Effect of root exudation on microbial community
Roots determine the assembly and recruitment of plant-specific
rhizosphere microbial communities by releasing exudates into the
rhizosphere (Bulgarelli et al., 2013). Despite this important functional
role in the plant-soil feedbacks, comprehensive and mechanistic evidence
of the processes underlying the influence of root exudates towards
rhizosphere microbiota is currently lacking. In this respect, rough
correlations between the accumulation of root exudates and microbial
communities (Chen et al., 2019) and few specific exudates included in
soil (Badri et al., 2013; Zwetsloot et al., 2020; Gu et al., 2020) or
growth medium (Zhalnina et al., 2018) indicated the effect(s) of root
exudates on soil microbial community. Differently to these works, we
applied a Multi-Omics Factor Analysis (MOFA+) using maize root exudome
and microbiome dataset collected within the same growth unit to extract
microbial taxa and maize root exudates that have a high probability to
be involved in root-microbiota interaction.
The metabolites extracted were amino acids (L-serine, L-histidine,
L-homocysteine), aminocyclopropane-1-carboxilic acid, phenolics
(p-coumaric, eugenol, quercetin 3-O -(6-acetyl-galactoside)
7-O -rhamnoside, rhamnetin and cinnamoyl glucose) together with
carnosic acid (supplemental material 1). Amino acids in root exudates
have been proposed as osmotically active compounds (Vives-Peris,
Gómez-Cadenas & Pérez-Clemente 2018), whereas phenolics play a direct
antioxidant activity and chemotaxis activity that has been proposed to
shape the rhizosphere community (Iannucci et al. 2021; Lucini et al.
2019; Zuluaga et al. 2021). Except carnosic acid, all these compounds
were negatively correlated with most gram-negative bacterial genus
(supplemental material 1) suggesting that the maize root exudates finely
modulated the depletion or enrichment of most diderm (or Gram negative)
lineages. Interestingly, the pattern of soil microbial compositional
shifts towards the gram-positive bacterial community is a universal
response to abiotic stress (Xu and Coleman-Derr, 2019). On the other
side, the increase of the abundance of specific bacteria belong to thePaenibacillus , Sphingomonas , Mesorhizobium andBacillus was also observed in our work (supplemental material 1)
which, altough being gram-negative, have been associated with the plant
tolerance to abiotic stress (Luo et al., 2019; Figueiredo, Burity,
Martínez & Chanway 2008; Khan, Mishra, Chauhan & Nautiyal 2011; Liu,
Sikora & Park 2020b; Yadav, Yadav, Singh, Singh & Singh 2021; Kang et
al. 2019; Khan et al. 2020 ).
An interesting finding of our work was that the root exudates affecting
bacterial taxa were stress-specific. In drought-stressed plants, we
found that p-coumaric acid ethyl ester and L-serine negatively correlate
with a pool of OTUs representing nine bacterial genera (supplementary
material 1). P-coumaric acid belongs to the phenolic acids, a class of
compounds that is well-known to affect the activity and diversity of the
rhizosphere microbial communities. Indeed, this compound has been
demonstrated to sharply affect the microbial community of the
rhizosphere of crops (Zhou and Wu, 2012; Zhou et al., 2018) and
specifically to reduce the abundance of Lysobacter (Folman et al.
2003), Haliangium (Fudou et al. 2001), and Gymnoascus spp.
(Liu et al. 2017b). These species pointed out plant-growth-promoting
and/or plant pathogen-inhibiting effects. In our study, we also found
that L-serine negatively correlated with different bacterial genera.
However, it has been also observed that amino acids as well as sugars
showed a lower impact than phenolic acids on the microbial community
(Badri et al., 2013). Hence, maize roots reducing the exudation of
p-coumaric and L-serine in presence of drought stress determined from
one side a lower soil accumulation of beneficial-microbial-inhibited
metabolites (p-coumaric) and, at the same time, the preservation of an
useful metabolite (L-serine) for the within-plant tolerance mechanisms.
Indeed, we found that p-coumaric is negatively correlated withMucilaginibacter that has been found to alleviate salt stress
(Fan, Subramanian & Smith 2020), Sphingomonas andMesorhizobium which contributed to alleviate the effects of
drought stress (Luo et al. , 2019; Yadav, Yadav, Singh, Singh &
Singh 2021) and Paenibacillus that are also well known to be
recruited by plants during drought stress episodes (Figueiredo, Burity,
Martínez & Chanway 2008; Khan, Mishra, Chauhan & Nautiyal 2011; Liu,
Sikora & Park 2020b).
In heat-stressed plants, we identified five compounds
(1-aminocyclopropane-1-carboxilic, L-histidine, quercetin, eugenol, and
rhamnetin) that explain most of the variation in the pattern of the root
exudates, and that significantly correlate with microbial taxa
(supplemental material 1). Also in this case, we observed an interaction
between these compounds and several bacterial taxa that have been
previously reported to have a beneficial influence on stressed plants.
In particular, species of Bacillus are widely recognized to be
beneficial microorganisms, helping plants to cope with a variety of
stressors including heat (Kang et al. 2019; Khan et al.2020). While Chitinophaga, Mesorhizobium and Rhizobacter are all
well-known plant-growth promoting rhizobacteria (Kour, Rana, Yadav &
Yadav 2019); no previous study reports a link betweenChitinophaga and abiotic stress.
Interestingly, in the combined-stressed plants, we identified three
metabolites (L-homocysteine, cinnamoyl glucose and carnosic acid) that
likely have a major role in the interaction between maize roots and soil
microbiota and are completely different to that obtained in the single
stress treatments (supplemental material 1). Similarly to what we
observed for the single stressors, also these exudates correlated with
taxa that have been previously reported to promote plant growth or
alleviate the effect of plant stress. Among these genera, we observed
(a) the gram negative Stenotrophomonas , including several species
that have been reported as plant growth promoters and elicitors of plant
resistance against biotic and abiotic stress (Singh and Jha, 2017), as
well as the suppression of pathogens in the rhizosphere (Schmidt et al.,
2012); (b) Microbacterium which improved the growth of sugarcane
(Pereira et al., 2019) and pepper in presence of drought stress (Vílchez
et al., 2018); (c) the Clavibacter that was observed in the
rhizosphere of the halophyte Salicornia europaea (Hrynkiewicz et
al., 2019); (d) the Dietzia whose specific strain, D.
cinnamea 55, was isolated in abiotic stress environment and promoted
the growth of maize plants (Khan et al., 2020) or the Dietzia
natronolimnaea which improved the tolerance of the wheat plants to salt
stress (Bharti et al., 2016).
Finally, within the same stress treatment, the identified metabolites
interact with the same group of bacterial taxa (supplemental material 1)
suggesting that, mechanistically, maize plants might modulate the
exudation of a specific blend of molecules acting in concert to shape
rhizosphere microbial communities.
Here we show that each individual stress (single and combined stress)
produces a specific signature in the composition of root exudates
targeting specific microbial taxa. In this respect, our results support
the existence of a mechanism by which some root exudates are used by
plants to recruit beneficial microorganisms (Naylor & Coleman-Derr
2018; Williams & de Vries 2020; Liu, Brettell, Qiu & Singh 2020a).
Root exudates are known to directly affect the availability of nutrients
in the rhizosphere (Canarini, Merchant & Dijkstra 2016). However, our
findings indicate that indirect effects related to the need to recruit
specific microbial communities is pivotal under drought, high
temperature or their combination. In fact, our findings highlight a role
of root exudates in the complex dynamics occurring in plant-microbe
interactions during single or combined stress. The correlations observed
confirm that specialized metabolites in root exudates may interfere with
the mutualistic interactions between roots and defined phylogroups, as a
well-known strategy to overcome stress conditions (O’Banion et al. 2020;
Zuluaga et al. 2021). Edaphoclimatic conditions are known to determine
plants’ ability to exude compounds able to recruit and sustain a defined
rhizosphere microbial community (Karlowsky etal. 2018) in a
genotype-related manner (Iannucci et al. 2021). Notwithstanding, such
modulation at rhizosphere community level is rather stress-specific and
cannot be generalized, even across relatively related abiotic stresses.