Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Genome-enabled metabolic reconstruction of dominant chemosynthetic colonizers in deep-sea massive sulfide deposits

(2018) Shingo Kato et al.   ENVIRONMENTAL MICROBIOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

(2018) Petra Pjevac et al.   Frontiers in Microbiology

In-situ incubation of iron-sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira

(2017) Roman A. Barco et al.   ENVIRONMENTAL MICROBIOLOGY

Mimicking microbial interactions under nitrate-reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio

(2017) Arslan Arshad et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH

(2017) E. Percak-Dennett et al.   Geobiology

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments

(2017) Marc Mußmann et al.   ISME Journal

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents

(2017) Dimitri V Meier et al.   ISME Journal

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Genomic Analysis of Neutrophilic Iron(II) Oxidizer Genomes for Candidate Genes in Extracellular Electron Transfer

(2017) Shaomei He et al.   Frontiers in Microbiology

Metatranscriptomics Supports the Mechanism for Biocathode Electroautotrophy by “ Candidatus Tenderia electrophaga”

(2017) Brian J. Eddie et al.   mSystems

Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting

(2016) Dimitri V. Meier et al.   ENVIRONMENTAL MICROBIOLOGY

Woeseia oceani gen. nov., sp. nov., a chemoheterotrophic member of the order Chromatiales, and proposal of Woeseiaceae fam. nov.

(2016) Zong-Jun Du et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

‘Candidatus Tenderia electrophaga', an uncultivated electroautotroph from a biocathode enrichment

(2016) Brian J. Eddie et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments

(2016) Stefan Dyksma et al.   ISME Journal

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

Emcibacter nanhaiensis gen. nov. sp. nov., isolated from sediment of the South China Sea

(2015) Xiupian Liu et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph

(2015) Roman A. Barco et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

(2015) Michael Richter et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Functional interactions among filamentousEpsilonproteobacteriaandBacteroidetesin a deep-sea hydrothermal vent biofilm

(2015) Runar Stokke 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

Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens

(2015) Beverly E. Flood et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Comparative Genomic Insights into Ecophysiology of Neutrophilic, Microaerophilic Iron Oxidizing Bacteria

(2015) Shingo Kato et al.   Frontiers in Microbiology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria

(2015) Brett J Baker et al.   Microbiome

The SuSu Knolls Hydrothermal Field, Eastern Manus Basin, Papua New Guinea: An Active Submarine High-Sulfidation Copper-Gold System

(2014) C. J. Yeats et al.   ECONOMIC GEOLOGY

Microbial lipids reveal carbon assimilation patterns on hydrothermal sulfide chimneys

(2014) Eoghan P. Reeves et al.   ENVIRONMENTAL MICROBIOLOGY

Potential for biogeochemical cycling of sulfur, iron and carbon within massive sulfide deposits below the seafloor

(2014) Shingo Kato et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial consumption of zero-valence sulfur in marine benthic habitats

(2014) Petra Pjevac et al.   ENVIRONMENTAL MICROBIOLOGY

Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas

(2014) K. Mori et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Geologic setting of PACManus hydrothermal area — High resolution mapping and in situ observations

(2014) Janis Thal et al.   MARINE GEOLOGY

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Assessing the influence of physical, geochemical and biological factors on anaerobic microbial primary productivity within hydrothermal vent chimneys

(2013) H. C. Olins et al.   Geobiology

Sulfide geochronology along the Endeavour Segment of the Juan de Fuca Ridge

(2013) John W. Jamieson et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

Mineralogy Drives Bacterial Biogeography of Hydrothermally Inactive Seafloor Sulfide Deposits

(2013) Brandy M. Toner et al.   GEOMICROBIOLOGY JOURNAL

Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents

(2013) Kiana L Frank et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low Temperature Geomicrobiology Follows Host Rock Composition Along a Geochemical Gradient in Lau Basin

(2013) Jason B. Sylvan et al.   Frontiers in Microbiology

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Radiometric Dating of Volcanogenic Massive Sulfides and Associated Iron Oxide Crusts with an Emphasis on 226Ra/Ba and 228Ra/226Ra in Volcanic and Hydrothermal Processes at Intraoceanic Arcs

(2012) R. G. Ditchburn et al.   ECONOMIC GEOLOGY

Characterization of the anaerobic microbial community in oil-polluted subtidal sediments: aromatic biodegradation potential after thePrestigeoil spill

(2012) Alejandro Acosta-González et al.   ENVIRONMENTAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Chemoautotrophy at Deep-Sea Vents: Past, Present, and Future

(2012) Stefan Sievert et al.   OCEANOGRAPHY

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Life and Death of Deep-Sea Vents: Bacterial Diversity and Ecosystem Succession on Inactive Hydrothermal Sulfides

(2012) J. B. Sylvan et al.   mBio

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean

(2011) Paola R. Gómez-Pereira et al.   ENVIRONMENTAL MICROBIOLOGY

Catabolic and anabolic energy for chemolithoautotrophs in deep-sea hydrothermal systems hosted in different rock types

(2011) Jan P. Amend et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

Biogeography and Biodiversity in Sulfide Structures of Active and Inactive Vents at Deep-Sea Hydrothermal Fields of the Southern Mariana Trough

(2010) S. Kato et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment

(2010) Sabine Lenk et al.   ENVIRONMENTAL MICROBIOLOGY

Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea)

(2010) Maria G. Pachiadaki et al.   FEMS MICROBIOLOGY ECOLOGY

Phylogeny of Gammaproteobacteria

(2010) K. P. Williams et al.   JOURNAL OF BACTERIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Ecology of Fe (hydr)oxide Mats and Basaltic Rock from Vailulu'u Seamount, American Samoa

(2009) Lisa A. Sudek et al.   GEOMICROBIOLOGY JOURNAL

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Endosymbioses between bacteria and deep-sea siboglinid tubeworms from an Arctic Cold Seep (Haakon Mosby Mud Volcano, Barents Sea)

(2008) Tina Lösekann et al.   ENVIRONMENTAL MICROBIOLOGY

Culture dependent and independent analyses of 16S rRNA and ATP citrate lyase genes: a comparison of microbial communities from different black smoker chimneys on the Mid-Atlantic Ridge

(2008) James W. Voordeckers et al.   EXTREMOPHILES

Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance

(2008) Satoshi Nakagawa et al.   FEMS MICROBIOLOGY ECOLOGY