Aguado-Norese, C. | bioRxiv Science

bioRxiv2025

The rhizosphere of Pappostipa frigida as a hotspot of active bacterial communities in the Andean steppe of the Atacama Desert

BackgroundThe rhizosphere is a resource-rich microenvironment where plants, soil nutrients, and microorganisms interact. In arid and semi-arid regions, this tripartite relationship must withstand long periods of drought followed by brief periods of rainfall. In the present study, we employed a combination of RNA/DNA metabarcoding and shotgun metagenomic sequencing to provide insights into the functional capabilities and activity levels of the bacterial communities present in the bulk soil and rhizosphere samples of Pappostipa frigida, a grass species endemic to the Andean steppe of the Atacama Desert. ResultsThe active bacterial community in the rhizosphere of P. frigida exhibited greater diversity and a higher Shannon index than the total bacterial community. In terms of beta diversity, the structures of the total and active communities differed markedly between the BS and the RZ. Furthermore, active bacteria in the RZ showed a stronger correlation with total bacterial populations than those in the BS. This finding is consistent with the low proportion of ASVs derived from RNA extractions detected in the BS. Notably, 64% of these putative inactive bacterial populations were identified as active RZ members and 73% grew in culture media, suggesting they were likely dormant. The bacterial communities of the BS exhibited higher abundances of sporulation genes. In contrast, active bacterial communities in the RZ consistently contained higher abundances of genes associated with halotolerance, siderophore synthesis, and resuscitation-promoting factors. ConclusionsThe results emphasize the importance of the conditions created by plants in recruiting bacterial populations from the soil and provide insights into how the rhizosphere of arid native plants influences the activity and functional traits of soil microorganisms in their natural habitat. Additionally, this study advances our understanding of the mechanisms employed by soil microorganisms to cope with desiccation in natural environments, establishing P. frigida as a model in plant science for studying grass traits and responses to extreme environments.

microbiology↗

bioRxiv2023

Convergent and divergent responses of the rhizosphere chemistry and bacterial communities to a stress gradient in the Atacama Desert.

Plants can modulate their rhizosphere chemistry, thereby influencing microbe communities. Although our understanding of rhizosphere chemistry is growing, knowledge of its responses to abiotic constraints is limited, especially in realistic ecological contexts. Here, we combined predictive metabolomics with bacterial sequencing data to investigate whether rhizosphere chemistry responded to environmental constraints and shaped bacterial communities across an elevation gradient in the Atacama Desert. We found that metabolic adjustments of rhizosphere chemistry predicted the environment of four plant species independently of year, identifying important rhizosphere metabolic biomarkers. Inter-species predictions unveiled significant biochemical convergences. Subsequently, we linked metabolic predictors to variation in the abundance of operational taxonomic units (OTUs). Chemical response influenced distinct and common bacterial families between species and vegetation belts. The annotation of chemical markers and correlated bacterial families highlighted critical biological processes such as nitrogen starvation, metal pollution and plant development and defence. Overall, this study demonstrates a unique metabolic set likely involved in improving plant resilience to harsh edaphic conditions. Besides, the results emphasise the need to integrate ecology with plant metabolome and microbiome approaches to explore plant-soil interactions and better predict their responses to climate change and consequences for ecosystem dynamics.

ecology↗