Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

Abstract

Background. Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, henceforth, the rhizobiome, can harbor beneficial microbes that alleviate stress impacts. However, the factors influencing the recruitment of the rhizobiome during stress are unclear. We conducted an experiment to understand bacterial rhizobiome responses to short-term drought for two crop species: switchgrass and common bean. We used 16S rRNA and 16S rRNA gene sequencing to investigate the impact of drought severity on the recruitment of active bacterial rhizobiome members. We included planted and unplanted conditions to distinguish the environment- versus plant-mediated drivers of the active rhizobiome. Results. Though each crop had a distinct rhizobiome, there were differences in the active microbiome structure between drought and watered and between planted and unplanted treatments. Despite their different community structures, the drought rhizobiome dynamics were similar across the two crops. However, the presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought only observed for the bean rhizobiome. The switchgrass rhizobiome was stable despite differences in the rhizosphere metabolite profiles between planted and unplanted treatments. Specifically, steroidal saponins and diterpennoids were enriched in drought, planted switchgrass soils. Conclusions. We conclude that rhizobiome benefits to resist short-term drought are crop-specific, with the possibility of decoupling of plant exudation and rhizobiome responses, as we observed in switchgrass. We propose bacterial taxa uniquely associated with common bean plants during the short-term drought, which could be further evaluated to determine any plant benefit during drought.

Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome

“…Members of Thermoproteota were among the most abundant ZOTUs so associations with the relatively rarer Mucoromycotina may exist but were not detected in the sparcc analysis. Future work would also benefit from the inclusion of non-plant controls to disentangle plant-specific microbiome responses distinct from responses of the soil microbiome alone to drought (Bandopadhyay et al, 2023).…”

“…Interestingly, while some compounds such as urea, arbutin, L-proline, and D-gluconic acid were only detected in the mild and severe drought treatment root exudates (Ulrich et al, 2022), no correlations between these compounds and shifts in the microbial community composition were detected here. As suggested by Bandopadhyay et al (2023), perennial grass species may not be as reliant on stress signaling to microbes via root exudation due to their relatively greater investment in belowground root architecture compared to many annual plant species. Another possibility, as suggested by Karlowsky et al (2018), is that root exudation during drought may be more important for the reinitiation of soil microbial activity following rewetting of the system.…”