Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats

Endemic and cosmopolitan fungal taxa exhibit differential abundances in total and active communities of Antarctic soils

(2019) Filipa Cox et al.   ENVIRONMENTAL MICROBIOLOGY

Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

(2019) Krista M. Ruppert et al.   Global Ecology and Conservation

Taxon-specific fungal preference for distinct soil particle size fractions

(2019) Michael Hemkemeyer et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Fungal richness contributes to multifunctionality in boreal forest soil

(2019) Jing Li et al.   SOIL BIOLOGY & BIOCHEMISTRY

Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

(2019) Charlie Pauvert et al.   Fungal Ecology

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

Estimation of Fungal Diversity and Identification of Major Abiotic Drivers Influencing Fungal Richness and Communities in Northern Temperate and Boreal Quebec Forests

(2019) Laperriere Genevieve et al.   Forests

The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen

(2018) César Nicolás et al.   ISME Journal

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

(2018) Lotus A. Lofgren et al.   MOLECULAR ECOLOGY

Mycobiome diversity: high-throughput sequencing and identification of fungi

(2018) R. Henrik Nilsson et al.   NATURE REVIEWS MICROBIOLOGY

Interactions between soil- and dead wood-inhabiting fungal communities during the decay of Norway spruce logs

(2017) Raisa Mäkipää et al.   ISME Journal

Tree species identity and diversity drive fungal richness and community composition along an elevational gradient in a Mediterranean ecosystem

(2017) Alessandro Saitta et al.   MYCORRHIZA

Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique

(2017) Witoon Purahong et al.   Frontiers in Microbiology

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

(2017) Olivier Laroche et al.   PeerJ

Multigene phylogeny of Endogonales, an early diverging lineage of fungi associated with plants

(2017) Alessandro Desirò et al.   IMA Fungus

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Location, location, location: priority effects in wood decay communities may vary between sites

(2016) Jennifer Hiscox et al.   ENVIRONMENTAL MICROBIOLOGY

Accumulation rates and sources of external nitrogen in decaying wood in a Norway spruce dominated forest

(2016) Katja T. Rinne et al.   FUNCTIONAL ECOLOGY

Fungi associated with decomposing deadwood in a natural beech-dominated forest

(2016) Petr Baldrian et al.   Fungal Ecology

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site

(2016) Olivier Laroche et al.   MARINE ENVIRONMENTAL RESEARCH

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Fine-scale spatial distribution of orchid mycorrhizal fungi in the soil of host-rich grasslands

(2016) Samuele Voyron et al.   NEW PHYTOLOGIST

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community

(2016) Vendula Brabcová et al.   NEW PHYTOLOGIST

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

(2016) Martina Peter et al.   Nature Communications

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

Low abundance of Archaeorhizomycetes among fungi in soil metatranscriptomes

(2016) Michal Choma et al.   Scientific Reports

Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria

(2016) Vincent J. Denef et al.   Frontiers in Microbiology

Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic

(2016) Sunil Mundra et al.   MicrobiologyOpen

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

(2016) Magdalena Guardiola et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

(2015) Lucia Žifčáková et al.   ENVIRONMENTAL MICROBIOLOGY

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

(2015) Joana Amorim Visco et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

(2015) Leho Tedersoo et al.   ISME Journal

Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils

(2015) Glade Dlott et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

(2015) X. Pochon et al.   MARINE POLLUTION BULLETIN

Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient

(2015) Rebecca C Mueller et al.   MICROBIAL ECOLOGY

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

(2014) Jan Pawlowski et al.   Molecular Ecology Resources

Influence of Different Forest System Management Practices on Leaf Litter Decomposition Rates, Nutrient Dynamics and the Activity of Ligninolytic Enzymes: A Case Study from Central European Forests

(2014) Witoon Purahong et al.   PLoS One

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

An overview of pre-ribosomal RNA processing in eukaryotes

(2014) Anthony K. Henras et al.   Wiley Interdisciplinary Reviews-RNA

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Effects of forest management on the diversity of deadwood-inhabiting fungi in Central European forests

(2013) Stefan Blaser et al.   FOREST ECOLOGY AND MANAGEMENT

Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus

(2013) F Rineau et al.   ISME Journal

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

(2013) Romain L Barnard et al.   ISME Journal

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

ITS1 versus ITS2 as DNA metabarcodes for fungi

(2013) R. Blaalid et al.   Molecular Ecology Resources

Biogeography of ectomycorrhizal fungi associated with alders (Alnusspp.) in relation to biotic and abiotic variables at the global scale

(2013) Sergei Põlme et al.   NEW PHYTOLOGIST

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

(2012) Coralie Damon et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi

(2011) A. Rosling et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Lignin-modifying enzymes in filamentous basidiomycetes - ecological, functional and phylogenetic review

(2010) Taina K. Lundell et al.   JOURNAL OF BASIC MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DNA- and RNA-derived assessments of fungal community composition in soil amended with sewage sludge rich in cadmium, copper and zinc

(2008) Ian C. Anderson et al.   SOIL BIOLOGY & BIOCHEMISTRY