ISME communications最新文献

{"title":"Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen","authors":"Yuto Fukuyama, Shigeru Shimamura, Sanae Sakai, Yuta Michimori, Tomomi Sumida, Yoshito Chikaraishi, Haruyuki Atomi, T. Nunoura","doi":"10.1093/ismeco/ycad006","DOIUrl":"https://doi.org/10.1093/ismeco/ycad006","url":null,"abstract":"\u0000 Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 μL of 100 nmol/L amino acids comparable to a mere 1 $times$ 104–105 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the occurrence of both the Wood-Ljungdahl pathway and an incomplete reductive tricarboxylic acid cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acid, genomic information, and public databases. Among them, the presence of alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS can be considered the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to any kind of isolated microbe.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"45 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139440958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wild plant species with broader precipitation niches exhibit stronger host selection in rhizosphere microbiome assembly","authors":"Haikun Ma, Jinming Liu, Lidong Mo, Luisa M Arias Giraldo, M. Xiang, Xingzhong Liu","doi":"10.1093/ismeco/ycad015","DOIUrl":"https://doi.org/10.1093/ismeco/ycad015","url":null,"abstract":"\u0000 Plants actively recruit microbes from the soil, forming species-specific root microbiomes. However, their relationship with plant adaptations to temperature and precipitation remains unclear. Here we examined the host-selected and conserved microbiomes of 13 native plant species in the Xinlingol steppe, Inner Mongolia, a semi-arid region in China. Through calculating plant global precipitation and temperature niches, plant phylogenetic distances and functional traits, we found that these factors significantly influenced rhizosphere microbiome assembly. We further quantified the strength of host selection and observed that plants with wider precipitation niches exhibited greater host selection strength in their rhizosphere microbiome assembly and higher rhizosphere bacterial diversity. In general, the rhizosphere microbiome showed a stronger link to plant precipitation niches than temperature niches. Haliangium exhibited consistent responsiveness to host characteristics. Our findings offer novel insights into host selection effects and ecological determinants of wild plant rhizosphere microbiome assembly, with implications for steering the root microbiomes of wild plants and understanding plant-microbiome evolution.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"85 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139440701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Horizontal metaproteomics and CAZymes analysis of lignocellulolytic microbial consortia selectively enriched from cow rumen and termite gut","authors":"Emeline Auer, Adèle Lazuka, Bertrand Huguenin-Bizot, Nico Jehmlich, Sébastien Déjean, Vincent Lombard, Bernard Henrissat, Michael O’Donohue, Guillermina Hernandez-Raquet","doi":"10.1038/s43705-023-00339-0","DOIUrl":"10.1038/s43705-023-00339-0","url":null,"abstract":"Selectively enriched microbial consortia are potentially useful for the conversion of lignocellulose (LC) into biofuels and commodity chemicals. Consortia are also of interest to elucidate the roles of individual microorganisms and the dynamics of enzymes involved in LC deconstruction. Using metaproteomics, 16 S rRNA gene amplicon sequencing and multivariate discriminant analysis, we revealed the temporal dynamics of microbial species and their proteins during anaerobic conversion of LC by microbial consortia derived from cow rumen (RWS) and termite gut (TWS) microbiomes. Bacteroidetes (Bacteroidota), Firmicutes (Bacillota) and Proteobacteria (Pseudomonadota) phyla were dominant, irrespective the inoculum origin, displaying functional complementarities. We identified a large variety of carbohydrate-active enzymes, distributed in 94 CAZy families, involved in biomass deconstruction. Additionally, proteins involved in short chain fatty acids biosynthesis were detected. Multivariate analysis clearly differentiates RWS and TWS metaproteomes, with differences originating in the initial inoculates. Further supervised discriminant analysis of the temporal succession of CAZymes revealed that both consortia consume easily accessible oligosaccharides during the early stage of incubation, degrading more complex hemicellulose and cellulose fractions at later stages, an action that pursues throughout the incubation period. Our results provide new insights regarding the functional roles and complementarities existing in lignocellulolytic consortia and highlight their potential for biorefinery applications.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":" ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43705-023-00339-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139643940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multiyear time series (2004–2012) of bacterial and archaeal community dynamics in a changing Arctic Ocean","authors":"Susanne A Kraemer, A. Ramachandran, Vera E. Onana, William K W Li, David A Walsh","doi":"10.1093/ismeco/ycad004","DOIUrl":"https://doi.org/10.1093/ismeco/ycad004","url":null,"abstract":"\u0000 Climate change is profoundly impacting the Arctic, leading to a loss of multiyear sea ice and a warmer, fresher upper Arctic Ocean. The response of microbial communities to these climate-mediated changes is largely unknown. Here, we document the interannual variation in bacterial and archaeal communities across a 9-year time series of the Canada Basin that includes two historic sea ice minima (2007 and 2012). We report an overall loss of bacterial and archaeal community richness and significant shifts in community composition. The magnitude and period of most rapid change differed between the stratified water layers. The most pronounced changes in the upper water layers (surface mixed layer and upper Arctic water) occurred earlier in the time series, while changes in the lower layer (Pacific-origin water) occurred later. Shifts in taxonomic composition across time were subtle, but a decrease in Bacteroidota taxa and increase in Thaumarchaeota and Euryarchaeota taxa were the clearest signatures of change. This time series provides a rare glimpse into the potential influence of climate change on Arctic microbial communities; extension to the present day should contribute to deeper insights into the trajectory of Arctic marine ecosystems in response to warming and freshening.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"30 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139455870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments","authors":"Blandine Trouche, Clemens Schauberger, Feriel Bouderka, Jean-Christophe Auguet, Caroline Belser, Julie Poulain, Bo Thamdrup, Patrick Wincker, Sophie Arnaud-Haond, Ronnie N. Glud, Loïs Maignien","doi":"10.1038/s43705-023-00341-6","DOIUrl":"10.1038/s43705-023-00341-6","url":null,"abstract":"Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade’s ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":" ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10746724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138886790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort","authors":"Guido Bonthond, Jan Beermann, Lars Gutow, Andreas Neumann, Francisco Rafael Barboza, Andrea Desiderato, Vera Fofonova, Stephanie B. Helber, Sahar Khodami, Casper Kraan, Hermann Neumann, Sven Rohde, Peter J. Schupp","doi":"10.1038/s43705-023-00336-3","DOIUrl":"10.1038/s43705-023-00336-3","url":null,"abstract":"Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":" ","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10724143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138815241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nitrogen and sulfur metabolisms encoded in prokaryotic communities associated with sea ice algae","authors":"Christopher M. Bellas, Karley Campbell, Martyn Tranter, Patricia Sánchez-Baracaldo","doi":"10.1038/s43705-023-00337-2","DOIUrl":"10.1038/s43705-023-00337-2","url":null,"abstract":"Sea ice habitats harbour seasonally abundant microalgal communities, which can be highly productive in the spring when the availability of light increases. An active, bloom-associated prokaryotic community relies on these microalgae for their organic carbon requirements, however an analysis of the encoded metabolic pathways within them is lacking. Hence, our understanding of biogeochemical cycling within sea ice remains incomplete. Here, we generated metagenomic assembled genomes from the bottom of first-year sea ice in northwestern Hudson Bay, during a spring diatom bloom. We show that the prokaryotic community had the metabolic potential to degrade algal derived dimethylsulphoniopropionate and oxidise sulfur. Facultative anaerobic metabolisms, specifically, dissimilatory nitrate reduction and denitrification were also prevalent here, suggesting some sea ice prokaryotes are metabolically capable of adapting to fluctuating oxygen levels during algal bloom conditions. Such denitrification could be an important loss of fixed-N2 in the changing Arctic marine system.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":" ","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43705-023-00337-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138584413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic","authors":"Taylor Priest, Silvia Vidal-Melgosa, Jan-Hendrik Hehemann, Rudolf Amann, Bernhard M. Fuchs","doi":"10.1038/s43705-023-00324-7","DOIUrl":"10.1038/s43705-023-00324-7","url":null,"abstract":"Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter and are key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by marine microbes have been centred on phytoplankton blooms in temperate regions, while far less is known from high-latitude waters and during later seasonal stages. Here, we combine glycan microarrays and analytical chromatography with metagenomics and metatranscriptomics to show the spatial heterogeneity in glycan distribution and potential carbohydrate utilisation by microbes in Atlantic waters of the Arctic. The composition and abundance of monomers and glycan structures in POM varied with location and depth. Complex fucose-containing sulfated polysaccharides, known to accumulate in the ocean, were consistently detected, while the more labile β-1,3-glucan exhibited a patchy distribution. Through ‘omics analysis, we identify variations in the abundance and transcription of carbohydrate degradation-related genes across samples at the community and population level. The populations contributing the most to transcription were taxonomically related to those known as primary responders and key carbohydrate degraders in temperate ecosystems, such as NS4 Marine Group and Formosa. The unique transcription profiles for these populations suggest distinct substrate utilisation potentials, with predicted glycan targets corresponding to those structurally identified in POM from the same sampling sites. By combining cutting-edge technologies and protocols, we provide insights into the carbohydrate component of the carbon cycle in the Arctic during late summer and present a high-quality dataset that will be of great value for future comparative analyses.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":" ","pages":"1-13"},"PeriodicalIF":0.0,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43705-023-00324-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138585726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Zea mays genotype influences microbial and viral rhizobiome community structure","authors":"Pooja Yadav, Amanda Quattrone, Yuguo Yang, Jacob Owens, Rebecca Kiat, Thirumurugen Kuppusamy, Sabrina E. Russo, Karrie A. Weber","doi":"10.1038/s43705-023-00335-4","DOIUrl":"10.1038/s43705-023-00335-4","url":null,"abstract":"Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":" ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10700569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138500369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes","authors":"Daniel E. Schäffer, Wenrui Li, Abdurrahman Elbasir, Dario C. Altieri, Qi Long, Noam Auslander","doi":"10.1038/s43705-023-00338-1","DOIUrl":"10.1038/s43705-023-00338-1","url":null,"abstract":"Local microbiome shifts are implicated in the development and progression of gastrointestinal cancers, and in particular, esophageal carcinoma (ESCA), which is among the most aggressive malignancies. Short-read RNA sequencing (RNAseq) is currently the leading technology to study gene expression changes in cancer. However, using RNAseq to study microbial gene expression is challenging. Here, we establish a new tool to efficiently detect viral and bacterial expression in human tissues through RNAseq. This approach employs a neural network to predict reads of likely microbial origin, which are targeted for assembly into longer contigs, improving identification of microbial species and genes. This approach is applied to perform a systematic comparison of bacterial expression in ESCA and healthy esophagi. We uncover bacterial genera that are over or underabundant in ESCA vs healthy esophagi both before and after correction for possible covariates, including patient metadata. However, we find that bacterial taxonomies are not significantly associated with clinical outcomes. Strikingly, in contrast, dozens of microbial proteins were significantly associated with poor patient outcomes and in particular, proteins that perform mitochondrial functions and iron-sulfur coordination. We further demonstrate associations between these microbial proteins and dysregulated host pathways in ESCA patients. Overall, these results suggest possible influences of bacteria on the development of ESCA and uncover new prognostic biomarkers based on microbial genes. In addition, this study provides a framework for the analysis of other human malignancies whose development may be driven by pathogens.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":" ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10696091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138483580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}