Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome

(2022) Kyle M. Meyer et al.   ISME Journal

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

(2022) Sana Romdhane et al.   Environmental Microbiome

Water deficit affects inter‐kingdom microbial connections in plant rhizosphere

(2022) Kathryn E. Bazany et al.   ENVIRONMENTAL MICROBIOLOGY

Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome

(2022) Lucas Schmitz et al.   ISME Journal

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons

(2022) Mingsheng Qi et al.   ISME Journal

Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health

(2022) Sai Guo et al.   ISME Journal

Life and death in the soil microbiome: how ecological processes influence biogeochemistry

(2022) Noah W. Sokol et al.   NATURE REVIEWS MICROBIOLOGY

Rare Species-Driven Diversity–Ecosystem Multifunctionality Relationships are Promoted by Stochastic Community Assembly

(2022) Zhengqing Zhang et al.   mBio

The Leaf Microbiome of Arabidopsis Displays Reproducible Dynamics and Patterns throughout the Growing Season

(2022) Juliana Almario et al.   mBio

Maize Field Study Reveals Covaried Microbiota and Metabolic Changes in Roots over Plant Growth

(2022) Amelia Bourceret et al.   mBio

The phyllosphere microbiome shifts toward combating melanose pathogen

(2022) Pu-Dong Li et al.   Microbiome

A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants

(2022) Liyu Zhang et al.   Nature Communications

The only constant is change: Endogenous circadian rhythms of soil microbial activities

(2022) Kankan Zhao et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fertilization alters protistan consumers and parasites in crop‐associated microbiomes

(2021) Anqi Sun et al.   ENVIRONMENTAL MICROBIOLOGY

Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root

(2021) Ahmed Abdelfattah et al.   ENVIRONMENTAL MICROBIOLOGY

Tracking, targeting, and conserving soil biodiversity

(2021) Carlos A. Guerra et al.   SCIENCE

Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

(2021) Sally Hilton et al.   Microbiome

Deciphering bacterial mechanisms of root colonization

(2021) Hayley E. Knights et al.   Environmental Microbiology Reports

Algae as New Kids in the Beneficial Plant Microbiome

(2021) Sang-Moo Lee et al.   Frontiers in Plant Science

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

(2021) Weibing Xun et al.   Microbiome

Light exposure mediates circadian rhythms of rhizosphere microbial communities

(2021) Kankan Zhao et al.   ISME Journal

Above‐ground parts of white grapevine Vitis vinifera cv. Furmint share core members of the fungal microbiome

(2021) Dániel G. Knapp et al.   Environmental Microbiology Reports

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

(2021) Ahmad Nuruddin Khoiri et al.   Frontiers in Microbiology

Protists as main indicators and determinants of plant performance

(2021) Sai Guo et al.   Microbiome

Holo-omics for deciphering plant-microbiome interactions

(2021) Ling Xu et al.   Microbiome

Microbial assembly and association network in watermelon rhizosphere after soil fumigation for Fusarium wilt control

(2021) An-Hui Ge et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Multiple strategies of plant colonization by beneficial endophytic Enterobacter sp. SA187

(2021) Lukas Synek et al.   ENVIRONMENTAL MICROBIOLOGY

Role of soil in the regulation of human and plant pathogens: soils' contributions to people

(2021) Sandipan Samaddar et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

(2021) Ling Xu et al.   Nature Communications

Plant developmental stage drives the differentiation in ecological role of the maize microbiome

(2021) Chao Xiong et al.   Microbiome

Disease-induced changes in plant microbiome assembly and functional adaptation

(2021) Min Gao et al.   Microbiome

Organic and conservation agriculture promote ecosystem multifunctionality

(2021) Raphaël A. Wittwer et al.   Science Advances

Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems

(2021) Shuo Jiao et al.   GLOBAL CHANGE BIOLOGY

Mycelial network-mediated rhizobial dispersal enhances legume nodulation

(2020) Wei Zhang et al.   ISME Journal

Next-generation physiology approaches to study microbiome function at single cell level

(2020) Roland Hatzenpichler et al.   NATURE REVIEWS MICROBIOLOGY

Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison

(2020) Andrzej Tkacz et al.   mBio

Rhizosphere protists are key determinants of plant health

(2020) Wu Xiong et al.   Microbiome

An amplification-selection model for quantified rhizosphere microbiota assembly

(2020) Xiaolin Wang et al.   Science Bulletin

Multiple elements of soil biodiversity drive ecosystem functions across biomes

(2020) Manuel Delgado-Baquerizo et al.   Nature Ecology & Evolution

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

(2020) Thorsten Thiergart et al.   Nature Ecology & Evolution

Functional roles of microbial symbionts in plant cold tolerance

(2020) Ian S. Acuña‐Rodríguez et al.   ECOLOGY LETTERS

Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

(2020) Shuo Jiao et al.   GLOBAL CHANGE BIOLOGY

Harnessing rhizosphere microbiomes for drought-resilient crop production

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

A plant’s diet, surviving in a variable nutrient environment

(2020) Giles E. D. Oldroyd et al.   SCIENCE

Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience

(2020) Inessa Arif et al.   TRENDS IN BIOTECHNOLOGY

Competition for iron drives phytopathogen control by natural rhizosphere microbiomes

(2020) Shaohua Gu et al.   Nature Microbiology

The Plant Microbiome: From Ecology to Reductionism and Beyond

(2020) Connor R. Fitzpatrick et al.   Annual Review of Microbiology

Expression of N‐cycling genes of root microbiomes provides insights for sustaining oilseed crop production

(2020) Li Wang et al.   ENVIRONMENTAL MICROBIOLOGY

Plant–microbiome interactions: from community assembly to plant health

(2020) Pankaj Trivedi et al.   NATURE REVIEWS MICROBIOLOGY

Heterosis of leaf and rhizosphere microbiomes in field‐grown maize

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

Imaging spatiotemporal evolution of molecules and active sites in zeolite catalyst during methanol-to-olefins reaction

(2020) Mingbin Gao et al.   Nature Communications

Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis

(2020) Christopher J. Harbort et al.   Cell Host & Microbe

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

(2020) Chao Xiong et al.   ENVIRONMENTAL MICROBIOLOGY

The plant endosphere world – bacterial life within plants

(2020) Stéphane Compant et al.   ENVIRONMENTAL MICROBIOLOGY

Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment

(2020) Kunkun Fan et al.   ISME Journal

Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease

(2020) Sang-Moo Lee et al.   ISME Journal

A single bacterial genus maintains root growth in a complex microbiome

(2020) Omri M. Finkel et al.   NATURE

Crop microbiome and sustainable agriculture

(2020) Brajesh K. Singh et al.   NATURE REVIEWS MICROBIOLOGY

Host selection shapes crop microbiome assembly and network complexity

(2020) Chao Xiong et al.   NEW PHYTOLOGIST

Microscale heterogeneity of the soil nitrogen cycling microbial functional structure and potential metabolism

(2020) Shun Han et al.   ENVIRONMENTAL MICROBIOLOGY

Engineering rhizobacteria for sustainable agriculture

(2020) Timothy L. Haskett et al.   ISME Journal

Evidence for the plant recruitment of beneficial microbes to suppress soil‐borne pathogens

(2020) Hongwei Liu et al.   NEW PHYTOLOGIST

Microbial communities in crop phyllosphere and root endosphere are more resistant than soil microbiota to fertilization

(2020) Anqi Sun et al.   SOIL BIOLOGY & BIOCHEMISTRY

Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.)

(2019) Tomislav Cernava et al.   Microbiome

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

(2019) Samiran Banerjee et al.   ISME Journal

The global burden of pathogens and pests on major food crops

(2019) Serge Savary et al.   Nature Ecology & Evolution

Ecology and Evolution of Plant Microbiomes

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

Maize synthesized benzoxazinoids affect the host associated microbiome

(2019) Enoch Narh Kudjordjie et al.   Microbiome

Common principles and best practices for engineering microbiomes

(2019) Christopher E. Lawson et al.   NATURE REVIEWS MICROBIOLOGY

Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat

(2019) Lydie Kerdraon et al.   Microbiome

Initial soil microbiome composition and functioning predetermine future plant health

(2019) Zhong Wei et al.   Science Advances

Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

(2019) Shuo Jiao et al.   ISME Journal

Soil microbiomes and climate change

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

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

(2019) Víctor J. Carrión et al.   SCIENCE

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

(2019) Keara L. Grady et al.   Nature Communications

Suppressed N fixation and diazotrophs after four decades of fertilization

(2019) Kunkun Fan et al.   Microbiome

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

(2019) Jennifer E. Schmidt et al.   Microbiome

Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization

(2019) Shuaimin Chen et al.   Microbiome

The Soil-Borne Legacy

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

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

(2018) Kelly Hamonts et al.   ENVIRONMENTAL MICROBIOLOGY

Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean

(2018) Lucas William Mendes et al.   ISME Journal

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Root microbiota shift in rice correlates with resident time in the field and developmental stage

(2018) Jingying Zhang et al.   Science China-Life Sciences

Microbial interactions within the plant holobiont

(2018) M. Amine Hassani et al.   Microbiome

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

(2018) Ramona Marasco et al.   Microbiome

A microorganisms’ journey between plant generations

(2018) Nathan Vannier et al.   Microbiome

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain

(2018) Yu Shi et al.   Microbiome

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

(2018) Kyle Hartman et al.   Microbiome

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

(2018) Allen Van Deynze et al.   PLOS BIOLOGY

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

Rhizosphere microbiome structure alters to enable wilt resistance in tomato

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

Arbuscular mycorrhizal fungi increase grain yields: a meta-analysis

(2018) Shujuan Zhang et al.   NEW PHYTOLOGIST

Poplar phyllosphere harbors disparate isoprene-degrading bacteria

(2018) Andrew T. Crombie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant compartment and genetic variation drive microbiome composition in switchgrass roots

(2018) Esther Singer et al.   Environmental Microbiology Reports

Soil protist communities form a dynamic hub in the soil microbiome

(2017) Wu Xiong et al.   ISME Journal

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function

(2017) Lucas William Mendes et al.   ISME Journal

Organic farming increases richness of fungal taxa in the wheat phyllosphere

(2017) Ida Karlsson et al.   MOLECULAR ECOLOGY

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Simplified and representative bacterial community of maize roots

(2017) Ben Niu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria

(2017) Francis M. Martin et al.   SCIENCE

The Plant Microbiota: Systems-Level Insights and Perspectives

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

Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis

(2016) Iris Bertani et al.   Environmental Microbiology Reports

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

(2016) Maggie R. Wagner et al.   Nature Communications

Networking in the Plant Microbiome

(2016) Marcel G. A. van der Heijden et al.   PLOS BIOLOGY

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

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

Isotopic evidence for the occurrence of biological nitrification and nitrogen deposition processing in forest canopies

(2015) Rossella Guerrieri et al.   GLOBAL CHANGE BIOLOGY

Structure, variation, and assembly of the root-associated microbiomes of rice

(2015) Joseph Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

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

(2012) Davide Bulgarelli et al.   NATURE

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil

(2012) Adela García-Salamanca et al.   Microbial Biotechnology

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

(2009) Stéphane Compant et al.   SOIL BIOLOGY & BIOCHEMISTRY

Arbuscular mycorrhiza: the mother of plant root endosymbioses

(2008) Martin Parniske   NATURE REVIEWS MICROBIOLOGY