Metabolic potentials of members of the class Acidobacteriia in metal‐contaminated soils revealed by metagenomic analysis

Microbial diversity in soils from antimony mining sites: geochemical control promotes species enrichment

(2020) Renjian Deng et al.   Environmental Chemistry Letters

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

(2020) Jasmine Chong et al.   Nature Protocols

Bacterial response to sharp geochemical gradients caused by acid mine drainage intrusion in a terrace: Relevance of C, N, and S cycling and metal resistance

(2020) Weimin Sun et al.   ENVIRONMENT INTERNATIONAL

Comparative characterization of microbial communities that inhabit arsenic-rich and antimony-rich contaminated sites: Responses to two different contamination conditions

(2020) Xiaoxu Sun et al.   ENVIRONMENTAL POLLUTION

Microbial communities associated with methylmercury degradation in paddy soils

(2020) Xin-Quan Zhou et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils

(2020) Anastasia A. Ivanova et al.   PLoS One

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling

(2020) Song-Can Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impacts of antimony and arsenic co-contamination on the river sedimentary microbial community in an antimony-contaminated river

(2020) Rui Xu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Concentration, Spatial Distribution, Contamination Degree and Human Health Risk Assessment of Heavy Metals in Urban Soils across China between 2003 and 2019—A Systematic Review

(2020) Shuangmei Tong et al.   International Journal of Environmental Research and Public Health

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage

(2020) Rui Xu et al.   ENVIRONMENTAL POLLUTION

Investigation of the ecological roles of putative keystone taxa during tailing revegetation

(2020) Xiaoxu Sun et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

(2020) Jialin Hou et al.   Microbiome

Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

(2020) Xiaoxu Sun et al.   Journal of Environmental Sciences-China

Mercury methylating microbial communities of boreal forest soils

(2019) Jingying Xu et al.   Scientific Reports

Biogeochemical gold cycling selects metal-resistant bacteria that promote gold particle transformation

(2019) Santonu Kumar Sanyal et al.   FEMS MICROBIOLOGY ECOLOGY

Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics

(2019) Sha Tan et al.   ISME Journal

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Vegetation type impacts microbial interaction with antimony contaminants in a mining-contaminated soil environment

(2019) Xiaoxu Sun et al.   ENVIRONMENTAL POLLUTION

Organic loading rate and hydraulic retention time shape distinct ecological networks of anaerobic digestion related microbiome

(2018) Rui Xu et al.   BIORESOURCE TECHNOLOGY

DNA-SIP Reveals the Diversity of Chemolithoautotrophic Bacteria Inhabiting Three Different Soil Types in Typical Karst Rocky Desertification Ecosystems in Southwest China

(2018) Baoqin Li et al.   MICROBIAL ECOLOGY

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants

(2018) Stefano Campanaro et al.   WATER RESEARCH

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Bacterial Survival Strategies in an Alkaline Tailing Site and the Physiological Mechanisms of Dominant Phylotypes As Revealed by Metagenomic Analyses

(2018) Weimin Sun et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Unraveling Microbial Communities Associated with Methylmercury Production in Paddy Soils

(2018) Yu-Rong Liu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Refining the taxonomic structure of the phylum Acidobacteria

(2018) Svetlana N. Dedysh et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic

(2017) Yong-Guan Zhu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

(2017) Achal Dhariwal et al.   NUCLEIC ACIDS RESEARCH

The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria

(2017) Olaf Tyc et al.   TRENDS IN MICROBIOLOGY

Soil Acidification Aggravates the Occurrence of Bacterial Wilt in South China

(2017) Shili Li et al.   Frontiers in Microbiology

Bacterial chromate reduction: A review of important genomic, proteomic, and bioinformatic analysis

(2016) Sukanta Kumar Pradhan et al.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil

(2016) Samiran Banerjee et al.   SOIL BIOLOGY & BIOCHEMISTRY

The Ecology of Acidobacteria: Moving beyond Genes and Genomes

(2016) Anna M. Kielak et al.   Frontiers in Microbiology

Microbial mercury methylation in Antarctic sea ice

(2016) Caitlin M. Gionfriddo et al.   Nature Microbiology

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

(2015) Dinghua Li et al.   BIOINFORMATICS

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

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

A Bacillus subtilis strain can reduce hexavalent chromium to trivalent and an nfrA gene is involved

(2015) Zhe Zheng et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Global prevalence and distribution of genes and microorganisms involved in mercury methylation

(2015) M. Podar et al.   Science Advances

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

(2014) Zheng-Shuang Hua et al.   ISME Journal

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Investigation on mechanism of Cr(VI) reduction and removal by Bacillus amyloliquefaciens, a novel chromate tolerant bacterium isolated from chromite mine soil

(2013) Sasmita Das et al.   CHEMOSPHERE

Escherichia coli NemA Is an Efficient Chromate Reductase That Can Be Biologically Immobilized to Provide a Cell Free System for Remediation of Hexavalent Chromium

(2013) Katherine J. Robins et al.   PLoS One

The Genetic Basis for Bacterial Mercury Methylation

(2013) J. M. Parks et al.   SCIENCE

A review of soil heavy metal pollution from mines in China: Pollution and health risk assessment

(2013) Zhiyuan Li et al.   SCIENCE OF THE TOTAL ENVIRONMENT

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Complete genome sequence of Granulicella mallensis type strain MP5ACTX8T, an acidobacterium from tundra soil

(2013) Suman R. Rawat et al.   Standards in Genomic Sciences

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

(2012) Astrid Naether et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Experimental in Situ Transformation of Pb Smelter Fly Ash in Acidic Soils

(2012) Vojtěch Ettler et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Acidobacteriadominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures

(2012) Minna K. Männistö et al.   FEMS MICROBIOLOGY ECOLOGY

Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

(2012) Acácio A. Navarrete et al.   FEMS MICROBIOLOGY ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure

(2012) Cody S. Sheik et al.   PLoS One

The Mercury Resistance Operon: From an Origin in a Geothermal Environment to an Efficient Detoxification Machine

(2012) Eric S. Boyd et al.   Frontiers in Microbiology

Bacteriocin Production: a Probiotic Trait?

(2011) Alleson Dobson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Chromium resistance strategies and toxicity: what makes Ochrobactrum tritici 5bvl1 a strain highly resistant

(2011) Paula Vasconcelos Morais et al.   BIOMETALS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Isolation and Characterization of Hexavalent Chromium-Reducing Rhizospheric Bacteria From a Wetland

(2010) Amparo Mauricio Gutiérrez et al.   INTERNATIONAL JOURNAL OF PHYTOREMEDIATION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A putative azoreductase gene is involved in the Shewanella oneidensis response to heavy metal stress

(2009) Irina Mugerfeld et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

(2009) Ryan T Jones et al.   ISME Journal

Heavy metals and soil microbes

(2009) Ken E. Giller et al.   SOIL BIOLOGY & BIOCHEMISTRY

Expression of chromate resistance genes fromShewanellasp. strain ANA-3 inEscherichia coli

(2008) Esther Aguilar-Barajas et al.   FEMS MICROBIOLOGY LETTERS

The influence of soil properties on the structure of bacterial and fungal communities across land-use types

(2008) Christian L. Lauber et al.   SOIL BIOLOGY & BIOCHEMISTRY