Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles DOI Creative Commons
Javier López-Simón, Marina Vila‐Nistal,

Aleksandra Rosenova

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Дек. 14, 2023

Abstract Viruses play an important role in the marine ecosystem. However, our comprehension of viruses inhabiting dark ocean, and particular, under Antarctic Ice Shelves, remains limited. Here, we mine single-cell genomic, transcriptomic, metagenomic data to uncover viral diversity, biogeography, activity, their as metabolic facilitators microbes beneath Ross Shelf. This is largest ice shelf with a major impact on global carbon cycle. The community found cavity mainly comprises endemic adapted polar mesopelagic environments. low abundance genes related lysogenic lifestyle (<3%) does not support predominance Piggyback-the-Winner hypothesis, consistent low-productivity habitat. Our results indicate actively infecting key ammonium sulfur-oxidizing chemolithoautotrophs (e.g. Nitrosopumilus spp, Thioglobus spp.), supporting “kill-the-winner” dynamic. Based genome analysis, these carry specific auxiliary potentially involved nitrogen, sulfur, phosphorus acquisition. Altogether, shelves are putatively programming metabolism ecologically relevant that maintain primary production chemosynthetically-driven ecosystems, which have nutrient cycles.

Язык: Английский

Biosynthetic potential of the global ocean microbiome DOI Creative Commons
Lucas Paoli, Hans‐Joachim Ruscheweyh, Clarissa C. Forneris

и другие.

Nature, Год журнала: 2022, Номер 607(7917), С. 111 - 118

Опубликована: Июнь 22, 2022

Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically biotechnologically relevant enzymes biochemical compounds2,3. However, studying identify genomic pathways the synthesis of such compounds4 assigning them their respective hosts remains challenging. The biosynthetic microorganisms in open ocean largely uncharted owing limitations analysis genome-resolved data at global scale. Here we investigated novelty gene clusters by integrating around 10,000 genomes from cultivated single cells with more than 25,000 newly reconstructed draft 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new clusters, several which were found previously unsuspected phylogenetic groups. Among these groups, identified lineage ('Candidatus Eudoremicrobiaceae') that belongs an uncultivated bacterial phylum includes some most biosynthetically diverse environment. From these, characterized phospeptin pythonamide pathways, revealing cases unusual bioactive compound structure enzymology, respectively. Together, research demonstrates how microbiomics-driven strategies can enable investigation undescribed natural products groups environments.

Язык: Английский

Процитировано

251
Microbial metabolites in the marine carbon cycle DOI
Mary Ann Moran, Elizabeth B. Kujawinski, William F. Schroer

и другие.

Nature Microbiology, Год журнала: 2022, Номер 7(4), С. 508 - 523

Опубликована: Апрель 1, 2022

Язык: Английский

Процитировано

152
EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes DOI Creative Commons
Daniel J. Richter, Cédric Berney, Jürgen F. H. Strassert

и другие.

Peer Community Journal, Год журнала: 2022, Номер 2

Опубликована: Сен. 20, 2022

EukProt is a database of published and publicly available predicted protein sets selected to represent the breadth eukaryotic diversity, currently including 993 species from all major supergroups as well orphan taxa. The goal provide single, convenient resource for gene-based research across spectrum life, such phylogenomics gene family evolution. Each placed within UniEuk taxonomic framework in order facilitate downstream analyses, each data set associated with unique, persistent identifier comparison replication among analyses. regularly updated, versions will be permanently stored made via FigShare. current version has number updates, notably 'The Comparative Set' (TCS), reduced high estimated completeness while maintaining substantial phylogenetic breadth, which comprises 196 proteomes. A BLAST web server graphical displays are at http://evocellbio.com/eukprot/. We invite community suggestions new annotation features included subsequent versions, building collaborative that promote understand diversity diversification.

Язык: Английский

Процитировано

124
Diversity and ecological footprint of Global Ocean RNA viruses DOI Open Access
Guillermo Domínguez-Huerta, Ahmed A. Zayed, James M. Wainaina

и другие.

Science, Год журнала: 2022, Номер 376(6598), С. 1202 - 1208

Опубликована: Июнь 9, 2022

DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global RNA virus diversity, ecology, ecosystem roles. In this study, we uncover patterns predictors of community- “species”-level diversity contextualize their ecological impacts from pole to pole. Our analyses revealed four zones, latitudinal depth patterns, environmental correlates for viruses. findings only partially parallel those cosampled plankton show unexpectedly high polar interactions. The influence on ecosystems appears be large, predicted hosts ecologically important. Moreover, the occurrence auxiliary metabolic genes indicates that cause reprogramming diverse host metabolisms, including photosynthesis carbon cycling, abundances predict ocean export.

Язык: Английский

Процитировано

84
Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments DOI Creative Commons
Xiyang Dong, Chuwen Zhang, Yongyi Peng

и другие.

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Авг. 19, 2022

Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs deep sea sediments. However, it is unclear whether other microbial groups can perform fixation such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, six metatranscriptomes derived from 11 globally distributed seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted provide ATP for fixation, suggesting diazotrophy seeps not necessarily associated with sulfate-dependent oxidation methane. Nitrogen among various inferred be genetically mobile subject purifying selection. Our findings extend the capacity five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota UBA6262), suggest that might contribute substantially global balance.

Язык: Английский

Процитировано

82
Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions DOI Creative Commons
Nguyễn Nhật Nam, Hoang Dang Khoa, Kieu The Loan Trinh

и другие.

Foods, Год журнала: 2023, Номер 12(11), С. 2140 - 2140

Опубликована: Май 25, 2023

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase discoveries related to microbial world. Newly discovered microbiomes different ecologies provide meaningful information on diversity functions of microorganisms Earth. Therefore, results metagenomic studies new microbe-based applications human health, agriculture, food industry, among others. This review summarizes fundamental procedures recent advances bioinformatic tools. It also explores up-to-date study, plant research, environmental sciences, other fields. Finally, is powerful tool for studying world, it still numerous that are currently hidden awaiting discovery. this discusses future perspectives

Язык: Английский

Процитировано

73
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean DOI
Marta Royo‐Llonch, Pablo Sánchez, Clara Ruiz‐González

и другие.

Nature Microbiology, Год журнала: 2021, Номер 6(12), С. 1561 - 1574

Опубликована: Ноя. 15, 2021

Язык: Английский

Процитировано

89
The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments DOI Creative Commons
Yosuke Nishimura, Susumu Yoshizawa

Scientific Data, Год журнала: 2022, Номер 9(1)

Опубликована: Июнь 17, 2022

Abstract Marine microorganisms are immensely diverse and play fundamental roles in global geochemical cycling. Recent metagenome-assembled genome studies, with particular attention to large-scale projects such as Tara Oceans, have expanded the genomic repertoire of marine microorganisms. However, published metagenome data is still underexplored. We collected 2,057 metagenomes covering various environments developed a new reconstruction pipeline. reconstructed 52,325 qualified genomes composed 8,466 prokaryotic species-level clusters spanning 59 phyla, including from deep-sea characterized deeper than 1,000 m (n = 3,337), low-oxygen zones <90 μmol O2 per kg water 7,884), polar regions 7,752). Novelty evaluation using taxonomy database shows that 6,256 species (73.9%) novel include high taxonomic novelty, class candidates. These collectively known phylogenetic diversity prokaryotes by 34.2%, representatives cover 26.5–42.0% prokaryote-enriched metagenomes. Thoroughly leveraging accumulated metagenomic data, this resource, named OceanDNA MAG catalog, illuminates uncharacterized microbial ‘dark matter’ lineages.

Язык: Английский

Процитировано

71
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes DOI Creative Commons
Caroline Vernette, Julien Lecubin, Pablo Sánchez

и другие.

Nucleic Acids Research, Год журнала: 2022, Номер 50(W1), С. W516 - W526

Опубликована: Май 11, 2022

Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware programming skills. The new release 'Ocean Gene Atlas' (OGA2) is a freely available intuitive online service to mine complex environmental genomic databases. OGA2 datasets have been extended now include, from portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 Ocean Microbial Reference Catalogue (46.8E+6 non-redundant (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs an Arctic MAG catalogue (1E+6 genes) (v) 1888 Bacterial Archaeal (4.5E+6 additional dataset Malaspina 2010 global circumnavigation: (vi) 317 Deep Metagenome (0.9E+6 genes). Novel analyses enabled by include phylogenetic tree inference visualize user queries within their context sequence homologues both RefSeq database. An Application Programming Interface (API) allows users query command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays any variables. Atlas v2.0 freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.

Язык: Английский

Процитировано

63
Analysis and Interpretation of metagenomics data: an approach DOI Creative Commons

Gauri S. Navgire,

Neha Goel, Gifty Sawhney

и другие.

Biological Procedures Online, Год журнала: 2022, Номер 24(1)

Опубликована: Ноя. 19, 2022

Abstract Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field one versatile applications microbiology, where any interaction environment involving microorganisms can be topic study. Due to this versatility, number omics technology reached its horizons. Agriculture a crucial sector crop plants and interacting together. Hence, studying these interactions through lenses would completely disclose new meaning health development. rhizosphere an essential reservoir microbial community for agricultural soil. we focus on R&D studies crops such as rice, wheat, legumes, chickpea, sorghum. These recent developments are impossible without continuous advancement seen platforms; thus, brief introduction analysis available platforms presented here clear picture workflow. Concluding discussion about different pipelines applied analyze data produced by techniques significant role interpreting outcome particular experiment. A plethora software tools incorporated automated or individually perform manual analysis. Here describe 8–10 advanced, efficient used that explain their respective workflows simplify whole process.

Язык: Английский

Процитировано

48