Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment

Involvement of polyhydroxyalkanoates in stress resistance of microbial cells: Biotechnological consequences and applications

(2018) Stanislav Obruca et al.   BIOTECHNOLOGY ADVANCES

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession

(2018) Rüdiger Ortiz-Álvarez et al.   ISME Journal

Peatland Acidobacteria with a dissimilatory sulfur metabolism

(2018) Bela Hausmann et al.   ISME Journal

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

Beyond the tip of the iceberg; a new view of the diversity of sulfite- and sulfate-reducing microorganisms

(2018) Adrien Vigneron et al.   ISME Journal

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters

(2017) Sonja Oberbeckmann et al.   FEMS MICROBIOLOGY ECOLOGY

Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps

(2016) Connor T Skennerton et al.   ISME Journal

Microbial colonization and degradation of polyethylene and biodegradable plastic bags in temperate fine-grained organic-rich marine sediments

(2016) Alice Nauendorf et al.   MARINE POLLUTION BULLETIN

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

A bacterium that degrades and assimilates poly(ethylene terephthalate)

(2016) Shosuke Yoshida et al.   SCIENCE

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre

(2016) Jessica A. Bryant et al.   mSystems

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea

(2015) Caroline A. De Tender et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Nutrient-Controlled Niche Differentiation of Western Lake Erie Cyanobacterial Populations Revealed via Metatranscriptomic Surveys

(2015) Matthew J. Harke et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

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

Microplastics in sediments: A review of techniques, occurrence and effects

(2015) Lisbeth Van Cauwenberghe et al.   MARINE ENVIRONMENTAL RESEARCH

Microbial Surface Colonization and Biofilm Development in Marine Environments

(2015) Hongyue Dang et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

(2015) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Plastic waste inputs from land into the ocean

(2015) J. R. Jambeck et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Rapid bacterial colonization of low-density polyethylene microplastics in coastal sediment microcosms

(2014) Jesse P Harrison et al.   BMC MICROBIOLOGY

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

(2014) Elizabeth G. Wilbanks et al.   ENVIRONMENTAL MICROBIOLOGY

Particle-associated extracellular enzyme activity and bacterial community composition across the Canadian Arctic Ocean

(2014) Colleen T.E. Kellogg et al.   FEMS MICROBIOLOGY ECOLOGY

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

(2014) Albert Leopold Müller et al.   ISME Journal

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of the model sulfate reducerDesulfovibrio gigas: a comparative analysis within theDesulfovibriogenus

(2014) Fabio O. Morais-Silva et al.   MicrobiologyOpen

Life in the “Plastisphere”: Microbial Communities on Plastic Marine Debris

(2013) Erik R. Zettler et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The plastic-associated microorganisms of the North Pacific Gyre

(2013) Henry S. Carson et al.   MARINE POLLUTION BULLETIN

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete genome, catabolic sub-proteomes and key-metabolites ofDesulfobacula toluolica Tol2, a marine, aromatic compound-degrading, sulfate-reducing bacterium

(2012) Lars Wöhlbrand et al.   ENVIRONMENTAL MICROBIOLOGY

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

(2012) Jennifer L Bowen et al.   ISME Journal

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Effect of substrate type on bacterial community composition in biofilms from the Great Barrier Reef

(2011) Verena Witt et al.   FEMS MICROBIOLOGY LETTERS

rRNASelector: A computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries

(2011) Jae-Hak Lee et al.   JOURNAL OF MICROBIOLOGY

Microplastics in the marine environment

(2011) Anthony L. Andrady   MARINE POLLUTION BULLETIN

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

(2010) Heng Li et al.   BIOINFORMATICS

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Plastics, the environment and human health: current consensus and future trends

(2009) R. C. Thompson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Accumulation and fragmentation of plastic debris in global environments

(2009) D. K. A. Barnes et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage

(2008) K. Robert Clarke et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY