Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome

PICRUSt2 for prediction of metagenome functions

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

Heterosis of leaf and rhizosphere microbiomes in field‐grown maize

(2020) Maggie R. Wagner et al.   NEW PHYTOLOGIST

Impacts of directed evolution and soil management legacy on the maize rhizobiome

(2020) Jennifer E. Schmidt et al.   SOIL BIOLOGY & BIOCHEMISTRY

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

Beyond Defense: Multiple Functions of Benzoxazinoids in Maize Metabolism

(2018) Shaoqun Zhou et al.   PLANT AND CELL PHYSIOLOGY

Eighty years of maize breeding alters plant nitrogen acquisition but not rhizosphere bacterial community composition

(2018) Bryan D. Emmett et al.   PLANT AND SOIL

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

Dynamic biochar effects on soil nitrous oxide emissions and underlying microbial processes during the maize growing season

(2018) Joseph D. Edwards et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nutrient- and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen

(2018) Maureen Berg et al.   CURRENT BIOLOGY

Modulating plant growth–metabolism coordination for sustainable agriculture

(2018) Shan Li et al.   NATURE

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota

(2018) Allen Van Deynze et al.   PLOS BIOLOGY

The structure and function of the global citrus rhizosphere microbiome

(2018) Jin Xu et al.   Nature Communications

Field-scale experiments reveal persistent yield gaps in low-input and organic cropping systems

(2017) Alexandra N. Kravchenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Plant Root Exudates Shape the Nitrogen Cycle

(2017) Devrim Coskun et al.   TRENDS IN PLANT SCIENCE

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

(2017) Yun Kit Yeoh et al.   Nature Communications

Research priorities for harnessing plant microbiomes in sustainable agriculture

(2017) Posy E. Busby et al.   PLOS BIOLOGY

Microbiome Datasets Are Compositional: And This Is Not Optional

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

Global nitrogen budgets in cereals: A 50-year assessment for maize, rice, and wheat production systems

(2016) J. K. Ladha et al.   Scientific Reports

Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity

(2015) Barbara Reinhold-Hurek et al.   Annual Review of Phytopathology

Long-term nitrogen addition causes the evolution of less-cooperative mutualists

(2015) Dylan J. Weese et al.   EVOLUTION

Evolution of US maize (Zea mays L.) root architectural and anatomical phenes over the past 100 years corresponds to increased tolerance of nitrogen stress

(2015) L. M. York et al.   JOURNAL OF EXPERIMENTAL BOTANY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Microfluidic Quantitative PCR for Simultaneous Quantification of Multiple Viruses in Environmental Water Samples

(2014) Satoshi Ishii et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structure and Functions of the Bacterial Microbiota of Plants

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

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Changes in Nitrogen Use Traits Associated with Genetic Improvement for Grain Yield of Maize Hybrids Released in Different Decades

(2013) Jason W. Haegele et al.   CROP SCIENCE

Generation Means Analysis of Elite Ex-Plant Variety Protection Commercial Inbreds: A New Public Maize Genetics Resource

(2013) Andrew L. Hauck et al.   CROP SCIENCE

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

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems

(2013) P. M. Vitousek et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Diversity and heritability of the maize rhizosphere microbiome under field conditions

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

Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction

(2013) Pankaj Trivedi et al.   TRENDS IN MICROBIOLOGY

FunGene: the functional gene pipeline and repository

(2013) Jordan A. Fish et al.   Frontiers in Microbiology

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Plant influence on nitrification

(2011) Marcin W. Skiba et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

Nitrogen in Agriculture: Balancing the Cost of an Essential Resource

(2009) G. Philip Robertson et al.   Annual Review of Environment and Resources

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS