Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination

Salinity determines performance, functional populations, and microbial ecology in consortia attenuating organohalide pollutants

(2023) Guofang Xu et al.   ISME Journal

Offshore Marine Sediment Microbiota Respire Structurally Distinct Organohalide Pollutants

(2022) Guofang Xu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Mechanistic insight into co-metabolic dechlorination of hexachloro-1,3-butadiene in Dehalococcoides

(2022) Rui Shen et al.   WATER RESEARCH

mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements

(2022) Connor L. Brown et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

(2022) Xiyang Dong et al.   Nature Communications

Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway

(2021) Jia-Wei Zhang et al.   ISME Journal

Challenges and opportunities for the biodegradation of chlorophenols: Aerobic, anaerobic and bioelectrochemical processes

(2021) Kaichao Yang et al.   WATER RESEARCH

Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon

(2021) Elena Cerro-Gálvez et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Potential Role of Methanogens in Microbial Reductive Dechlorination of Organic Chlorinated Pollutants In Situ

(2021) Jing Yuan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Growth inhibition of methanogens for the enhancement of TCE dechlorination

(2021) W.H. Lin et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Microbial diversity in extreme environments

(2021) Wen-Sheng Shu et al.   NATURE REVIEWS MICROBIOLOGY

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

(2021) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Analysis Reveals Microbial Interactions at the Biocathode of a Bioelectrochemical System Capable of Simultaneous Trichloroethylene and Cr(VI) Reduction

(2021) Bruna Matturro et al.   Frontiers in Microbiology

Organohalide-respiring Desulfoluna species isolated from marine environments

(2020) Peng Peng et al.   ISME Journal

Influence of non-dechlorinating microbes on trichloroethene reduction based on vitamin B12 synthesis in anaerobic cultures

(2020) Li-Lian Wen et al.   ENVIRONMENTAL POLLUTION

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

Anthropogenic dissolved organic carbon and marine microbiomes

(2020) Maria Vila-Costa et al.   ISME Journal

Sharing vitamins: Cobamides unveil microbial interactions

(2020) Olga M. Sokolovskaya et al.   SCIENCE

Global diversity of microbial communities in marine sediment

(2020) Tatsuhiko Hoshino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia

(2020) Yi Yang et al.   Frontiers in Microbiology

Microbial community response to the toxic effect of pentachlorophenol in paddy soil amended with an electron donor and shuttle

(2020) Manjia Chen et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Reduction in sulfate inhibition of microbial dechlorination of polychlorinated biphenyls in Hudson and Grasse River sediments through fatty acid supplementation

(2019) Yan Xu et al.   CHEMOSPHERE

Microbial synergistic interactions for reductive dechlorination of polychlorinated biphenyls

(2019) Shanquan Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Synchronous response in methanogenesis and anaerobic degradation of pentachlorophenol in flooded soil

(2019) Min Zhu et al.   JOURNAL OF HAZARDOUS MATERIALS

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

MetaboLights: a resource evolving in response to the needs of its scientific community

(2019) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Electron transport chains in organohalide-respiring bacteria and bioremediation implications

(2018) Shanquan Wang et al.   BIOTECHNOLOGY ADVANCES

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Desulfitobacterium contributes to the microbial transformation of 2,4,5-T by methanogenic enrichment cultures from a Vietnamese active landfill

(2018) Ute Lechner et al.   Microbial Biotechnology

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Anaerobic Dehalogenation of Chloroanilines by Dehalococcoides mccartyi Strain CBDB1 and Dehalobacter Strain 14DCB1 via Different Pathways as Related to Molecular Electronic Structure

(2017) Shangwei Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Elucidation of roles for vitamin B12in regulation of folate, ubiquinone, and methionine metabolism

(2017) Margaret F. Romine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

‘ Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

(2017) Sara Kleindienst et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Spatial Abundance and Distribution of Potential Microbes and Functional Genes Associated with Anaerobic Mineralization of Pentachlorophenol in a Cylindrical Reactor

(2016) Zhi-Ling Li et al.   Scientific Reports

Microbial dehalogenation of organohalides in marine and estuarine environments

(2015) Giulio Zanaroli et al.   CURRENT OPINION IN BIOTECHNOLOGY

Anaerobic Microbial Transformation of Halogenated Aromatics and Fate Prediction Using Electron Density Modeling

(2015) Myriel Cooper 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

Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses

(2015) Etienne A. Thévenot et al.   JOURNAL OF PROTEOME RESEARCH

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Improved Vitamin B12 Fermentation Process by Adding Rotenone to Regulate the Metabolism of Pseudomonas denitrificans

(2014) Xin Cheng et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

The “bacterial heterodisulfide” DsrC is a key protein in dissimilatory sulfur metabolism

(2014) S.S. Venceslau et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin

(2014) Anne-Kristin Kaster et al.   ISME Journal

Genomic, Proteomic, and Biochemical Analysis of the Organohalide Respiratory Pathway in Desulfitobacterium dehalogenans

(2014) Thomas Kruse et al.   JOURNAL OF BACTERIOLOGY

Variable influence on projection (VIP) for orthogonal projections to latent structures (OPLS)

(2014) Beatriz Galindo-Prieto et al.   JOURNAL OF CHEMOMETRICS

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation

(2014) Karl A. P. Payne et al.   NATURE

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

(2014) Mikihiko Kawai et al.   Frontiers in Microbiology

Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions

(2013) Yujie Men et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Isolation and characterization of a novel Dehalobacter species strain TCP1 that reductively dechlorinates 2,4,6-trichlorophenol

(2013) Shanquan Wang et al.   BIODEGRADATION

Dechlorination of Commercial PCBs and Other Multiple Halogenated Compounds by a Sediment-Free Culture ContainingDehalococcoidesandDehalobacter

(2013) Shanquan Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Identification of a reductive tetrachloroethene dehalogenase in Shewanella sediminis

(2013) S. T. Lohner et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Guided cobalamin biosynthesis supports Dehalococcoides mccartyi reductive dechlorination activity

(2013) J. Yan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bacterial Chemotaxis: The Early Years of Molecular Studies

(2012) Gerald L. Hazelbauer   Annual Review of Microbiology

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Metagenomics of microbial life in extreme temperature environments

(2012) Anna Lewin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Long-Term Anaerobic Mineralization of Pentachlorophenol in a Continuous-Flow System Using Only Lactate as an External Nutrient

(2012) Zhiling Li et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme

(2012) S. Craciun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses

(2011) Yujie Men et al.   ISME Journal

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst

(2011) Jianguo Xia et al.   Nature Protocols

Natural organobromine in marine sediments: New evidence of biogeochemical Br cycling

(2010) Alessandra C. Leri et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Genome sequence ofDesulfobacterium autotrophicumHRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide

(2009) Axel W. Strittmatter et al.   ENVIRONMENTAL MICROBIOLOGY

Methanogenic archaea: ecologically relevant differences in energy conservation

(2008) Rudolf K. Thauer et al.   NATURE REVIEWS MICROBIOLOGY

Levels and spatial distribution of chlorophenols – 2,4-Dichlorophenol, 2,4,6-trichlorophenol, and pentachlorophenol in surface water of China

(2007) Jijun Gao et al.   CHEMOSPHERE