Microbiome of vineyard soils is shaped by geography and management

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

(2019) Samiran Banerjee et al.   ISME Journal

Modelling microbiome recovery after antibiotics using a stability landscape framework

(2019) Liam P. Shaw et al.   ISME Journal

A few Ascomycota taxa dominate soil fungal communities worldwide

(2019) Eleonora Egidi et al.   Nature Communications

How sample heterogeneity can obscure the signal of microbial interactions

(2019) David W. Armitage et al.   ISME Journal

Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

(2018) Ruvishika S. Jayawardena et al.   FUNGAL DIVERSITY

Why do microbes exhibit weak biogeographic patterns?

(2018) Kyle M. Meyer et al.   ISME Journal

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

(2018) Alexander Crits-Christoph et al.   NATURE

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts

(2018) Ming-Yi Chou et al.   Scientific Reports

A practical tool for maximal information coefficient analysis

(2018) Davide Albanese et al.   GigaScience

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

(2018) Kyle Hartman et al.   Microbiome

High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity

(2018) Ales Eichmeier et al.   Fungal Ecology

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships

(2017) Isabelle Laforest-Lapointe et al.   NATURE

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Is microbial terroir related to geographic distance between vineyards?

(2017) Toshiko Miura et al.   Environmental Microbiology Reports

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

(2017) Zachary S. L. Foster et al.   PLoS Computational Biology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

(2017) Yong Zhang et al.   Scientific Reports

Spatial scale drives patterns in soil bacterial diversity

(2016) Sarah L. O'Brien et al.   ENVIRONMENTAL MICROBIOLOGY

Dimensions of biodiversity in the Earth mycobiome

(2016) Kabir G. Peay et al.   NATURE REVIEWS MICROBIOLOGY

Status of the Archaeal and Bacterial Census: an Update

(2016) Patrick D. Schloss et al.   mBio

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

(2016) Nicholas A. Bokulich et al.   mBio

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility

(2015) Acacio Aparecido Navarrete et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Land-use system shapes soil bacterial communities in Southeastern Amazon region

(2015) Lucas William Mendes et al.   APPLIED SOIL ECOLOGY

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Soil biodiversity and human health

(2015) Diana H. Wall et al.   NATURE

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Increasing aridity reduces soil microbial diversity and abundance in global drylands

(2015) Fernando T. Maestre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Continental-scale distributions of dust-associated bacteria and fungi

(2015) Albert Barberán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

(2015) Jonathan W. Leff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

(2015) Davide Albanese et al.   Scientific Reports

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

(2015) Sarah Knight et al.   Scientific Reports

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Do bacterial and fungal communities assemble differently during primary succession?

(2014) S. K. Schmidt et al.   MOLECULAR ECOLOGY

Sebacinales, but not total root associated fungal communities, are affected by land-use intensity

(2014) Erik Verbruggen et al.   NEW PHYTOLOGIST

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

(2014) K. S. Ramirez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Plant growth promoting rhizobia: challenges and opportunities

(2014) Subramaniam Gopalakrishnan et al.   3 Biotech

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Microbial terroir for wine grapes

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

What if esca disease of grapevine were not a fungal disease?

(2012) Valérie Hofstetter et al.   FUNGAL DIVERSITY

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

Not every fungus is everywhere: scaling to the biogeography of fungal-plant interactions across roots, shoots and ecosystems

(2010) Kabir G. Peay et al.   NEW PHYTOLOGIST

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

Scale-Free Networks: A Decade and Beyond

(2009) Albert-László Barabási   SCIENCE