Table 1.

Overview of chemical structures, metabolic precursors, and microbial effects for secondary metabolites that shape the root microbiome

Secondary metabolite	Example chemical structure	Precursor primary metabolite	Mechanistic action on microbes
Benzoxazinoids		• Chorismate	• Chemoattractant (Neal et al., 2012a) • Modification of -SH and -NH2 groups in proteins, leading to enzyme inactivation (Wouters et al., 2016)
Camalexin		• Tryptophan	• Disruption of membrane integrity (Rogers et al., 1996)
Coumarins		• Phenylalanine	• Disruption of transcription (Yang et al., 2016) • Disruption of quorum sensing and biofilm formation (Yang et al., 2016) • Damage to membranes (Yang et al., 2016)
Flavonoids		• Phenylalanine	• Induction of nod gene expression in Rhizobium (Redmond et al., 1986) • Damage to membranes (Tsuchiya and Iinuma, 2000) • Inhibition of enzymes (Zhang and Rock, 2004) • Disruption of nucleic acid synthesis (Mori et al., 1987) • Disruption of biofilm formation (Vikram et al., 2010)
Glucosinolates		• Tryptophan • Phenylalanine • Methionine	• Isothiocyanate-mediated enzyme inactivation (Aires et al., 2009) • Isothiocyanate-mediated disruption of membrane integrity (Borges et al., 2015)
Strigolactones		• Isopentenyl pyrophosphate • β-Carotene	• Induction of hyphal branching in mycorrhizal fungi (Akiyama et al., 2005)
Triterpenes		• Isopentenyl pyrophosphate • Squalene	• Disruption of membrane integrity (de León et al., 2010)