Marine microbial community dynamics and their ecological interpretation

COEXISTENCE OF EVOLVING BACTERIA STABILIZED BY A SHARED BLACK QUEEN FUNCTION

(2014) J. Jeffrey Morris et al.   EVOLUTION

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing

(2014) Anna Klindworth et al.   Marine Genomics

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

Master recyclers: features and functions of bacteria associated with phytoplankton blooms

(2014) Alison Buchan et al.   NATURE REVIEWS MICROBIOLOGY

Microbial oceanography and the Hawaii Ocean Time-series programme

(2014) David M. Karl et al.   NATURE REVIEWS MICROBIOLOGY

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages

(2014) E. A. Ottesen et al.   SCIENCE

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

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

Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California

(2013) AAY Lie et al.   AQUATIC MICROBIAL ECOLOGY

Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean

(2013) KL Vergin et al.   AQUATIC MICROBIAL ECOLOGY

Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates

(2013) JL Clasen et al.   AQUATIC MICROBIAL ECOLOGY

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

Sea change: Charting the course for biogeochemical ocean time-series research in a new millennium

(2013) Matthew J. Church et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Beta diversity of marine bacteria depends on temporal scale

(2013) Stephen M. Hatosy et al.   ECOLOGY

Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode-water eddy

(2013) Craig E. Nelson et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

(2013) David M Needham 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

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

(2013) Kevin L Vergin et al.   ISME Journal

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Pattern and synchrony of gene expression among sympatric marine microbial populations

(2013) E. A. Ottesen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

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

(2012) Li C. Xia et al.   BIOINFORMATICS

Population Genomics: How Bacterial Species Form and Why They Don't Exist

(2012) W. Ford Doolittle   CURRENT BIOLOGY

Seasonality and monthly dynamics of marine myovirus communities

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

Basin-scale patterns in the abundance of SAR11 subclades, marine Actinobacteria (OM1), members of the Roseobacter clade and OCS116 in the South Atlantic

(2012) Robert M. Morris et al.   ENVIRONMENTAL MICROBIOLOGY

A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA

(2012) Emily L Kara et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Rapid diversification of coevolving marine Synechococcus and a virus

(2012) M. F. Marston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seasonality in Ocean Microbial Communities

(2012) S. J. Giovannoni et al.   SCIENCE

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

(2012) L. Deng et al.   mBio

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Diversity and Distribution of Marine Synechococcus: Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive Measurement of Clades in the Ocean

(2012) Nathan A. Ahlgren et al.   Frontiers in Microbiology

Abundance and Distribution of Synechococcus spp. and Cyanophages in the Chesapeake Bay

(2011) Kui Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR

(2011) Ryan W. Paerl et al.   ENVIRONMENTAL MICROBIOLOGY

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

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea

(2011) Rachel J Parsons et al.   ISME Journal

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

(2011) Albert Barberán et al.   ISME Journal

Genomic island variability facilitates Prochlorococcus–virus coexistence

(2011) Sarit Avrani et al.   NATURE

Nutrient Cycles and Marine Microbes in a CO2-Enriched Ocean

(2011) David Hutchins et al.   OCEANOGRAPHY

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

Targeted Sorting of Single Virus-Infected Cells of the Coccolithophore Emiliania huxleyi

(2011) Joaquín Martínez Martínez et al.   PLoS One

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Long Term Seasonal Dynamics of Synechococcus Population Structure in the Gulf of Aqaba, Northern Red Sea

(2011) Anton F. Post et al.   Frontiers in Microbiology

Modeling Diverse Communities of Marine Microbes

(2010) Michael J. Follows et al.   Annual Review of Marine Science

Nitrogen Cycle of the Open Ocean: From Genes to Ecosystems

(2010) Jonathan P. Zehr et al.   Annual Review of Marine Science

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

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

Time-series analyses of Monterey Bay coastal microbial picoplankton using a ‘genome proxy’ microarray

(2010) Virginia I. Rich et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans

(2010) Rex R Malmstrom 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

Short-term variability in primary productivity during a wind-driven diatom bloom in the Gulf of Eilat (Aqaba)

(2009) D Iluz et al.   AQUATIC MICROBIAL ECOLOGY

Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences

(2009) Feng Chen et al.   ENVIRONMENTAL MICROBIOLOGY

The seasonal structure of microbial communities in the Western English Channel

(2009) Jack A. Gilbert et al.   ENVIRONMENTAL MICROBIOLOGY

The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity

(2009) M. S. Schwalbach et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal variation of Synechococcus clades at a coastal Pacific Ocean monitoring site

(2009) Vera Tai et al.   ISME Journal

Seasonality and vertical structure of microbial communities in an ocean gyre

(2009) Alexander H Treusch et al.   ISME Journal

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Viral Glycosphingolipids Induce Lytic Infection and Cell Death in Marine Phytoplankton

(2009) A. Vardi et al.   SCIENCE

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

Community structure of marine bacterioplankton: patterns, networks, and relationships to function

(2008) JA Fuhrman et al.   AQUATIC MICROBIAL ECOLOGY

Microbial dynamics in cyclonic and anticyclonic mode-water eddies in the northwestern Sargasso Sea

(2008) Courtney S. Ewart et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Long-term observation of a pollination network: fluctuation in species and interactions, relative invariance of network structure and implications for estimates of specialization

(2008) Theodora Petanidou et al.   ECOLOGY LETTERS

Microbial diversity and the genetic nature of microbial species

(2008) Mark Achtman et al.   NATURE REVIEWS MICROBIOLOGY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

(2008) D. E. Hunt et al.   SCIENCE

Spreading Dead Zones and Consequences for Marine Ecosystems

(2008) R. J. Diaz et al.   SCIENCE