Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept

The development of the protistan species-maximum concept for the critical salinity zone

(2017) S. O. Skarlato et al.   Russian Journal of Marine Biology

Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine

(2016) Oleksandra Bobrova et al.   ACTA BIOCHIMICA POLONICA

Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea)

(2016) Christina Pavloudi et al.   Marine Genomics

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon

(2016) Matthew P. Highton et al.   Frontiers in Microbiology

Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea

(2016) Daniel P. R. Herlemann et al.   Frontiers in Microbiology

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Resilience vs. historical contingency in microbial responses to environmental change

(2015) Christine V. Hawkes et al.   ECOLOGY LETTERS

Size, seasonality, or salinity: What drives the protistan species maximum in the horohalinicum?

(2015) Irena V. Telesh et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Saltwater intrusion history shapes the response of bacterial communities upon rehydration

(2015) Tiffanie M. Nelson et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

(2014) Jingxu Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

UProC: tools for ultra-fast protein domain classification

(2014) Peter Meinicke   BIOINFORMATICS

Can the freshwater bacterial communities shift to the “marine-like” taxa?

(2014) Lei Zhang et al.   JOURNAL OF BASIC MICROBIOLOGY

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

(2014) Chris L. Dupont et al.   PLoS One

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Life in the salinity gradient: Discovering mechanisms behind a new biodiversity pattern

(2013) Irena Telesh et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River

(2013) C. Staley et al.   JOURNAL OF APPLIED MICROBIOLOGY

Functional changes in benthic communities along a salinity gradient– a western Baltic case study

(2013) Alexander Darr et al.   JOURNAL OF SEA RESEARCH

Illumina Sequencing of 16S rRNA Tag Revealed Spatial Variations of Bacterial Communities in a Mangrove Wetland

(2013) Xiao-Tao Jiang et al.   MICROBIAL ECOLOGY

Coastal Microbial Mat Diversity along a Natural Salinity Gradient

(2013) Henk Bolhuis et al.   PLoS One

Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags

(2012) Yu Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of salinity on nitrogenase activity and composition of the active diazotrophic community in intertidal microbial mats

(2012) Ina Severin et al.   ARCHIVES OF MICROBIOLOGY

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

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

(2012) Barbara J Campbell et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

The role of freshwater inflow in lagoons, rivers, and bays

(2011) Terence A. Palmer et al.   HYDROBIOLOGIA

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

(2011) Daniel PR Herlemann et al.   ISME Journal

Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient

(2011) Caroline S Fortunato et al.   ISME Journal

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing

(2011) Henk Bolhuis et al.   ISME Journal

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

(2011) Lucie Zinger et al.   PLoS One

Short-Term Response of Carbon Cycling to Salinity Pulses in a Freshwater Wetland

(2011) Lisa G. Chambers et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Microbes do not follow the elevational diversity patterns of plants and animals

(2010) Noah Fierer et al.   ECOLOGY

Global patterns in the biogeography of bacterial taxa

(2010) Diana R. Nemergut et al.   ENVIRONMENTAL MICROBIOLOGY

Fjord water circulation patterns and dysoxic/anoxic conditions in a Mediterranean semi-enclosed embayment in the Amvrakikos Gulf, Greece

(2010) George Ferentinos et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Revisiting Remane’s concept: evidence for high plankton diversity and a protistan species maximum in the horohalinicum of the Baltic Sea

(2010) IV Telesh et al.   MARINE ECOLOGY PROGRESS SERIES

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Denitrifier abundance and activity across the San Francisco Bay estuary

(2010) Annika C. Mosier et al.   Environmental Microbiology Reports

Microbial Community Response to Seawater Amendment in Low-Salinity Tidal Sediments

(2009) Jennifer W. Edmonds et al.   MICROBIAL ECOLOGY

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

(2008) Annika C. Mosier et al.   ENVIRONMENTAL MICROBIOLOGY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

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