ISME Journal最新文献_第7页

Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress. 盐胁迫下淡水厌氧甲烷氧化古细菌的渗透调节。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae137

Maider J Echeveste Medrano, Andy O Leu, Martin Pabst, Yuemei Lin, Simon J McIlroy, Gene W Tyson, Jitske van Ede, Irene Sánchez-Andrea, Mike S M Jetten, Robert Jansen, Cornelia U Welte

{"title":"Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress.","authors":"Maider J Echeveste Medrano, Andy O Leu, Martin Pabst, Yuemei Lin, Simon J McIlroy, Gene W Tyson, Jitske van Ede, Irene Sánchez-Andrea, Mike S M Jetten, Robert Jansen, Cornelia U Welte","doi":"10.1093/ismejo/wrae137","DOIUrl":"10.1093/ismejo/wrae137","url":null,"abstract":"Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.","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/PMC11337218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141728216","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

Nitrite-oxidizing bacteria adapted to low-oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones. 适应低氧条件的亚硝酸盐氧化细菌在海洋最小含氧区的亚硝酸盐氧化中占主导地位。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae160

Samantha G Fortin, Xin Sun, Amal Jayakumar, Bess B Ward

{"title":"Nitrite-oxidizing bacteria adapted to low-oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones.","authors":"Samantha G Fortin, Xin Sun, Amal Jayakumar, Bess B Ward","doi":"10.1093/ismejo/wrae160","DOIUrl":"10.1093/ismejo/wrae160","url":null,"abstract":"Nitrite is a central molecule in the nitrogen cycle because nitrite oxidation to nitrate (an aerobic process) retains fixed nitrogen in a system and its reduction to dinitrogen gas (anaerobic) reduces the fixed nitrogen inventory. Despite its acknowledged requirement for oxygen, nitrite oxidation is observed in oxygen-depleted layers of the ocean's oxygen minimum zones (OMZs), challenging the current understanding of OMZ nitrogen cycling. Previous attempts to determine whether nitrite-oxidizing bacteria in the anoxic layer differ from known nitrite oxidizers in the open ocean were limited by cultivation difficulties and sequencing depth. Here, we construct 31 draft genomes of nitrite-oxidizing bacteria from global OMZs. The distribution of nitrite oxidation rates, abundance and expression of nitrite oxidoreductase genes, and relative abundance of nitrite-oxidizing bacterial draft genomes from the same samples all show peaks in the core of the oxygen-depleted zone (ODZ) and are all highly correlated in depth profiles within the major ocean oxygen minimum zones. The ODZ nitrite oxidizers are not found in the Tara Oceans global dataset (the most complete oxic ocean dataset), and the major nitrite oxidizers found in the oxygenated ocean do not occur in ODZ waters. A pangenomic analysis shows the ODZ nitrite oxidizers have distinct gene clusters compared to oxic nitrite oxidizers and are microaerophilic. These findings all indicate the existence of nitrite oxidizers whose niche is oxygen-deficient seawater. Thus, specialist nitrite-oxidizing bacteria are responsible for fixed nitrogen retention in marine oxygen minimum zones, with implications for control of the ocean's fixed nitrogen inventory.","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/PMC11373643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141983776","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

Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function. 肠道微生物群失调会通过结肠吲哚和 LBP/HTR2B 介导的巨噬细胞功能来恶化色氨酸的免疫调节作用。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae166

Lili Jiang, Youling Hao, Dandan Han, Wenjian Dong, Aoyu Yang, Zhiyuan Sun, Yao Ge, Shuai Duan, Xiuwen Zhang, Zhaolai Dai

{"title":"Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function.","authors":"Lili Jiang, Youling Hao, Dandan Han, Wenjian Dong, Aoyu Yang, Zhiyuan Sun, Yao Ge, Shuai Duan, Xiuwen Zhang, Zhaolai Dai","doi":"10.1093/ismejo/wrae166","DOIUrl":"10.1093/ismejo/wrae166","url":null,"abstract":"Tryptophan (Trp) has been shown to regulate immune function by modulating gut serotonin (5-HT) metabolism and signaling. However, the mechanisms underlying the microbial modulation of gut 5-HT signaling in gut inflammation with gut microbiota dysbiosis require further investigation. Here, we investigated the effects of Trp supplementation on the composition and metabolism of the gut microbiome and 5-HT signaling-related gut immune function using a dextran sodium sulfate (DSS)-induced colitis mouse model coupled with antibiotic exposure. The results showed that antibiotic treatment before but not during DSS treatment decreased the immunoregulatory effects of Trp and aggravated gut inflammation and body weight loss in mice. Metagenomic analysis revealed that the fecal microbiota transplantation of Trp-enriched gut microbiota to recipient mice subject to antibiotic pre-exposure and DSS treatment alleviated inflammation by increasing the relative abundances of Lactobacillus and Parabacteroides and the microbial production of indole coupled with the activation of the 5-HT receptor 2B (HTR2B) in the colon. Transcriptomic analysis showed that HTR2B agonist administration strengthened the beneficial effects of Trp in DSS-induced colitis mice with antibiotic exposure by reducing gut lipopolysaccharide-binding protein (LBP) production, IκB-α/nuclear factor-κB signaling, and M1 macrophage polarization. Indole treatment reduced LBP production and M1 macrophage polarization both in mice with DSS-induced colitis and in lipopolysaccharide-treated mouse macrophages; however, the HTR2B antagonist reversed the effects of indole. Our findings provide the basis for developing new dietary and therapeutic interventions to improve gut microbiota dysbiosis-associated inflammatory gut disorders and diseases.","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/PMC11421149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047399","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

Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback. 一氧化二氮对甲烷生成的抑制是一种未被充分重视的温室气体排放反馈。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae027

Yongchao Yin, Fadime Kara-Murdoch, Robert W Murdoch, Jun Yan, Gao Chen, Yongchao Xie, Yanchen Sun, Frank E Löffler

{"title":"Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback.","authors":"Yongchao Yin, Fadime Kara-Murdoch, Robert W Murdoch, Jun Yan, Gao Chen, Yongchao Xie, Yanchen Sun, Frank E Löffler","doi":"10.1093/ismejo/wrae027","DOIUrl":"10.1093/ismejo/wrae027","url":null,"abstract":"Methane (CH4) and nitrous oxide (N2O) are major greenhouse gases that are predominantly generated by microbial activities in anoxic environments. N2O inhibition of methanogenesis has been reported, but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth yield and kinetic measurements and showed that micromolar concentrations of N2O suppress the growth of methanogens and CH4 production from major methanogenic substrate classes. Acetoclastic methanogenesis, estimated to account for two-thirds of the annual 1 billion metric tons of biogenic CH4, was most sensitive to N2O, with inhibitory constants (KI) in the range of 18-25 μM, followed by hydrogenotrophic (KI, 60-90 μM) and methylotrophic (KI, 110-130 μM) methanogenesis. Dissolved N2O concentrations exceeding these KI values are not uncommon in managed (i.e. fertilized soils and wastewater treatment plants) and unmanaged ecosystems. Future greenhouse gas emissions remain uncertain, particularly from critical zone environments (e.g. thawing permafrost) with large amounts of stored nitrogenous and carbonaceous materials that are experiencing unprecedented warming. Incorporating relevant feedback effects, such as the significant N2O inhibition on methanogenesis, can refine climate models and improve predictive capabilities.","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/PMC10960958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140050874","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

Strategies for tailoring functional microbial synthetic communities. 定制功能性微生物合成群落的策略。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae049

Jiayi Jing, Paolina Garbeva, Jos M Raaijmakers, Marnix H Medema

{"title":"Strategies for tailoring functional microbial synthetic communities.","authors":"Jiayi Jing, Paolina Garbeva, Jos M Raaijmakers, Marnix H Medema","doi":"10.1093/ismejo/wrae049","DOIUrl":"10.1093/ismejo/wrae049","url":null,"abstract":"Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.","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/PMC11008692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140307688","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

Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change. 全球变化下海洋 Synechococcus 元素配比的蛋白质组特征调控。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae046

Nathan S Garcia, Mingyu Du, Michele Guindani, Matthew R McIlvin, Dawn M Moran, Mak A Saito, Adam C Martiny

{"title":"Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change.","authors":"Nathan S Garcia, Mingyu Du, Michele Guindani, Matthew R McIlvin, Dawn M Moran, Mak A Saito, Adam C Martiny","doi":"10.1093/ismejo/wrae046","DOIUrl":"10.1093/ismejo/wrae046","url":null,"abstract":"Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature and nutrient stress on Synechococcus chemistry using laboratory chemostats, chemical analyses, and data-independent acquisition mass spectrometry proteomics. Nutrient supply accounted for most C:N:Pcell variability and induced tradeoffs between nutrient acquisition and ribosomal proteins. High temperature prompted heat-shock, whereas thermal effects via the \"translation-compensation hypothesis\" were only seen under P-stress. A Nonparametric Bayesian Local Clustering algorithm suggested that changes in lipopolysaccharides, peptidoglycans, and C-rich compatible solutes may also contribute to C:N:P regulation. Physiological responses match field-based trends in ecosystem stoichiometry and suggest a hierarchical environmental regulation of current and future ocean C:N: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/PMC11020310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186231","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

Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients. 与温度相关的营养关联沿着纬度梯度调节土壤细菌群落。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae145

Xing Huang, Jianjun Wang, Kenneth Dumack, Karthik Anantharaman, Bin Ma, Yan He, Weiping Liu, Hongjie Di, Yong Li, Jianming Xu

{"title":"Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients.","authors":"Xing Huang, Jianjun Wang, Kenneth Dumack, Karthik Anantharaman, Bin Ma, Yan He, Weiping Liu, Hongjie Di, Yong Li, Jianming Xu","doi":"10.1093/ismejo/wrae145","DOIUrl":"10.1093/ismejo/wrae145","url":null,"abstract":"Understanding the environmental and biological mechanisms shaping latitudinal patterns in microbial diversity is challenging in the field of ecology. Although multiple hypotheses have been proposed to explain these patterns, a consensus has rarely been reached. Here, we conducted a large-scale field survey and microcosm experiments to investigate how environmental heterogeneity and putative trophic interactions (exerted by protist-bacteria associations and T4-like virus-bacteria associations) affect soil bacterial communities along a latitudinal gradient. We found that the microbial latitudinal diversity was kingdom dependent, showing decreasing, clumped, and increasing trends in bacteria, protists, and T4-like viruses, respectively. Climatic and edaphic drivers played predominant roles in structuring the bacterial communities; the intensity of the climatic effect increased sharply from 30°N to 32°N, whereas the intensity of the edaphic effect remained stable. Biotic associations were also essential in shaping the bacterial communities, with protist-bacteria associations showing a quadratic distribution, whereas virus-bacteria associations were significant only at high latitudes. The microcosm experiments further revealed that the temperature component, which is affiliated with climate conditions, is the primary regulator of trophic associations along the latitudinal gradient. Overall, our study highlights a previously underestimated mechanism of how the putative biotic interactions influence bacterial communities and their response to environmental gradients.","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/PMC11334336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903451","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

Leveraging genome-scale metabolic models to understand aerobic methanotrophs. 利用基因组尺度代谢模型了解需氧甲烷营养体。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae102

Magdalena Wutkowska, Vojtěch Tláskal, Sergio Bordel, Lisa Y Stein, Justus Amuche Nweze, Anne Daebeler

{"title":"Leveraging genome-scale metabolic models to understand aerobic methanotrophs.","authors":"Magdalena Wutkowska, Vojtěch Tláskal, Sergio Bordel, Lisa Y Stein, Justus Amuche Nweze, Anne Daebeler","doi":"10.1093/ismejo/wrae102","DOIUrl":"10.1093/ismejo/wrae102","url":null,"abstract":"Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.","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/PMC11195481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307286","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

Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles. 大规模单病毒基因组学揭示了河水病毒隐藏的多样性和多样化的基因特征。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae124

Yohei Nishikawa, Ryota Wagatsuma, Yuko Tsukada, Lin Chia-Ling, Rieka Chijiiwa, Masahito Hosokawa, Haruko Takeyama

{"title":"Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles.","authors":"Yohei Nishikawa, Ryota Wagatsuma, Yuko Tsukada, Lin Chia-Ling, Rieka Chijiiwa, Masahito Hosokawa, Haruko Takeyama","doi":"10.1093/ismejo/wrae124","DOIUrl":"10.1093/ismejo/wrae124","url":null,"abstract":"Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental viral genomes, we developed a new single-viral genome sequencing platform with microfluidic-generated gel beads. Amplification of individual DNA viral genomes in mass-produced gel beads allows high-throughput genome sequencing compared to conventional single-virus genomics. The sequencing analysis of river water samples yielded 1431 diverse viral single-amplified genomes, whereas viral metagenomics recovered 100 viral metagenome-assembled genomes at the comparable sequence depth. The 99.5% of viral single-amplified genomes were determined novel at the species level, most of which could not be recovered by a metagenomic assembly. The large-scale acquisition of diverse viral genomes identified protein clusters commonly detected in different viral strains, allowing the gene transfer to be tracked. Moreover, comparative genomics within the same viral species revealed that the profiles of various methyltransferase subtypes were diverse, suggesting an enhanced escape from host bacterial internal defense mechanisms. Our use of gel bead-based single-virus genomics will contribute to exploring the nature of viruses by accelerating the accumulation of draft genomes of environmental DNA viruses.","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/PMC11283719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555842","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

Diversity alone does not reliably indicate the healthiness of an animal microbiome. 仅凭多样性并不能可靠地说明动物微生物群的健康状况。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae133

Claire E Williams, Tobin J Hammer, Candace L Williams

引用次数: 0