A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
Published 2023 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
Authors
Keywords
-
Journal
Nature Microbiology
Volume 8, Issue 6, Pages 1137-1148
Publisher
Springer Science and Business Media LLC
Online
2023-04-25
DOI
10.1038/s41564-023-01374-2
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf
- (2022) Clara Martínez-Pérez et al. Nature Communications
- Phylogeny and Metabolic Potential of the Candidate Phylum SAR324
- (2022) Lukas Malfertheiner et al. Biology-Basel
- Prokaryotic Life in the Deep Ocean's Water Column
- (2022) Gerhard J. Herndl et al. Annual Review of Marine Science
- Biosynthetic potential of the global ocean microbiome
- (2022) Lucas Paoli et al. NATURE
- The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments
- (2022) Yosuke Nishimura et al. Scientific Data
- Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny
- (2022) Robert C. Edgar Nature Communications
- clinker & clustermap.js: automatic generation of gene cluster comparison figures
- (2021) Cameron L M Gilchrist et al. BIOINFORMATICS
- Twelve years of SAMtools and BCFtools
- (2021) Petr Danecek et al. GigaScience
- Sulfur cycling in oceanic oxygen minimum zones
- (2021) Cameron M. Callbeck et al. LIMNOLOGY AND OCEANOGRAPHY
- Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
- (2021) Ivica Letunic et al. NUCLEIC ACIDS RESEARCH
- Microbes mediating the sulfur cycle in the Atlantic Ocean and their link to chemolithoautotrophy
- (2021) Daniele De Corte et al. ENVIRONMENTAL MICROBIOLOGY
- Structural and Mechanistic Insights Into Dimethylsulfoxide Formation Through Dimethylsulfide Oxidation
- (2021) Xiu-Juan Wang et al. Frontiers in Microbiology
- Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
- (2020) Lucas Czech et al. BIOINFORMATICS
- Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean
- (2020) Yao Zhang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics
- (2020) Shunan Cao et al. Microbiome
- Rfam 14: expanded coverage of metagenomic, viral and microRNA families
- (2020) Ioanna Kalvari et al. NUCLEIC ACIDS RESEARCH
- Sulfur metabolites that facilitate oceanic phytoplankton–bacteria carbon flux
- (2019) Marine Landa et al. ISME Journal
- Bacteria are important dimethylsulfoniopropionate producers in coastal sediments
- (2019) Beth T. Williams et al. Nature Microbiology
- KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold
- (2019) Takuya Aramaki et al. BIOINFORMATICS
- Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
- (2019) Guillem Salazar et al. CELL
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- A novel bacterial sulfur oxidation pathway provides a new link between the cycles of organic and inorganic sulfur compounds
- (2018) Tobias Koch et al. ISME Journal
- Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria
- (2018) Cameron M. Callbeck et al. Nature Communications
- A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
- (2018) Donovan H Parks et al. NATURE BIOTECHNOLOGY
- EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
- (2018) Pierre Barbera et al. SYSTEMATIC BIOLOGY
- 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
- Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents
- (2017) Dimitri V Meier et al. ISME Journal
- Crustacean zooplankton release copious amounts of dissolved organic matter as taurine in the ocean
- (2017) Elisabeth L. Clifford et al. LIMNOLOGY AND OCEANOGRAPHY
- The MAR databases: development and implementation of databases specific for marine metagenomics
- (2017) Terje Klemetsen et al. NUCLEIC ACIDS RESEARCH
- Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation
- (2017) Maria G. Pachiadaki et al. SCIENCE
- Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
- (2017) Donovan H. Parks et al. Nature Microbiology
- Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic
- (2016) Federico Baltar et al. Frontiers in Microbiology
- Structure and function of the global ocean microbiome
- (2015) S. Sunagawa et al. SCIENCE
- Tara Oceans studies plankton at planetary scale
- (2015) P. Bork et al. SCIENCE
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- (2014) Lam-Tung Nguyen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Infernal 1.1: 100-fold faster RNA homology searches
- (2013) E. P. Nawrocki et al. BIOINFORMATICS
- Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
- (2013) Ramiro Logares et al. ENVIRONMENTAL MICROBIOLOGY
- Microbial control of the dark end of the biological pump
- (2013) Gerhard J. Herndl et al. Nature Geoscience
- CD-HIT: accelerated for clustering the next-generation sequencing data
- (2012) Limin Fu et al. BIOINFORMATICS
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- (2012) Christian Quast et al. NUCLEIC ACIDS RESEARCH
- Microbial oceanography of anoxic oxygen minimum zones
- (2012) O. Ulloa et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Carboxylases in Natural and Synthetic Microbial Pathways
- (2011) Tobias J. Erb APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Aligning short reads to reference alignments and trees
- (2011) Simon A. Berger et al. BIOINFORMATICS
- Microbial metatranscriptomics in a permanent marine oxygen minimum zone
- (2011) Frank J. Stewart et al. ENVIRONMENTAL MICROBIOLOGY
- Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean
- (2011) B. K. Swan et al. SCIENCE
- Mechanisms and Evolution of Oxidative Sulfur Metabolism in Green Sulfur Bacteria
- (2011) Lea H. Gregersen et al. Frontiers in Microbiology
- mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models forIn SilicoEvaluation of Oligonucleotide Probes for FluorescenceIn SituHybridization
- (2010) L. Safak Yilmaz et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior
- (2010) Thomas Reinthaler et al. DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
- Significance of non-sinking particulate organic carbon and dark CO2fixation to heterotrophic carbon demand in the mesopelagic northeast Atlantic
- (2010) Federico Baltar et al. GEOPHYSICAL RESEARCH LETTERS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Biopython: freely available Python tools for computational molecular biology and bioinformatics
- (2009) P. J. A. Cock et al. BIOINFORMATICS
- Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones
- (2009) D. A. Walsh et al. SCIENCE
- A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation
- (2008) Sean R. Eddy PLoS Computational Biology
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