A global microbiome survey of vineyard soils highlights the microbial dimension of viticultural terroirs

Network Properties of Local Fungal Communities Reveal the Anthropogenic Disturbance Consequences of Farming Practices in Vineyard Soils

(2021) Rüdiger Ortiz-Álvarez et al.   mSystems

Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

(2020) Alex Gobbi et al.   Scientific Reports

Using soil bacterial communities to predict physico-chemical variables and soil quality

(2020) Syrie M. Hermans et al.   Microbiome

Community succession of the grapevine fungal microbiome in the annual growth cycle

(2020) Di Liu et al.   ENVIRONMENTAL MICROBIOLOGY

Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR

(2019) Alex Gobbi et al.   PLoS One

A few Ascomycota taxa dominate soil fungal communities worldwide

(2019) Eleonora Egidi et al.   Nature Communications

Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

(2019) Charlie Pauvert et al.   Fungal Ecology

A meta-analysis of global fungal distribution reveals climate-driven patterns

(2019) Tomáš Větrovský et al.   Nature Communications

Rarefaction, Alpha Diversity, and Statistics

(2019) Amy D. Willis   Frontiers in Microbiology

Microbiome of vineyard soils is shaped by geography and management

(2019) Emanuela Coller et al.   Microbiome

Plant litter composition selects different soil microbial structures and in turn drives different litter decomposition pattern and soil carbon sequestration capability

(2018) Jianfang Yan et al.   GEODERMA

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Yeasts of the soil - obscure but precious

(2018) Andrey M. Yurkov   YEAST

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

(2017) Marvin N. Wright et al.   Journal of Statistical Software

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production

(2017) Valerio Mezzasalma et al.   PLoS One

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests

(2017) Luis E. Castañeda et al.   PeerJ

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain)

(2016) Maria del Carmen Portillo et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure

(2016) Suzanne L. Ishaq et al.   MICROBIAL ECOLOGY

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management

(2016) Kayla N. Burns et al.   SOIL BIOLOGY & BIOCHEMISTRY

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

(2016) Nicholas A. Bokulich et al.   mBio

Networking in the Plant Microbiome

(2016) Marcel G. A. van der Heijden et al.   PLOS BIOLOGY

Unraveling the Enzymatic Basis of Wine “Flavorome”: A Phylo-Functional Study of Wine Related Yeast Species

(2016) Ignacio Belda et al.   Frontiers in Microbiology

Soil Biodiversity and the Environment

(2015) Uffe N. Nielsen et al.   Annual Review of Environment and Resources

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

(2015) Kayla N. Burns et al.   SOIL BIOLOGY & BIOCHEMISTRY

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir

(2015) Sarah Knight et al.   Scientific Reports

Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities

(2015) Andreas Henschel et al.   PLoS Computational Biology

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Bayesian-multiplicative treatment of count zeros in compositional data sets

(2014) Josep-Antoni Martín-Fernández et al.   STATISTICAL MODELLING

Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil

(2014) Ralfo G. Pacchioni et al.   MicrobiologyOpen

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples

(2013) Tatiana A. Vishnivetskaya et al.   FEMS MICROBIOLOGY ECOLOGY

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

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

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

Microbial terroir for wine grapes

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

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

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

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

(2013) Kateryna Zhalnina et al.   Frontiers in Microbiology

The adult intestinal core microbiota is determined by analysis depth and health status

(2012) A. Salonen et al.   CLINICAL MICROBIOLOGY AND INFECTION

Testing the metabolic theory of ecology

(2012) Charles A. Price et al.   ECOLOGY LETTERS

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

The microbial ecology of wine grape berries

(2011) A. Barata et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Influence of fungicide treatments on the occurrence of yeast flora associated with wine grapes

(2009) Francesca Comitini et al.   ANNALS OF MICROBIOLOGY

Whole ecosystem metabolic pulses following precipitation events

(2008) G. D. Jenerette et al.   FUNCTIONAL ECOLOGY