Metagenomic analysis displays the potential predictive biodegradation pathways of the persistent pesticides in agricultural soil with a long record of pesticide usage

Taxonomical and functional bacterial community profiling in disease-resistant and disease-susceptible soybean cultivars

(2022) Anamika Dubey et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Emerging frontiers in microbe-mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment

(2022) Muneer Ahmad Malla et al.   ENVIRONMENTAL POLLUTION

Electrical conductivity as a driver of biological and geological spatial heterogeneity in the Puquios, Salar de Llamara, Atacama Desert, Chile

(2021) R. P. Reid et al.   Scientific Reports

Tapping the Role of Microbial Biosurfactants in Pesticide Remediation: An Eco-Friendly Approach for Environmental Sustainability

(2021) Aman Raj et al.   Frontiers in Microbiology

Exploring Soil Factors Determining Composition and Structure of the Bacterial Communities in Saline-Alkali Soils of Songnen Plain

(2020) Shuang Wang et al.   Frontiers in Microbiology

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Pesticide-tolerant bacteria isolated from a biopurification system to remove commonly used pesticides to protect water resources

(2020) Gabriela Briceño et al.   PLoS One

Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8

(2020) Dean Thompson et al.   Frontiers in Microbiology

Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production

(2020) Ashwani Kumar et al.   Journal of Advanced Research

Plants endophytes: unveiling hidden agenda for bioprospecting toward sustainable agriculture

(2020) Anamika Dubey et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Microbial diversity and co-occurrence patterns in deep soils contaminated by polycyclic aromatic hydrocarbons (PAHs)

(2020) Shuying Geng et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Biodegradation of Pesticides at the Limit: Kinetics and Microbial Substrate Use at Low Concentrations

(2020) Johannes Wirsching et al.   Frontiers in Microbiology

Tolerance of Bradyrhizobium sp. BR 3901 to herbicides and their ability to use these pesticides as a nutritional source

(2020) Gabriela Madureira Barroso et al.   ECOLOGICAL INDICATORS

Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment

(2019) Muneer Ahmad Malla et al.   Frontiers in Immunology

A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico

(2019) Keni Cota-Ruiz et al.   ENVIRONMENT INTERNATIONAL

Soil microbiome: a key player for conservation of soil health under changing climate

(2019) Anamika Dubey et al.   BIODIVERSITY AND CONSERVATION

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities

(2019) Raj Kumar Regar et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Metagenomic insights into the microbiota profiles and bioaugmentation mechanism of organics removal in coal gasification wastewater in an anaerobic/anoxic/oxic system by methanol

(2018) Weichao Xu et al.   BIORESOURCE TECHNOLOGY

Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

(2018) Madan Kumar et al.   Biotechnology for Biofuels

Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation

(2018) Shuai Zhao et al.   Scientific Reports

Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils

(2018) Thomas C. Jeffries et al.   Frontiers in Microbiology

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

(2018) Muneer A. Malla et al.   Frontiers in Microbiology

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

(2018) Nicholas A. Bokulich et al.   Microbiome

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

(2018) Shin Haruta et al.   CURRENT GENOMICS

Biodegradation of Organochlorine Pesticides by Paenibacillus sp. Strain

(2018) El-Sayed B. Belal et al.   ENVIRONMENTAL ENGINEERING SCIENCE

Exploring bacterial communities and biodegradation genes in activated sludge from pesticide wastewater treatment plants via metagenomic analysis

(2018) Hua Fang et al.   ENVIRONMENTAL POLLUTION

Isolation and characterization of a lead (Pb) tolerant Pseudomonas aeruginosa strain HF5 for decolorization of reactive red-120 and other azo dyes

(2018) Farhan Hafeez et al.   ANNALS OF MICROBIOLOGY

Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants

(2018) Jong-Hyun Jung et al.   Standards in Genomic Sciences

Microbial communities in pesticide-contaminated soils in Kyrgyzstan and bioremediation possibilities

(2017) Tinatin Doolotkeldieva et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Pseudomonas sp. ZXY-1, a newly isolated and highly efficient atrazine-degrading bacterium, and optimization of biodegradation using response surface methodology

(2017) Xinyue Zhao et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

Identification of the key amino acid sites of the carbendazim hydrolase (MheI) from a novel carbendazim-degrading strain Mycobacterium sp. SD-4

(2017) Yingkun Zhang et al.   JOURNAL OF HAZARDOUS MATERIALS

Stenotrophomonas maltophilia as an Emerging Ubiquitous Pathogen: Looking Beyond Contemporary Antibiotic Therapy

(2017) Anthony A. Adegoke et al.   Frontiers in Microbiology

Effect of pesticides on microbial communities in container aquatic habitats

(2017) Ephantus J. Muturi et al.   Scientific Reports

Structure and function of the microbial consortia of activated sludge in typical municipal wastewater treatment plants in winter

(2017) Bo Zhang et al.   Scientific Reports

Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism

(2016) Xin Yan et al.   ENVIRONMENTAL MICROBIOLOGY

Contamination from organochlorine pesticides (OCPs) in agricultural soils of Kuttanad agroecosystem in India and related potential health risk

(2016) S. N. Sruthi et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Bacterial assisted degradation of chlorpyrifos: The key role of environmental conditions, trace metals and organic solvents

(2016) Saira Khalid et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation

(2016) Saranya Kuppusamy et al.   JOURNAL OF HAZARDOUS MATERIALS

Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea

(2016) Jeong Myeong Kim et al.   JOURNAL OF MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Effects of heavy metals on soil microbial community structure and diversity in the rice (Oryza sativa L. subsp. Japonica, Food Crops Institute of Jiangsu Academy of Agricultural Sciences) rhizosphere

(2016) Zili Ding et al.   SOIL SCIENCE AND PLANT NUTRITION

Characterization and genome functional analysis of a novel metamitron-degrading strain Rhodococcus sp. MET via both triazinone and phenyl rings cleavage

(2016) Hua Fang et al.   Scientific Reports

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Involvement of the Cytochrome P450 System EthBAD in theN-Deethoxymethylation of Acetochlor by Rhodococcus sp. Strain T3-1

(2015) Fei Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam

(2015) Katja Sonja Nitzsche et al.   CHEMOSPHERE

Quantitative response relationships between degradation rates and functional genes during the degradation of beta-cypermethrin in soil

(2015) Zhong-Hua Yang et al.   JOURNAL OF HAZARDOUS MATERIALS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Properties of bacterial laccases and their application in bioremediation of industrial wastes

(2015) Ram Chandra et al.   Environmental Science-Processes & Impacts

Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer

(2015) Andreas H. Keller et al.   Frontiers in Microbiology

Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India

(2015) Gagandeep Kaur et al.   3 Biotech

Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India

(2015) Gagandeep Kaur et al.   3 Biotech

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Potential use of polyphenol oxidases (PPO) in the bioremediation of phenolic contaminants containing industrial wastewater

(2013) Suprabhat Mukherjee et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge

(2012) Hua Fang et al.   BIORESOURCE TECHNOLOGY

Chlorpyrifos biodegradation and 3,5,6-trichloro-2-pyridinol production by actinobacteria isolated from soil

(2012) G. Briceño et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

IBD—what role do Proteobacteria play?

(2012) Indrani Mukhopadhya et al.   Nature Reviews Gastroenterology & Hepatology

METAGENassist: a comprehensive web server for comparative metagenomics

(2012) D. Arndt et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

(2012) Etienne Yergeau et al.   PLoS One

Biosorption of lead from aqueous solutions by Bacillus strains possessing heavy-metal resistance

(2011) Ferdağ Çolak et al.   CHEMICAL ENGINEERING JOURNAL

Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

(2011) Casey R. J. Hubert et al.   ENVIRONMENTAL MICROBIOLOGY

Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities

(2011) Hikaru Suenaga   ENVIRONMENTAL MICROBIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments

(2010) Emily B Hollister et al.   ISME Journal

The effects of nutrient amendment on biodegradation and cytochrome P450 activity of an n-alkane degrading strain of Burkholderia sp. GS3C

(2010) Ren-Ren Wu et al.   JOURNAL OF HAZARDOUS MATERIALS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genetic diversity and characterization of heavy metal-resistant-endophytic bacteria from two copper-tolerant plant species on copper mine wasteland

(2009) Le-Ni Sun et al.   BIORESOURCE TECHNOLOGY

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria

(2008) Graeme W. Nicol et al.   ENVIRONMENTAL MICROBIOLOGY