ISME communications最新文献

{"title":"Active microbiota persist in dry permafrost and active layer from elephant head, Antarctica","authors":"Claudia Wood, Alyssa Bruinink, Elizabeth Trembath-Reichert, M. Wilhelm, Chanel Vidal, Edward Balaban, Christopher P McKay, Robert Swan, Barney Swan, Jackie Goordial","doi":"10.1093/ismeco/ycad002","DOIUrl":"https://doi.org/10.1093/ismeco/ycad002","url":null,"abstract":"\u0000 Dry permafrost is a challenging environment for microbial life due to the cold, dry, and often oligotrophic conditions. In 2016, Elephant Head, Antarctica was confirmed as the second site on Earth to contain dry permafrost. It is geographically distinct from the McMurdo Dry Valleys where dry permafrost has been studied previously. Here we present the first study of the microbial activity, diversity, and functional potential of Elephant Head dry permafrost. Microbial activity was measured using radiorespiration assays with radiolabelled acetate as a carbon source at 5, 0 and − 5°C. Low, but detectable, rates of microbial activity were measured in some samples at 0 and − 5°C. This is distinct from previous studies of McMurdo Dry Valley dry permafrost which concluded that dry permafrost represents a cold-arid limit to life on the planet. The isolation of cold adapted organisms from these soils, including one capable of sub-zero growth further supports that Elephant Head dry active layer and dry permafrost harbor viable microbial life which may be active in situ. Metagenomic, 16S rRNA gene and ITS and amplicon sequencing identified similar microbial communities to other Antarctic and cold environments. The Elephant Head microbial community appears adapted for survival in cold, dry, and oligotrophic conditions based on the presence of cold adaptation and stress response genes in the metagenomes. Together our results show that dry permafrost environments do not exclude active microbial life at sub-zero temperatures and suggests that the cold, dry soils of Mars may also not be as inhospitable as previously thought.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139438895","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":"Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses","authors":"L. F. Kop, Hanna Koch, M. Jetten, H. Daims, Sebastian Lücker","doi":"10.1093/ismeco/ycad017","DOIUrl":"https://doi.org/10.1093/ismeco/ycad017","url":null,"abstract":"\u0000 The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, while Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes (MAGs) have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2–12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a non-redundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"10 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139439035","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":"Host species and geography impact bee-associated RNA virus communities with evidence for isolation-by-distance in viral populations","authors":"Chris R. P. Robinson, Adam G. Dolezal, Irene L. G. Newton","doi":"10.1093/ismeco/ycad003","DOIUrl":"https://doi.org/10.1093/ismeco/ycad003","url":null,"abstract":"\u0000 Virus symbionts are important mediators of ecosystem function, yet we know little of their diversity and ecology in natural populations. The alarming decline of pollinating insects in many regions of the globe, especially the European honey bee, Apis mellifera, has been driven in part by worldwide transmission of virus pathogens. Previous work has examined the transmission of known honey bee virus pathogens to wild bee populations, but only a handful of studies have investigated the native viromes associated with wild bees, limiting epidemiological predictors associated with viral pathogenesis. Further, variation among different bee species might have important consequences in the acquisition and maintenance of bee-associated virome diversity.\u0000 We utilized comparative metatranscriptomics to develop a baseline description of the RNA viromes associated with wild bee pollinators and to document viral diversity, community composition, and structure. Our sampling includes five wild-caught, native bee species that vary in social behavior as well as managed honey bees. We describe 26 putatively new RNA virus species based on RdRP phylogeny and show that each sampled bee species was associated with a specific virus community composition, even among sympatric populations of distinct host species. From 17 samples of a single host species, we recovered a single virus species despite over 600 km of distance between host populations and found strong evidence for isolation-by distance in associated viral populations. Our work adds to the small number of studies examining viral prevalence and community composition in wild bees.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"9 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139440362","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":"Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture","authors":"M. Oshiki, Emi Morimoto, Kanae Kobayashi, H. Satoh, Satoshi Okabe","doi":"10.1093/ismeco/ycad007","DOIUrl":"https://doi.org/10.1093/ismeco/ycad007","url":null,"abstract":"\u0000 Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2-. Remineralization of organic nitrogen compounds including urea and cyanate (OCN-) into NH4+ has been believed as an NH4+ source of the anammox process in OMZs. However, urea- or OCN-- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN- degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN- degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN- was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32 – 42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"89 21","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139440422","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":"Functional prediction of proteins from the human gut archaeome.","authors":"Polina V Novikova, Susheel Bhanu Busi, Alexander J Probst, Patrick May, Paul Wilmes","doi":"10.1093/ismeco/ycad014","DOIUrl":"10.1093/ismeco/ycad014","url":null,"abstract":"<p><p>The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, <i>Methanobrevibacter smithii</i> represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of <i>M. smithii</i> proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and <i>M. smithii</i>. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with <i>N</i>-linked and <i>O</i>-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between <i>Clostridia</i> species and <i>M. smithii</i>, which includes <i>sporulation Stage V proteins AE and AD</i>. Our study broadens the understanding of archaeal biology, particularly <i>M. smithii</i>, and highlights the importance of considering both sequence and structure for the prediction of protein function.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycad014"},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10939349/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140133383","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":"Rich diversity and active spatial–temporal dynamics of Thalassiosira species revealed by time-series metabarcoding analysis","authors":"Kuiyan Liu, Shuya Liu, Zongmei Cui, Yongfang Zhao, Nansheng Chen","doi":"10.1093/ismeco/ycad009","DOIUrl":"https://doi.org/10.1093/ismeco/ycad009","url":null,"abstract":"\u0000 Thalassiosira is a species-rich genus in Bacillariophyta that not only contributes positively as primary producer, but also poses negative impacts on ecosystems by causing harmful algal blooms (HABs). Although taxonomical studies have identified a large number of Thalassiosira species, however, the composition of Thalassiosira species and their geographical distribution in marine ecosystems were not well understood due primarily to the lack of resolution of morphology-based approaches used previously in ecological expeditions. In this study, we systematically analyzed the composition and spatial–temporal dynamic distributions of Thalassiosira in the model marine ecosystem Jiaozhou Bay by applying metabarcoding analysis. Through analyzing samples collected monthly from 12 sampling sites, 14 Thalassiosira species were identified, including five species that were not previously reported in Jiaozhou Bay, demonstrating the resolution and effectiveness of metabarcoding analysis in ecological research. Many Thalassiosira species showed prominent temporal preferences in Jiaozhou Bay, with some displaying spring–winter preference represented by T. tenera, while others displaying summer-autumn preference represented by T. lundiana and T. minuscula, indicating that the temperature as an important driving factor in the temporal dynamics. The application of metabarcoding analysis, equipped with appropriate molecular markers with high resolution and high specificity and databases of reference molecular marker sequences for potential all Thalassiosira species, will revolutionize ecological research of Thalassiosira species in Jiaozhou Bay and other marine ecosystems.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139439066","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":"Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom <i>Phaeodactylum tricornutum</i>.","authors":"Timothée Chaumier, Feng Yang, Eric Manirakiza, Ouardia Ait-Mohamed, Yue Wu, Udita Chandola, Bruno Jesus, Gwenael Piganeau, Agnès Groisillier, Leila Tirichine","doi":"10.1093/ismeco/ycad008","DOIUrl":"https://doi.org/10.1093/ismeco/ycad008","url":null,"abstract":"<p><p>Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom <i>Phaeodactylum tricornutum</i> including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the <i>P. tricornutum</i> population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycad008"},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139673792","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":"Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets","authors":"Mazel Florent, Pitteloud Camille, Guisan Antoine, Pellissier Loïc","doi":"10.1093/ismeco/ycad013","DOIUrl":"https://doi.org/10.1093/ismeco/ycad013","url":null,"abstract":"\u0000 Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont community are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e., harbor host specificity) and host phylogeny (i.e., harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g., endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g., most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e., hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. While elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher specificity in endosymbionts corroborates the idea that -everything else being equal- vertically transmitted microbes harbor stronger specificity signal, but the absence of phylosymbiosis suggests that specificity changes quickly on evolutionary time scales.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"2 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139439355","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":"Homogenization of bacterial plastisphere community in soil: a continental-scale microcosm study","authors":"Yuanze Sun, Mochen Wu, Siyuan Xie, Jingxi Zang, Xiang Wang, Yuyi Yang, Changchao Li, Jie Wang","doi":"10.1093/ismeco/ycad012","DOIUrl":"https://doi.org/10.1093/ismeco/ycad012","url":null,"abstract":"\u0000 Microplastics alter niches of soil microbiota by providing trillions of artificial microhabitats, termed the “plastisphere”. Due to the ever-increasing accumulation of microplastics in ecosystems, it is urgent to understand the ecology of microbes associated with the plastisphere. Here, we present a continental-scale study of the bacterial plastisphere on polyethylene microplastics compared with adjacent soil communities across 99 sites collected from across China through microcosm experiments. In comparison with the soil bacterial communities, we found that plastispheres had a greater proportion of Actinomycetota and Bacillota, but lower proportions of Pseudomonadota, Acidobacteriota, Gemmatimonadota, and Bacteroidota. The spatial dispersion and the dissimilarity among plastisphere communities were less variable than those among the soil bacterial communities, suggesting highly homogenized bacterial communities on microplastics. The relative importance of homogeneous selection in plastispheres was greater than that in soil samples, possibly because of the more uniform properties of PE microplastics compared to the surrounding soil. Importantly, we found that the degree to which plastisphere and soil bacterial communities differed was negatively correlated with the soil pH and carbon content and positively related to the mean annual temperature of sampling sites. Our work provides a more comprehensive continental-scale perspective on the microbial communities that form in the plastisphere and highlights the potential impacts of microplastics on the maintenance of microbial biodiversity and ecosystem functioning.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"64 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139441109","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":"Genotype-associated heritable rumen bacteria can be a stable microbiota passed to the offspring","authors":"Xinwei Zang, Huizeng Sun, Mingyuan Xue, Shulin Liang, Le Luo Guan, Jianxin Liu","doi":"10.1093/ismeco/ycad020","DOIUrl":"https://doi.org/10.1093/ismeco/ycad020","url":null,"abstract":"\u0000 Recent studies have reported that some rumen microbes are “heritable” (those have significant narrow sense heritability) and can significantly contribute to host phenotype variations. However, it is unknown if these heritable rumen bacteria can be passed to the next generation. In this study, the rumen bacteria from mother cows (sampled in 2016) and their offspring (sampled in 2019) were assessed to determine if vertical transmission occurred between the two generations. The analysis of relationship between host genotypes and heritable bacterial abundances showed that potential of five host genotypes can affect the relative abundances of two unclassified species level heritable bacteria (Pseudoscardovia, and p-251-o5). The G allele of BTB-01532239 and A allele of ARS-BFGL-NGS-8960 were associated with a higher relative abundance of p-251-o5. The A allele of BTB-00740910 and BovineHD1300021786, and G allele of BovineHD1900005868 were associated with a higher relative abundance of Pseudoscardovia. The mother-offspring comparison revealed that the heritable rumen bacteria had higher compositional similarity than nonheritable bacteria between two generations, and the predicted heritable microbial functions had higher stability than those from non-heritable bacteria. These findings suggest that a high stability exists in heritable rumen bacteria, which could be passed to the next generation in dairy cows.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139439188","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}