Exploring the roles of microbes in facilitating plant adaptation to climate change

Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential

(2021) Lu Zhou et al.   BMC GENOMICS

Microbiota-root-shoot-environment axis and stress tolerance in plants

(2021) Shiji Hou et al.   CURRENT OPINION IN PLANT BIOLOGY

Editorial: Novel Insights Into the Response of the Plant Microbiome to Abiotic Factors

(2021) Feth el Zahar Haichar et al.   Frontiers in Plant Science

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics

(2021) Vittorio Tracanna et al.   mSystems

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

(2021) Daniel Petras et al.   NATURE METHODS

Harnessing rhizosphere microbiomes for drought-resilient crop production

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

Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function

(2020) Devin R. Leopold et al.   CURRENT BIOLOGY

More than words: the chemistry behind the interactions in the plant holobiont

(2020) María Victoria Berlanga‐Clavero et al.   ENVIRONMENTAL MICROBIOLOGY

Plant–microbiome interactions: from community assembly to plant health

(2020) Pankaj Trivedi et al.   NATURE REVIEWS MICROBIOLOGY

Climate Disruption of Plant-Microbe Interactions

(2020) Jennifer A. Rudgers et al.   Annual Review of Ecology Evolution and Systematics

Unraveling the sugar code: the role of microbial extracellular glycans in plant-microbe interactions

(2020) Alan Wanke et al.   JOURNAL OF EXPERIMENTAL BOTANY

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

MAGI: A method for metabolite, annotation, and gene integration

(2019) Onur Erbilgin et al.   ACS Chemical Biology

Ecology and Evolution of Plant Microbiomes

(2019) Viviane Cordovez et al.   Annual Review of Microbiology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

EcoFABs: advancing microbiome science through standardized fabricated ecosystems

(2019) Karsten Zengler et al.   NATURE METHODS

Scientists’ warning to humanity: microorganisms and climate change

(2019) Ricardo Cavicchioli et al.   NATURE REVIEWS MICROBIOLOGY

Root exudates: from plant to rhizosphere and beyond

(2019) Vicente Vives-Peris et al.   PLANT CELL REPORTS

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

(2019) Ashish A. Malik et al.   ISME Journal

Plant root exudation under drought: implications for ecosystem functioning

(2019) Alex Williams et al.   NEW PHYTOLOGIST

Impacts of experimental alteration of water table regime and vascular plant community composition on peat mercury profiles and methylmercury production

(2019) Kristine M. Haynes et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Initial soil microbiome composition and functioning predetermine future plant health

(2019) Zhong Wei et al.   Science Advances

Interactions between plants and soil shaping the root microbiome under abiotic stress

(2019) Kyle Hartman et al.   BIOCHEMICAL JOURNAL

Soil microbiomes and climate change

(2019) Janet K. Jansson et al.   NATURE REVIEWS MICROBIOLOGY

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

(2019) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

Climate change effects on plant-soil feedbacks and consequences for biodiversity and functioning of terrestrial ecosystems

(2019) Francisco I. Pugnaire et al.   Science Advances

Bridging the Gap Between Single-Strain and Community-Level Plant-Microbe Chemical Interactions

(2019) Bridget S. O’Banion et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

High-order interactions distort the functional landscape of microbial consortia

(2019) Alicia Sanchez-Gorostiaga et al.   PLOS BIOLOGY

Field study reveals core plant microbiota and relative importance of their drivers

(2018) Kelly Hamonts et al.   ENVIRONMENTAL MICROBIOLOGY

From climate chambers to biodiversity chambers

(2018) Nico Eisenhauer et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Cell wall extensins in root–microbe interactions and root secretions

(2018) Romain Castilleux et al.   JOURNAL OF EXPERIMENTAL BOTANY

Climate-smart crops with enhanced photosynthesis

(2018) Christer Jansson et al.   JOURNAL OF EXPERIMENTAL BOTANY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

(2018) Ling Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

(2018) Joelle Sasse et al.   TRENDS IN PLANT SCIENCE

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

(2018) Tami L. Swenson et al.   Nature Communications

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

(2018) Lingfei Hu et al.   Nature Communications

Design of synthetic bacterial communities for predictable plant phenotypes

(2018) Sur Herrera Paredes et al.   PLOS BIOLOGY

Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions

(2018) Jian Gao et al.   Jove-Journal of Visualized Experiments

Microbial interactions within the plant holobiont

(2018) M. Amine Hassani et al.   Microbiome

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

(2018) Kateryna Zhalnina et al.   Nature Microbiology

Past and future global transformation of terrestrial ecosystems under climate change

(2018) Connor Nolan et al.   SCIENCE

Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities

(2018) Xinyun Cao et al.   BIOCHEMISTRY

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

(2018) Joelle Sasse et al.   NEW PHYTOLOGIST

Genomes OnLine database (GOLD) v.7: updates and new features

(2018) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Cheating fosters species co-existence in well-mixed bacterial communities

(2017) Anne Leinweber et al.   ISME Journal

Polysaccharide Utilization Loci: Fueling Microbial Communities

(2017) Julie M. Grondin et al.   JOURNAL OF BACTERIOLOGY

Genomic features of bacterial adaptation to plants

(2017) Asaf Levy et al.   NATURE GENETICS

Root exudate ofSolanum tuberosumis enriched in galactose-containing molecules and impacts the growth ofPectobacterium atrosepticum

(2016) Abdoul Salam Koroney et al.   ANNALS OF BOTANY

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction

(2016) Christopher S. Henry et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Root exudates drive interspecific facilitation by enhancing nodulation and N2fixation

(2016) Bai Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities

(2016) Anna Hanke et al.   Frontiers in Microbiology

Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction

(2015) A Ranjitha Dhanasekaran et al.   BMC BIOINFORMATICS

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

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

The plant microbiome explored: implications for experimental botany

(2015) Gabriele Berg et al.   JOURNAL OF EXPERIMENTAL BOTANY

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arbuscular mycorrhizal fungi reduce decomposition of woody plant litter while increasing soil aggregation

(2015) E.F. Leifheit et al.   SOIL BIOLOGY & BIOCHEMISTRY

Biochemistry and genetics of ACC deaminase: a weapon to “stress ethylene” produced in plants

(2015) Rajnish P. Singh et al.   Frontiers in Microbiology

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Climate Change, Aboveground-Belowground Interactions, and Species' Range Shifts

(2012) Wim H. Van der Putten   Annual Review of Ecology Evolution and Systematics

Evidence of a strong coupling between root exudation, C and N availability, and stimulated SOM decomposition caused by rhizosphere priming effects

(2012) Per Bengtson et al.   Ecology and Evolution

Elevated CO2 stimulates grassland soil respiration by increasing carbon inputs rather than by enhancing soil moisture

(2011) E. Carol Adair et al.   GLOBAL CHANGE BIOLOGY

The RootChip: An Integrated Microfluidic Chip for Plant Science

(2011) G. Grossmann et al.   PLANT CELL

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Climate change effects on beneficial plant-microorganism interactions

(2010) Stéphane Compant et al.   FEMS MICROBIOLOGY ECOLOGY

Dealing with the unknown: Metabolomics and Metabolite Atlases

(2010) Benjamin P. Bowen et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis

(2010) Paola Bonfante et al.   Nature Communications

DNA Stable-Isotope Probing (DNA-SIP)

(2010) Eric A. Dunford et al.   Jove-Journal of Visualized Experiments

Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats

(2009) Rashid Nazir et al.   FEMS MICROBIOLOGY ECOLOGY