The role of elevation and time in structuring soil microbial communities in the Sierra Nevada, California
Biogeographic patterns and community responses to climate change can be assessed using elevational gradients, which function as space-for-time substitutions. While surveys across multiple elevations have frequently been used to determine climate and other environmental controls on aboveground (e.g., plant and animal) communities, only recently have soil microbial communities been investigated in the same way. As a result, our ability to generalize and predict trends in microbial structure (composition and diversity) across elevational gradients - and to infer the mechanisms that shape elevational biogeographic patterns over time - remains limited. In order to determine spatial and temporal patterns of soil bacterial and archaeal community structure in the Sierra Nevada, California, we sampled soil from three elevations (varying from 400 m to 2000 m) along the Southern Sierra Critical Zone Observatory. Ten replicate soil cores (0-15 cm depth) were taken from each site in April, June, and July 2014 using a sterile soil auger. Microbial DNA was extracted from the soils, amplified for the V3 – V4 region of the 16S ribosomal RNA gene, and subsequently sequenced on the Illumina MiSeq platform.
Principal coordinates analysis (PCoA) of the UniFrac metric illustrated clustering of soil communities by elevation, which was confirmed using perMANOVA (Pseudo-F = 12.8; P-value < 0.001). However, alpha diversity, as indicated by the number of observed OTUs, Faith’s phylogenetic diversity, and Chao1 richness estimator, did not vary systematically across space or time. Within a given site, community composition remained relatively stable over time, indicating that elevation was a stronger determinant of microbial community structure than sampling date. Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Verrucomicrobia, and Chloroflexi tended to predominate across all samples, although the relative abundances varied. Notably, soils from the middle elevation site (Soaproot) had a relatively high abundance of Chloroflexi compared to the lower (SJER) and upper (Providence) sites during June and July. In addition, Planctomycetes were consistently more abundant at the lower elevation site than the other two sites. These results demonstrate that soil microbial community richness is consistent across space and time, while community composition varies with elevation. Continuing research will investigate the potential driving mechanisms, in addition to the functional importance, of these trends within the Sierra Nevada.