Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

Taxonomic patterns in the nitrogen assimilation of soil prokaryotes

(2018) Ember M. Morrissey et al.   ENVIRONMENTAL MICROBIOLOGY

Peatland Acidobacteria with a dissimilatory sulfur metabolism

(2018) Bela Hausmann et al.   ISME Journal

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

Ecology and evolution of seafloor and subseafloor microbial communities

(2018) William D. Orsi   NATURE REVIEWS MICROBIOLOGY

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

(2018) Nicholas D. Youngblut et al.   PLoS One

Estimating taxon-specific population dynamics in diverse microbial communities

(2018) Benjamin J. Koch et al.   Ecosphere

A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform

(2018) Monica Pichler et al.   MicrobiologyOpen

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

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter

(2017) Ember M Morrissey et al.   ISME Journal

Decline in global oceanic oxygen content during the past five decades

(2017) Sunke Schmidtko et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

(2017) Kenneth Wasmund et al.   Environmental Microbiology Reports

Stable isotope probing with 18 O-water to investigate microbial growth and death in environmental samples

(2016) Egbert Schwartz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia

(2016) Alyssa Cornall et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Phylogenetic organization of bacterial activity

(2016) Ember M Morrissey et al.   ISME Journal

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments

(2016) Stefan Dyksma et al.   ISME Journal

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

(2016) William D Orsi et al.   ISME Journal

Complete genome of Zhongshania aliphaticivorans SM-2T, an aliphatic hydrocarbon-degrading bacterium isolated from tidal flat sediment

(2016) Baolei Jia et al.   JOURNAL OF BIOTECHNOLOGY

Intertidal salt marshes as an important source of inorganic carbon to the coastal ocean

(2016) Zhaohui Aleck Wang et al.   LIMNOLOGY AND OCEANOGRAPHY

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

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

Identification of growing bacteria during litter decomposition in freshwater through H218O quantitative stable isotope probing

(2016) Michaela Hayer et al.   Environmental Microbiology Reports

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

(2016) Patrick J. Kearns et al.   Nature Communications

phylosignal: an R package to measure, test, and explore the phylogenetic signal

(2016) François Keck et al.   Ecology and Evolution

Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea

(2016) Qi Ye et al.   MicrobiologyOpen

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2015) Brett J Baker et al.   Microbiome

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)

(2015) Noha H. Youssef et al.   PLoS One

Cytochrome bd oxidase and bacterial tolerance to oxidative and nitrosative stress

(2014) Alessandro Giuffrè et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Characterization of growing bacterial populations in McMurdo Dry Valley soils through stable isotope probing with18O-water

(2014) Egbert Schwartz et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2014) Albert Leopold Müller et al.   ISME Journal

Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions

(2014) Anuj Camanocha et al.   Journal of Oral Microbiology

Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil

(2013) Steven J. Blazewicz et al.   ECOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Microbial life under extreme energy limitation

(2013) Tori M. Hoehler et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria

(2013) Rohit Ghai et al.   Scientific Reports

Microbial ecology of expanding oxygen minimum zones

(2012) Jody J. Wright et al.   NATURE REVIEWS MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Identification of a Toluene-Degrading Bacterium from a Soil Sample through H218O DNA Stable Isotope Probing

(2011) Angela Woods et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial community composition in sediments resists perturbation by nutrient enrichment

(2011) Jennifer L Bowen et al.   ISME Journal

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland

(2010) Michael Pester et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

DNA Stable-Isotope Probing (DNA-SIP)

(2010) Eric A. Dunford et al.   Jove-Journal of Visualized Experiments

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Oxygen dynamics of marine sediments

(2008) Ronnie N. Glud   Marine Biology Research

Detoxification of sulphidic African shelf waters by blooming chemolithotrophs

(2008) Gaute Lavik et al.   NATURE

Spreading Dead Zones and Consequences for Marine Ecosystems

(2008) R. J. Diaz et al.   SCIENCE