Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments
Published 2022 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments
Authors
Keywords
-
Journal
Nature Communications
Volume 13, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2022-08-19
DOI
10.1038/s41467-022-32503-w
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Reconstruction of nitrogenase predecessors suggests origin from maturase-like proteins
- (2022) Amanda K Garcia et al. Genome Biology and Evolution
- Improved metagenome binning and assembly using deep variational autoencoders
- (2021) Jakob Nybo Nissen et al. NATURE BIOTECHNOLOGY
- inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
- (2021) Matthew R. Olm et al. NATURE BIOTECHNOLOGY
- Asgard archaea in the haima cold seep: Spatial distribution and genomic insights
- (2021) Rui Lu et al. DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
- Examining horizontal gene transfer in microbial communities
- (2021) Ilana Lauren Brito NATURE REVIEWS MICROBIOLOGY
- Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
- (2021) Ivica Letunic et al. NUCLEIC ACIDS RESEARCH
- Microbial metabolism and adaptations in Atribacteria ‐dominated methane hydrate sediments
- (2021) Jennifer B. Glass et al. ENVIRONMENTAL MICROBIOLOGY
- Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef
- (2021) Molly A. Moynihan et al. ISME Journal
- Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea
- (2021) Hang Yu et al. ISME Journal
- Crystal structure of a key enzyme for anaerobic ethane activation
- (2021) Cedric J. Hahn et al. SCIENCE
- Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods
- (2021) Juan José Pierella Karlusich et al. Nature Communications
- Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue
- (2021) Miriam Philippi et al. Nature Communications
- Diverse ATPase Proteins in Mobilomes Constitute a Large Potential Sink for Prokaryotic Host ATP
- (2021) Hyunjin Shim et al. Frontiers in Microbiology
- Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea
- (2021) Amrit Koirala et al. Microorganisms
- Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
- (2021) Silvia G. Acinas et al. Communications Biology
- Microbial ecology of sulfur cycling near the sulfate–methane transition of deep‐sea cold seep sediments
- (2021) Wen‐Li Li et al. ENVIRONMENTAL MICROBIOLOGY
- Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean
- (2021) Tom O. Delmont et al. ISME Journal
- Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization
- (2020) Amanda K. Garcia et al. Geobiology
- Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment
- (2020) Bennett J. Kapili et al. ISME Journal
- Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae
- (2020) Andy O. Leu et al. ISME Journal
- FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
- (2020) Arkadiy I. Garber et al. Frontiers in Microbiology
- The Geology and Biogeochemistry of Hydrocarbon Seeps
- (2020) Samantha B. Joye Annual Review of Earth and Planetary Sciences
- Changing perspectives in marine nitrogen fixation
- (2020) Jonathan P. Zehr et al. SCIENCE
- Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico
- (2020) Rui Zhao et al. Scientific Reports
- Iron-Only and Vanadium Nitrogenases: Fail-Safe Enzymes or Something More?
- (2020) Caroline S. Harwood Annual Review of Microbiology
- Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog
- (2020) Raphaël Méheust et al. ISME Journal
- DRAM for distilling microbial metabolism to automate the curation of microbiome function
- (2020) Michael Shaffer et al. NUCLEIC ACIDS RESEARCH
- Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake
- (2020) Leyden Fernandez et al. Frontiers in Microbiology
- Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy
- (2020) Kyle S. Metcalfe et al. ISME Journal
- Biological nitrogen fixation detected under Antarctic sea ice
- (2020) Takuhei Shiozaki et al. Nature Geoscience
- A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis
- (2020) Justin A. North et al. SCIENCE
- A prominent isotopic fingerprint of nitrogen uptake by anaerobic methanotrophic archaea
- (2020) Yu Hu et al. CHEMICAL GEOLOGY
- Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
- (2020) M. Consuelo Gazitúa et al. ISME Journal
- Anaerobic methane oxidation coupled to denitrification is an important potential methane sink in deep-sea cold seeps
- (2020) Hongmei Jing et al. SCIENCE OF THE TOTAL ENVIRONMENT
- Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep
- (2020) Xiyang Dong et al. Nature Communications
- Expanding anaerobic alkane metabolism in the domain of Archaea
- (2019) Yinzhao Wang et al. Nature Microbiology
- Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea
- (2019) Guillaume Borrel et al. Nature Microbiology
- Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep
- (2019) Song-Can Chen et al. NATURE
- Geobiological feedbacks, oxygen, and the evolution of nitrogenase
- (2019) Florence Mus et al. FREE RADICAL BIOLOGY AND MEDICINE
- Diverse anaerobic methane‐ and multi‐carbon alkane‐metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment
- (2019) Yinzhao Wang et al. ENVIRONMENTAL MICROBIOLOGY
- The EMBL-EBI search and sequence analysis tools APIs in 2019
- (2019) Fábio Madeira et al. NUCLEIC ACIDS RESEARCH
- Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments
- (2019) Xiyang Dong et al. Nature Communications
- Diversity, Genomics, and Distribution of Phytoplankton-Cyanobacterium Single-Cell Symbiotic Associations
- (2019) Rachel A. Foster et al. Annual Review of Microbiology
- Anaerobic Degradation of Non-Methane Alkanes by “Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico
- (2019) Rafael Laso-Pérez et al. mBio
- Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
- (2019) Guillem Salazar et al. CELL
- An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
- (2019) Xiaoli Dong et al. Frontiers in Genetics
- Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading
- (2018) Anne E. Dekas et al. ENVIRONMENTAL MICROBIOLOGY
- Seasonal resource conditions favor a summertime increase in North Pacific diatom–diazotroph associations
- (2018) Christopher L. Follett et al. ISME Journal
- GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
- (2018) Joel A Boyd et al. NUCLEIC ACIDS RESEARCH
- Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes
- (2018) Tom O. Delmont et al. Nature Microbiology
- In situ development of a methanotrophic microbiome in deep-sea sediments
- (2018) S. E. Ruff et al. ISME Journal
- MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
- (2018) Gherman V. Uritskiy et al. Microbiome
- High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
- (2018) Chirag Jain et al. Nature Communications
- dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
- (2017) Matthew R Olm et al. ISME Journal
- Salmon provides fast and bias-aware quantification of transcript expression
- (2017) Rob Patro et al. NATURE METHODS
- Microbial community assembly and evolution in subseafloor sediment
- (2017) Piotr Starnawski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep
- (2017) Blair G. Paul et al. Frontiers in Microbiology
- A simple method to control over-alignment in the MAFFT multiple sequence alignment program
- (2016) Kazutaka Katoh et al. BIOINFORMATICS
- BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
- (2016) Minoru Kanehisa et al. JOURNAL OF MOLECULAR BIOLOGY
- Thermophilic archaea activate butane via alkyl-coenzyme M formation
- (2016) Rafael Laso-Pérez et al. NATURE
- MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
- (2015) Dinghua Li et al. BIOINFORMATICS
- An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment
- (2015) Ernesto Arias-Palomo et al. CELL
- Endomicrobium proavitum, the first isolate ofEndomicrobiaclass. nov. (phylumElusimicrobia) - an ultramicrobacterium with an unusual cell cycle that fixes nitrogen with a Group IV nitrogenase
- (2015) Hao Zheng et al. ENVIRONMENTAL MICROBIOLOGY
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses
- (2015) Anne E Dekas et al. ISME Journal
- Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival
- (2015) Chris Greening et al. ISME Journal
- Evolution of Molybdenum Nitrogenase during the Transition from Anaerobic to Aerobic Metabolism
- (2015) Eric S. Boyd et al. JOURNAL OF BACTERIOLOGY
- Nitrogenase MoFe protein fromClostridium pasteurianumat 1.08 Å resolution: comparison with theAzotobacter vinelandiiMoFe protein
- (2015) Li-Mei Zhang et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage
- (2014) Brian M. Hoffman et al. CHEMICAL REVIEWS
- Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean
- (2014) Pia H Moisander et al. ISME Journal
- Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps
- (2014) Sara Kleindienst et al. ISME Journal
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- (2014) Lam-Tung Nguyen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Fast and sensitive protein alignment using DIAMOND
- (2014) Benjamin Buchfink et al. NATURE METHODS
- Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes
- (2014) Jian-Bo Xie et al. PLoS Genetics
- Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea
- (2013) Anne E. Dekas et al. ENVIRONMENTAL MICROBIOLOGY
- Environment-Dependent Distribution of the Sediment nifH -Harboring Microbiota in the Northern South China Sea
- (2012) Hongyue Dang et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
- (2012) Evguenia Kopylova et al. BIOINFORMATICS
- Genomic variation landscape of the human gut microbiome
- (2012) Siegfried Schloissnig et al. NATURE
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- An Alternative Path for the Evolution of Biological Nitrogen Fixation
- (2011) Eric S. Boyd et al. Frontiers in Microbiology
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Heterogeneous energetic pathways and carbon sources on deep eastern Mediterranean cold seep communities
- (2010) Antoine Carlier et al. MARINE BIOLOGY
- Molecular Characterization of Potential Nitrogen Fixation by Anaerobic Methane-Oxidizing Archaea in the Methane Seep Sediments at the Number 8 Kumano Knoll in the Kumano Basin, Offshore of Japan
- (2009) J. Miyazaki et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Diverse and Novel nifH and nifH-Like Gene Sequences in the Deep-Sea Methane Seep Sediments of the Okhotsk Sea
- (2009) H. Dang et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
- (2009) S. Capella-Gutierrez et al. BIOINFORMATICS
- Jalview Version 2--a multiple sequence alignment editor and analysis workbench
- (2009) A. M. Waterhouse et al. BIOINFORMATICS
- Catalytic activities of NifEN: Implications for nitrogenase evolution and mechanism
- (2009) Y. Hu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia
- (2009) A. E. Dekas et al. SCIENCE
- The Take and Give Between Retrotransposable Elements and their Hosts
- (2008) Arthur Beauregard et al. Annual Review of Genetics
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started