Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

Fungi in the future: interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities

(2015) T. E. Anne Cotton et al.   NEW PHYTOLOGIST

Arbuscular mycorrhizal fungal succession in a long-lived perennial

(2014) Miranda M. Hart et al.   Botany

Back to the future: natural history and the way forward in modern fungal ecology

(2014) Kabir G. Peay   Fungal Ecology

Evaluation of six primer pairs targeting the nuclear rRNA operon for characterization of arbuscular mycorrhizal fungal (AMF) communities using 454 pyrosequencing

(2014) Maarten Van Geel et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Sequencing and comparison of the mitochondrial COI gene from isolates of Arbuscular Mycorrhizal Fungi belonging to Gigasporaceae and Glomeraceae families

(2014) Roberto Borriello et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?

(2014) Martina Janoušková et al.   MYCORRHIZA

Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi

(2014) Mohammad Bahram et al.   NEW PHYTOLOGIST

Where the wild things are: looking for uncultured Glomeromycota

(2014) Brian M. Ohsowski et al.   NEW PHYTOLOGIST

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

(2014) Inga Hiiesalu et al.   NEW PHYTOLOGIST

Will different OTU delineation methods change interpretation of arbuscular mycorrhizal fungal community patterns?

(2014) Ylva Lekberg et al.   NEW PHYTOLOGIST

Parsing ecological signal from noise in next generation amplicon sequencing

(2014) Nhu H. Nguyen et al.   NEW PHYTOLOGIST

The Largest Subunit of RNA Polymerase II as a New Marker Gene to Study Assemblages of Arbuscular Mycorrhizal Fungi in the Field

(2014) Herbert Stockinger et al.   PLoS One

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

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

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

(2014) Kui Lin et al.   PLoS Genetics

How distinct are arbuscular mycorrhizal fungal communities associating with grapevines?

(2013) Taylor C. Holland et al.   BIOLOGY AND FERTILITY OF SOILS

DNA-based detection and identification of Glomeromycota: the virtual taxonomy of environmental sequences

(2013) Maarja Öpik et al.   Botany

Root-colonizing and soil-borne communities of arbuscular mycorrhizal fungi in a temperate forest understorey

(2013) Ülle Saks et al.   Botany

Severe plant invasions can increase mycorrhizal fungal abundance and diversity

(2013) Ylva Lekberg et al.   ISME Journal

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Fungal communities in soils along a vegetative ecotone

(2013) Justine Karst et al.   MYCOLOGIA

Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi

(2013) Maarja Öpik et al.   MYCORRHIZA

Still scratching the surface: how much of the ‘black box’ of soil ectomycorrhizal communities remains in the dark?

(2013) Brian J. Pickles et al.   NEW PHYTOLOGIST

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Assessing the Consequences of Denoising Marker-Based Metagenomic Data

(2013) John M. Gaspar et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

(2013) E. Tisserant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Illumina metabarcoding of a soil fungal community

(2013) Philipp-André Schmidt et al.   SOIL BIOLOGY & BIOCHEMISTRY

Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: Is there a universal solution?

(2013) Petr Kohout et al.   SOIL BIOLOGY & BIOCHEMISTRY

Testing Potential Effects of Maize Expressing the Bacillus thuringiensis Cry1Ab Endotoxin (Bt Maize) on Mycorrhizal Fungal Communities via DNA- and RNA-Based Pyrosequencing and Molecular Fingerprinting

(2012) Erik Verbruggen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mycoheterotrophic interactions are not limited to a narrow phylogenetic range of arbuscular mycorrhizal fungi

(2012) VINCENT S. F. T. MERCKX et al.   MOLECULAR ECOLOGY

Spatial analysis of ectomycorrhizal fungi reveals that root tip communities are structured by competitive interactions

(2012) Brian J. Pickles et al.   MOLECULAR ECOLOGY

First cloning and characterization of two functional aquaporin genes from an arbuscular mycorrhizal fungusGlomus intraradices

(2012) Tao Li et al.   NEW PHYTOLOGIST

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

(2012) V. G. Fonseca et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Arbuscular mycorrhizal fungal communities change among three stages of primary sand dune succession but do not alter plant growth

(2012) Benjamin A. Sikes et al.   OIKOS

PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution

(2012) Stéphane Mahé 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

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

(2012) Patricio S. La Rosa 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

Inter- and intrasporal nuclear ribosomal gene sequence variation within one isolate of arbuscular mycorrhizal fungus, Diversispora sp.

(2012) Odile Thiéry et al.   SYMBIOSIS

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes

(2011) Daniel Aguirre de Cárcer 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

Importance of dispersal and thermal environment for mycorrhizal communities: lessons from Yellowstone National Park

(2011) Ylva Lekberg et al.   ECOLOGY

Arbuscular mycorrhizal fungal communities in plant roots are not random assemblages

(2011) John Davison et al.   FEMS MICROBIOLOGY ECOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

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

(2011) Daniel McDonald 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

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

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

(2011) Leho Tedersoo et al.   PLoS One

Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

(2011) David S. Hibbett et al.   Fungal Biology Reviews

High diversity of root associated fungi in both alpine and arctic Dryas octopetala

(2010) Marit Bjorbækmo et al.   BMC PLANT BIOLOGY

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

Patterns of fungal diversity and composition along a salinity gradient

(2010) Devon J Mohamed et al.   ISME Journal

Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

(2010) K. O'Donnell et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Differential effect of sample preservation methods on plant and arbuscular mycorrhizal fungal DNA

(2010) L.D. Bainard et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories

(2010) JEFF R. POWELL et al.   MOLECULAR ECOLOGY

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

(2010) M. Öpik 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

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

DNA barcoding of arbuscular mycorrhizal fungi

(2010) Herbert Stockinger et al.   NEW PHYTOLOGIST

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

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Relative roles of niche and neutral processes in structuring a soil microbial community

(2009) Alex J Dumbrell et al.   ISME Journal

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

Spatial characterization of arbuscular mycorrhizal fungal molecular diversity at the submetre scale in a temperate grassland

(2008) Daniel L. Mummey et al.   FEMS MICROBIOLOGY ECOLOGY

Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi

(2008) Jaikoo Lee et al.   FEMS MICROBIOLOGY ECOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Preserving Accuracy in GenBank

(2008) M. I. Bidartondo   SCIENCE