Response of soil protozoa to acid mine drainage in a contaminated terrace

Soil bacterial community functions and distribution after mining disturbance

(2021) Enzong Xiao et al.   SOIL BIOLOGY & BIOCHEMISTRY

Rhizosphere protists are key determinants of plant health

(2020) Wu Xiong et al.   Microbiome

The global-scale distributions of soil protists and their contributions to belowground systems

(2020) Angela M. Oliverio et al.   Science Advances

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

Characterization of nitrate-dependent As(III)-oxidizing communities in arsenic-contaminated soil and investigation of their metabolic potentials by the combination of DNA-SIP and metagenomics

(2020) Miaomiao Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

A practical guide to amplicon and metagenomic analysis of microbiome data

(2020) Yong-Xin Liu et al.   Protein & Cell

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

Metagenomic approach reveals the fate of antibiotic resistance genes in a temperature-raising anaerobic digester treating municipal sewage sludge

(2020) Rui Xu et al.   JOURNAL OF CLEANER PRODUCTION

Microbial co-occurrence network analysis of soils receiving short- and long-term applications of alkaline treated biosolids

(2020) G.W. Price et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem

(2020) Andrew R. Thompson et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial adaptation in vertical soil profiles contaminated by antimony smelting plant

(2020) Rui Xu et al.   FEMS MICROBIOLOGY ECOLOGY

Root microbiome assembly of As‐hyperaccumulator Pteris vittata and its efficacy in arsenic requisition

(2020) Enzong Xiao et al.   ENVIRONMENTAL MICROBIOLOGY

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

Metagenomic analysis reveals the effects of long-term antibiotic pressure on sludge anaerobic digestion and antimicrobial resistance risk

(2019) Rui Xu et al.   BIORESOURCE TECHNOLOGY

Functional Traits and Spatio-Temporal Structure of a Major Group of Soil Protists (Rhizaria: Cercozoa) in a Temperate Grassland

(2019) Anna Maria Fiore-Donno et al.   Frontiers in Microbiology

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

(2018) Rui Xu et al.   BIORESOURCE TECHNOLOGY

The ecology and diversity of microbial eukaryotes in geothermal springs

(2018) Angela M. Oliverio et al.   ISME Journal

Rapid startup of thermophilic anaerobic digester to remove tetracycline and sulfonamides resistance genes from sewage sludge

(2018) Rui Xu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

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

Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study

(2018) Alessia Rossi et al.   MICROBIAL ECOLOGY

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function

(2017) Sebastian Flues et al.   ENVIRONMENTAL MICROBIOLOGY

Soil protist communities form a dynamic hub in the soil microbiome

(2017) Wu Xiong et al.   ISME Journal

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture

(2017) S Emilia Hannula et al.   ISME Journal

Biodiversity and species competition regulate the resilience of microbial biofilm community

(2017) Kai Feng et al.   MOLECULAR ECOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Soil protistology rebooted: 30 fundamental questions to start with

(2017) Stefan Geisen et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

(2017) Olaf Tyc et al.   TRENDS IN MICROBIOLOGY

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs

(2016) A. Ö. C. Dupont et al.   ENVIRONMENTAL MICROBIOLOGY

The prey’s scent – Volatile organic compound mediated interactions between soil bacteria and their protist predators

(2016) Kristin Schulz-Bohm et al.   ISME Journal

Metagenomes provide valuable comparative information on soil microeukaryotes

(2016) Samuel Jacquiod et al.   RESEARCH IN MICROBIOLOGY

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

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

(2015) S. Geisen et al.   MOLECULAR ECOLOGY

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

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Contrasting elevational diversity patterns between eukaryotic soil microbes and plants

(2014) Congcong Shen et al.   ECOLOGY

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

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

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

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

Soil water availability strongly alters the community composition of soil protists

(2014) Geisen Stefan et al.   PEDOBIOLOGIA

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

(2013) Cheryl-Emiliane T Chow et al.   ISME Journal

Fungal diversity in deep-sea extreme environments

(2012) Yuriko Nagano et al.   Fungal Ecology

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

Ecological niche models reveal the importance of climate variability for the biogeography of protosteloid amoebae

(2012) María Aguilar et al.   ISME Journal

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Community structure of cultivable protists in different grassland and forest soils of Thuringia

(2012) Anne Domonell et al.   PEDOBIOLOGIA

GENETIC ADAPTATION AND ACCLIMATION OF PHYTOPLANKTON ALONG A STRESS GRADIENT IN THE EXTREME WATERS OF THE AGRIO RIVER-CAVIAHUE LAKE (ARGENTINA)1

(2011) Victoria López-Rodas et al.   JOURNAL OF PHYCOLOGY

Closely related protist strains have different grazing impacts on natural bacterial communities

(2010) Edvard Glücksman et al.   ENVIRONMENTAL MICROBIOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Molecular systematics of marine gregarines (Apicomplexa) from North-eastern Pacific polychaetes and nemerteans, with descriptions of three novel species: Lecudina phyllochaetopteri sp. nov., Difficilina tubulani sp. nov. and Difficilina paranemertis sp. nov.

(2009) S. Rueckert et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana

(2009) Katja Rosenberg et al.   ISME Journal

Global ecological patterns in uncultured Archaea

(2009) Jean-Christophe Auguet et al.   ISME Journal

Phylogeny, Taxonomy, and Astounding Genetic Diversity of Glissomonadida ord. nov., The Dominant Gliding Zooflagellates in Soil (Protozoa: Cercozoa)

(2009) Alexis T. Howe et al.   PROTIST