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References from Plant immunity-microbiome interactions: Assembly, stress adaptation, and translation. Local targets link to admitted publications; unresolved targets remain external evidence.
NLR singletons, pairs, and networks: evolution, assembly, and regulation of the intracellular immunoreceptor circuitry of plants
10.1016/j.pbi.2019.04.007 · 2019 · External reference
Regulation and function of root exudates
10.1111/j.1365-3040.2009.01926.x · 2009 · External reference
Functional overlap of the Arabidopsis leaf and root microbiota
10.1038/nature16192 · 2015 · External reference
The soil-borne legacy
10.1016/j.cell.2018.02.024 · 2018 · External reference
The ‘prime-ome’: towards a holistic approach to priming
10.1016/j.tplants.2015.04.002 · 2015 · External reference
Keystone taxa as drivers of microbiome structure and functioning
10.1038/s41579-018-0024-1 · 2018 · External reference
Use of metatranscriptomics in microbiome research
10.4137/bbi.s34610 · 2016 · External reference
The rhizosphere microbiome and plant health
10.1016/j.tplants.2012.04.001 · 2012 · External reference
Evolution of hormone signaling networks in plant defense
10.1146/annurev-phyto-080516-035544 · 2017 · External reference
Signaling mechanisms in pattern-triggered immunity (PTI)
10.1016/j.molp.2014.12.022 · 2015 · External reference
A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors
10.1146/annurev.arplant.57.032905.105346 · 2009 · External reference
Structure and functions of the bacterial microbiota of plants
10.1146/annurev-arplant-050312-120106 · 2013 · External reference
Rewiring of jasmonate and phytochrome B signalling uncouples plant growth-defense tradeoffs
10.1038/ncomms12570 · 2016 · External reference
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
10.1126/science.aaw9285 · 2019 · External reference
Linking jasmonic acid signaling, root exudates, and rhizosphere microbiomes
10.1094/mpmi-01-15-0016-r · 2015 · External reference
Root microbiota drive direct integration of phosphate stress and immunity
10.1038/nature21417 · 2017 · External reference
Rhizosphere microbiome assemblage is affected by plant development
10.1038/ismej.2013.196 · 2014 · External reference
Mechanisms and impact of rhizosphere microbial metabolites on crop health, traits, functional components: a comprehensive review
10.3390/molecules29245922 · 2024 · External reference
A plant genetic network for preventing dysbiosis in the phyllosphere
10.1038/s41586-020-2185-0 · 2020 · External reference
Harnessing the plant microbiome for sustainable crop production
10.1038/s41579-024-01079-1 · 2025 · External reference
A review on the plant microbiome: ecology, functions, and emerging trends in microbial application
10.1016/j.jare.2019.03.004 · 2019 · External reference
Ecology and evolution of plant microbiomes
10.1146/annurev-micro-090817-062524 · 2019 · External reference
Regulation of pattern recognition receptor signalling in plants
10.1038/nri.2016.77 · 2016 · External reference
Effector-triggered immunity: from pathogen perception to robust defense
10.1146/annurev-arplant-050213-040012 · 2015 · External reference
Plant–rhizobacteria interactions alleviate abiotic stress conditions
10.1111/j.1365-3040.2009.02028.x · 2009 · External reference
Plant immunity: towards an integrated view of plant–pathogen interactions
10.1038/nrg2812 · 2010 · External reference
Microbial interkingdom interactions in roots promote Arabidopsis survival
10.1016/j.cell.2018.10.020 · 2018 · External reference
Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice
10.1371/journal.pbio.2003862 · 2018 · External reference
Structure, variation, and assembly of the root-associated microbiomes of rice
10.1073/pnas.1414592112 · 2015 · External reference
Phytohormones and beneficial microbes: essential components for plants to balance stress and fitness
10.3389/fmicb.2017.02104 · 2017 · External reference
Dynamic chemical communication between plants and bacteria through airborne signals: induced resistance by bacterial volatiles
10.1007/s10886-013-0317-9 · 2013 · External reference
Plant NLRs get by with a little help from their friends
10.1016/j.pbi.2020.04.006 · 2020 · External reference
Embracing the unknown: disentangling the complexities of the soil microbiome
10.1038/nrmicro.2017.87 · 2017 · External reference
The plant microbiome: from ecology to reductionism and beyond
10.1146/annurev-micro-022620-014327 · 2020 · External reference
Emerging strategies for precision microbiome management in diverse agroecosystems
10.1038/s41477-020-00830-9 · 2021 · External reference
Historical contingency in community assembly: integrating niches, species pools, and priority effects
10.1146/annurev-ecolsys-110411-160340 · 2015 · External reference
Competition for iron drives phytopathogen control by natural rhizosphere microbiomes
10.1038/s41564-020-0719-8 · 2020 · External reference
Resolution of growth–defense conflict: mechanistic insights from jasmonate signaling
10.1016/j.pbi.2018.02.009 · 2018 · External reference
Interplay between innate immunity and the plant microbiota
10.1146/annurev-phyto-080516-035623 · 2017 · External reference
Associations with rhizosphere bacteria can confer an adaptive advantage to plants
10.1038/nplants.2015.51 · 2015 · External reference
Root-secreted coumarins and the microbiota interact to improve iron nutrition in Arabidopsis
10.1016/j.chom.2020.09.006 · 2020 · External reference
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming
10.1186/s40168-017-0389-9 · 2018 · External reference
The role of flavonoids in root–rhizosphere signalling: opportunities and challenges for improving plant–microbe interactions
10.1093/jxb/err430 · 2012 · External reference
Design of synthetic bacterial communities for predictable plant phenotypes
10.1371/journal.pbio.2003962 · 2018 · External reference
A specialized metabolic network selectively modulates Arabidopsis root microbiota
10.1126/science.aau6389 · 2019 · External reference
Pinpointing secondary metabolites that shape the composition and function of the plant microbiome
10.1093/jxb/eraa424 · 2021 · External reference
The plant immune system
10.1038/nature05286 · 2006 · External reference
Intracellular innate immune surveillance devices in plants and animals
10.1126/science.aaf6395 · 2016 · External reference
Bacterial-plant-interactions: approaches to unravel the biological function of bacterial volatiles in the rhizosphere
10.3389/fmicb.2016.00108 · 2016 · External reference
Mechanisms to mitigate the trade-off between growth and defense
10.1105/tpc.16.00931 · 2017 · External reference
Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice
10.1038/ismej.2011.192 · 2012 · External reference
Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana
10.1094/mpmi-20-12-1512 · 2007 · External reference
Rhizosphere microbiome mediates systemic root metabolite exudation by root-to-root signaling
10.1073/pnas.1912130117 · 2020 · External reference
Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa
10.1126/science.aaa8764 · 2015 · External reference
Microbiology of the phyllosphere
10.1128/aem.69.4.1875-1883.2003 · 2003 · External reference
Microbiome-mediated stress resistance in plants
10.1016/j.tplants.2020.03.014 · 2020 · External reference
Microbiome-mediated plant immunity: molecular signalling, community assembly, and emerging intergenerational feedback
10.1016/j.micres.2026.128591 · 2026 · External reference
Reductionist synthetic community approaches in root microbiome research
10.1016/j.mib.2019.10.010 · 2019 · External reference
Defining the core Arabidopsis thaliana root microbiome
10.1038/nature11237 · 2012 · External reference
Coordination of microbe–host homeostasis by crosstalk with plant innate immunity
10.1038/s41477-021-00920-2 · 2021 · External reference
Live imaging of root–bacteria interactions in a microfluidics setup
10.1073/pnas.1618584114 · 2017 · External reference
Deciphering the rhizosphere microbiome for disease-suppressive bacteria
10.1126/science.1203980 · 2011 · External reference
The chemistry of plant–microbe interactions in the rhizosphere and the potential for metabolomics to reveal signaling related to defense priming and induced systemic resistance
10.3389/fpls.2018.00112 · 2018 · External reference
The plant microbiota: systems-level insights and perspectives
10.1146/annurev-genet-120215-034952 · 2016 · External reference
Drought and host selection influence bacterial community dynamics in the grass root microbiome
10.1038/ismej.2017.118 · 2017 · External reference
Patterns and processes of microbial community assembly
10.1128/mmbr.00051-12 · 2013 · External reference
Mutual potentiation of plant immunity by cell-surface and intracellular receptors
10.1038/s41586-021-03315-7 · 2021 · External reference
Simplified and representative bacterial community of maize roots
10.1073/pnas.1616148114 · 2017 · External reference
Sampling root exudates–mission impossible?
10.1016/j.rhisph.2018.06.004 · 2018 · External reference
Road MAPs to engineer host microbiomes
10.1016/j.mib.2017.11.023 · 2018 · External reference
Linking plant secondary metabolites and plant microbiomes: a review
10.3389/fpls.2021.621276 · 2021 · External reference
Jasmonic acid and ethylene signaling pathways regulate glucosinolate levels in plants during rhizobacteria-induced systemic resistance against a leaf-chewing herbivore
10.1007/s10886-016-0787-7 · 2016 · External reference
Diversity and heritability of the maize rhizosphere microbiome under field conditions
10.1073/pnas.1302837110 · 2013 · External reference
Impact of plant domestication on rhizosphere microbiome assembly and functions
10.1007/s11103-015-0337-7 · 2016 · External reference
The soil-borne supremacy
10.1016/j.tplants.2016.01.018 · 2016 · External reference
Hormonal modulation of plant immunity
10.1146/annurev-cellbio-092910-154055 · 2012 · External reference
Induced systemic resistance by beneficial microbes
10.1146/annurev-phyto-082712-102340 · 2014 · External reference
Phyllosphere microbiology: at the interface between microbial individuals and the plant host
10.1111/nph.15054 · 2018 · External reference
Plant genomic and microbial interplay in the rhizosphere under salt stress: a review
10.3389/fpls.2025.1667328 · 2026 · External reference
Crying out for help with root exudates: adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes
10.1016/j.mib.2019.10.003 · 2019 · External reference
Bacterial volatiles induce systemic resistance in Arabidopsis
10.1104/pp.103.026583 · 2004 · External reference
Plant growth-promoting bacterial endophytes
10.1016/j.micres.2015.11.008 · 2016 · External reference
Feed your friends: do plant exudates shape the root microbiome?
10.1016/j.tplants.2017.09.003 · 2018 · External reference
Coevolution of plant-microbe interactions, friend-foe continuum, and microbiome engineering for a sustainable future
10.1016/j.molp.2026.01.010 · 2026 · External reference
Crop microbiome and sustainable agriculture
10.1038/s41579-020-00446-y · 2020 · External reference
Plant growth-promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae
10.1111/1462-2920.14486 · 2019 · External reference
The age of coumarins in plant–microbe interactions
10.1093/pcp/pcz076 · 2019 · External reference
MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health
10.1073/pnas.1722335115 · 2018 · External reference
Receptor kinases in plant-pathogen interactions: more than pattern recognition
10.1105/tpc.16.00891 · 2017 · External reference
Beyond pathogens: microbiota interactions with the plant immune system
10.1016/j.mib.2019.08.003 · 2019 · External reference
Root microbiota assembly and adaptive differentiation among European Arabidopsis populations
10.1038/s41559-019-1063-3 · 2020 · External reference
Core microbiomes for sustainable agroecosystems
10.1038/s41477-018-0139-4 · 2018 · External reference
Plant-pathogen effectors: cellular probes interfering with plant defenses in spatial and temporal manners
10.1146/annurev-phyto-080615-100204 · 2016 · External reference
Plant–microbiome interactions: from community assembly to plant health
10.1038/s41579-020-0412-1 · 2020 · External reference
The importance of the microbiome of the plant holobiont
10.1111/nph.13312 · 2015 · External reference
Microbiota-mediated disease resistance in plants
10.1371/journal.ppat.1007740 · 2019 · External reference
Signaling in the rhizosphere
10.1016/j.tplants.2016.01.005 · 2016 · External reference
Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome
10.1073/pnas.1820691116 · 2019 · External reference
Microbial life in the phyllosphere
10.1038/nrmicro2910 · 2012 · External reference
Establishing causality: opportunities of synthetic communities for plant microbiome research
10.1016/j.chom.2017.07.004 · 2017 · External reference
Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
10.1038/ncomms12151 · 2016 · External reference
Large-scale replicated field study of maize rhizosphere identifies heritable microbes
10.1073/pnas.1800918115 · 2018 · External reference
Genetic control of rhizosphere microbiome of the cotton plants under field conditions
10.1007/s00253-024-13143-0 · 2024 · External reference
Soil-borne legacy facilitates the dissemination of antibiotic resistance genes in soil–plant continua
10.1002/imt2.70094 · 2025 · External reference
Host selection shapes crop microbiome assembly and network complexity
10.1111/nph.16890 · 2021 · External reference
The structure and function of the global citrus rhizosphere microbiome
10.1038/s41467-018-07343-2 · 2018 · External reference
Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria
10.1073/pnas.1717308115 · 2018 · External reference
Plant exudates-driven microbiome recruitment and assembly facilitates plant health management
10.1093/femsre/fuaf008 · 2025 · External reference
Beneficial microbes going underground of root immunity
10.1111/pce.13632 · 2019 · External reference
From chaos to harmony: responses and signaling upon microbial pattern recognition
10.1146/annurev-phyto-080516-035649 · 2017 · External reference
Root exudates drive the soil-borne legacy of aboveground pathogen infection
10.1186/s40168-018-0537-x · 2018 · External reference
Pattern-recognition receptors are required for NLR-mediated plant immunity
10.1038/s41586-021-03316-6 · 2021 · External reference
Modulation of host immunity by beneficial microbes
10.1094/mpmi-06-11-0179 · 2012 · External reference
Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly
10.1038/s41564-018-0129-3 · 2018 · External reference
Stochastic community assembly: does it matter in microbial ecology?
10.1128/mmbr.00002-17 · 2017 · External reference
Plant pattern-recognition receptors
10.1016/j.it.2014.05.004 · 2014 · External reference