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

Metabolic and genetic patterns of soil microbial communities in response to different amendments under organic farming system

(2017) Stefano Dumontet et al.   GEODERMA

A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia

(2017) Antonella Succurro et al.   JOURNAL OF BACTERIOLOGY

Root microbiota drive direct integration of phosphate stress and immunity

(2017) Gabriel Castrillo et al.   NATURE

Small molecules below-ground: the role of specialized metabolites in the rhizosphere

(2017) Hassan Massalha et al.   PLANT JOURNAL

Research priorities for harnessing plant microbiomes in sustainable agriculture

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

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

(2017) Kamlesh K. Meena et al.   Frontiers in Plant Science

The Plant Microbiota: Systems-Level Insights and Perspectives

(2016) Daniel B. Müller et al.   Annual Review of Genetics

Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes

(2016) Florence Mus et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Monitoring soil bacteria with community-level physiological profiles using Biolog™ ECO-plates in the Netherlands and Europe

(2016) Michiel Rutgers et al.   APPLIED SOIL ECOLOGY

Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems

(2016) Fabian Bergkemper et al.   ENVIRONMENTAL MICROBIOLOGY

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Synthetic Ecology of Microbes: Mathematical Models and Applications

(2016) Ali R. Zomorrodi et al.   JOURNAL OF MOLECULAR BIOLOGY

Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics

(2016) Laurent Kamel et al.   NEW PHYTOLOGIST

Plant root-microbe communication in shaping root microbiomes

(2016) Andrew Lareen et al.   PLANT MOLECULAR BIOLOGY

Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria

(2016) Paul C. A. Wintermans et al.   PLANT MOLECULAR BIOLOGY

Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula)

(2016) Mahmoud W. Yaish et al.   PLoS One

Root nodule symbiosis inLotus japonicusdrives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

(2016) Rafal Zgadzaj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Bacteria Are Smartphones and Mobile Genes Are Apps

(2016) J. Peter W. Young   TRENDS IN MICROBIOLOGY

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza

(2016) Kevin Garcia et al.   TRENDS IN PLANT SCIENCE

Mechanisms of Early Microbial Establishment on Growing Root Surfaces

(2016) Lionel X. Dupuy et al.   VADOSE ZONE JOURNAL

Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges

(2016) Martin J. Blaser et al.   mBio

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

(2016) Octavio Perez-Garcia et al.   Frontiers in Microbiology

Cooperation through Competition—Dynamics and Microeconomics of a Minimal Nutrient Trade System in Arbuscular Mycorrhizal Symbiosis

(2016) Stephan Schott et al.   Frontiers in Plant Science

Crop management as a driving force of plant growth promoting rhizobacteria physiology

(2016) Juliana Melo et al.   SpringerPlus

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat

(2016) Akitomo Kawasaki et al.   PLoS One

Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data

(2016) Susann Mönchgesang et al.   Scientific Reports

Critical assessment of genome-scale metabolic networks: the need for a unified standard

(2015) A. Ravikrishnan et al.   BRIEFINGS IN BIOINFORMATICS

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

Tracing the evolutionary path to nitrogen-fixing crops

(2015) Pierre-Marc Delaux et al.   CURRENT OPINION IN PLANT BIOLOGY

Updates in metabolomics tools and resources: 2014-2015

(2015) Biswapriya B. Misra et al.   ELECTROPHORESIS

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

(2015) Dylan J. Weese et al.   EVOLUTION

Linking alkaline phosphatase activity with bacterial phoD gene abundance in soil from a long-term management trial

(2015) Tandra Fraser et al.   GEODERMA

Housing helpful invaders: the evolutionary and molecular architecture underlying plant root-mutualist microbe interactions

(2015) B. Lagunas et al.   JOURNAL OF EXPERIMENTAL BOTANY

Non-targeted profiling of semi-polar metabolites in Arabidopsis root exudates uncovers a role for coumarin secretion and lignification during the local response to phosphate limitation

(2015) Jörg Ziegler et al.   JOURNAL OF EXPERIMENTAL BOTANY

Root phenotyping: from component trait in the lab to breeding: Table 1.

(2015) René C.P. Kuijken et al.   JOURNAL OF EXPERIMENTAL BOTANY

Linking Jasmonic Acid Signaling, Root Exudates, and Rhizosphere Microbiomes

(2015) Lilia C. Carvalhais et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Wheat roots efflux a diverse array of organic N compounds and are highly proficient at their recapture

(2015) Charles R. Warren   PLANT AND SOIL

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

Planetary boundaries: Guiding human development on a changing planet

(2015) W. Steffen et al.   SCIENCE

Soil and human security in the 21st century

(2015) R. Amundson et al.   SCIENCE

Microbial Malaise: How Can We Classify the Microbiome?

(2015) Robert G. Beiko   TRENDS IN MICROBIOLOGY

Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

(2015) N. Kumar et al.   Open Biology

Collaboration between grass seedlings and rhizobacteria to scavenge organic nitrogen in soils

(2015) James F. White et al.   AoB Plants

Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

(2015) Collin M. Timm et al.   Frontiers in Microbiology

Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices

(2015) Ye Xia et al.   Frontiers in Plant Science

Associations with rhizosphere bacteria can confer an adaptive advantage to plants

(2015) Cara H. Haney et al.   Nature Plants

Song, H.-S., et al. Mathematical Modeling of Microbial Community Dynamics: A Methodological Review. Processes 2014, 2, 711–752

(2015) Hyun-Seob Song et al.   Processes

Life's Bottleneck: Sustaining the World's Phosphorus for a Food Secure Future

(2014) Dana Cordell et al.   Annual Review of Environment and Resources

Distinct soil microbial diversity under long-term organic and conventional farming

(2014) Martin Hartmann et al.   ISME Journal

The zigzag model of plant-microbe interactions: is it time to move on?

(2014) Leighton Pritchard et al.   MOLECULAR PLANT PATHOLOGY

Root exudation of phytosiderophores from soil-grown wheat

(2014) Eva Oburger et al.   NEW PHYTOLOGIST

Profiling of secondary metabolites in root exudates of Arabidopsis thaliana

(2014) Nadine Strehmel et al.   PHYTOCHEMISTRY

Long-term effects of mineral fertilizers on soil microorganisms – A review

(2014) Daniel Geisseler et al.   SOIL BIOLOGY & BIOCHEMISTRY

Lasting influence of biochemically contrasting organic inputs on abundance and community structure of total and proteolytic bacteria in tropical soils

(2014) Frank Rasche et al.   SOIL BIOLOGY & BIOCHEMISTRY

Going underground: root traits as drivers of ecosystem processes

(2014) Richard D. Bardgett et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome-wide association study of Arabidopsis thaliana leaf microbial community

(2014) Matthew W. Horton et al.   Nature Communications

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota

(2014) Natacha Bodenhausen et al.   PLoS Genetics

Biological nitrogen fixation in non-legume plants

(2013) Carole Santi et al.   ANNALS OF BOTANY

Chemical Signaling Between Plants and Plant-Pathogenic Bacteria

(2013) Vittorio Venturi et al.   Annual Review of Phytopathology

Transport and Metabolism in Legume-Rhizobia Symbioses

(2013) Michael Udvardi et al.   Annual Review of Plant Biology

Structure and Functions of the Bacterial Microbiota of Plants

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

Indicators of soil ecosystem services in conventional and organic arable fields along a gradient of landscape heterogeneity in southern Sweden

(2013) Alwyn Williams et al.   APPLIED SOIL ECOLOGY

Metabolic potential of endophytic bacteria

(2013) Günter Brader et al.   CURRENT OPINION IN BIOTECHNOLOGY

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

Flavonoids: Their Structure, Biosynthesis and Role in the Rhizosphere, Including Allelopathy

(2013) Leslie A. Weston et al.   JOURNAL OF CHEMICAL ECOLOGY

Methods of collection of plant root exudates in relation to plant metabolism and purpose: A review

(2013) Valerie Vranova et al.   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance

(2013) Yakov Kuzyakov et al.   NEW PHYTOLOGIST

Consequences of human modification of the global nitrogen cycle

(2013) J. W. Erisman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013)

(2013) Yoav Bashan et al.   PLANT AND SOIL

Feruloyl-CoA 6'-Hydroxylase1-Dependent Coumarins Mediate Iron Acquisition from Alkaline Substrates in Arabidopsis

(2013) N. B. Schmid et al.   PLANT PHYSIOLOGY

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

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

(2013) K. Schlaeppi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively-managed agricultural landscape

(2013) Timothy M. Bowles et al.   SOIL BIOLOGY & BIOCHEMISTRY

DATA MINING METHODS FOR OMICS AND KNOWLEDGE OF CRUDE MEDICINAL PLANTS TOWARD BIG DATA BIOLOGY

(2013) Farit M. Afendi et al.   Computational and Structural Biotechnology Journal

Receptor Kinase Signaling Pathways in Plant-Microbe Interactions

(2012) Meritxell Antolín-Llovera et al.   Annual Review of Phytopathology

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

(2012) Kai Xue et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Soil microbial biomass, functional microbial diversity, and nematode community structure as affected by cover crops and compost in an organic vegetable production system

(2012) Ajay Nair et al.   APPLIED SOIL ECOLOGY

The effect of organic acids from tomato root exudates on rhizosphere colonization of Bacillus amyloliquefaciens T-5

(2012) Shiyong Tan et al.   APPLIED SOIL ECOLOGY

Evaluation of a novel tool for sampling root exudates from soil-grown plants compared to conventional techniques

(2012) Eva Oburger et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

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

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

The role of flavonoids in root-rhizosphere signalling: opportunities and challenges for improving plant-microbe interactions

(2012) S. Hassan et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Genetic and Molecular Basis of Plant Resistance to Pathogens

(2012) Yan Zhang et al.   Journal of Genetics and Genomics

Strigolactones and the Regulation of Pea Symbioses in Response to Nitrate and Phosphate Deficiency

(2012) Eloise Foo et al.   Molecular Plant

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

A sensitive LC-ESI-Q-TOF-MS method reveals novel phytosiderophores and phytosiderophore-iron complexes in barley

(2012) Munkhtsetseg Tsednee et al.   NEW PHYTOLOGIST

Past, present and future of organic nutrients

(2012) Chanyarat Paungfoo-Lonhienne et al.   PLANT AND SOIL

Benzoxazinoids in Root Exudates of Maize Attract Pseudomonas putida to the Rhizosphere

(2012) Andrew L. Neal et al.   PLoS One

Diversity in phosphorus mobilisation and uptake in ectomycorrhizal fungi

(2011) Claude Plassard et al.   ANNALS OF FOREST SCIENCE

Roles of Arbuscular Mycorrhizas in Plant Nutrition and Growth: New Paradigms from Cellular to Ecosystem Scales

(2011) Sally E. Smith et al.   Annual Review of Plant Biology

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

Natural variation of Arabidopsis response to nitrogen availability

(2011) Sobia Ikram et al.   JOURNAL OF EXPERIMENTAL BOTANY

Legume-Nodulating Betaproteobacteria: Diversity, Host Range, and Future Prospects

(2011) Prasad Gyaneshwar et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Solutions for a cultivated planet

(2011) Jonathan A. Foley et al.   NATURE

Soil Microorganisms Mediating Phosphorus Availability Update on Microbial Phosphorus

(2011) A. E. Richardson et al.   PLANT PHYSIOLOGY

Incidence and diversity of phosphate-solubilising bacteria are linked to phosphorus status in grassland soils

(2011) Carolyn Mander et al.   SOIL BIOLOGY & BIOCHEMISTRY

Increased plant uptake of nitrogen from 15N-depleted fertilizer using plant growth-promoting rhizobacteria

(2010) A.O. Adesemoye et al.   APPLIED SOIL ECOLOGY

Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems

(2010) Kelly S. Ramirez et al.   ECOLOGY

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

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

Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency

(2010) Lilia C. Carvalhais et al.   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Release of plant-borne flavonoids into the rhizosphere and their role in plant nutrition

(2010) Stefano Cesco et al.   PLANT AND SOIL

Fruit and Soil Quality of Organic and Conventional Strawberry Agroecosystems

(2010) John P. Reganold et al.   PLoS One

The biodiversity of beneficial microbe-host mutualism: the case of rhizobia

(2010) Kristina Lindström et al.   RESEARCH IN MICROBIOLOGY

Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates

(2009) Shirley A. Micallef et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Population size and specific potential of P-mineralizing and -solubilizing bacteria under long-term P-deficiency fertilization in a sandy loam soil

(2009) Junli Hu et al.   PEDOBIOLOGIA

Rhizosphere fauna: the functional and structural diversity of intimate interactions of soil fauna with plant roots

(2009) Michael Bonkowski et al.   PLANT AND SOIL

Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms

(2009) Alan E. Richardson et al.   PLANT AND SOIL

Regulation and function of root exudates

(2009) Dayakar V. Badri et al.   PLANT CELL AND ENVIRONMENT

Fertilizer-dependent efficiency of Pseudomonads for improving growth, yield, and nutrient use efficiency of wheat (Triticum aestivum L.)

(2008) Baby Shaharoona et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

The role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different sulfur fertilization regimes

(2008) Achim Schmalenberger et al.   ENVIRONMENTAL MICROBIOLOGY

New approach for capturing soluble root exudates in forest soils

(2008) Richard P. Phillips et al.   FUNCTIONAL ECOLOGY

16S rDNA analysis reveals low microbial diversity in community level physiological profile assays

(2008) Margarita Ros et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Response to flavonoids as a factor influencing competitiveness and symbiotic activity of Rhizobium leguminosarum

(2008) Dominika Maj et al.   MICROBIOLOGICAL RESEARCH

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Plant-driven selection of microbes

(2008) Anton Hartmann et al.   PLANT AND SOIL

Flavones and flavonols play distinct critical roles during nodulation ofMedicago truncatulabySinorhizobium meliloti

(2008) Juan Zhang et al.   PLANT JOURNAL

Root-Secreted Malic Acid Recruits Beneficial Soil Bacteria

(2008) T. Rudrappa et al.   PLANT PHYSIOLOGY

Plants can use protein as a nitrogen source without assistance from other organisms

(2008) C. Paungfoo-Lonhienne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Suitability of enzyme activities for the monitoring of soil quality improvement in organic agricultural systems

(2008) Roberto García-Ruiz et al.   SOIL BIOLOGY & BIOCHEMISTRY