Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field

Spatial comparison and temporal evolution of two marine iron-rich microbial mats from the Lucky Strike Hydrothermal Field, related to environmental variations

(2023) Aina Astorch-Cardona et al.   Frontiers in Marine Science

Multiple parameters enable deconvolution of water-rock reaction paths in low-temperature vent fluids of the Kamaʻehuakanaloa (Lōʻihi) seamount

(2023) Vincent Milesi et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge

(2022) Ying-Wen Zhong et al.   Microbiology Spectrum

Mineralogical distribution and genetic aspects of cobalt at the active Fåvne and Loki’s Castle seafloor massive sulfide deposits, Arctic Mid-Ocean Ridges

(2022) Fredrik Sahlström et al.   ORE GEOLOGY REVIEWS

Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics

(2021) Congyu Lu et al.   BMC BIOLOGY

A late Paleoproterozoic (1.74 Ga) deep‐sea, low‐temperature, iron‐oxidizing microbial hydrothermal vent community from Arizona, USA

(2021) Crispin T. S. Little et al.   Geobiology

An evolving view on biogeochemical cycling of iron

(2021) Andreas Kappler et al.   NATURE REVIEWS MICROBIOLOGY

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

(2021) Dongwook Kim et al.   JOURNAL OF MICROBIOLOGY

Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

(2021) Marie-Anne Cambon-Bonavita et al.   Microbiome

Iron Oxidation by a Fused Cytochrome-Porin Common to Diverse Iron-Oxidizing Bacteria

(2021) Jessica L. Keffer et al.   mBio

Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export

(2021) Elif Koeksoy et al.   Frontiers in Microbiology

Microbial processes during deposition and diagenesis of Banded Iron Formations

(2021) Carolin L. Dreher et al.   Palaeontologische Zeitschrift

Evidence for auxiliary anaerobic metabolism in obligately aerobic Zetaproteobacteria

(2020) Abhiney Jain 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

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

Genomic insights into two novel Zetaproteobacteria Fe(II)-oxidizing isolates reveal lifestyle adaption to coastal marine sediments

(2020) Nia Blackwell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Abiotic redox reactions in hydrothermal mixing zones: Decreased energy availability for the subsurface biosphere

(2020) Jill M. McDermott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution

(2020) Nina Dombrowski et al.   Nature Communications

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

(2020) Irene Sánchez-Andrea et al.   Nature Communications

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

(2020) Lauren M. Seyler et al.   ISME Journal

Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents

(2020) Sean M. McAllister et al.   ISME Journal

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

The role of iron-oxidizing bacteria in biocorrosion: a review

(2019) David Emerson   BIOFOULING

The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally

(2019) Gregory J. Dick   NATURE REVIEWS MICROBIOLOGY

Predicting the optimal growth temperatures of prokaryotes using only genome derived features

(2019) David B Sauer et al.   BIOINFORMATICS

Environmental Evidence and Genomic Insight of Iron-oxidizing Bacteria Preference Towards More Corrosion Resistant Stainless Steel at Higher Salinities

(2019) Cody E Garrison et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

Fine-Scale Biogeography and the Inference of Ecological Interactions Among Neutrophilic Iron-Oxidizing Zetaproteobacteria as Determined by a Rule-Based Microbial Network

(2019) Katherine Duchinski et al.   Frontiers in Microbiology

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Geochemistry of fluids from Earth’s deepest ridge-crest hot-springs: Piccard hydrothermal field, Mid-Cayman Rise

(2018) Jill M. McDermott et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

(2018) Jongsik Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Biological rejuvenation of iron oxides in bioturbated marine sediments

(2018) Jacob P. Beam et al.   ISME Journal

Potential for primary productivity in a globally-distributed bacterial phototroph

(2018) E. D. Graham et al.   ISME Journal

Establishing anaerobic hydrocarbon-degrading enrichment cultures of microorganisms under strictly anoxic conditions

(2018) Rafael Laso-Pérez et al.   Nature Protocols

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

(2018) David W. Waite et al.   Frontiers in Microbiology

Energy Landscapes in Hydrothermal Chimneys Shape Distributions of Primary Producers

(2018) Håkon Dahle et al.   Frontiers in Microbiology

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields

(2018) Jan Vander Roost 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

Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō‘ihi Seamount

(2017) Jarrod J. Scott et al.   ENVIRONMENTAL MICROBIOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Environmental controls on biomineralization and Fe-mound formation in a low-temperature hydrothermal system at the Jan Mayen Vent Fields

(2017) Karen C. Johannessen et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Sorption of arsenic to biogenic iron (oxyhydr)oxides produced in circumneutral environments

(2017) Tyler D. Sowers et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

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

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

(2017) Benjamin J Tully et al.   ISME Journal

Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov.

(2017) Jiro F Mori et al.   ISME Journal

Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i

(2017) Heather Fullerton et al.   ISME Journal

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Microbial analysis of Zetaproteobacteria and co-colonizers of iron mats in the Troll Wall Vent Field, Arctic Mid-Ocean Ridge

(2017) Jan Vander Roost et al.   PLoS One

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

(2017) Shaomei He et al.   Frontiers in Microbiology

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

(2017) Kevin W. Hager et al.   Frontiers in Microbiology

Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic–Anoxic Transition Zone

(2017) Beverly K. Chiu et al.   Frontiers in Microbiology

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Peeking under the Iron Curtain: Development of a Microcosm for Imaging the Colonization of Steel Surfaces by Mariprofundus sp. Strain DIS-1, an Oxygen-Tolerant Fe-Oxidizing Bacterium

(2016) Adam C. Mumford et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative Analysis of Microbial Communities in Iron-Dominated Flocculent Mats in Deep-Sea Hydrothermal Environments

(2016) Hiroko Makita et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mariprofundus micogutta sp. nov., a novel iron-oxidizing zetaproteobacterium isolated from a deep-sea hydrothermal field at the Bayonnaise knoll of the Izu-Ogasawara arc, and a description of Mariprofundales ord. nov. and Zetaproteobacteria classis nov.

(2016) Hiroko Makita et al.   ARCHIVES OF MICROBIOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations

(2016) C. S. Chan et al.   Geobiology

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Structural Iron (II) of Basaltic Glass as an Energy Source for Zetaproteobacteria in an Abyssal Plain Environment, Off the Mid Atlantic Ridge

(2016) Pauline A. Henri et al.   Frontiers in Microbiology

Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems

(2016) Ida H. Steen et al.   Frontiers in Microbiology

The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

(2016) Clara S. Chan 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

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

(2015) Dinghua Li et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko 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

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese 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

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Microbial Iron Mats at the Mid-Atlantic Ridge and Evidence that Zetaproteobacteria May Be Restricted to Iron-Oxidizing Marine Systems

(2015) Jarrod J. Scott et al.   PLoS One

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Carbon adsorption onto Fe oxyhydroxide stalks produced by a lithotrophic iron-oxidizing bacteria

(2014) S. A. Bennett et al.   Geobiology

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

(2014) Erin K Field 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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics

(2013) Tim Urich et al.   ENVIRONMENTAL MICROBIOLOGY

Hidden in plain sight: discovery of sheath-forming, iron-oxidizingZetaproteobacteriaat Loihi Seamount, Hawaii, USA

(2013) Emily J. Fleming et al.   FEMS MICROBIOLOGY ECOLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Iron oxide nanoparticles in geomicrobiology: from biogeochemistry to bioremediation

(2013) Juliane Braunschweig et al.   New Biotechnology

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l

(2013) Esther Singer et al.   Frontiers in Microbiology

Elimination of Manganese(II,III) Oxidation in Pseudomonas putida GB-1 by a Double Knockout of Two Putative Multicopper Oxidase Genes

(2012) Kati Geszvain et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

A precision multi-sampler for deep-sea hydrothermal microbial mat studies

(2012) J.A. Breier et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Håkon Dahle et al.   Environmental Microbiology Reports

Iron-Based Microbial Ecosystem on and Below the Seafloor: A Case Study of Hydrothermal Fields of the Southern Mariana Trough

(2012) Shingo Kato et al.   Frontiers in Microbiology

Mineralogy of Iron Microbial Mats from Loihi Seamount

(2012) Brandy M. Toner et al.   Frontiers in Microbiology

Toward a Mechanistic Understanding of Anaerobic Nitrate-Dependent Iron Oxidation: Balancing Electron Uptake and Detoxification

(2012) Hans K. Carlson et al.   Frontiers in Microbiology

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biodiversity and Emerging Biogeography of the Neutrophilic Iron-Oxidizing Zetaproteobacteria

(2011) Sean M. McAllister et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis ofin situmanganese(II) oxidation in the Columbia River and offshore plume: linkingAurantimonasand the associated microbial community to an active biogeochemical cycle

(2011) C. R. Anderson et al.   ENVIRONMENTAL MICROBIOLOGY

A new Fe/Mn geothermometer for hydrothermal systems: Implications for high-salinity fluids at 13°N on the East Pacific Rise

(2011) Nicholas J. Pester et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

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

Microbiology of Seamounts: Common Patterns Observed in Community Structure

(2011) David Emerson et al.   OCEANOGRAPHY

Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium

(2011) Esther Singer et al.   PLoS One

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Neutrophilic Iron-Oxidizing “Zetaproteobacteria” and Mild Steel Corrosion in Nearshore Marine Environments

(2010) Joyce M. McBeth et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes

(2010) N. L. FORGET et al.   Geobiology

Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation

(2010) Clara S Chan et al.   ISME Journal

Mn(II) Oxidation Is Catalyzed by Heme Peroxidases in "Aurantimonas manganoxydans" Strain SI85-9A1 and Erythrobacter sp. Strain SD-21

(2009) C. R. Anderson 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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough

(2009) Shingo Kato et al.   ENVIRONMENTAL MICROBIOLOGY

Biogeochemical Redox Processes and their Impact on Contaminant Dynamics

(2009) Thomas Borch et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

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

Removal of phosphorus from solution using biogenic iron oxides

(2009) Jeremy A. Rentz et al.   WATER RESEARCH

Molecular Comparison of Bacterial Communities within Iron-Containing Flocculent Mats Associated with Submarine Volcanoes along the Kermadec Arc

(2008) T. W. Hodges et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community

(2008) Chris Jeans et al.   ISME Journal

A New Iron-oxidizing/O2-reducing Supercomplex Spanning Both Inner and Outer Membranes, Isolated from the Extreme AcidophileAcidithiobacillus ferrooxidans

(2008) Cindy Castelle et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle

(2008) Murray Ronald Badger et al.   JOURNAL OF EXPERIMENTAL BOTANY

Extreme spatial and temporal variability of hydrothermal microbial mat communities along the Mariana Island Arc and southern Mariana back-arc system

(2008) Richard E. Davis et al.   JOURNAL OF GEOPHYSICAL RESEARCH

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH