Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria

Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla

(2016) Marian L. Schmidt et al.   ENVIRONMENTAL MICROBIOLOGY

Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1Compound Oxidation

(2015) Vincent J. Denef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Major contribution of both zooplankton and protists to the top-down regulation of freshwater aerobic anoxygenic phototrophic bacteria

(2015) MC Garcia-Chaves et al.   AQUATIC MICROBIAL ECOLOGY

The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign

(2015) Michaela M Salcher et al.   ISME Journal

Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary

(2015) Thomas S Lankiewicz et al.   ISME Journal

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

(2015) Özgul İnceoğlu et al.   MICROBIAL ECOLOGY

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

(2015) Guillem Salazar et al.   MOLECULAR ECOLOGY

Different bulk and active bacterial communities in cryoconite from the margin and interior of the Greenland ice sheet

(2015) Marek Stibal et al.   Environmental Microbiology Reports

A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan

(2015) Ryan J. Newton et al.   Frontiers in Microbiology

Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre

(2015) Kristina M. Fontanez et al.   Frontiers in Microbiology

RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

(2015) Ann McCarthy et al.   PLoS One

Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization

(2014) Mina Bižić-Ionescu et al.   ENVIRONMENTAL MICROBIOLOGY

Leucine incorporation by aerobic anoxygenic phototrophic bacteria in the Delaware estuary

(2014) Monica R Stegman et al.   ISME Journal

Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

(2014) Yao Zhang et al.   MOLECULAR ECOLOGY

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities

(2014) Despina Tsementzi et al.   Environmental Microbiology Reports

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography

(2014) Heather E. Adams et al.   Frontiers 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

Community composition and activity state of estuarine bacterioplankton assessed using differential staining and metagenomic analysis of 16S rDNA and rRNA

(2013) RB Franklin et al.   AQUATIC MICROBIAL ECOLOGY

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

(2013) Romain L Barnard et al.   ISME Journal

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters

(2012) Dana E. Hunt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Acidobacteriadominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures

(2012) Minna K. Männistö et al.   FEMS MICROBIOLOGY ECOLOGY

Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient

(2012) Barbara J Campbell et al.   ISME Journal

In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake

(2012) Michaela M Salcher et al.   ISME Journal

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny 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

Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns

(2012) Stefan Rösel et al.   MICROBIAL ECOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom

(2011) Ester M. Eckert et al.   ENVIRONMENTAL MICROBIOLOGY

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)

(2011) Michaela M Salcher et al.   ISME Journal

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Activity of abundant and rare bacteria in a coastal ocean

(2011) B. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dreissena and the disappearance of the spring phytoplankton bloom in Lake Michigan

(2010) Henry A. Vanderploeg et al.   JOURNAL OF GREAT LAKES RESEARCH

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea

(2009) Jean-François Ghiglione et al.   FEMS MICROBIOLOGY LETTERS

Annual patterns of presence and activity of marine bacteria monitored by 16S rDNA–16S rRNA fingerprints in the coastal NW Mediterranean Sea

(2008) R Lami et al.   AQUATIC MICROBIAL ECOLOGY

Current Status and Trends in Muskegon Lake, Michigan

(2008) Alan D. Steinman et al.   JOURNAL OF GREAT LAKES RESEARCH

A single-cell view on the ecophysiology of anaerobic phototrophic bacteria

(2008) N. Musat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA