ISME Journal最新文献

{"title":"Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.","authors":"María Dolores Ramos-Barbero, Clara Gómez-Gómez, Gloria Vique, Laura Sala-Comorera, Lorena Rodríguez-Rubio, Maite Muniesa","doi":"10.1093/ismejo/wrae192","DOIUrl":"10.1093/ismejo/wrae192","url":null,"abstract":"<p><p>The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11475920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environment-specific virocell metabolic reprogramming.","authors":"Cristina Howard-Varona, Morgan M Lindback, Jane D Fudyma, Azriel Krongauz, Natalie E Solonenko, Ahmed A Zayed, William B Andreopoulos, Heather M Olson, Young-Mo Kim, Jennifer E Kyle, Tijana Glavina Del Rio, Joshua N Adkins, Malak M Tfaily, Subhadeep Paul, Matthew B Sullivan, Melissa B Duhaime","doi":"10.1093/ismejo/wrae055","DOIUrl":"10.1093/ismejo/wrae055","url":null,"abstract":"<p><p>Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a \"virocell,\" is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11170926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140327350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents.","authors":"Raphael Gollnisch, Dag Ahrén, Karin Rengefors","doi":"10.1093/ismejo/wrae045","DOIUrl":"10.1093/ismejo/wrae045","url":null,"abstract":"<p><p>The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the USA. Our aim was to investigate if populations of Gonyostomum semen in Europe and in the USA are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a novel method based on single-amplified genomes combined with Restriction-site Associated DNA sequencing that allows de novo genotyping of natural single-cell isolates without the need for culturing. We amplified over 900 single-cell genomes from 25 lake populations across Europe and the USA and identified two distinct population clusters, one in Europe and another in the USA. Low genetic diversity in European populations supports the hypothesized recent expansion of Gonyostomum semen on this continent. Geographic population structure within each continent was associated with differences in environmental variables that may have led to ecological divergence of population clusters. Overall, our results show that single-amplified genomes combined with Restriction-site Associated DNA sequencing can be used to analyze microalgal population structure and differentiation based on single-cell isolates from natural, uncultured samples.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140137463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Warming effects on grassland soil microbial communities are amplified in cool months.","authors":"Jiesi Lei, Yuanlong Su, Siyang Jian, Xue Guo, Mengting Yuan, Colin T Bates, Zhou Jason Shi, Jiabao Li, Yifan Su, Daliang Ning, Liyou Wu, Jizhong Zhou, Yunfeng Yang","doi":"10.1093/ismejo/wrae088","DOIUrl":"10.1093/ismejo/wrae088","url":null,"abstract":"<p><p>Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass prairie ecosystem. The interplay between warming and time altered (P < 0.05) the taxonomic and functional compositions of microbial communities. During the cool months (January to February and October to December), warming induced a soil microbiome with a higher genomic potential for carbon decomposition, community-level ribosomal RNA operon (rrn) copy numbers, and microbial metabolic quotients, suggesting that warming stimulated fast-growing microorganisms that enhanced carbon decomposition. Modeling analyses further showed that warming reduced the temperature sensitivity of microbial carbon use efficiency (CUE) by 28.7% when monthly average temperature was low, resulting in lower microbial CUE and higher heterotrophic respiration (Rh) potentials. Structural equation modeling showed that warming modulated both Rh and RS directly by altering soil temperature and indirectly by influencing microbial community traits, soil moisture, nitrate content, soil pH, and gross primary productivity. The modulation of Rh by warming was more pronounced in cooler months compared to warmer ones. Together, our findings reveal distinct warming-induced effects on microbial functional traits in cool months, challenging the norm of soil sampling only in the peak growing season, and advancing our mechanistic understanding of the seasonal pattern of RS and Rh sensitivity to warming.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11170927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression.","authors":"Silvia Coolen, Magda A Rogowska-van der Molen, Ineke Kwakernaak, Johan A van Pelt, Jelle L Postma, Theo van Alen, Robert S Jansen, Cornelia U Welte","doi":"10.1093/ismejo/wrae097","DOIUrl":"10.1093/ismejo/wrae097","url":null,"abstract":"<p><p>The Southern green shield bug, Nezara viridula, is an invasive piercing and sucking pest insect that feeds on crop plants and poses a threat to global food production. Given that insects are known to live in a close relationship with microorganisms, our study provides insights into the community composition and function of the N. viridula-associated microbiota and its effect on host-plant interactions. We discovered that N. viridula hosts both vertically and horizontally transmitted microbiota throughout different developmental stages and their salivary glands harbor a thriving microbial community that is transmitted to the plant while feeding. The N. viridula microbiota was shown to aid its host with the detoxification of a plant metabolite, namely 3-nitropropionic acid, and repression of host plant defenses. Our results demonstrate that the N. viridula-associated microbiota plays an important role in interactions between insects and plants and could therefore be considered a valuable target for the development of sustainable pest control strategies.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11195473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141248860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders.","authors":"Owen G Osborne, Randall R Jiménez, Allison Q Byrne, Brian Gratwicke, Amy Ellison, Carly R Muletz-Wolz","doi":"10.1093/ismejo/wrae104","DOIUrl":"10.1093/ismejo/wrae104","url":null,"abstract":"<p><p>Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via the evolution of host traits, habitat preferences, diets, and the co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis in Appalachian salamander skin in the context of infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd), while accounting for environmental microbiome exposure. We sampled ten salamander species representing >150M years of divergence, assessed their Bd infection status, and analysed their skin and environmental microbiomes. Our results reveal a significant signal of phylosymbiosis, whereas the local environmental pool of microbes, climate, geography, and Bd infection load had a smaller impact. Host-microbe co-speciation was not evident, indicating that the effect stems from the evolution of host traits influencing microbiome assembly. Bd infection is correlated with host phylogeny and the abundance of Bd-inhibitory bacterial strains, suggesting that the long-term evolutionary dynamics between salamander hosts and their skin microbiomes affect the present-day distribution of the pathogen, along with habitat-linked exposure risk. Five Bd-inhibitory bacterial strains showed unusual generalism: occurring in most host species and habitats. These generalist strains may enhance the likelihood of probiotic manipulations colonising and persisting on hosts. Our results underscore the substantial influence of host-microbiome eco-evolutionary dynamics on environmental health and disease outcomes.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11195472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Root-associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonization.","authors":"Clément Nicolle, Damien Gayrard, Alba Noël, Marion Hortala, Aurélien Amiel, Sabine Grat, Aurélie Le Ru, Guillaume Marti, Jean-Luc Pernodet, Sylvie Lautru, Bernard Dumas, Thomas Rey","doi":"10.1093/ismejo/wrae112","DOIUrl":"10.1093/ismejo/wrae112","url":null,"abstract":"<p><p>The rhizosphere, which serves as the primary interface between plant roots and the soil, constitutes an ecological niche for a huge diversity of microbial communities. Currently, there is little knowledge on the nature and the function of the different metabolites released by rhizospheric microbes to facilitate colonization of this highly competitive environment. Here, we demonstrate how the production of galbonolides, a group of polyene macrolides that inhibit plant and fungal inositol phosphorylceramide synthase (IPCS), empowers the rhizospheric Streptomyces strain AgN23, to thrive in the rhizosphere by triggering the plant's defence mechanisms. Metabolomic analysis of AgN23-inoculated Arabidopsis roots revealed a strong induction in the production of an indole alkaloid, camalexin, which is a major phytoalexin in Arabidopsis. By using a plant mutant compromised in camalexin synthesis, we show that camalexin production is necessary for the successful colonization of the rhizosphere by AgN23. Conversely, hindering galbonolides biosynthesis in AgN23 knock-out mutant resulted in loss of inhibition of IPCS, a deficiency in plant defence activation, notably the production of camalexin, and a strongly reduced development of the mutant bacteria in the rhizosphere. Together, our results identified galbonolides as important metabolites mediating rhizosphere colonization by Streptomyces.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11463028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141421709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining-impacted habitats.","authors":"Xiaoxu Sun, Qizhi Chen, Max M Häggblom, Guoqiang Liu, Tianle Kong, Duanyi Huang, Zhenyu Chen, Fangbai Li, Baoqin Li, Weimin Sun","doi":"10.1093/ismejo/wrae110","DOIUrl":"10.1093/ismejo/wrae110","url":null,"abstract":"<p><p>Arsenate [As(V)] reduction is a major cause of arsenic (As) release from soils, which threatens more than 200 million people worldwide. While heterotrophic As(V) reduction has been investigated extensively, the mechanism of chemolithotrophic As(V) reduction is less studied. Since As is frequently found as a sulfidic mineral in the environment, microbial mediated sulfur oxidation coupled to As(V) reduction (SOAsR), a chemolithotrophic process, may be more favorable in sites impacted by oligotrophic mining (e.g. As-contaminated mine tailings). While SOAsR is thermodynamically favorable, knowledge regarding this biogeochemical process is still limited. The current study suggested that SOAsR was a more prevalent process than heterotrophic As(V) reduction in oligotrophic sites, such as mine tailings. The water-soluble reduced sulfur concentration was predicted to be one of the major geochemical parameters that had a substantial impact on SOAsR potentials. A combination of DNA stable isotope probing and metagenome binning revealed members of the genera Sulfuricella, Ramlibacter, and Sulfuritalea as sulfur oxidizing As(V)-reducing bacteria (SOAsRB) in mine tailings. Genome mining further expanded the list of potential SOAsRB to diverse phylogenetic lineages such as members associated with Burkholderiaceae and Rhodocyclaceae. Metagenome analysis using multiple tailing samples across southern China confirmed that the putative SOAsRB were the dominant As(V) reducers in these sites. Together, the current findings expand our knowledge regarding the chemolithotrophic As(V) reduction process, which may be harnessed to facilitate future remediation practices in mine tailings.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11283718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141433267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat.","authors":"Tessa E Reid, Vanessa N Kavamura, Adriana Torres-Ballesteros, Monique E Smith, Maïder Abadie, Mark Pawlett, Ian M Clark, Jim A Harris, Tim H Mauchline","doi":"10.1093/ismejo/wrae131","DOIUrl":"10.1093/ismejo/wrae131","url":null,"abstract":"<p><p>The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification has been limited. This study investigated how endogenous (genome polyploidization) and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture-independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root-soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11292143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut.","authors":"","doi":"10.1093/ismejo/wrae143","DOIUrl":"10.1093/ismejo/wrae143","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"18 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141972254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}