Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments

Trace gas oxidizers are widespread and active members of soil microbial communities

(2021) Sean K. Bay et al.   Nature Microbiology

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem

(2021) Ya-Jou Chen et al.   ISME Journal

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

(2021) Marguerite V. Langwig et al.   ISME Journal

Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean

(2020) Katharina Kitzinger et al.   Nature Communications

Pontiella desulfatans gen. nov., sp. nov., and Pontiella sulfatireligans sp. nov., Two Marine Anaerobes of the Pontiellaceae fam. nov. Producing Sulfated Glycosaminoglycan-like Exopolymers

(2020) Daan M. van Vliet et al.   Microorganisms

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments

(2019) Adam J. Kessler et al.   Nature Microbiology

Autometa: automated extraction of microbial genomes from individual shotgun metagenomes

(2019) Ian J Miller et al.   NUCLEIC ACIDS RESEARCH

Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide

(2019) Zahra F. Islam et al.   ISME Journal

Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism

(2019) Anja Spang et al.   Nature Microbiology

Diverse hydrogen production and consumption pathways influence methane production in ruminants

(2019) Chris Greening et al.   ISME Journal

Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival

(2019) Paul R. F. Cordero et al.   ISME Journal

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

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

(2019) Dongwan D. Kang et al.   PeerJ

Microbiome data science

(2019) Sudarshan A Shetty et al.   JOURNAL OF BIOSCIENCES

Biogeochemical Controls on the Relative Importance of Denitrification and Dissimilatory Nitrate Reduction to Ammonium in Estuaries

(2018) Adam J. Kessler et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Metabolic specialization of denitrifiers in permeable sediments controls N2 O emissions

(2018) Hannah K. Marchant et al.   ENVIRONMENTAL MICROBIOLOGY

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Uncultured Gammaproteobacteria and Desulfobacteraceae Account for Major Acetate Assimilation in a Coastal Marine Sediment

(2018) Stefan Dyksma et al.   Frontiers in Microbiology

Evidence for H2 consumption by uncultured Desulfobacterales in coastal sediments

(2017) Stefan Dyksma et al.   ENVIRONMENTAL MICROBIOLOGY

Permeability shapes bacterial communities in sublittoral surface sediments

(2017) D. Probandt et al.   ENVIRONMENTAL MICROBIOLOGY

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations

(2017) Sainab Saad et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

(2017) Marc Mußmann et al.   ISME Journal

Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously

(2017) Hannah K Marchant et al.   ISME Journal

Microbial life on a sand grain: from bulk sediment to single grains

(2017) David Probandt 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

Grain-size distributions on high-energy sandy beaches and their relation to wave dissipation

(2017) Sam Prodger et al.   SEDIMENTOLOGY

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

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

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

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

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

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments

(2016) Stefan Dyksma et al.   ISME Journal

Coupled nitrification-denitrification leads to extensive N loss in subtidal permeable sediments

(2016) Hannah K. Marchant et al.   LIMNOLOGY AND OCEANOGRAPHY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation

(2016) Michael F. Bourke et al.   Nature Geoscience

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments

(2016) Y. He et al.   Nature Microbiology

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

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

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

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

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

(2015) Luis M Rodriguez-R et al.   ISME Journal

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

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

(2015) Brett J Baker et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The Fate of Nitrate in Intertidal Permeable Sediments

(2014) Hannah K. Marchant et al.   PLoS One

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Benthic Exchange and Biogeochemical Cycling in Permeable Sediments

(2013) Markus Huettel et al.   Annual Review of Marine Science

Transport Zonation Limits Coupled Nitrification-Denitrification in Permeable Sediments

(2013) Adam J. Kessler et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Membrane-bound oxygen reductases of the anaerobic sulfate-reducing Desulfovibrio vulgaris Hildenborough: roles in oxygen defence and electron link with periplasmic hydrogen oxidation

(2013) F. Ramel et al.   MICROBIOLOGY-SGM

The kinetics of denitrification in permeable sediments

(2012) Victor Evrard et al.   BIOGEOCHEMISTRY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

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

The driving forces of porewater and groundwater flow in permeable coastal sediments: A review

(2011) Isaac R. Santos et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

(2011) Angélique Gobet et al.   ISME Journal

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

(2010) Sabine Lenk et al.   ENVIRONMENTAL MICROBIOLOGY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aerobic denitrification in permeable Wadden Sea sediments

(2009) Hang Gao et al.   ISME Journal

Modeling the polaronic nature of p-type defects in Cu2O: The failure of GGA and GGA+U

(2009) David O. Scanlon et al.   JOURNAL OF CHEMICAL PHYSICS

Oxygen dynamics of marine sediments

(2008) Ronnie N. Glud   Marine Biology Research