Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater

Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity

(2017) Sophie-Marie Martirani-Von Abercron et al.   Microbial Biotechnology

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community

(2016) Kevin M. Posman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Targeted metagenomics of active microbial populations with stable-isotope probing

(2016) Sara Coyotzi et al.   CURRENT OPINION IN BIOTECHNOLOGY

Tracking microbial interactions with NanoSIMS

(2016) Niculina Musat et al.   CURRENT OPINION IN BIOTECHNOLOGY

Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

(2016) David J. Beaudoin et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Phylogenetic organization of bacterial activity

(2016) Ember M Morrissey et al.   ISME Journal

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

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

Extracellular electron transfer mechanisms between microorganisms and minerals

(2016) Liang Shi et al.   NATURE REVIEWS MICROBIOLOGY

Enhanced removal of petroleum hydrocarbons using a bioelectrochemical remediation system with pre-cultured anodes

(2016) Krishnaveni Venkidusamy et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Identification of Electrode Respiring, Hydrocarbonoclastic Bacterial Strain Stenotrophomonas maltophilia MK2 Highlights the Untapped Potential for Environmental Bioremediation

(2016) Krishnaveni Venkidusamy et al.   Frontiers in Microbiology

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

(2015) Sebastián Fuentes et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reconstructing 16S rRNA genes in metagenomic data

(2015) Cheng Yuan et al.   BIOINFORMATICS

Ciliated protists from the nepheloid layer and water column of sites affected by the Deepwater Horizon oil spill in the Northeastern Gulf of Mexico

(2015) Joseph A. Moss et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

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

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples

(2015) Boonfei Tan et al.   ISME Journal

In situexpression of nitrite-dependent anaerobic methane oxidation proteins byCandidatusMethylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer

(2015) Buck T. Hanson et al.   Environmental Microbiology Reports

The Split-Apply-Combine Strategy for Data Analysis

(2015) Hadley Wickham   Journal of Statistical Software

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Microbial Metabolism and Community Structure in Response to Bioelectrochemically Enhanced Remediation of Petroleum Hydrocarbon-Contaminated Soil

(2014) Lu Lu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Functional response of an adapted subtidal macrobenthic community to an oil spill: macrobenthic structure and bioturbation activity over time throughout an 18-month field experiment

(2014) Franck Gilbert et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

(2014) Shinjini Mukherjee et al.   ISME Journal

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Methylobacterium populiVP2: Plant Growth-Promoting Bacterium Isolated from a Highly Polluted Environment for Polycyclic Aromatic Hydrocarbon (PAH) Biodegradation

(2014) Valeria Ventorino et al.   TheScientificWorldJOURNAL

Intra-genomic variation in G + C content and its implications for DNA stable isotope probing

(2014) Nicholas D. Youngblut et al.   Environmental Microbiology Reports

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Impact of protist grazing on a key bacterial group for biogeochemical cycling in Baltic Sea pelagic oxic/anoxic interfaces

(2013) Ruth Anderson et al.   ENVIRONMENTAL MICROBIOLOGY

The Morphology of ThreeLoxophyllumSpecies (Ciliophora, Pleurostomatida) from Southern China,L. lembumsp. n.,L. vesiculosumsp. n. andL. perihoplophorumBuddenbrock, 1920, with Notes on the Molecular Phylogeny ofLoxophyllum

(2013) Lei Wu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Fear in the dark? Community-level effects of non-lethal predators change with light regime

(2013) Coreen Forbes et al.   OIKOS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

One-year monitoring of meta-cleavage dioxygenase gene expression and microbial community dynamics reveals the relevance of subfamily I.2.C extradiol dioxygenases in hypoxic, BTEX-contaminated groundwater

(2013) András Táncsics et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Stable Isotope Probing and Raman Spectroscopy for Monitoring Carbon Flow in a Food Chain and Revealing Metabolic Pathway

(2012) Mengqiu Li et al.   ANALYTICAL CHEMISTRY

Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation

(2012) María-Eugenia Guazzaroni 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

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

(2011) T. Magoc et al.   BIOINFORMATICS

Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

(2011) Florence Martin et al.   ENVIRONMENTAL POLLUTION

Assimilation of benzene carbon through multiple trophic levels traced by different stable isotope probing methodologies

(2011) Felipe Bastida et al.   FEMS MICROBIOLOGY ECOLOGY

Subsurface Cycling of Nitrogen and Anaerobic Aromatic Hydrocarbon Biodegradation Revealed by Nucleic Acid and Metabolic Biomarkers

(2010) J. M. Yagi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of Ciliate Grazers of Autotrophic Bacteria in Ammonia-Oxidizing Activated Sludge by RNA Stable Isotope Probing

(2010) A. M. Moreno et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a Fatty Acid and RNA Stable Isotope Probing-Based Method for Tracking Protist Grazing on Bacteria in Wastewater

(2010) S. Kuppardt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil

(2010) Kathryn G. Eilers et al.   SOIL BIOLOGY & BIOCHEMISTRY

Diversity, Abundance, and Consistency of Microbial Oxygenase Expression and Biodegradation in a Shallow Contaminated Aquifer

(2009) J. M. Yagi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Monitored Natural Attenuation of Manufactured Gas Plant Tar Mono- and Polycyclic Aromatic Hydrocarbons in Ground Water: A 14-Year Field Study

(2009) Edward F. Neuhauser et al.   GROUND WATER MONITORING AND REMEDIATION

Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community

(2009) Jane M Yagi et al.   ISME Journal

A novel bacterial isolate Stenotrophomonas maltophilia as living factory for synthesis of gold nanoparticles

(2009) Yogesh Nangia et al.   Microbial Cell Factories

The versatility and adaptation of bacteria from the genus Stenotrophomonas

(2009) Robert P. Ryan et al.   NATURE REVIEWS MICROBIOLOGY

A Filamentous Hemagglutinin-Like Protein of Xanthomonas axonopodis pv. citri, the Phytopathogen Responsible for Citrus Canker, Is Involved in Bacterial Virulence

(2009) Natalia Gottig et al.   PLoS One

Molecular characteristics of xenobiotic-degrading sphingomonads

(2008) Andreas Stolz   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Dynamic SIMS ion microscopy imaging of individual bacterial cells for studies of isotopically labeled molecules

(2008) Subhash Chandra et al.   APPLIED SURFACE SCIENCE

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Microbial fuel cell in enhancing anaerobic biodegradation of diesel

(2008) Jeffrey M. Morris et al.   CHEMICAL ENGINEERING JOURNAL

Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metabolizing microorganisms in freshwater sediment

(2008) J. S.-C. Liou et al.   ENVIRONMENTAL MICROBIOLOGY

Dynamic secondary ion mass spectrometry imaging of microbial populations utilizing13C-labelled substrates in pure culture and in soil

(2008) Graham M. Pumphrey et al.   ENVIRONMENTAL MICROBIOLOGY

Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters

(2008) Jorge Frias-Lopez et al.   ENVIRONMENTAL MICROBIOLOGY