Table 1.

Representative studies where plants under different stresses can select/modulate the assembly of the root-associated microbiome. For each study (when possible) the trigger leading to plant activity that modulates the microbiome, the identified mechanism of action, the effect on the microbiome, the host plant and the reference is mentioned.

Trigger	Mechanisms	Effect	Host	Reference
Pathogen-triggered
Fusarium oxysporum f. sp. lycopersici	Disease -induced recruitment from suppressive compost	Enrichment of Proteobacteria, Actinobacteria, and Firmicutes (Bacillus)	Tomato	Antoniou et al., 2017
Hyaloperonospora arabidopsidis/Pseudomonas syringae pv. tomato	Legacy-mediated development of soil suppressiveness	Assemblage of beneficial rhizosphere microbiome	Arabidopsis/Tomato	Berendsen et al., 2018/ Yuan et al., 2018
Rhizoctonia solani	Activation of bacterial stress responses and activation of antagonistic traits that restrict pathogen infection	Shifts in microbiome composition and enrichment of Oxalobacteraceae, Burkholderiaceae, Sphingobacteriaceae, and Sphingomonadaceae	Sugar beet	Chapelle et al., 2016
Botrytis cinerea	Chemoattraction induced by root-exuded peroxidases and oxylipins	Attraction of Trichoderma harzianum and inhibition of Fusarium oxysporum	Tomato; Cucumber	Lombardi et al., 2018
Rhizoctonia solani	Pathogen-induced taxa enrichment from suppressive soils	Recruitment of specific taxa from rhizosphere of sugar beet infected with Rhizoctonia solani	Sugar beet	Mendes et al., 2011
Pseudomonas syringae pv. tomato	Root-secreted malic acid	Recruitment of Bacillus subtilis FB17	Arabidopsis	Rudrappa et al., 2008
Fusarium oxysporum f. sp. lini	Disease-induced recruitment of beneficial microbes from Fusarium suppressive soils	Increase of taxa associated to Fusarium wilt suppressiveness	Flax	Siegel-Hertz et al., 2018
Huanglongbing (HLB) caused by Candidatus Liberibacter spp.	Putative mechanisms: HLB significantly altered the structure or functional potential of the citrus endosphere	Decrease in abundance of taxa and loss of functions in the rhizoplane-rhizosphere enriched microbiome of HLB- infected citrus roots	Citrus	Zhang et al., 2017
Insects-triggered
Aphids	Elicitation of plant immunity via SA/JA systemic signaling and expression of pathogenesis-related (PR) proteins in roots	Recruitment of the beneficial bacteria Bacillus subtilis and decrease of the population of Ralstonia solanacearum	Pepper	Lee et al., 2012
Whitefly	Whitefly infestation elicited SA and JA signaling in above and below ground tissues and overexpression of PR genes in the roots resulting in a differential microbiome assembly	The differential microbiome assembly induced resistance against to Xanthomonas axonopodis pv. vesicatoria and Ralstonia solanacearum	Pepper	Yang et al., 2011
Abiotic stress/nutrient deficiency-triggered
Phosphate deficiency	Phosphate starvation response via PHR1 and PHL1 and PHO2	Differential assemblage of bacterial and fungal microbiota	Arabidopsis	Castrillo et al., 2017/ Fabianska et al., 2019
Gradients of phosphate, salinity, pH, temperature	-	Assembly of different modules of co-occurring strains	Arabidopsis	Finkel et al., 2019
wounding; salt stress	Chemoattraction induced by root-exuded peroxidases and oxylipins	Exudates attracted Trichoderma harzianum and showed deterrent activity against Fusarium oxysporum	Tomato; Cucumber	Lombardi et al., 2018
Iron deficiency/colonization by PGPR	Increased accumulation and secretion of the coumarin scopoletin exerts selective antimicrobial activity in rhizosphere	Differential microbiome assembly, repelling potential against phytopathogens and thus, recruiting potential beneficial microbes	Arabidopsis	Stringlis et al., 2018b
Iron deficiency	Catecholic coumarins show differential antimicrobial activity	Shift in microbial composition of SynCom in vitro	Arabidopsis	Voges et al., 2019
Endogenous/exogenous plant-derived molecules-triggered
-	Overexpression of genes involved biosynthesis and transport of root-exuded secondary metabolites	Greater abundance of potentially beneficial bacteria	Arabidopsis	Badri et al., 2009
-	Differential exudation of root secondary metabolites regulated by Benzoxazinoids (BXs)	Enrichment of Methylophilaceae, Nitrosomonadaceae, Oxalobactereraceae, Syntrophobacteriaceae, and Gaiellaceae	Maize	Cotton et al., 2019
-	Benzoxazinoids (BXs) drive plant-soil feedback	BXs shape the microbiota of the next generation of plants	Maize	Hu et al., 2018
-	Differential secretion of triterpene-derived metabolites by altering triterpene gene cluster	Differential assembly of Arabidopsis root microbiome	Arabidopsis	Huang et al., 2019
-	Microbial sulfatase cleaves root-exuded sulfate esters produced by the camalexin biosynthetic pathway	Stimulation of microbial sulfatase activity in soil and is required for the plant growth-promoting effects of several bacterial strains	Arabidopsis	Koprivova et al., 2019
-	Assembly of differential microbiome between tomato cultivars susceptible and resistant to Ralstonia solanacearum	Enrichment of Flavobacterium in the microbiome of tomato cultivars resistant to Ralstonia, Flavobacterium application confers resistance to susceptible cultivar	Tomato	Kwak et al., 2018
SA	Compromised innate immune system impairing SA biosynthetic pathway	SA-dependent modulation of root microbiome and enrichment of Flavobacterium, Terracoccus, and Streptomyces in SA-treated roots and bulk soils	Arabidopsis	Lebeis et al., 2015
-	DIMBOA Benzoxazinoids (BXs) induce chemotaxis-associated genes in Pseudomonas putida	Enhanced rhizosphere colonization by P. putida	Maize	Neal et al., 2012
ACC; JA	ACC and JA application, induced altered expression of PRR and RLK and cell wall biosynthesis and maintenance related genes	Inhibition of the secondary stage of root colonization by Laccaria bicolor	Poplar	Plett et al., 2014b