Bacterial Endophytic Communities in the Grapevine Depend on Pest Management

Unravelling the Diversity of Grapevine Microbiome

(2014) Cátia Pinto et al.   PLoS One

Pyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere

(2014) Sohail Yousaf et al.   Frontiers in Microbiology

The arable ecosystem as battleground for emergence of new human pathogens

(2014) Leonard S. van Overbeek et al.   Frontiers in Microbiology

Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis

(2013) Paulina Estrada-de los Santos et al.   CURRENT MICROBIOLOGY

Microbial community structure in vineyard soils across altitudinal gradients and in different seasons

(2013) Paola E. Corneo et al.   FEMS MICROBIOLOGY ECOLOGY

Resistance and resilience of the forest soil microbiome to logging-associated compaction

(2013) Martin Hartmann et al.   ISME Journal

The Endophytic Lifestyle ofEscherichia coliO157:H7: Quantification and Internal Localization in Roots

(2013) Kathryn M. Wright et al.   PHYTOPATHOLOGY

Impact of Shortened Crop Rotation of Oilseed Rape on Soil and Rhizosphere Microbial Diversity in Relation to Yield Decline

(2013) Sally Hilton 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

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies

(2013) Jonas Ghyselinck et al.   PLoS One

Fungal endophytes and their interaction with plant pathogens: a review

(2013) I. Zabalgogeazcoa   SPANISH JOURNAL OF AGRICULTURAL RESEARCH

How are plant and fungal communities linked to each other in belowground ecosystems? A massively parallel pyrosequencing analysis of the association specificity of root-associated fungi and their host plants

(2013) Hirokazu Toju et al.   Ecology and Evolution

Fungal Endophytic Communities in Grapevines (Vitis vinifera L.) Respond to Crop Management

(2012) Michael Pancher et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Martin Hartmann et al.   ISME Journal

Burkholderia phytofirmansPsJN Acclimates Grapevine to Cold by Modulating Carbohydrate Metabolism

(2012) Olivier Fernandez et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The Vineyard Yeast Microbiome, a Mixed Model Microbial Map

(2012) Mathabatha Evodia Setati et al.   PLoS One

Functional and Structural Microbial Diversity in Organic and Conventional Viticulture: Organic Farming Benefits Natural Biocontrol Agents

(2011) Florian Schmid et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Restructuring of Endophytic Bacterial Communities in Grapevine Yellows-Diseased and Recovered Vitis vinifera L. Plants

(2011) Daniela Bulgari et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Projecting the impacts of climate change on the phenology of grapevine in a mountain area

(2011) A. CAFFARRA et al.   AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Rice root-associated bacteria: insights into community structures across 10 cultivars

(2011) Pablo Rodrigo Hardoim et al.   FEMS MICROBIOLOGY ECOLOGY

The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments

(2011) Christina Bienhold et al.   ISME Journal

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

(2011) Daniel McDonald et al.   ISME Journal

Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis

(2011) A. Sessitsch et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Burkholderia phytofirmansPsJN PrimesVitis viniferaL. and Confers a Better Tolerance to Low Nonfreezing Temperatures

(2011) Andreas Theocharis et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

(2011) Heiko Nacke et al.   PLoS One

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The characterization and diversity of bacterial endophytes of grapevine

(2010) E. R. West et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Pyrosequencing Reveals a Highly Diverse and Cultivar-Specific Bacterial Endophyte Community in Potato Roots

(2010) Daniel K. Manter et al.   MICROBIAL 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

Community- and Genome-Based Views of Plant-Associated Bacteria: Plant–Bacterial Interactions in Soybean and Rice

(2010) Seishi Ikeda et al.   PLANT AND CELL PHYSIOLOGY

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

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Soil management effects on entomopathogenic fungi during the transition to organic agriculture in a feed grain rotation

(2009) Randa Jabbour et al.   BIOLOGICAL CONTROL

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Diversity of endophytic bacterial communities in poplar grown under field conditions

(2009) Kristina Ulrich et al.   FEMS MICROBIOLOGY ECOLOGY

Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR

(2009) Daniela Bulgari et al.   JOURNAL OF MICROBIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete Genome Sequence of Citrus Huanglongbing Bacterium, ‘CandidatusLiberibacter asiaticus’ Obtained Through Metagenomics

(2009) Yongping Duan et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

(2009) Stéphane Compant et al.   SOIL BIOLOGY & BIOCHEMISTRY

Culturable Fungi of Stored ‘Golden Delicious’ Apple Fruits: A One-Season Comparison Study of Organic and Integrated Production Systems in Switzerland

(2008) José Granado et al.   MICROBIAL ECOLOGY

The metagenomics of disease-suppressive soils – experiences from the METACONTROL project

(2008) Jan Dirk van Elsas et al.   TRENDS IN BIOTECHNOLOGY