Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy

ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes

(2018) Yu-Wei Wu   BMC GENOMICS

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane-Oxidizing Upland Soil Cluster α

(2018) Jennifer Pratscher et al.   ENVIRONMENTAL MICROBIOLOGY

High-throughput metaproteomics data analysis with Unipept: A tutorial

(2018) Bart Mesuere et al.   Journal of Proteomics

Comparative Genomics and Mutational Analysis Reveals a Novel XoxF-Utilizing Methylotroph in the Roseobacter Group Isolated From the Marine Environment

(2018) Alexandra M. Howat et al.   Frontiers in Microbiology

Microbial metabolism of methanol and methylamine in the Gulf of Mexico: insight into marine carbon and nitrogen cycling

(2018) Guang-Chao Zhuang et al.   ENVIRONMENTAL MICROBIOLOGY

Differential incorporation of one-carbon substrates among microbial populations identified by stable isotope probing from the estuary to South China Sea

(2018) Wenchao Deng et al.   Scientific Reports

Shallow submarine seep of abiotic methane from serpentinized peridotite off the Island of Elba, Italy

(2018) Alessandra Sciarra et al.   APPLIED GEOCHEMISTRY

High-quality genome sequences of uncultured microbes by assembly of read clouds

(2018) Alex Bishara et al.   NATURE BIOTECHNOLOGY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Anaerobic methane oxidation inducing carbonate precipitation at abiogenic methane seeps in the Tuscan archipelago (Italy)

(2018) Patrick Meister et al.   PLoS One

Evolutionary History of Copper Membrane Monooxygenases

(2018) Roshan Khadka et al.   Frontiers in Microbiology

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

(2017) John Vollmers et al.   PLoS One

Natural Selection in Synthetic Communities Highlights the Roles of Methylococcaceae and Methylophilaceae and Suggests Differential Roles for Alternative Methanol Dehydrogenases in Methane Consumption

(2017) Zheng Yu et al.   Frontiers in Microbiology

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning

(2017) John Vollmers et al.   Frontiers in Microbiology

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

(2016) Jarone Pinhassi et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph

(2015) Carolina Grob et al.   ENVIRONMENTAL MICROBIOLOGY

Methane oxidation coupled to nitrate reduction under hypoxia by the GammaproteobacteriumMethylomonas denitrificans, sp. nov. type strain FJG1

(2015) K. Dimitri Kits et al.   ENVIRONMENTAL MICROBIOLOGY

XoxFencoding an alternative methanol dehydrogenase is widespread in coastal marine environments

(2015) Martin Taubert 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

Annual study of oxygenated volatile organic compounds in UK shelf waters

(2015) Rachael Beale et al.   MARINE CHEMISTRY

Global dispersion and local diversification of the methane seep microbiome

(2015) S. Emil Ruff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation

(2015) Maria E. Hernandez et al.   PeerJ

PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference

(2014) Jan T. Keltjens et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Shear-velocity structure of the Tyrrhenian Sea: Tectonics, volcanism and mantle (de)hydration of a back-arc basin

(2014) Sonja Greve et al.   EARTH AND PLANETARY SCIENCE LETTERS

The more, the merrier: heterotroph richness stimulates methanotrophic activity

(2014) Adrian Ho et al.   ISME Journal

Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN

(2014) Marc G. Dumont et al.   Frontiers in Microbiology

Seafloor oxygen consumption fuelled by methane from cold seeps

(2013) Antje Boetius et al.   Nature Geoscience

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Microbial Communities of Deep-Sea Methane Seeps at Hikurangi Continental Margin (New Zealand)

(2013) S. Emil Ruff et al.   PLoS One

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between theMethylococcaceaeand theMethylophilaceae

(2013) David A.C. Beck et al.   PeerJ

Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium

(2012) Martin Taubert et al.   ISME Journal

Protein-based stable isotope probing (protein-SIP) in functional metaproteomics

(2012) Jana Seifert et al.   MASS SPECTROMETRY REVIEWS

Methane uncovered

(2012) Giuseppe Etiope   Nature Geoscience

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

Abundance and distribution of diverse membrane-bound monooxygenase (Cu-MMO) genes within the Costa Rica oxygen minimum zone

(2012) Patricia L. Tavormina et al.   Environmental Microbiology Reports

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

(2011) T. Magoc et al.   BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera

(2011) M. G. Kalyuzhnaya et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

One Carbon Metabolism in SAR11 Pelagic Marine Bacteria

(2011) Jing Sun et al.   PLoS One

Methane in shallow cold seeps at Mocha Island off central Chile

(2010) Gerdhard L. Jessen et al.   CONTINENTAL SHELF RESEARCH

Anaerobic Oxidation of Methane: Progress with an Unknown Process

(2009) Katrin Knittel et al.   Annual Review of Microbiology

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

Diversity, ecology, and genomics of the Roseobacter clade: a short overview

(2008) Thorsten Brinkhoff et al.   ARCHIVES OF MICROBIOLOGY

The small genome of an abundant coastal ocean methylotroph

(2008) Stephen J. Giovannoni et al.   ENVIRONMENTAL MICROBIOLOGY

Oxygen dynamics of marine sediments

(2008) Ronnie N. Glud   Marine Biology Research

High-resolution metagenomics targets specific functional types in complex microbial communities

(2008) Marina G Kalyuzhnaya et al.   NATURE BIOTECHNOLOGY