ISME Journal最新文献_第9页

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

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 10.8 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":10.8,"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

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

Comment on "Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone" by Yuanxu Song et al. 就宋元旭等人《依赖腐殖酸的乙酰甲烷虫呼吸生长涉及吡咯喹啉醌》发表的评论

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae020

Derek R Lovley, Dawn E Holmes

引用次数: 0

Response to comment on "Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone" by Yuanxu Song et al. 对Yuanxu song等人关于 "Methanosarcina acetivorans的腐殖酸依赖性呼吸生长涉及吡咯喹啉醌 "的评论的回应

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae019

Yuanxu Song, Rui Huang, Ling Li, Mingyu Wang, Shuguang Wang, James G Ferry, Zhen Yan

引用次数: 0

Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats. 需氧甲烷营养体在限氧淡水生境中的神秘持久性。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae041

Paula C J Reis, Jackson M Tsuji, Cerrise Weiblen, Sherry L Schiff, Matthew Scott, Lisa Y Stein, Josh D Neufeld

引用次数: 0

High-sugar diet leads to loss of beneficial probiotics in housefly larvae guts. 高糖饮食导致家蝇幼虫肠道中有益益生菌的流失

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae193

Anna Voulgari-Kokota, Francesco Boatta, Ruud Rijkers, Bregje Wertheim, Leo W Beukeboom, Jacintha Ellers, Joana Falcao Salles

{"title":"High-sugar diet leads to loss of beneficial probiotics in housefly larvae guts.","authors":"Anna Voulgari-Kokota, Francesco Boatta, Ruud Rijkers, Bregje Wertheim, Leo W Beukeboom, Jacintha Ellers, Joana Falcao Salles","doi":"10.1093/ismejo/wrae193","DOIUrl":"10.1093/ismejo/wrae193","url":null,"abstract":"The housefly (Musca domestica) is a common insect species with only a few recurrent bacterial taxa in its gut microbiota, because the numerous microbial acquisition routes in its septic habitats can favor transient microbes. Here, we investigated the role of the diet on the microbiota and the developmental success of a housefly strain reared on three substrates. We used a control wheat bran-based substrate, and added clotted cream and sucrose to make a high-fat, and a high-sugar substrate, respectively. The conducted survey revealed that, in contrast to the high-fat diet, the high-sugar diet caused lower developmental success and less diverse microbiota, in which several lactobacilli were replaced with Weissella bacterial phylotypes. Cultures with sucrose as the sole carbon source confirmed that a Weissella confusa strain, isolated from larvae, could utilize sucrose more efficiently than other tested lactic acid bacteria; a result also supported by gene function prediction analysis. Enhancing the rearing substrate with Limosilactobacillus fermentum and Lactiplantibacillus plantarum strains, which were isolated from control larvae, could not only revert the negative effect of the high-sucrose diet on development, but also increase the gut bacterial diversity. In our study, we show that the microbiota shifts in response to the high-sucrose diet did not benefit the host, that showed lower developmental success. In contrast, high-sucrose favored specific components of the microbiota, that continued to be enriched even after multiple generations, outcompeting beneficial bacteria. Also, microbiome manipulation showed the potential of probiotics to rescue host performance and restore the microbiome.","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/PMC11495414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373436","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