Integration of metabolome and microbiota datasets
To test our hypothesis in which stress-specific root exudates can
influence the relative abundance of microbial taxa, we built a framework
that integrates microbiota and metabolome data. This investigation
targets at elucidating the influence of each treatment on both exudates
and microbiota, and to identify microbial taxa and compounds that may
coordinately interact in response to stress(es). Excitingly, the
variance decomposition step revealed three factors explaining a high
proportion of the variance, jointly for metabolome and microbiota in the
three different treatments (Supplementary material 1). For each
treatment, we then selected the top 0.1% of bacterial taxa and the top
10% of metabolites that mostly contribute to explain the variation
within each factor, and then we correlated the abundance of the
bacterial taxa and metabolites, then extracting significative
correlations.
The analysis of drought-stresses plants suggests that two compounds
(p-coumaric acid ethyl ester and L-serine) negatively correlate with
several bacterial taxa. Both compounds were negatively correlated with
the same pool of taxa (Mucilaginibacter , Sphingomonas ,Acidibacter, Paenibacillus, Filimonas, Labrys, Mesorhizobium,
Heliimonas, Rudaea ) with the only difference that L-serine negatively
correlated with a single unidentified bacterium, while p-coumaric acid
ethyl ester negatively correlated with 2 unidentified bacterial OTUs
(Supplementary material 1).
Plants exposed to heat treatment showed five compounds
[aminocyclopropane-1-carboxilic, rhamnetin, L-histidine, Quercetin
3-O -(6-acetyl-galactoside) 7-O -rhamnoside and
2-methoxy-5-prop-1-enylphenol/eugenol] correlating negatively with a
total of 23 bacterial taxa (Supplementary material 2). Interestingly,
the first four molecules negatively correlated with a common pool of 22
taxa (Supplementary Material 1) including the genera Bacillus ,Bacteriovorax , Caulobacter , Chitinophaga ,Dyadobacter , Heliimonas , Mesorhizobium ,Micromonospora , Niastella , Pseudonocardia ,Rhizobacter together with 6 OTUs of unidentified bacteria.
2-Methoxy-5-prop-1-enylphenol/Eugenol negatively correlated with 4 OTUs:
one belonging to the genus Alsobacter and three toCaulobacter (Supplementary material 1).
When plants were exposed to combined stress, the analysis suggests that
two compounds (L-homocysteine and cinnamoyl glucose) negatively
correlate with bacterial taxa, while a positive correlation was observed
only for carnosic acid. L-homocysteine influenced the abundance of 25
taxa (Supplementary material 1) including Bacillus ,Clavibacter , Devosia , Dietzia ,Microbacterium , Paenibacillus , Paracoccus ,Rhizobium , Rhodococcus , Stenotrophomonas . Cinnamoyl
glucose and carnosic acid affected, in opposite direction, a single OTU
of Paenibacillus (Supplementary material 1).