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

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

Sodium azide used as microbial inhibitor caused unwanted by-products in anaerobic geochemical studies

(2019) Katrien Hendrix et al.   APPLIED GEOCHEMISTRY

Iron targeted transcriptome study draws attention to novel redox protein candidates involved in ferrous iron oxidation in “ Ferrovum ” sp. JA12

(2018) Sophie R. Ullrich et al.   RESEARCH IN MICROBIOLOGY

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

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

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

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

25 years of serving the community with ribosomal RNA gene reference databases and tools

(2017) Frank Oliver Glöckner et al.   JOURNAL OF BIOTECHNOLOGY

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

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

(2017) Elaina D. Graham et al.   PeerJ

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

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

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer

(2016) Talia N M Jewell et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

GenBank

(2016) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Expression of multiplecbb3cytochromecoxidase isoforms by combinations of multiple isosubunits inPseudomonas aeruginosa

(2016) Takehiro Hirai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

(2016) Julie L. Meyer et al.   Scientific Reports

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

Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis

(2015) Danilo J. P. Rocha 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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME 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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

(2014) Erin K Field et al.   ISME Journal

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Using in situ voltammetry as a tool to identify and characterize habitats of iron-oxidizing bacteria: from fresh water wetlands to hydrothermal vent sites

(2014) Daniel J. MacDonald et al.   Environmental Science-Processes & Impacts

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

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

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics

(2013) David Emerson et al.   Frontiers in Microbiology

Insight into the evolution of the iron oxidation pathways

(2012) Marianne Ilbert et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova 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

Abiotic oxidation of Fe(II) by reactive nitrogen species in cultures of the nitrate-reducing Fe(II) oxidizerAcidovoraxsp. BoFeN1 - questioning the existence of enzymatic Fe(II) oxidation

(2012) N. Klueglein et al.   Geobiology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1

(2012) Juan Liu et al.   Frontiers in Microbiology

Biodiversity and Emerging Biogeography of the Neutrophilic Iron-Oxidizing Zetaproteobacteria

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

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Iron-Oxidizing Bacteria: An Environmental and Genomic Perspective

(2010) David Emerson et al.   Annual Review of Microbiology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Clara S Chan et al.   ISME Journal

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Potential for Iron-reduction and Iron-cycling in Iron Oxyhydroxide-rich Microbial Mats at Loihi Seamount

(2009) David Emerson   GEOMICROBIOLOGY JOURNAL

Redox Speciation and Distribution within Diverse Iron-dominated Microbial Habitats at Loihi Seamount

(2009) Brian T. Glazer et al.   GEOMICROBIOLOGY JOURNAL

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

The cbb3 Oxidases Are an Ancient Innovation of the Domain Bacteria

(2008) A.-L. Ducluzeau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY