Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat

Niche-directed evolution modulates genome architecture in freshwater Planctomycetes

(2019) Adrian-Ştefan Andrei et al.   ISME Journal

Unexpected host dependency of Antarctic Nanohaloarchaeota

(2019) Joshua N. Hamm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered lakes

(2018) Patricia Tran et al.   ENVIRONMENTAL MICROBIOLOGY

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

(2018) Michael W. Henson et al.   ISME Journal

Lake Baikal's response to remote earthquakes: Lake-level fluctuations and near-bottom water layer temperature change

(2018) Nikolay G. Granin et al.   MARINE AND PETROLEUM GEOLOGY

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

(2018) Jose M. Haro-Moreno et al.   Microbiome

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria

(2018) Sarahi L. Garcia et al.   mSphere

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS MICROBIOLOGY

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

(2018) Charlotte D. Vavourakis et al.   Microbiome

Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

(2018) Alexandra M. Linz et al.   PeerJ

Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi

(2018) Maliheh Mehrshad et al.   Microbiome

Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems

(2018) Sara F. Paver et al.   mSystems

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

(2017) Maliheh Mehrshad et al.   ISME Journal

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

(2017) Alex W Hernsdorf et al.   ISME Journal

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

(2017) Meinhard Simon et al.   ISME Journal

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria

(2017) Stefan M Neuenschwander et al.   ISME Journal

Particulate fluxes in South Baikal: Evidence from sediment trap experiments

(2017) E.G. Vologina et al.   Russian Geology and Geophysics

Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs

(2017) Pedro J. Cabello-Yeves et al.   Frontiers in Microbiology

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

(2017) Pedro J. Cabello-Yeves et al.   Frontiers in Microbiology

Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

(2017) R. E. Danczak et al.   Microbiome

Environmental drivers of a microbial genomic transition zone in the ocean’s interior

(2017) Daniel R. Mende et al.   Nature Microbiology

Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

(2016) Maliheh Mehrshad et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes

(2016) Rudiger Ortiz-Alvarez et al.   Environmental Microbiology Reports

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

(2016) Karthik Anantharaman et al.   Nature Communications

Similarity of structure of taxonomic bacterial communities in the photic layer of Lake Baikal’s three basins differing in spring phytoplankton composition and abundance

(2015) I. S. Mikhailov et al.   Doklady Biochemistry and Biophysics

The mechanism of oxygen aeration of bottom waters of Lake Baikal

(2015) M. N. Shimaraev et al.   DOKLADY EARTH SCIENCES

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

Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines

(2015) David Kamanda Ngugi et al.   ISME Journal

Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia

(2015) Maria V. Bashenkhaeva et al.   MICROBIAL ECOLOGY

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing

(2014) Rohit Ghai et al.   MOLECULAR ECOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

(2013) Alexander Eiler et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

The Diversity of the Limnohabitans Genus, an Important Group of Freshwater Bacterioplankton, by Characterization of 35 Isolated Strains

(2013) Vojtěch Kasalický et al.   PLoS One

The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal

(2013) Yulia R. Zakharova et al.   PLoS One

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Gas hydrate of Lake Baikal: Discovery and varieties

(2012) Oleg Khlystov et al.   JOURNAL OF ASIAN EARTH SCIENCES

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem

(2011) Seungdae Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Renewal of deep waters of Lake Baikal revisited

(2011) M. N. Shimaraev et al.   DOKLADY EARTH SCIENCES

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

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

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

A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

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

Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)

(2009) R. Logares et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sixty years of environmental change in the world's largest freshwater lake - Lake Baikal, Siberia

(2008) STEPHANIE E. HAMPTON et al.   GLOBAL CHANGE BIOLOGY