Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems

Microplastic pollution increases gene exchange in aquatic ecosystems

(2018) Maria Arias-Andres et al.   ENVIRONMENTAL POLLUTION

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities

(2018) Tim N. Enke et al.   Nature Communications

Microbial interactions and community assembly at microscales

(2016) Otto X Cordero et al.   CURRENT OPINION IN MICROBIOLOGY

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria

(2016) Steven Smriga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial interactions lead to rapid micro-scale successions on model marine particles

(2016) Manoshi S. Datta et al.   Nature Communications

High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)

(2016) Christian Wurzbacher et al.   MycoKeys

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

The microbial carbon pump concept: Potential biogeochemical significance in the globally changing ocean

(2015) Louis Legendre et al.   PROGRESS IN OCEANOGRAPHY

The value of protein structure classification information-Surveying the scientific literature

(2015) Naomi K. Fox et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Standard filtration practices may significantly distort planktonic microbial diversity estimates

(2015) Cory C. Padilla et al.   Frontiers in Microbiology

A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect

(2015) Danny Ionescu et al.   Scientific Reports

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

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

Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison

(2014) Lindsay D'Ambrosio et al.   ISME Journal

Importance of Saprotrophic Freshwater Fungi for Pollen Degradation

(2014) Christian Wurzbacher et al.   PLoS One

Temporal changes in particle-associated microbial communities after interception by nonlethal sediment traps

(2013) Gary R. LeCleir et al.   FEMS MICROBIOLOGY ECOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Diversity and Spatial Distribution of Hydrazine Oxidoreductase (hzo) Gene in the Oxygen Minimum Zone Off Costa Rica

(2013) Liangliang Kong et al.   PLoS One

Identification of Pseudomonas aeruginosa Phenazines that Kill Caenorhabditis elegans

(2013) Brent Cezairliyan et al.   PLoS Pathogens

Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

(2013) Maria W. Smith et al.   Frontiers in Microbiology

Sizing up metatranscriptomics

(2012) Mary Ann Moran et al.   ISME Journal

Interactions between Diatoms and Bacteria

(2012) S. A. Amin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

(2012) Nadine Ziemert et al.   PLoS One

Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea

(2012) Danny Ionescu et al.   PLoS One

Marine Microbes See a Sea of Gradients

(2012) R. Stocker   SCIENCE

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

(2012) H. Teeling et al.   SCIENCE

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Prokaryotic community structure and respiration during long-term incubations

(2012) Federico Baltar et al.   MicrobiologyOpen

Decrease in the Autotrophic-to-Heterotrophic Biomass Ratio of Picoplankton in Oligotrophic Marine Waters Due to Bottle Enclosure

(2011) Alejandra Calvo-Díaz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Particle size distributions in the upper 100m water column and their implications for animal feeding in the plankton

(2011) George A. Jackson et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Zooplankton and aggregates as refuge for aquatic bacteria: protection from UV, heat and ozone stresses used for water treatment

(2010) Kam W. Tang et al.   ENVIRONMENTAL MICROBIOLOGY

Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii

(2010) Astrid Gärdes et al.   ISME Journal

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

(2010) Frank J Stewart et al.   ISME Journal

Variability in the average sinking velocity of marine particles

(2010) Andrew M. P. McDonnell et al.   LIMNOLOGY AND OCEANOGRAPHY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Pseudomonas aeruginosa-Candida albicans Interactions: Localization and Fungal Toxicity of a Phenazine Derivative

(2008) J. Gibson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Elevated Lytic Phage Production as a Consequence of Particle Colonization by a Marine Flavobacterium (Cellulophaga sp.)

(2008) Lasse Riemann et al.   MICROBIAL ECOLOGY

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

(2007) Rotem Sorek et al.   NATURE REVIEWS MICROBIOLOGY