Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation

New insights into marine group III Euryarchaeota, from dark to light

(2017) Jose M Haro-Moreno et al.   ISME Journal

Marine Group II Dominates Planktonic Archaea in Water Column of the Northeastern South China Sea

(2017) Haodong Liu et al.   Frontiers in Microbiology

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

(2016) William D Orsi et al.   ISME Journal

Resistant Microbial Cooccurrence Patterns Inferred by Network Topology

(2015) Sari Peura et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CCLasso: correlation inference for compositional data through Lasso

(2015) Huaying Fang et al.   BIOINFORMATICS

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

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

Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter

(2015) William D Orsi et al.   ISME Journal

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

(2015) Masaru K Nobu et al.   ISME Journal

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

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

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea

(2015) Meng Li et al.   Nature Communications

Marine Group II Archaea, potentially important players in the global ocean carbon cycle

(2015) Chuanlun L. Zhang et al.   Frontiers in Microbiology

Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea

(2014) Wei Xie et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables

(2014) Wei Xie et al.   ENVIRONMENTAL MICROBIOLOGY

Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters

(2014) Alexandre B. de Menezes et al.   ENVIRONMENTAL MICROBIOLOGY

Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota

(2014) Philippe Deschamps et al.   Genome Biology and Evolution

Crenarchaeal heterotrophy in salt marsh sediments

(2014) Lauren M Seyler et al.   ISME Journal

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

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

Identification of Photosynthetic Plankton Communities Using Sedimentary Ancient DNA and Their Response to late-Holocene Climate Change on the Tibetan Plateau

(2014) Weiguo Hou et al.   Scientific Reports

Assessing ecosystem response to phosphorus and nitrogen limitation in the Pearl River plume using the Regional Ocean Modeling System (ROMS)

(2014) Jianping Gan et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

Single-cell genomics shedding light on marine Thaumarchaeota diversification

(2013) Haiwei Luo et al.   ISME Journal

Short-term observations of marine bacterial and viral communities: patterns, connections and resilience

(2013) David M Needham et al.   ISME Journal

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang 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

Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses

(2013) Jun Meng et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

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

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

(2013) Jeremy A. Dodsworth et al.   Nature Communications

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Transcriptomic analysis of the red seaweed Laurencia dendroidea (Florideophyceae, Rhodophyta) and its microbiome

(2012) Louisi de Oliveira et al.   BMC GENOMICS

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from Marine Sediment

(2012) S.-J. Park et al.   JOURNAL OF BACTERIOLOGY

The Pst system of Streptococcus mutans is important for phosphate transport and adhesion to abiotic surfaces

(2012) D.E. Luz et al.   Molecular Oral Microbiology

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

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

(2012) V. Iverson et al.   SCIENCE

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

(2011) Céline Brochier-Armanet et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Coherent dynamics and association networks among lake bacterioplankton taxa

(2011) Alexander Eiler et al.   ISME Journal

Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1

(2011) B. K. Kim et al.   JOURNAL OF BACTERIOLOGY

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

Dependence of the Cyanobacterium Prochlorococcus on Hydrogen Peroxide Scavenging Microbes for Growth at the Ocean's Surface

(2011) J. Jeffrey Morris et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil

(2011) M. Tourna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prokaryotic functional diversity in different biogeochemical depth zones in tidal sediments of  the Severn Estuary, UK, revealed by stable-isotope probing

(2010) Gordon Webster et al.   FEMS MICROBIOLOGY ECOLOGY

Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage

(2010) James T Hollibaugh et al.   ISME Journal

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

(2010) Wei Xie et al.   ISME Journal

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

Allelopathic effects of Cochlodinium polykrikoides isolates and blooms from the estuaries of Long Island, New York, on co-occurring phytoplankton

(2010) YZ Tang et al.   MARINE ECOLOGY PROGRESS SERIES

Population Dynamics of Crenarchaeota and Euryarchaeota in the Mixing Front of River and Marine Waters

(2010) Do Manh Hao et al.   MICROBES AND ENVIRONMENTS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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

Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing

(2009) Pierre E Galand et al.   ISME Journal

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Physical–biological coupling in the Pearl River Estuary

(2008) Paul J. Harrison et al.   CONTINENTAL SHELF RESEARCH

Linkages between bacterioplankton community composition, heterotrophic carbon cycling and environmental conditions in a highly dynamic coastal ecosystem

(2008) Eva Teira et al.   ENVIRONMENTAL MICROBIOLOGY

Measurement and Implications of Nonphotochemically Generated Superoxide in the Equatorial Pacific Ocean

(2008) Andrew L. Rose et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Electron microscopy encounters with unusual thermophiles helps direct genomic analysis of Aciduliprofundum boonei

(2008) A.-L. REYSENBACH et al.   Geobiology

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

(2008) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Heterogeneous archaeal communities in the particle-rich environment of an arctic shelf ecosystem

(2008) Pierre E. Galand et al.   JOURNAL OF MARINE SYSTEMS

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH