ISME communications最新文献_第2页

Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments. 瑞士湖泊沉积物中微生物氮转化潜力和基因表达的元基因组和转录组分析。

IF 5.1

ISME communications Pub Date : 2024-10-15 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae110

Kathrin B L Baumann, Alessandra Mazzoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Beat Müller, Robert Niederdorfer, Shinichi Sunagawa, Mark A Lever, Moritz F Lehmann, Helmut Bürgmann

{"title":"Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments.","authors":"Kathrin B L Baumann, Alessandra Mazzoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Beat Müller, Robert Niederdorfer, Shinichi Sunagawa, Mark A Lever, Moritz F Lehmann, Helmut Bürgmann","doi":"10.1093/ismeco/ycae110","DOIUrl":"https://doi.org/10.1093/ismeco/ycae110","url":null,"abstract":"The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae110"},"PeriodicalIF":5.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11476906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142486154","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}

引用次数: 0

Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis. 确定微生物接种对植物性状有效性的生物和实验因素：荟萃分析。

IF 5.1

ISME communications Pub Date : 2024-10-14 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae122

Hamed Azarbad, Robert R Junker

{"title":"Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis.","authors":"Hamed Azarbad, Robert R Junker","doi":"10.1093/ismeco/ycae122","DOIUrl":"10.1093/ismeco/ycae122","url":null,"abstract":"Bacterial and fungal microbiomes associated with plants can significantly affect the host's phenotype. Inoculating plants with one or multiple bacterial and fungal species can affect specific plant traits, which is exploited in attempts to increase plant performance and stress tolerance by microbiome engineering. Currently, we lack a comprehensive synthesis on the generality of these effects related to different biological (e.g. plant models, plant traits, and microbial taxa) and experimental factors. In a meta-analysis, we showed that the plant trait under consideration and the microbial taxa used to inoculate plants significantly influenced the strength of the effect size. In a methodological context, experiments under sterilized conditions and short-term periods resulted in larger positive effects on plant traits than those of unsterilized and long-term experiments. We recommend that future studies should not only consider (short-term) laboratory experiments with sterilized plants and single inoculants but also and more often (long-term) field or greenhouse experiments with naturally occurring microbial communities associated with the plants and inoculated consortia including both bacteria and fungi.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae122"},"PeriodicalIF":5.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11538580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592454","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}

引用次数: 0

Rhizospheric miRNAs affect the plant microbiota. 根瘤层 miRNA 对植物微生物群的影响

IF 5.1

ISME communications Pub Date : 2024-10-12 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae120

Harriet Middleton, Jessica Ann Dozois, Cécile Monard, Virginie Daburon, Emmanuel Clostres, Julien Tremblay, Jean-Philippe Combier, Étienne Yergeau, Abdelhak El Amrani

{"title":"Rhizospheric miRNAs affect the plant microbiota.","authors":"Harriet Middleton, Jessica Ann Dozois, Cécile Monard, Virginie Daburon, Emmanuel Clostres, Julien Tremblay, Jean-Philippe Combier, Étienne Yergeau, Abdelhak El Amrani","doi":"10.1093/ismeco/ycae120","DOIUrl":"https://doi.org/10.1093/ismeco/ycae120","url":null,"abstract":"Small ribonucleic acids (RNAs) have been shown to play important roles in cross-kingdom communication, notably in plant-pathogen relationships. Plant micro RNAs (miRNAs)-one class of small RNAs-were even shown to regulate gene expression in the gut microbiota. Plant miRNAs could also affect the rhizosphere microbiota. Here we looked for plant miRNAs in the rhizosphere of model plants, and if these miRNAs could affect the rhizosphere microbiota. We first show that plant miRNAs were present in the rhizosphere of Arabidopsis thaliana and Brachypodium distachyon. These plant miRNAs were also found in or on bacteria extracted from the rhizosphere. We then looked at the effect these plants miRNAs could have on two typical rhizosphere bacteria, Variovorax paradoxus and Bacillus mycoides. The two bacteria took up a fluorescent synthetic miRNA but only V. paradoxus shifted its transcriptome when confronted to a mixture of six plant miRNAs. V. paradoxus also changed its transcriptome when it was grown in the rhizosphere of Arabidopsis that overexpressed a miRNA in its roots. As there were differences in the response of the two isolates used, we looked for shifts in the larger microbial community. We observed shifts in the rhizosphere bacterial communities of Arabidopsis mutants that were impaired in their small RNA pathways, or overexpressed specific miRNAs. We also found differences in the growth and community composition of a simplified soil microbial community when exposed in vitro to a mixture of plant miRNAs. Our results support the addition of miRNAs to the plant tools shaping rhizosphere microbial assembly.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae120"},"PeriodicalIF":5.1,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549350","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}

引用次数: 0

NovoLign: metaproteomics by sequence alignment. NovoLign：通过序列比对进行元蛋白质组学研究。

IF 5.1

ISME communications Pub Date : 2024-10-12 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae121

Hugo B C Kleikamp, Ramon van der Zwaan, Ramon van Valderen, Jitske M van Ede, Mario Pronk, Pim Schaasberg, Maximilienne T Allaart, Mark C M van Loosdrecht, Martin Pabst

{"title":"NovoLign: metaproteomics by sequence alignment.","authors":"Hugo B C Kleikamp, Ramon van der Zwaan, Ramon van Valderen, Jitske M van Ede, Mario Pronk, Pim Schaasberg, Maximilienne T Allaart, Mark C M van Loosdrecht, Martin Pabst","doi":"10.1093/ismeco/ycae121","DOIUrl":"10.1093/ismeco/ycae121","url":null,"abstract":"Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae121"},"PeriodicalIF":5.1,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11530927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142570521","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}

引用次数: 0

Imbalanced intracellular nutrient stoichiometries drive the regional structural variation of microeukaryotic communities in paddy fields. 细胞内养分比例失调导致稻田中微真核生物群落的区域结构变化。

IF 5.1

ISME communications Pub Date : 2024-10-10 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae119

Pengfei Sun, Eleonora Silvano, Yin Chen, Yonghong Wu

{"title":"Imbalanced intracellular nutrient stoichiometries drive the regional structural variation of microeukaryotic communities in paddy fields.","authors":"Pengfei Sun, Eleonora Silvano, Yin Chen, Yonghong Wu","doi":"10.1093/ismeco/ycae119","DOIUrl":"10.1093/ismeco/ycae119","url":null,"abstract":"Periphytons serve as critical microbial nutrient sinks at the soil-water interface, influencing biogeochemical cycles and nutrient migration in paddy fields. Despite their importance, the impact of accumulated intracellular nutrients on the spatial dynamics and community assembly of periphytons, particularly their microeukaryote communities, remains unclear. To address this gap, we examined the nutrient accumulation potential and its effects on microeukaryotes in periphytons from 220 paddy fields spanning up to 3469 km across three temperature zones. Our study reveals that the periphytons exhibit varying capacities to accumulate carbon, nitrogen, and phosphorus, leading to imbalanced intracellular nutrient stoichiometries (carbon-to-nitrogen ratio = 10.3 ± 2.1, carbon-to-phosphorus ratio = 30.9 ± 13.1, nitrogen-to-phosphorus ratio = 3.1 ± 1.3). This stoichiometric imbalance induces intracellular environmental heterogeneity, which partially influences the local species richness of microeukaryotic communities and their regional structural variations on a large scale. Contrary to the typical latitudinal diversity gradient theory, local microeukaryotic species richness follows a distance-decay model, with both deterministic and stochastic processes contributing to community assembly. These results underscore the complex interplay of environmental filtering, species interactions, and dispersal dynamics in shaping the structure and adaptability of microeukaryotic communities within periphytons. This study contributes to a broader understanding of the factors driving regional structural variations of microeukaryotes at the soil-water interface in agricultural landscapes.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae119"},"PeriodicalIF":5.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11512751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514079","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}

引用次数: 0

Land use effects on soil microbiome composition and traits with consequences for soil carbon cycling. 土地利用对土壤微生物组组成和性状的影响以及对土壤碳循环的影响。

IF 5.1

ISME communications Pub Date : 2024-10-07 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae116

Lisa Cole, Tim Goodall, Nico Jehmlich, Robert I Griffiths, Gerd Gleixner, Cecile Gubry-Rangin, Ashish A Malik

{"title":"Land use effects on soil microbiome composition and traits with consequences for soil carbon cycling.","authors":"Lisa Cole, Tim Goodall, Nico Jehmlich, Robert I Griffiths, Gerd Gleixner, Cecile Gubry-Rangin, Ashish A Malik","doi":"10.1093/ismeco/ycae116","DOIUrl":"10.1093/ismeco/ycae116","url":null,"abstract":"The soil microbiome determines the fate of plant-fixed carbon. The shifts in soil properties caused by land use change leads to modifications in microbiome function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated using metaproteomics, metabarcoding, and a 13C-labeled litter decomposition experiment across two temperate sites with differing soil pH each with a paired land use intensity contrast. 13C incorporation into microbial biomass increased with land use intensification in low-pH soil but decreased in high-pH soil, with potential impact on carbon use efficiency in opposing directions. Reduction in biosynthesis traits was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. We observed divergent pH-controlled pathways of SOC cycling. In low-pH soil, land use intensification alleviates microbial abiotic stress resulting in increased biomass production but promotes decomposition and SOC loss. In contrast, in high-pH soil, land use intensification increases microbial physiological constraints and decreases biomass production, leading to reduced necromass build-up and SOC stabilization. We demonstrate how microbial biomass production and respiration dynamics and therefore carbon use efficiency can be decoupled from SOC highlighting the need for its careful consideration in managing SOC storage for soil health and climate change mitigation.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae116"},"PeriodicalIF":5.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633660","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}

引用次数: 0

Amplicon sequencing with internal standards yields accurate picocyanobacteria cell abundances as validated with flow cytometry. 经流式细胞仪验证，使用内部标准进行扩增子测序可获得准确的皮蓝藻细胞丰度。

IF 5.1

ISME communications Pub Date : 2024-09-25 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae115

Alexandra E Jones-Kellett, Jesse C McNichol, Yubin Raut, Kelsy R Cain, François Ribalet, E Virginia Armbrust, Michael J Follows, Jed A Fuhrman

{"title":"Amplicon sequencing with internal standards yields accurate picocyanobacteria cell abundances as validated with flow cytometry.","authors":"Alexandra E Jones-Kellett, Jesse C McNichol, Yubin Raut, Kelsy R Cain, François Ribalet, E Virginia Armbrust, Michael J Follows, Jed A Fuhrman","doi":"10.1093/ismeco/ycae115","DOIUrl":"https://doi.org/10.1093/ismeco/ycae115","url":null,"abstract":"To understand ecosystem state and function, marine microbial ecologists seek measurements of organismal abundance and diversity at high taxonomic resolution. Conventional flow cytometry accurately estimates microbial cell abundance but only discerns broad groups with distinct optical properties. While amplicon sequencing resolves more comprehensive diversity within microbiomes, it typically only provides relative organismal abundances within samples, not absolute abundance changes. Internal genomic standards offer a solution for absolute amplicon-based measures. Here, we spiked genomic standards into plankton samples from surface seawater, gathered at 46-km intervals along a cruise transect spanning the southern California Current System and the oligotrophic North Pacific Subtropical Gyre. This enabled evaluation of the absolute volumetric gene copy abundances of 16S rRNA amplicon sequence variants (amplified with 515Y-926R universal primers, quantitatively validated with mock communities) and cell abundances of picocyanobacteria with known genomic 16S copy numbers. Comparison of amplicon-derived cell abundances of Prochlorococcus and Synechococcus with flow cytometry data from nearby locations yielded nearly identical results (slope = 1.01; Pearson's r = 0.9942). Our findings show that this amplicon sequencing protocol combined with genomic internal standards accurately measures absolute cell counts of marine picocyanobacteria in complex field samples. By extension, we expect this approach to reasonably estimate volumetric gene copies for other amplified taxa in these samples.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae115"},"PeriodicalIF":5.1,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11459381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395743","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}

引用次数: 0

Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters. 新的候选类群有助于芬诺斯坎地盾深层地下水的关键代谢过程。

IF 5.1

ISME communications Pub Date : 2024-09-23 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae113

Mark Dopson, Maryam Rezaei Somee, Carolina González-Rosales, Lauren M Lui, Stephanie Turner, Moritz Buck, Emelie Nilsson, George Westmeijer, Kamal Ashoor, Torben N Nielsen, Maliheh Mehrshad, Stefan Bertilsson

{"title":"Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.","authors":"Mark Dopson, Maryam Rezaei Somee, Carolina González-Rosales, Lauren M Lui, Stephanie Turner, Moritz Buck, Emelie Nilsson, George Westmeijer, Kamal Ashoor, Torben N Nielsen, Maliheh Mehrshad, Stefan Bertilsson","doi":"10.1093/ismeco/ycae113","DOIUrl":"https://doi.org/10.1093/ismeco/ycae113","url":null,"abstract":"The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood-Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community's capacity, with up to 9.9% of fermentation, 6.4% of the Wood-Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae113"},"PeriodicalIF":5.1,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11484514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482376","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}

引用次数: 0

Quantifying microbial DNA in metagenomes improves microbial trait estimation. 对元基因组中的微生物 DNA 进行定量分析可改进微生物性状的估算。

IF 5.1

ISME communications Pub Date : 2024-09-08 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae111

Raphael Eisenhofer, Antton Alberdi, Ben J Woodcroft

{"title":"Quantifying microbial DNA in metagenomes improves microbial trait estimation.","authors":"Raphael Eisenhofer, Antton Alberdi, Ben J Woodcroft","doi":"10.1093/ismeco/ycae111","DOIUrl":"https://doi.org/10.1093/ismeco/ycae111","url":null,"abstract":"Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae111"},"PeriodicalIF":5.1,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11439404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333881","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}

引用次数: 0

Denitrification genotypes of endospore-forming Bacillota. 内孢子形成芽孢杆菌的脱硝基因型。

IF 5.1

ISME communications Pub Date : 2024-09-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae107

Emma Bell, Jianwei Chen, William D L Richardson, Milovan Fustic, Casey R J Hubert

{"title":"Denitrification genotypes of endospore-forming Bacillota.","authors":"Emma Bell, Jianwei Chen, William D L Richardson, Milovan Fustic, Casey R J Hubert","doi":"10.1093/ismeco/ycae107","DOIUrl":"https://doi.org/10.1093/ismeco/ycae107","url":null,"abstract":"Denitrification is a key metabolic process in the global nitrogen cycle and is performed by taxonomically diverse microorganisms. Despite the widespread importance of this metabolism, challenges remain in identifying denitrifying populations and predicting their metabolic end-products based on their genotype. Here, genome-resolved metagenomics was used to explore the denitrification genotype of Bacillota enriched in nitrate-amended high temperature incubations with confirmed N2O and N2 production. A set of 12 hidden Markov models (HMMs) was created to target the diversity of denitrification genes in members of the phylum Bacillota. Genomic potential for complete denitrification was found in five metagenome-assembled genomes from nitrate-amended enrichments, including two novel members of the Brevibacillaceae family. Genomes of complete denitrifiers encode N2O reductase gene clusters with clade II-type nosZ and often include multiple variants of the nitric oxide reductase gene. The HMM set applied to all genomes of Bacillota from the Genome Taxonomy Database identified 17 genera inferred to contain complete denitrifiers based on their gene content. Among complete denitrifiers it was common for three distinct nitric oxide reductases to be present (qNOR, bNOR, and sNOR) that may reflect the metabolic adaptability of Bacillota in environments with variable redox conditions.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae107"},"PeriodicalIF":5.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11388526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302629","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}

引用次数: 0