Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

(2018) Robin R. Rohwer et al.   mSphere

Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the ‘Proteobacteria’, and four new families within the orders Nitrosomonadales and Rhodocyclales

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

(2017) Simon Roux et al.   Nature Communications

Ananke: temporal clustering reveals ecological dynamics of microbial communities

(2017) Michael W. Hall et al.   PeerJ

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

(2017) Shaomei He et al.   mSphere

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI

(2017) Joshua J. Hamilton et al.   mSystems

Algae–bacteria interactions: Evolution, ecology and emerging applications

(2016) Rishiram Ramanan et al.   BIOTECHNOLOGY ADVANCES

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

(2016) Alexander Eiler et al.   ISME Journal

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

(2015) John W. Peters et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

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

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

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

(2015) Michaela M Salcher et al.   ISME Journal

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Aquatic carbon cycling in the conterminous United States and implications for terrestrial carbon accounting

(2015) David Butman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes

(2015) Sari Peura et al.   Scientific Reports

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Microcystin mcyA and mcyE Gene Abundances Are Not Appropriate Indicators of Microcystin Concentrations in Lakes

(2015) Lucas J. Beversdorf et al.   PLoS One

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

(2014) Trevor W Ghylin et al.   ISME Journal

Global rates of marine sulfate reduction and implications for sub-sea-floor metabolic activities

(2014) M. W. Bowles et al.   SCIENCE

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Green sulphur bacteria as a component of the photosynthetic plankton community in small dimictic humic lakes with an anoxic hypolimnion

(2013) J Karhunen et al.   AQUATIC MICROBIAL ECOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

The Role of Nitrogen Fixation in Cyanobacterial Bloom Toxicity in a Temperate, Eutrophic Lake

(2013) Lucas J. Beversdorf et al.   PLoS One

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

(2012) Sari Peura 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

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

(2012) J Gregory Caporaso et al.   ISME Journal

The Passive Yet Successful Way of Planktonic Life: Genomic and Experimental Analysis of the Ecology of a Free-Living Polynucleobacter Population

(2012) Martin W. Hahn et al.   PLoS One

Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

(2012) Manuel Martinez-Garcia et al.   PLoS One

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera

(2011) M. G. Kalyuzhnaya et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Reconstructing the various facets of dissolved organic carbon bioavailability in freshwater ecosystems

(2011) François Guillemette et al.   LIMNOLOGY AND OCEANOGRAPHY

A Guide to the Natural History of Freshwater Lake Bacteria

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

Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system

(2011) C. Holkenbrink et al.   MICROBIOLOGY-SGM

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton

(2011) Xiaozhen Mou et al.   Environmental Microbiology Reports

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Both Forward and Reverse TCA Cycles Operate in Green Sulfur Bacteria

(2010) Kuo-Hsiang Tang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Temporal Patterns in Glycolate-Utilizing Bacterial Community Composition Correlate with Phytoplankton Population Dynamics in Humic Lakes

(2010) Sara F. Paver et al.   MICROBIAL ECOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Biogenic Amines in Fish: Roles in Intoxication, Spoilage, and Nitrosamine Formation—A Review

(2009) Ismail Al Bulushi et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Lakes and streams as sentinels of environmental change in terrestrial and atmospheric processes

(2008) Craig E Williamson et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT