Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype

Assembly and ecological function of the root microbiome across angiosperm plant species

(2018) Connor R. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

(2018) M. A. Cregger et al.   Microbiome

Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees

(2017) Jessica M. Vélez et al.   Fungal Ecology

Atractiella rhizophila, sp. nov., an endorrhizal fungus isolated from the Populus root microbiome

(2017) Gregory Bonito et al.   MYCOLOGIA

Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species

(2017) Kyriaki Glynou et al.   NEW PHYTOLOGIST

Tree genetics defines fungal partner communities that may confer drought tolerance

(2017) Catherine A. Gehring et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil

(2017) Behnoushsadat Ghodsalavi et al.   PLoS One

Propagation technique of arbuscular mycorrhizal fungi isolated from coastal reclamation land

(2016) Gopal Selvakumar et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Isolating a functionally relevant guild of fungi from the root microbiome of Populus

(2016) Gregory Bonito et al.   Fungal Ecology

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

(2016) Citlali Fonseca-García et al.   Frontiers in Microbiology

Influence of exogenous organic matter on prokaryotic and eukaryotic microbiota in an agricultural soil. A multidisciplinary approach

(2015) Daniela Pezzolla et al.   SOIL BIOLOGY & BIOCHEMISTRY

3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics

(2015) Deborah A Weighill et al.   PLoS Computational Biology

Fold change rank ordering statistics: a new method for detecting differentially expressed genes

(2014) Doulaye Dembélé et al.   BMC BIOINFORMATICS

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

(2014) Gregory Bonito et al.   MOLECULAR ECOLOGY

Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

(2014) Björn Hoppe 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

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

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

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Genetic variation for resistance to herbivores and plant pathogens: hypotheses, mechanisms and evolutionary implications

(2013) R. Keith et al.   PLANT PATHOLOGY

Host Genotype Shapes the Foliar Fungal Microbiome of Balsam Poplar (Populus balsamifera)

(2013) Miklós Bálint 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

A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees

(2013) Migun Shakya et al.   PLoS One

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

(2012) John H Morris et al.   BMC BIOINFORMATICS

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities

(2012) L. Danielsen et al.   Ecology and Evolution

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

(2011) Johan Bengtsson et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

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

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival

(2011) Michelle H. Hersh et al.   ECOLOGY

Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

(2011) Brendan P. Hodkinson et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level

(2011) Manuela Krüger et al.   NEW PHYTOLOGIST

Clone history shapes Populus drought responses

(2011) S. Raj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Improving indicator species analysis by combining groups of sites

(2010) Miquel De Cáceres et al.   OIKOS

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Refining the stress-gradient hypothesis for competition and facilitation in plant communities

(2009) Fernando T. Maestre et al.   JOURNAL OF ECOLOGY

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

(2008) Jaikoo Lee et al.   FEMS MICROBIOLOGY ECOLOGY

Graph Clustering Via a Discrete Uncoupling Process

(2008) Stijn Van Dongen   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS