Rhizosphere microbial communities explain positive effects of diverse crop rotations on maize and soybean performance

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Harnessing rhizosphere microbiomes for drought-resilient crop production

(2020) Franciska T. de Vries et al.   SCIENCE

Fossil energy use, climate change impacts, and air quality-related human health damages of conventional and diversified cropping systems in Iowa, USA

(2020) Natalie Dawn Hunt et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Consistent and correctable bias in metagenomic sequencing experiments

(2019) Michael R McLaren et al.   eLife

Diversifying crop rotation increased metabolic soil diversity and activity of the microbial community

(2018) Luciana D’Acunto et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

(2018) Laura E. MacConaill et al.   BMC GENOMICS

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Cropping System Diversification Reduces Severity and Incidence of Soybean Sudden Death Syndrome Caused by Fusarium virguliforme

(2018) L. F. S. Leandro et al.   PLANT DISEASE

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

(2018) William A. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Where is the USA Corn Belt, and how is it changing?

(2018) Timothy R. Green et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems

(2018) Anil Somenahally et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil quality – A critical review

(2018) Else K. Bünemann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota

(2018) Lingfei Hu et al.   Nature Communications

Crop rotational diversity increases disease suppressive capacity of soil microbiomes

(2018) Ariane L. Peralta et al.   Ecosphere

Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

(2018) Xue Guo et al.   Frontiers in Microbiology

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

(2018) Kyle Hartman et al.   Microbiome

Rhizosphere microbiome structure alters to enable wilt resistance in tomato

(2018) Min-Jung Kwak et al.   NATURE BIOTECHNOLOGY

Intensification for redesigned and sustainable agricultural systems

(2018) Jules Pretty   SCIENCE

Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists

(2017) Ioannis A. Stringlis et al.   PLANT JOURNAL

Diversified No-Till Crop Rotation Reduces Nitrous Oxide Emissions, Increases Soybean Yields, and Promotes Soil Carbon Accrual

(2017) R. Michael Lehman et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions

(2017) Richard Jacoby et al.   Frontiers in Plant Science

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome

(2017) Maria-Soledad Benitez et al.   Scientific Reports

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The impact of crop rotation on soil microbial diversity: A meta-analysis

(2016) Zander Samuel Venter et al.   PEDOBIOLOGIA

Long-term fertilizer and crop-rotation treatments differentially affect soil bacterial community structure

(2016) Chinmay Soman et al.   PLANT AND SOIL

Eleven years of crop diversification alters decomposition dynamics of litter mixtures incubated with soil

(2016) M. D. McDaniel et al.   Ecosphere

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

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Definitions and determination of crop yield, yield gaps, and of rates of change

(2015) R.A. Fischer   FIELD CROPS RESEARCH

From patterns to causal understanding: Structural equation modeling (SEM) in soil ecology

(2015) Nico Eisenhauer et al.   PEDOBIOLOGIA

lavaan: AnRPackage for Structural Equation Modeling

(2015) Yves Rosseel   Journal of Statistical Software

Increasing Crop Diversity Mitigates Weather Variations and Improves Yield Stability

(2015) Amélie C. M. Gaudin et al.   PLoS One

Sustainable intensification in agricultural systems

(2014) Jules Pretty et al.   ANNALS OF BOTANY

Structural Equation Modeling Facilitates Transdisciplinary Research on Agriculture and Climate Change

(2014) Richard. G. Smith et al.   CROP SCIENCE

Accounting for soil biotic effects on soil health and crop productivity in the design of crop rotations

(2014) Teresa Dias et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

An Affinity–Effect Relationship for Microbial Communities in Plant–Soil Feedback Loops

(2014) Yi Lou et al.   MICROBIAL ECOLOGY

Parsing ecological signal from noise in next generation amplicon sequencing

(2014) Nhu H. Nguyen et al.   NEW PHYTOLOGIST

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Soil Attributes, Soybean Mineral Nutrition, and Yield in Diverse Crop Rotations under No-Till Conditions

(2013) Walter E. Riedell et al.   AGRONOMY JOURNAL

Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? A meta-analysis

(2013) M. D. McDaniel et al.   ECOLOGICAL APPLICATIONS

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

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

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

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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Increasing Cropping System Diversity Balances Productivity, Profitability and Environmental Health

(2012) Adam S. Davis et al.   PLoS One

Meeting the demand for crop production: the challenge of yield decline in crops grown in short rotations

(2011) Amanda J. Bennett et al.   BIOLOGICAL REVIEWS

Roles of Arbuscular Mycorrhizas in Plant Phosphorus Nutrition: Interactions between Pathways of Phosphorus Uptake in Arbuscular Mycorrhizal Roots Have Important Implications for Understanding and Manipulating Plant Phosphorus Acquisition

(2011) S. E. Smith et al.   PLANT PHYSIOLOGY

Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?

(2010) Paul G. Dennis et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Testing the significance of canonical axes in redundancy analysis

(2010) Pierre Legendre et al.   Methods in Ecology and Evolution

Distributional Equivalence and Subcompositional Coherence in the Analysis of Compositional Data, Contingency Tables and Ratio-Scale Measurements

(2009) Michael Greenacre et al.   JOURNAL OF CLASSIFICATION

Simultaneous Inference in General Parametric Models

(2008) Torsten Hothorn et al.   BIOMETRICAL JOURNAL

Break crop benefits in temperate wheat production

(2008) John Kirkegaard et al.   FIELD CROPS RESEARCH

Plant host habitat and root exudates shape soil bacterial community structure

(2008) Feth el Zahar Haichar et al.   ISME Journal