findings of other studies of plant (Allen et al., 2002; Hawkins et al., 2003; Currie et al., 2004) and microbial (Fierer and Jackson, 2006) diversity.
It is well documented that the scale over which biodiversity is sampled will strongly influence observed patterns. For example, recent empirical studies have shown that decreasing the spatial grain at which organisms are sampled shifts their diversity patterns (Rahbek, 2005; Cavender-Bares et al., 2006; Slingsby and Verboom, 2006; Swenson et al., 2006, 2007). Although the spatial extent of our study was the same for bacteria and plants, the grain of our sample observations was different between these two groups. The spatial scales over which bacteria interact with each other are likely to be several orders of magnitude smaller than the scale at which they were sampled. Therefore, relative to plants, bacteria were likely sampled at a coarser grain, and thus we may have included a greater amount of environmental heterogeneity within a bacterial sample. Sampling bacteria at a spatial scale that more closely approaches the “ecologically equivalent” grain of plants may result in convergent biodiversity patterns between these two groups.
Taxonomic scale also influences biodiversity patterns. For example, taxonomic breadth, which defines how broadly or narrowly a target community is defined from a phylogenetic perspective (e.g., bacteria versus Acidobacteria), can shift the degree of observed overdispersion or clustering in that community (Swenson et al., 2006). Species are a natural taxonomic unit by which to measure plants (Mayr, 1942). Such an intuitive unit does not exist for prokaryotes. In this study we classified partial Acidobacteria 16S ribosomal DNA sequences into taxonomic units based on the commonly used 99% sequence similarity designation (see Materials and Methods). It is unknown how taxonomic resolution, defined as the threshold at which individuals are binned into taxonomic units, should influence phylogenetic patterns, although it has been shown to impact taxonomic patterns such as the taxa–area relationship (Horner-Devine et al., 2004b). We found that binning bacteria into increasingly broader taxonomic units (i.e., 97%, 94%, and 90% sequence similarity) tended to dampen the strength of all observed elevational diversity patterns. However, general trends did not qualitatively change (Figs. 7.4–7.6), suggesting that taxonomic resolution is not the cause of disparate bacterial and plant biodiversity patterns in this study. Alternative approaches to defining bacterial taxonomic units such as “ecotypes” (Cohan and Perry, 2007) could significantly change the results and lead to plant and microbial diversity patterns that more resemble one another.
Differences in the approach to building the Acidobacteria and angiosperm phylogenetic trees should also be considered when comparing phylogenetic patterns between these two groups. The Acidobacteria phylogeny was estimated solely from molecular data identified in this study, whereas