Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla

Comparison of the rhizosphere and bulk soil microbial communities showed significantly higher species richness in the former than in the latter, although these differences were not sig- nificant at site level. In addition, there were slightly different species composition per sample type/microhabitat. Our PCoA ordination revealed clusters by sites, with sub-clusters by micro- habitat suggesting that rhizosphere microbial communities are distinct from those of the bulk soil at all geologies. These results are not surprising since the micro-conditions of the rhizo- sphere are distinct from those of the soil. For instance, rhizosphere holds higher nutrients and water levels than the soil [33], which probably allows different bacterial and archaeal species to colonize. Indeed, we found taxa characterized by being nodulating nitrogen-fixing bacteria in significant abundance in rhizosphere compared to soils. Differences in composition and abun- dance between rhizosphere and bulk soil communities was also found in arctic soils [34]. Most bulk soils are more diverse than rhizosphere but this is likely true in nutrient-replete soils, compared to tropical soils where frequent rainfall may leach nutrients away; indeed, drier sites had higher bulk soil diversity while sites of high elevation had more diverse rhizospheres. We hypothesized that environmental interactions could modify rhizosphere microbes and their functions, which in turn would have an impact in the plant’s phenotype. Indeed, we found that the most distinct microbiomes, as shown in the beta diversity plots, were from low

altitude karst which had very high mean annual temperature and low precipitation; these cor- respond to the shortest trees, with markedly different leaf morphology. Seminal evidence from other studies suggests that microbiomes alter plant phenotypic plasticity in a broad range of traits [35] and common garden experiments also suggest a role of plant genotypes shaping its microbiota and the microbes in turn participate in the development of plant phenotypes [36]. To test the hypothesis that climate will alter the rhizosphere microbial communities, we focused on two sites of the same geology but with the most contrasting climatic conditions. Serpentine sites (S3 and S4 Figs), which had a difference in the mean annual temperature of 2.2˚C and 1041 mm of rain, had significantly higher rhizosphere diversity between both sites and compared to other sites. However, their microbial community compositions aren’t nota- bly different from each other, except for the greater abundance of Chloracidobacteria and Betaproteobacteria in the high elevation site. These differences in the microbial communities can be ascribed to differences in the environmental conditions at the different altitudes, emphasizing the importance of variables such precipitation and temperature, as previously shown in other geographical studies [37, 38]. Indeed, studies have observed greater environ- mental fluctuations in low altitude sites, whereas high altitude sites have normally lower tem- perature, nutrient, and water availability [39–41]. Indeed a recent study found selective

proliferation of Gram negative bacteria at high altitude, including psychrophilic diazotrophs, along with a decrease in Gram positive bacteria [41], however these studies were done at signif- icantly higher altitudes than those assessed in this manuscript. For the hypothesis that geology will alter the microbial community in the rhizosphere, hav- ing an indirect effect over the phenotype, we chose sites with similar climatic conditions but originating from different parental material. Sites 2 (volcanic) and 6 (karst) possess a differ- ence of only 0.6˚C and 203.5mm of rain (Table 1), and differ significantly in their diversity lev- els, as well as in their microbial community composition. These results suggest that geology may have a greater effect on the microbial community composition of the rhizosphere as well as on the leaf phenology/phenotype, than other environmental factors. Changes in microbial community composition across sites were related to temperature, precipitation, pH, and geology. The highest diversity was observed in the serpentine samples, which possess ~neutral pH and temperatures near 24˚C. This diversity peak is consistent with a previous study of geothermal environments, where the highest diversity was also observed in samples collected at pH 7 with temperatures of 24˚C [42]. As in their study, we also found that PLOS ONE Rhizobiota of the tropical tree Tabebuia heterophylla PLOS ONE | https://doi.org/10.1371/journal.pone.0231083 April 7, 2020 11 / 16