ISME Journal最新文献_第2页

Warming effects on grassland soil microbial communities are amplified in cool months. 气候变暖对草地土壤微生物群落的影响在凉爽的月份会被放大。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae088

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

{"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":"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.","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}

引用次数: 0

Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression. 害虫 Nezara viridula 的微生物群介导解毒和植物防御抑制。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae097

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

{"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":"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.","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}

引用次数: 0

Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders. 系统共生塑造了阿巴拉契亚蝾螈的皮肤细菌群落和病原体保护功能。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae104

Owen G Osborne, Randall R Jiménez, Allison Q Byrne, Brian Gratwicke, Amy Ellison, Carly R Muletz-Wolz

{"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":"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.","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}

引用次数: 0

Root-associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonization. 与根相关的链霉菌会产生半苯甲酮类化合物，以调节植物免疫力并促进根瘤菌群的定植。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae112

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

{"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":"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.","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}

引用次数: 0

Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining-impacted habitats. 在受采矿影响的寡营养生境中，微生物介导的硫氧化作用与砷酸盐还原作用相结合。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae110

Xiaoxu Sun, Qizhi Chen, Max M Häggblom, Guoqiang Liu, Tianle Kong, Duanyi Huang, Zhenyu Chen, Fangbai Li, Baoqin Li, Weimin Sun

{"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":"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.","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}

引用次数: 0

Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat. 农业集约化减少了小麦中假定的植物生长促进根瘤菌的选择。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae131

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

{"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":"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.","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}

引用次数: 0

Correction to: Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut. 更正：超病毒性肺炎克雷伯氏菌利用基因组岛编码的毒素对付肠道中的细菌竞争者。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae143

引用次数: 0

Temperature modulates dominance of a superinfecting Arctic virus in its unicellular algal host. 温度调节北极超级感染病毒在其单细胞藻类宿主中的优势。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae161

Claudia Meyer, Victoria L N Jackson, Keith Harrison, Ioanna Fouskari, Henk Bolhuis, Yael A Artzy-Randrup, Jef Huisman, Adam Monier, Corina P D Brussaard

{"title":"Temperature modulates dominance of a superinfecting Arctic virus in its unicellular algal host.","authors":"Claudia Meyer, Victoria L N Jackson, Keith Harrison, Ioanna Fouskari, Henk Bolhuis, Yael A Artzy-Randrup, Jef Huisman, Adam Monier, Corina P D Brussaard","doi":"10.1093/ismejo/wrae161","DOIUrl":"10.1093/ismejo/wrae161","url":null,"abstract":"Complex virus-virus interactions can arise when multiple viruses coinfect the same host, impacting infection outcomes with broader ecological and evolutionary significance for viruses and host. Yet, our knowledge regarding virus competition is still limited, especially for single-celled eukaryotic host-virus systems. Here, we report on mutual interference of two dsDNA viruses, MpoV-45T and MpoV-46T, competing for their Arctic algal host Micromonas polaris. Both viruses affected each other's gene expression and displayed reduced genome replication during coinfection. MpoV-45T was the dominant virus, likely due to interference in the DNA replication of is competitor. Even when its coinfection was delayed, the dominant virus still prevailed while genome production of the other virus was strongly suppressed. This contrasts with typical superinfection exclusion, where the primary infection prevents secondary infection by other viruses. Higher temperature made the suppressed virus a stronger competitor, signifying that global warming is likely to alter virus-virus interactions in Arctic waters.","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/PMC11370638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037596","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}

引用次数: 0

Correction to: Anaerobic hydrocarbon biodegradation by alkylotrophic methanogens in deep oil reservoirs. 更正：深层油藏中烷基甲烷菌的厌氧碳氢化合物生物降解。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae196

引用次数: 0

Leveraging genomic information to predict environmental preferences of bacteria. 利用基因组信息预测细菌的环境偏好。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae195

Josep Ramoneda, Michael Hoffert, Elias Stallard-Olivera, Emilio O Casamayor, Noah Fierer

{"title":"Leveraging genomic information to predict environmental preferences of bacteria.","authors":"Josep Ramoneda, Michael Hoffert, Elias Stallard-Olivera, Emilio O Casamayor, Noah Fierer","doi":"10.1093/ismejo/wrae195","DOIUrl":"10.1093/ismejo/wrae195","url":null,"abstract":"Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.","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/PMC11488383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373437","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}

引用次数: 0