression was upregulated after shifting from a microoxic to an oxic condition. Seventy-three reconstructed metagenome-assembled genomes (>74% of the total) from 11 bacterial phyla harbored genes encoding proteins involved in nitrate respiration; 39 (~53%) carried N2O reductase (nosZ) genes with the predominance of clade II nosZ (31 metagenome-assembled genomes), and 24 (~33%) possessed nitrite reductase (ammonia-forming) genes (nrfA). Clade II nosZ and nrfA genes exhibited the highest and second-highest expressions among nitrogen metabolism genes, indicating robust N2O consumption and ammonification. Non-denitrifying clade II nosZ bacteria, Cloacibacterium spp., in the most abundant and active phylum Bacteroioda, were likely major N2O sinks. Elevated dissolved oxygen concentration inhibited clade II nosZ expression but not nrfA expression, potentially switching phenotypes from N2O reduction to ammonification. Collectively, the multi-omics analysis illuminated bacteria responsible for N2O reduction and ammonification in microoxic and oxic conditions, facilitating high-performance ammonia recovery.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258562","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}

{"title":"Metabolism of hemicelluloses by root-associated Bacteroidota species","authors":"Hannah Martin, Lucy A Rogers, Laila Moushtaq, Amanda A Brindley, Polly Forbes, Amy R Quintion, Andrew R J Murphy, Helen Hipperson, Tim J Daniell, Didier Ndeh, Sam Amsbury, Andrew Hitchcock, Ian D E A Lidbury","doi":"10.1093/ismejo/wraf022","DOIUrl":"https://doi.org/10.1093/ismejo/wraf022","url":null,"abstract":"Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression. Determining the mechanisms that enable bacteroidota to colonise plant roots may therefore provide opportunities for enhancing crop production through microbiome engineering. By focusing on nutrient acquisition mechanisms, we discovered Bacteroidota species lack high affinity ATP-binding cassette transporters common in other plant bacteria for capturing simple carbon exudates. Instead, bacteroidota possess TonB-dependent transporters predicted to import glycans produced by plant polysaccharide breakdown. Metatranscriptomics (oat rhizosphere) identified several TonB-dependent transporters genes that were highly expressed in Flavobacterium (phylum Bacteroidota). Using Flavobacterium johnsoniae as the model, we experimentally validated the function of one highly expressed TonB-dependent transporters, identifying a conserved Xyloglucan Utilisation Loci conferring an ability to import xyloglucan, the major hemicellulose secreted from plant roots. Xyloglucan utilisation loci harbour an endoxyloglucanase related to family 5 subfamily 4 subclade 2D glycoside hydrolases carrying a mutation that we demonstrate is required for full activity towards xyloglucan. Based on analysing 700 soil metagenomes, subclade 2D glycoside hydrolases have radiated in soil and are prevalent among plant-associated bacteroidota and certain taxa affiliated with Gammaproteobacteria. In bacteroidota, particularly Flavobacterium species, xyloglucan utilisation loci organisation was highly conserved, which may increase their competitive ability to utilise xyloglucan. Given bacteroidota lack high-affinity nutrient transporters for simple carbon, instead possessing xyloglucan utilisation loci and similar gene clusters, our data suggests hemicellulose exudates provide them with an important carbon source in the rhizosphere.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258458","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}

{"title":"Metabolic labour division trade-offs in denitrifying microbiomes","authors":"Nina Roothans, Mark C M van Loosdrecht, Michele Laureni","doi":"10.1093/ismejo/wraf020","DOIUrl":"https://doi.org/10.1093/ismejo/wraf020","url":null,"abstract":"Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification – the stepwise reduction of nitrate and nitrite to nitrogenous gases – is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143125126","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}

{"title":"Microbial reaction rate estimation using proteins and proteomes","authors":"J Scott P McCain, Gregory L Britten, Sean R Hackett, Michael J Follows, Gene-Wei Li","doi":"10.1093/ismejo/wraf018","DOIUrl":"https://doi.org/10.1093/ismejo/wraf018","url":null,"abstract":"Microbes transform their environments using diverse enzymatic reactions. However, it remains challenging to measure microbial reaction rates in natural environments. Despite advances in global quantification of enzyme abundances, the individual relationships between enzyme abundances and their reaction rates have not been systematically examined. Using matched proteomic and reaction rate data from microbial cultures, we show that enzyme abundance is often insufficient to predict its corresponding reaction rate. However, we discovered that global proteomic measurements can be used to make accurate rate predictions of individual reaction rates (median R2 = 0.78). Accurate rate predictions required only a small number of proteins and they did not need explicit prior mechanistic knowledge or environmental context. These results indicate that proteomes are encoders of cellular reaction rates, potentially enabling proteomic measurements in situ to estimate the rates of microbially mediated reactions in natural systems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072509","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}

{"title":"Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota","authors":"Guido Zampieri, Davide Santinello, Matteo Palù, Esteban Orellana, Paola Costantini, Lorenzo Favaro, Stefano Campanaro, Laura Treu","doi":"10.1093/ismejo/wraf017","DOIUrl":"https://doi.org/10.1093/ismejo/wraf017","url":null,"abstract":"Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised. In this work, we investigate the activity in a microbial community evolved to efficiently convert carbon dioxide into methane and predominantly populated by Methanothermobacter wolfeii. Through multi-omics, biochemical analysis and constraint-based modelling, we identify a potential formate cross-feeding from an uncharacterised Limnochordia species to M. wolfeii, driven by the recently discovered reductive glycine pathway and upregulated when hydrogen and carbon dioxide are limited. The quantitative consistency of this metabolic exchange with experimental data is shown by metagenome-scale metabolic models integrating condition-specific metatranscriptomics, which also indicate a broader three-way interaction involving M. wolfeii, the Limnochordia species, and Sphaerobacter thermophilus. Under limited hydrogen and carbon dioxide, aspartate released by M. wolfeii is fermented by S. thermophilus into acetate, which in turn is convertible into formate by Limnochordia, possibly forming a cooperative loop sustaining hydrogenotrophic methanogenesis. These findings expand our knowledge on the modes of carbon dioxide reduction into methane within natural microbial communities and provide an example of cooperative plasticity surrounding this process.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072510","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}

{"title":"Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance","authors":"Chenshuo Lin, Li-Juan Li, Kai Yang, Jia-Yang Xu, Xiao-Ting Fan, Qing-Lin Chen, Yong-Guan Zhu","doi":"10.1093/ismejo/wraf009","DOIUrl":"https://doi.org/10.1093/ismejo/wraf009","url":null,"abstract":"Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes. However, the effects of protozoan predation on antibiotic resistance genes dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse transcription quantitative PCR, to unveil how protozoa (Colpoda steinii and Acanthamoeba castellanii) influence the plasmid-mediated transfer of antibiotic resistance genes to soil microbial communities. Protozoan predation reduced the absolute abundance of plasmids but promoted the expression of conjugation-associated genes, leading to a 5-fold and 4.5-fold increase in conjugation frequency in the presence of C. steinii and A. castellanii, respectively. Excessive oxidative stress, increased membrane permeability, and the provoked SOS response closely associated with the increased conjugative transfer. Protozoan predation also altered the plasmid host range and selected for specific transconjugant taxa along with antibiotic resistance genes and virulence factors carried by transconjugant communities. This study underscores the role of protozoa in the plasmid-mediated conjugative transfer of antibiotic resistance genes, providing new insights into microbial mechanisms that drive the dissemination of environmental antibiotic resistance.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143050153","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}

{"title":"Microbial competition for iron determines its availability to the ferrous wheel","authors":"Robert F Strzepek, Pauline Latour, Michael J Ellwood, Yeala Shaked, Philip W Boyd","doi":"10.1093/ismejo/wraf015","DOIUrl":"https://doi.org/10.1093/ismejo/wraf015","url":null,"abstract":"Iron plays a pivotal role in regulating ocean primary productivity. Iron is supplied from diverse sources such as the atmosphere and the geosphere, and hence iron biogeochemical research has focused on identifying and quantifying such sources of “new” iron. However, the recycling of this new iron fuels up to 90% of the productivity in vast oceanic regions. Evidence points to the key role of microbes in mediating this recycling, referred to as the “ferrous wheel”, that remobilises iron initially supplied to ocean biota. In the iron-limited subantarctic waters of the Southern Ocean, iron uptake is dominated by microbes smaller than 2 μm and exhibits seasonal and depth-related variations. The microbial community within the <2 μm size fraction comprises heterotrophic bacteria and picophytoplankton, both competing for iron. Here, we dissect the demand component of the ferrous wheel by separately assessing iron uptake by heterotrophic bacteria and photoautotrophic picophytoplankton. To explore the seasonal and depth-related variability in iron uptake, the influence of light on iron uptake in both bacterial and phytoplankton communities was examined. We observed that picoeukaryote phytoplankton demonstrated iron uptake rates 10 times greater than those observed in bacteria when normalized to biomass. Light was shown to stimulate iron uptake by 8- to 16-fold in phytoplankton and by 4- to 8-fold in heterotrophic bacteria. These results highlight the unexpectedly significant role of picoeukaryotic phytoplankton in driving the speed of the ferrous wheel, with implications for iron recycling across diurnal cycles, different oceanic depths, and seasonally.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"73 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143050105","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}