Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents

(2020) Sean M. McAllister et al.   mSystems

Expanding anaerobic alkane metabolism in the domain of Archaea

(2019) Yinzhao Wang et al.   Nature Microbiology

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments

(2019) Stefanie Böhnke et al.   Frontiers in Microbiology

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

(2018) Shingo Kato et al.   ENVIRONMENTAL MICROBIOLOGY

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

Primary productivity below the seafloor at deep-sea hot springs

(2018) Jesse McNichol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

(2018) Petra Pjevac et al.   Frontiers in Microbiology

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits

(2018) Yuchen Han et al.   Scientific Reports

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

(2018) Dimitri V. Meier et al.   ENVIRONMENTAL MICROBIOLOGY

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments

(2018) Nina Dombrowski et al.   Nature Communications

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

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH

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

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

Colonization of Black Smokers by Hyperthermophilic Microorganisms

(2017) Reinhard Wirth   TRENDS IN MICROBIOLOGY

Oxidative Weathering and Microbial Diversity of an Inactive Seafloor Hydrothermal Sulfide Chimney

(2017) Jiangtao Li et al.   Frontiers in Microbiology

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

(2017) David W. Waite et al.   Frontiers in Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

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

(2017) Brian J. Eddie et al.   mSystems

Assessing microbial processes in deep-sea hydrothermal systems by incubation at in situ temperature and pressure

(2016) Jesse McNichol et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent

(2016) Caroline S Fortunato et al.   ISME Journal

Dynamics of a seafloor-spreading episode at the East Pacific Rise

(2016) Yen Joe Tan et al.   NATURE

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Genome Analysis of Thermosulfurimonas dismutans, the First Thermophilic Sulfur-Disproportionating Bacterium of the Phylum Thermodesulfobacteria

(2016) Andrey V. Mardanov et al.   Frontiers in Microbiology

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

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

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu 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

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge

(2015) Håkon Dahle et al.   ISME Journal

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

(2015) Shingo Kato et al.   Frontiers in Microbiology

Handling Temperature Bursts Reaching 464°C: Different Microbial Strategies in the Sisters Peak Hydrothermal Chimney

(2014) Mirjam Perner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

(2014) Albert Leopold Müller et al.   ISME Journal

Microbial distribution in different spatial positions within the walls of a black sulfide hydrothermal chimney

(2014) J Li et al.   MARINE ECOLOGY PROGRESS SERIES

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

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

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

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Microbial diversity of Loki's Castle black smokers at the Arctic Mid-Ocean Ridge

(2012) A. Jaeschke et al.   Geobiology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

The East Pacific Rise Between 9°N and 10°N: Twenty-Five Years of Integrated, Multidisciplinary Oceanic Spreading Center Studies

(2012) Daniel Fornari et al.   OCEANOGRAPHY

The versatilein situgene expression of anEpsilonproteobacteria-dominated biofilm from a hydrothermal chimney

(2012) Håkon Dahle et al.   Environmental Microbiology Reports

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

(2012) J. B. Sylvan et al.   mBio

Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge

(2011) Gilberto E. Flores et al.   ENVIRONMENTAL MICROBIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

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

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Methanocaldococcus villosus sp. nov., a heavily flagellated archaeon that adheres to surfaces and forms cell-cell contacts

(2010) A. Bellack et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

(2010) Wei Xie et al.   ISME Journal

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Variability in Microbial Communities in Black Smoker Chimneys at the NW Caldera Vent Field, Brothers Volcano, Kermadec Arc

(2009) Ken Takai et al.   GEOMICROBIOLOGY JOURNAL

Microbial diversity of a sulfide black smoker in main endeavour hydrothermal vent field, Juan de Fuca Ridge

(2009) Huaiyang Zhou et al.   JOURNAL OF MICROBIOLOGY

GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent

(2009) F. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal and spatial archaeal colonization of hydrothermal vent deposits

(2008) Antoine Pagé et al.   ENVIRONMENTAL MICROBIOLOGY

Culture-independent characterization of a novel microbial community at a hydrothermal vent at Brothers volcano, Kermadec arc, New Zealand

(2008) M. B. Stott et al.   JOURNAL OF GEOPHYSICAL RESEARCH