Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

A better understanding of functional roles of fungi in the decomposition process: using precursor rRNA containing ITS regions as a marker for the active fungal community

(2012) Witoon Purahong et al.   ANNALS OF FOREST SCIENCE

Pyrosequencing-Derived Bacterial, Archaeal, and Fungal Diversity of Spacecraft Hardware Destined for Mars

(2012) Myron T. La Duc et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Long-Term Balanced Fertilization Decreases Arbuscular Mycorrhizal Fungal Diversity in an Arable Soil in North China Revealed by 454 Pyrosequencing

(2012) Xiangui Lin et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Occurrence and impact of the root-rot biocontrol agent Phlebiopsis gigantea on soil fungal communities in Picea abies forests of northern Europe

(2012) Audrius Menkis et al.   FEMS MICROBIOLOGY ECOLOGY

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

Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers

(2012) Martina Štursová et al.   FEMS MICROBIOLOGY ECOLOGY

Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica)

(2012) Tristan Cordier et al.   Fungal Ecology

Estimation of fungal biomass in forest litter and soil

(2012) Petr Baldrian et al.   Fungal Ecology

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

(2012) Martin Hartmann et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Fungal community on decomposing leaf litter undergoes rapid successional changes

(2012) Jana Voříšková et al.   ISME Journal

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform

(2012) Andrew S. Whiteley et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Patterns of fungal communities among and within decaying logs, revealed by 454 sequencing

(2012) A. Kubartová et al.   MOLECULAR ECOLOGY

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing

(2012) Marie L. Davey et al.   NEW PHYTOLOGIST

Molecular characterization of root-associated fungal communities in relation to health status of Pisum sativum using barcoded pyrosequencing

(2012) L. Yu et al.   PLANT AND SOIL

Diversity Measures in Environmental Sequences Are Highly Dependent on Alignment Quality—Data from ITS and New LSU Primers Targeting Basidiomycetes

(2012) Dirk Krüger et al.   PLoS One

Communities of Arbuscular Mycorrhizal Fungi Detected in Forest Soil Are Spatially Heterogeneous but Do Not Vary throughout the Growing Season

(2012) John Davison 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

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

(2011) Neil R. Gottel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Influence of DNA extraction and PCR amplification on studies of soil fungal communities based on amplicon sequencing

(2011) Lihui Xu et al.   CANADIAN JOURNAL OF MICROBIOLOGY

EcM fungal community structure, but not diversity, altered in a Pb-contaminated shooting range in a boreal coniferous forest site in Southern Finland

(2011) Nan Hui et al.   FEMS MICROBIOLOGY ECOLOGY

Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa

(2011) Yonathan Arfi et al.   FEMS MICROBIOLOGY ECOLOGY

Assessment of soil fungal diversity in different alpine tundra habitats by means of pyrosequencing

(2011) Guillaume Lentendu et al.   FUNGAL DIVERSITY

Fungal diversity in anoxic-sulfidic sediments in a mangrove soil

(2011) Yonathan Arfi et al.   Fungal Ecology

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

(2011) Anthony S Amend et al.   ISME Journal

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

(2011) Petr Baldrian et al.   ISME Journal

Alien plants associate with widespread generalist arbuscular mycorrhizal fungal taxa: evidence from a continental-scale study using massively parallel 454 sequencing

(2011) Mari Moora et al.   JOURNAL OF BIOGEOGRAPHY

454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities

(2011) Ylva Lekberg et al.   JOURNAL OF ECOLOGY

Host Identity Impacts Rhizosphere Fungal Communities Associated with Three Alpine Plant Species

(2011) Katie M. Becklin et al.   MICROBIAL ECOLOGY

Fungal Community Composition in Neotropical Rain Forests: the Influence of Tree Diversity and Precipitation

(2011) Krista L. McGuire et al.   MICROBIAL ECOLOGY

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

(2011) HOLLY M. BIK et al.   MOLECULAR ECOLOGY

Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing

(2011) RAKEL BLAALID et al.   MOLECULAR ECOLOGY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds

(2011) Antonietta Mello et al.   MYCOLOGIA

High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples

(2011) Håvard Kauserud et al.   MYCORRHIZA

Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing

(2011) Alex J. Dumbrell et al.   NEW PHYTOLOGIST

Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities

(2011) R. Henrik Nilsson et al.   NEW PHYTOLOGIST

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Identifying wood-inhabiting fungi with 454 sequencing – what is the probability that BLAST gives the correct species?

(2010) Otso Ovaskainen et al.   Fungal Ecology

An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology

(2010) R. Henrik Nilsson et al.   Fungal Ecology

Massively parallel 454-sequencing of fungal communities inQuercusspp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites

(2010) ARI JUMPPONEN et al.   MOLECULAR ECOLOGY

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

Vertical distribution of fungal communities in tallgrass prairie soil

(2010) Ari Jumpponen et al.   MYCOLOGIA

Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests

(2010) Håkan Wallander et al.   NEW PHYTOLOGIST

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments

(2010) A. Jumpponen et al.   NEW PHYTOLOGIST

Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics

(2010) A. S. Amend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere

(2009) A. Jumpponen et al.   NEW PHYTOLOGIST

Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest

(2009) M. Öpik et al.   NEW PHYTOLOGIST