Depth-dependent loss of microbiome diversity and Firmicutes compositional shift induced by ureolytic biostimulation in Aridisols

Abstract

Soil microbiomes regulate biogeochemical cycles and fulfill essential ecosystem functions, particularly in arid environments. One beneficial function of various edaphic microbes is the ability to participate in the precipitation of calcium carbonate. Microbial Induced Calcite Precipitation (MICP) is a biomineralization process that has been extensively investigated as a soil improvement technique for various purposes, including mitigating drought-related soil degradation and controlling erosion. One aspect seldom addressed in MICP studies is the microbial heterogeneity of the ecosystem in which it is applied and its post-treatment consequences. In this study, we examined MICP biostimulation rates in an Aridisol, considering the microbial heterogeneity across different soil depths relevant to surface reinforcement applications (from the topsoil to 1 m below the surface). Biostimulation was achieved by inducing ureolysis, one of the most studied metabolic pathways to stimulate MICP. We characterized the native microbial communities and their response to biostimulation across the depths under consideration using 16S sequencing. We found that ureolysis rates were affected by soil depth, with higher rates detected in the topsoil. Before biostimulation, the native soils were dominated by Actinobacteria and contained diverse communities. The microbial communities of the deeper soil layers were richer in Firmicutes, and the deepest layer was less diverse than the topsoil. Following biostimulation, alpha-diversity and microbial richness were drastically reduced at all depths, resulting in homogenized communities dominated by Firmicutes, although microbial DNA concentrations increased. A notable decrease was detected in autotrophs (e.g., Cyanobacteria, Chloroflexi), which are important for the formation and function of biocrusts and, hence, to the entire ecosystem. We also found that biostimulation led to a shift in the composition of the Firmicutes phylum, where specific members of the Planococcaceae family became the most prevalent Firmicutes, replacing Paenibacillaceae and Bacillaceae as the dominant families. Our findings demonstrate that environmental heterogeneity across soil depth is an influential variable affecting ureolytic biostimulation. In turn, biostimulation affects microbial diversity consistently, regardless of preexisting differences resulting from spatial heterogeneity. Although feasible, implementing biostimulated MICP in arid environments induces a strong selective pressure with negative consequences for the native edaphic microbiomes.