Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks

The Soil-Borne Legacy

(2018) Peter A.H.M. Bakker et al.   CELL

Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe

(2018) Zhongmin Dai et al.   GLOBAL CHANGE BIOLOGY

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

N addition undermines N supplied by arbuscular mycorrhizal fungi to native perennial grasses

(2018) Laura C. Jach-Smith et al.   SOIL BIOLOGY & BIOCHEMISTRY

Community-level plant-soil feedbacks explain landscape distribution of native and non-native plants

(2018) Andrew Kulmatiski   Ecology and Evolution

Plant compartment and genetic variation drive microbiome composition in switchgrass roots

(2018) Esther Singer et al.   Environmental Microbiology Reports

Fungal diversity regulates plant-soil feedbacks in temperate grassland

(2018) Marina Semchenko et al.   Science Advances

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture

(2017) S Emilia Hannula et al.   ISME Journal

Verrucomicrobial elevational distribution was strongly influenced by soil pH and carbon/nitrogen ratio

(2017) Congcong Shen et al.   JOURNAL OF SOILS AND SEDIMENTS

Plant growth promoting rhizobacteria are more effective under drought: a meta-analysis

(2017) Rachel L. Rubin et al.   PLANT AND SOIL

Research priorities for harnessing plant microbiomes in sustainable agriculture

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

Microbial Phosphorus Solubilization and Its Potential for Use in Sustainable Agriculture

(2017) Elizabeth T. Alori et al.   Frontiers in Microbiology

The economic value of grassland species for carbon storage

(2017) Bruce A. Hungate et al.   Science Advances

Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization

(2016) Lawrence G. Oates et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

The Phyllosphere: Microbial Jungle at the Plant–Climate Interface

(2016) Corinne Vacher et al.   Annual Review of Ecology Evolution and Systematics

The role of locally adapted mycorrhizas and rhizobacteria in plant-soil feedback systems

(2016) Daniel Revillini et al.   FUNCTIONAL ECOLOGY

Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems

(2016) Geoffrey P. Morris et al.   Global Change Biology Bioenergy

Effects of switchgrass cultivars and intraspecific differences in root structure on soil carbon inputs and accumulation

(2016) Jaron Adkins et al.   GEODERMA

An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability

(2016) S. Franz Bender et al.   TRENDS IN ECOLOGY & EVOLUTION

Plant-fungus competition for nitrogen erases mycorrhizal growth benefits ofAndropogon gerardiiunder limited nitrogen supply

(2016) David Püschel et al.   Ecology and Evolution

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

Plant preferential allocation and fungal reward decline with soil phosphorus: implications for mycorrhizal mutualism

(2016) Baoming Ji et al.   Ecosphere

Comparison of biochemical and microscopic methods for quantification of arbuscular mycorrhizal fungi in soil and roots

(2015) Mahaveer P. Sharma et al.   APPLIED SOIL ECOLOGY

A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment

(2015) Marcel GA van der Heijden et al.   ISME Journal

Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

(2015) Jessica A. M. Moore et al.   JOURNAL OF ECOLOGY

The Plant Microbiome at Work

(2015) Klaus Schlaeppi et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts

(2015) James D. Bever   NEW PHYTOLOGIST

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Effects of 44 years of chronic nitrogen fertilization on the soil nitrifying community of permanent grassland

(2015) Xue Zhou et al.   SOIL BIOLOGY & BIOCHEMISTRY

Mycorrhizal fungi associated with high soil N:P ratios are more likely to be lost upon conversion from grasslands to arable agriculture

(2015) Erik Verbruggen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nutrient cycling in the mycorrhizosphere

(2015) C Azcón-Aguilar et al.   Journal of Soil Science and Plant Nutrition

Diversity of Nitrogen-Fixing Bacteria Associated with Switchgrass in the Native Tallgrass Prairie of Northern Oklahoma

(2014) Rahul A. Bahulikar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

(2014) Suzanne M. Prober et al.   ECOLOGY LETTERS

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Mycorrhizal phenotypes and the Law of the Minimum

(2014) Nancy Collins Johnson et al.   NEW PHYTOLOGIST

Shading decreases plant carbon preferential allocation towards the most beneficial mycorrhizal mutualist

(2014) Chaoyuan Zheng et al.   NEW PHYTOLOGIST

Arbuscular mycorrhiza and nitrogen: implications for individual plants through to ecosystems

(2014) Angela Hodge et al.   PLANT AND SOIL

Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems

(2014) David J. Levy-Booth et al.   SOIL BIOLOGY & BIOCHEMISTRY

Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates

(2014) Yuejian Mao et al.   Environmental Microbiology Reports

Unraveling the plant microbiome: looking back and future perspectives

(2014) Gabriele Berg et al.   Frontiers in Microbiology

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

Evidence that soil nutrient stoichiometry controls the competitive abilities of arbuscular mycorrhizal vs. root-borne non-mycorrhizal fungi

(2013) Pierre-Luc Chagnon et al.   Fungal Ecology

Nitrogen deposition weakens plant-microbe interactions in grassland ecosystems

(2013) Cunzheng Wei et al.   GLOBAL CHANGE BIOLOGY

Plant-soil feedbacks: the past, the present and future challenges

(2013) Wim H. van der Putten et al.   JOURNAL OF ECOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

(2013) N. Fierer et al.   SCIENCE

Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes

(2012) Kelly S. Ramirez et al.   GLOBAL CHANGE BIOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Nitrogen-fixing bacteria, arbuscular mycorrhizal fungi, and the productivity and structure of prairie grassland communities

(2012) Jonathan T. Bauer et al.   OECOLOGIA

A Comprehensive Evaluation of PCR Primers to Amplify the nifH Gene of Nitrogenase

(2012) John Christian Gaby et al.   PLoS One

Functional Ecology of Free-Living Nitrogen Fixation: A Contemporary Perspective

(2011) Sasha C. Reed et al.   Annual Review of Ecology Evolution and Systematics

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

(2011) Daniel McDonald et al.   ISME Journal

Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing

(2011) Alex J. Dumbrell et al.   NEW PHYTOLOGIST

Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis

(2011) E. T. Kiers et al.   SCIENCE

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Multiple Climate Change Factors Interact to Alter Soil Microbial Community Structure in an Old-Field Ecosystem

(2011) Sharon B. Gray et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

A new method for non-parametric multivariate analysis of variance

(2010) MARTI J. ANDERSON   AUSTRAL ECOLOGY

Switchgrass selection as a “model” bioenergy crop: A history of the process

(2010) Lynn Wright et al.   BIOMASS & BIOENERGY

A meta-analysis of context-dependency in plant response to inoculation with mycorrhizal fungi

(2010) Jason D. Hoeksema et al.   ECOLOGY LETTERS

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

(2010) M. Öpik et al.   NEW PHYTOLOGIST

Improving indicator species analysis by combining groups of sites

(2010) Miquel De Cáceres et al.   OIKOS

Resource limitation is a driver of local adaptation in mycorrhizal symbioses

(2010) N. C. Johnson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications

(2010) Michael S. Strickland et al.   SOIL BIOLOGY & BIOCHEMISTRY

Use and misuse of PLFA measurements in soils

(2010) Åsa Frostegård et al.   SOIL BIOLOGY & BIOCHEMISTRY

The interactive effects of plant microbial symbionts: a review and meta-analysis

(2010) Anna L. Larimer et al.   SYMBIOSIS

Plant-Growth-Promoting Rhizobacteria

(2009) Ben Lugtenberg et al.   Annual Review of Microbiology

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

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

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

(2009) Miquel De Cáceres et al.   ECOLOGY

Global patterns in belowground communities

(2009) Noah Fierer et al.   ECOLOGY LETTERS

Plant Growth-Promoting Rhizobacteria Allow Reduced Application Rates of Chemical Fertilizers

(2009) A. O. Adesemoye et al.   MICROBIAL ECOLOGY

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

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

Resource stoichiometry elucidates the structure and function of arbuscular mycorrhizas across scales

(2009) Nancy Collins Johnson   NEW PHYTOLOGIST

Regulation and function of root exudates

(2009) DAYAKAR V. BADRI et al.   PLANT CELL AND ENVIRONMENT

Sanctions, Cooperation, and the Stability of Plant-Rhizosphere Mutualisms

(2008) E. Toby Kiers et al.   Annual Review of Ecology Evolution and Systematics

Preferential allocation to beneficial symbiont with spatial structure maintains mycorrhizal mutualism

(2008) James D. Bever et al.   ECOLOGY LETTERS

The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling

(2008) Diana R. Nemergut et al.   ENVIRONMENTAL MICROBIOLOGY

Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi

(2008) Jaikoo Lee et al.   FEMS MICROBIOLOGY ECOLOGY