Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor

Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems

(2017) Nathan A. Ahlgren et al.   ENVIRONMENTAL MICROBIOLOGY

Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters

(2016) Bradley B Tolar 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

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom

(2016) David M. Needham et al.   Nature Microbiology

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains

(2015) Li C. Xia et al.   BMC BIOINFORMATICS

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

Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter

(2015) William D Orsi et al.   ISME Journal

Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters

(2015) Pierre E. Galand et al.   MOLECULAR ECOLOGY

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

(2015) Guillem Salazar et al.   MOLECULAR ECOLOGY

Genomic and proteomic characterization of “CandidatusNitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

(2015) Alyson E. Santoro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of temperature on rates of ammonium uptake and nitrification in the western coastal Arctic during winter, spring, and summer

(2014) Steven E. Baer et al.   GLOBAL BIOGEOCHEMICAL CYCLES

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

(2014) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years

(2014) Jacob A Cram et al.   ISME Journal

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

(2014) W. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Archaeal distribution and abundance in water masses of the Arctic Ocean, Pacific sector

(2013) C Amano-Sato et al.   AQUATIC MICROBIAL ECOLOGY

Single-cell genomics shedding light on marine Thaumarchaeota diversification

(2013) Haiwei Luo et al.   ISME Journal

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

(2013) Cheryl-Emiliane T Chow et al.   ISME Journal

Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle

(2013) Jody J Wright et al.   ISME Journal

Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight

(2013) Cheryl-Emiliane T Chow et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters

(2013) M. Hugoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Analysis of Thaumarchaeota Populations from the Northern Gulf of Mexico

(2013) Bradley B. Tolar et al.   Frontiers in Microbiology

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data

(2012) Li C. Xia et al.   BIOINFORMATICS

Seasonality and monthly dynamics of marine myovirus communities

(2012) Cheryl-Emiliane T. Chow et al.   ENVIRONMENTAL MICROBIOLOGY

Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

(2012) Jean-Christophe Auguet et al.   ISME Journal

Quantification of ammonia oxidation rates and ammonia-oxidizing archaea and bacteria at high resolution in the Gulf of California and eastern tropical North Pacific Ocean

(2012) J. Michael Beman et al.   LIMNOLOGY AND OCEANOGRAPHY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

(2011) Li C Xia et al.   BMC Systems Biology

Particle fluxes in San Pedro Basin, California: A four-year record of sedimentation and physical forcing

(2011) Lisa E. Collins et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Ammonia oxidation rates and nitrification in the Arabian Sea

(2011) Silvia E. Newell et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California

(2011) J Michael Beman et al.   ISME Journal

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation

(2011) Julie C Robidart et al.   ISME Journal

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight

(2010) J. Michael Beman et al.   ENVIRONMENTAL MICROBIOLOGY

Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current

(2010) Alyson E. Santoro et al.   ENVIRONMENTAL MICROBIOLOGY

Inter-annual recurrence of archaeal assemblages in the coastal NW Mediterranean Sea (Blanes Bay Microbial Observatory)

(2010) Pierre E. Galand et al.   LIMNOLOGY AND OCEANOGRAPHY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic

(2008) Marta M. Varela et al.   ENVIRONMENTAL MICROBIOLOGY

Archaeal diversity and a gene for ammonia oxidation are coupled to oceanic circulation

(2008) Pierre E. Galand et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California

(2008) J Michael Beman et al.   ISME Journal