Emergence Shapes the Structure of the Seed Microbiota

Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome onTriticumandBrassicaseeds

(2014) Matthew G. Links et al.   NEW PHYTOLOGIST

Analyses of the Temporal Dynamics of Fungal Communities Colonizing the Healthy Wood Tissues of Esca Leaf-Symptomatic and Asymptomatic Vines

(2014) Emilie Bruez et al.   PLoS One

Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities

(2014) L. Maignien et al.   mBio

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

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

Onychomycosis Caused byChaetomium globosum

(2013) Dong Min Kim et al.   Annals of Dermatology

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches

(2013) Gurdeep Rastogi et al.   FEMS MICROBIOLOGY LETTERS

Diversity of the spinach (Spinacia oleracea) spermosphere and phyllosphere bacterial communities

(2013) Gabriela Lopez-Velasco et al.   FEMS MICROBIOLOGY LETTERS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns

(2013) Anjuli Meiser et al.   NEW PHYTOLOGIST

The root microbiota—a fingerprint in the soil?

(2013) Aleklett Kristin et al.   PLANT AND SOIL

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

(2013) Tomáš Větrovský et al.   PLoS One

Unexpected Diversity during Community Succession in the Apple Flower Microbiome

(2013) A. Shade et al.   mBio

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

(2013) Johan Bengtsson-Palme et al.   Methods in Ecology and Evolution

Functional Analysis of the Degradation of Cellulosic Substrates by a Chaetomium globosum Endophytic Isolate

(2012) Paolo Longoni et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The diversity and importance of fungi associated with marine sponges

(2012) Trichur S. Suryanarayanan   BOTANICA MARINA

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity

(2012) Michiel Vos et al.   PLoS One

Dynamics of Seed-Borne Rice Endophytes on Early Plant Growth Stages

(2012) Pablo R. Hardoim et al.   PLoS One

Ecology of Root Colonizing Massilia (Oxalobacteraceae)

(2012) Maya Ofek et al.   PLoS One

The Chaperonin-60 Universal Target Is a Barcode for Bacteria That Enables De Novo Assembly of Metagenomic Sequence Data

(2012) Matthew G. Links 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

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

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level

(2011) Evy Battaglia et al.   BMC GENOMICS

Colonization of cucumber seeds by bacteria during germination

(2011) Maya Ofek et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial Communities Associated with Chenopodium album and Stellaria media Seeds from Arable Soils

(2011) Leonard S. van Overbeek et al.   MICROBIAL ECOLOGY

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Conservation and Diversity of Seed Associated Endophytes in Zea across Boundaries of Evolution, Ethnography and Ecology

(2011) David Johnston-Monje et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Transmission of Plant-Pathogenic Bacteria by Nonhost Seeds without Induction of an Associated Defense Reaction at Emergence

(2010) A. Darrasse et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture

(2009) Gabriele Berg   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) M. Buée et al.   NEW PHYTOLOGIST

The Type III Secretion System of Xanthomonas fuscans subsp. fuscans Is Involved in the Phyllosphere Colonization Process and in Transmission to Seeds of Susceptible Beans

(2008) A. Darsonval et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH