Indicator species drive the key ecological functions of microbiota in a river impacted by acid mine drainage generated by rare earth elements mining in South China

Nitrate assimilation, dissimilatory nitrate reduction to ammonium, and denitrification coexist in Pseudomonas putida Y-9 under aerobic conditions

(2020) Xuejiao Huang et al.   BIORESOURCE TECHNOLOGY

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

(2020) Rui Xu et al.   ENVIRONMENTAL POLLUTION

Baseline of distribution and origin of Rare Earth Elements in marine sediment of the coastal area of the Eastern Gulf of Tigullio (Ligurian Sea, North-West Italy)

(2020) Sirio Consani et al.   MARINE POLLUTION BULLETIN

Factors influencing heavy metal availability and risk assessment of soils at typical metal mines in Eastern China

(2020) Xi Zhong et al.   JOURNAL OF HAZARDOUS MATERIALS

MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

(2019) Weizhi Song et al.   Microbiome

Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes

(2019) Jing Huang et al.   ISME Journal

Controls on rare-earth element transport in a river impacted by ion-adsorption rare-earth mining

(2019) Wen-Shen Liu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The Biogeochemical Sulfur Cycle of Marine Sediments

(2019) Bo Barker Jørgensen et al.   Frontiers in Microbiology

Cryptic footprints of rare earth elements on natural resources and living organisms

(2019) Muhammad Adeel et al.   ENVIRONMENT INTERNATIONAL

Laboratory evolution reveals the metabolic and regulatory basis of ethylene glycol metabolism by Pseudomonas putida KT2440

(2019) Wing‐Jin Li et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Nitrate addition promotes the nitrogen cycling processes under the co-contaminated tetrabromobisphenol A and copper condition in river sediment

(2019) Linqiong Wang et al.   ENVIRONMENTAL POLLUTION

Rare earth element bioaccumulation in the yellow and silver European eel (Anguilla anguilla): A case study in the Loire estuary (France)

(2019) Marjorie Lortholarie et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Denitrification and dissimilatory nitrate reduction to ammonium in freshwater lakes of the Eastern Plain, China: Influences of organic carbon and algal bloom

(2019) Xingyu Jiang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Mineralogical controls on mobility of rare earth elements in acid mine drainage environments

(2018) T.O. Soyol-Erdene et al.   CHEMOSPHERE

Biogeochemical sulfur cycling coupling with dissimilatory nitrate reduction processes in freshwater sediments

(2018) Jin Zhu et al.   ENVIRONMENTAL REVIEWS

Homologs from sulfur oxidation (Sox) and methanol dehydrogenation (Xox) enzyme systems collaborate to give rise to a novel pathway of chemolithotrophic tetrathionate oxidation

(2018) Prosenjit Pyne et al.   MOLECULAR MICROBIOLOGY

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

Biogeochemical sulfur cycling coupling with dissimilatory nitrate reduction processes in freshwater sediments

(2018) Jin Zhu et al.   ENVIRONMENTAL REVIEWS

Lanthanide-Dependent Methanol Dehydrogenases of XoxF4 and XoxF5 Clades Are Differentially Distributed Among Methylotrophic Bacteria and They Reveal Different Biochemical Properties

(2018) Jing Huang et al.   Frontiers in Microbiology

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

Environmental Drivers of Rare Earth Element Bioaccumulation in Freshwater Zooplankton

(2018) Gwyneth A. MacMillan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Bed and suspended sediment-associated rare earth element concentrations and fluxes in a polluted Brazilian river system

(2018) Yuri Jacques Agra Bezerra da Silva et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Water, sediment and agricultural soil contamination from an ion-adsorption rare earth mining area

(2018) Wen-Shen Liu et al.   CHEMOSPHERE

Response of Soil Microbial Communities to Elevated Antimony and Arsenic Contamination Indicates the Relationship between the Innate Microbiota and Contaminant Fractions

(2017) Weimin Sun et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Sources of rare earth elements in shells and soft-tissues of bivalves from Tokyo Bay

(2017) Tasuku Akagi et al.   MARINE CHEMISTRY

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Functional Role of Lanthanides in Enzymatic Activity and Transcriptional Regulation of Pyrroloquinoline Quinone-Dependent Alcohol Dehydrogenases in Pseudomonas putida KT2440

(2017) Matthias Wehrmann et al.   mBio

‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ

(2017) Olga V. Golyshina et al.   Nature Communications

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

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

Microbial communities, processes and functions in acid mine drainage ecosystems

(2016) Lin-xing Chen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Increases in Anthropogenic Gadolinium Anomalies and Rare Earth Element Concentrations in San Francisco Bay over a 20 Year Record

(2016) Vanessa Hatje et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Pyrroloquinoline Quinone Ethanol Dehydrogenase in Methylobacterium extorquens AM1 Extends Lanthanide-Dependent Metabolism to Multicarbon Substrates

(2016) Nathan M. Good et al.   JOURNAL OF BACTERIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Archaea catalyze iron-dependent anaerobic oxidation of methane

(2016) Katharina F. Ettwig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lanthanides: New life metals?

(2016) Ludmila Chistoserdova   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Effects of Simulated Rare Earth Recycling Wastewaters on Biological Nitrification

(2015) Yoshiko Fujita 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

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Just add lanthanides

(2015) E. Skovran et al.   SCIENCE

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

(2015) Dongwan D. Kang et al.   PeerJ

PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference

(2014) Jan T. Keltjens et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage

(2014) Lin-xing Chen et al.   ISME Journal

Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities

(2014) Daniela S Aliaga Goltsman et al.   ISME Journal

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

(2014) Celia Méndez-García et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The environmental controls that govern the end product of bacterial nitrate respiration

(2014) B. Kraft et al.   SCIENCE

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities

(2013) Frank O. Aylward et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings

(2013) Lin-xing Chen et al.   ENVIRONMENTAL MICROBIOLOGY

Rare earth metals are essential for methanotrophic life in volcanic mudpots

(2013) Arjan Pol et al.   ENVIRONMENTAL MICROBIOLOGY

State of rare earth elements in different environmental components in mining areas of China

(2013) Tao Liang et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria

(2013) Sibylle Ziegler et al.   ISME Journal

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Evaluating Rare Earth Element Availability: A Case with Revolutionary Demand from Clean Technologies

(2012) Elisa Alonso et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Contemporary environmental variation determines microbial diversity patterns in acid mine drainage

(2012) Jia-Liang Kuang et al.   ISME Journal

Effect of Ce3+ on membrane permeability of Escherichia coli cell

(2012) Aimei CHEN et al.   JOURNAL OF RARE EARTHS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Spatial and Temporal Analysis of the Microbial Community in the Tailings of a Pb-Zn Mine Generating Acidic Drainage

(2011) Li-Nan Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Modularity of methylotrophy, revisited

(2011) Ludmila Chistoserdova   ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Improving indicator species analysis by combining groups of sites

(2010) Miquel De Cáceres et al.   OIKOS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ECOLOGY: Controlling Eutrophication: Nitrogen and Phosphorus

(2009) D. J. Conley et al.   SCIENCE

Effect of some rare earth elements on the growth and lanthanide accumulation in different Trichoderma strains

(2009) Luigi d'Aquino et al.   SOIL BIOLOGY & BIOCHEMISTRY