Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons

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

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

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

Network modules and hubs in plant-root fungal biomes

(2016) Hirokazu Toju et al.   Journal of the Royal Society Interface

Ericaceous plant-fungus network in a harsh alpine-subalpine environment

(2016) H. Toju et al.   MOLECULAR ECOLOGY

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

(2016) James L. O’Donnell et al.   PLoS One

Root-associated fungi of Vaccinium carlesii in subtropical forests of China: intra- and inter-annual variability and impacts of human disturbances

(2016) Yanhua Zhang et al.   Scientific Reports

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

Lack of host specificity leads to independent assortment of dipterocarps and ectomycorrhizal fungi across a soil fertility gradient

(2015) Kabir G. Peay et al.   ECOLOGY LETTERS

Fine-scale hydrological niche differentiation through the lens of multi-species co-occurrence models

(2015) Andrew D. Letten et al.   JOURNAL OF ECOLOGY

Diversity of Fungi on Decomposing Leaf Litter in a Sugarcane Plantation and Their Response to Tillage Practice and Bagasse Mulching: Implications for Management Effects on Litter Decomposition

(2015) Toshiko Miura et al.   MICROBIAL ECOLOGY

Competitive avoidance not edaphic specialization drives vertical niche partitioning among sister species of ectomycorrhizal fungi

(2015) Alija B. Mujic et al.   NEW PHYTOLOGIST

High-throughput DNA barcoding for ecological network studies

(2015) Hirokazu Toju   POPULATION ECOLOGY

So Many Variables: Joint Modeling in Community Ecology

(2015) David I. Warton et al.   TRENDS IN ECOLOGY & EVOLUTION

Using latent variable models to identify large networks of species-to-species associations at different spatial scales

(2015) Otso Ovaskainen et al.   Methods in Ecology and Evolution

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Below-ground plant-fungus network topology is not congruent with above-ground plant-animal network topology

(2015) H. Toju et al.   Science Advances

Spore dispersal of basidiomycete fungi at the landscape scale is driven by stochastic and deterministic processes and generates variability in plant-fungal interactions

(2014) Kabir G. Peay et al.   NEW PHYTOLOGIST

Order of arrival structures arbuscular mycorrhizal colonization of plants

(2014) Gijsbert D. A. Werner et al.   NEW PHYTOLOGIST

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Spatial Segregation and Aggregation of Ectomycorrhizal and Root-Endophytic Fungi in the Seedlings of Two Quercus Species

(2014) Satoshi Yamamoto et al.   PLoS One

Endemism and functional convergence across the North American soil mycobiome

(2014) J. M. Talbot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Assembly of complex plant–fungus networks

(2014) Hirokazu Toju et al.   Nature Communications

Missing checkerboards? An absence of competitive signal inAlnus-associated ectomycorrhizal fungal communities

(2014) Peter Kennedy et al.   PeerJ

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

(2013) J. Zhang et al.   BIOINFORMATICS

Slowing PCR ramp speed reduces chimera formation from environmental samples

(2013) Julia L. Stevens et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome

(2013) Matthew G. Bakker et al.   MOLECULAR ECOLOGY

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants

(2013) Akifumi S. Tanabe et al.   PLoS One

Community composition of root-associated fungi in aQuercus-dominated temperate forest: “codominance” of mycorrhizal and root-endophytic fungi

(2013) Hirokazu Toju et al.   Ecology and Evolution

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

On the application of network theory to arbuscular mycorrhizal fungi-plant interactions: the importance of basic assumptions

(2012) Tancredi Caruso et al.   NEW PHYTOLOGIST

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

(2012) Hirokazu Toju et al.   PLoS One

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

A meta-analysis of plant responses to dark septate root endophytes

(2011) K. K. Newsham   NEW PHYTOLOGIST

Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis

(2011) E. T. Kiers et al.   SCIENCE

Using null models to disentangle variation in community dissimilarity from variation in α-diversity

(2011) Jonathan M. Chase et al.   Ecosphere

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Negative plant–soil feedback predicts tree-species relative abundance in a tropical forest

(2010) Scott A. Mangan et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks

(2010) E. Thebault et al.   SCIENCE

Ascomycetes associated with ectomycorrhizas: molecular diversity and ecology with particular reference to theHelotiales

(2009) Leho Tedersoo et al.   ENVIRONMENTAL MICROBIOLOGY

Soil fungal community composition at Mars Oasis, a southern maritime Antarctic site, assessed by PCR amplification and cloning

(2009) Paul D. Bridge et al.   Fungal Ecology

Architecture of the wood-wide web: Rhizopogon spp. genets link multiple Douglas-fir cohorts

(2009) Kevin J. Beiler 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

Fungal endophytes: diversity and functional roles

(2009) R. J. Rodriguez et al.   NEW PHYTOLOGIST

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

Further compatibility tests of the entomopathogenic fungusLecanicillium muscariumwith conventional insecticide products for control of sweetpotato whitefly,Bemisia tabacion poinsettia plants

(2008) Andrew G. S. Cuthbertson et al.   Insect Science

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS