Analysis of combined prokaryotic and eukaryotic microbial communities in a geothermal biological soil crust through bar-coded pyrosequencing

Background/Question/Methods

Soils hold microbial communities that are among the most species-rich and diverse of any habitat, but the drivers of the inherent heterogeneity of these communities are not fully understood.  High-throughput DNA sequencing has dramatically improved our ability to generate microbial community data, and analysis methods have improved to deal with these advances.  Bar-coded pyrosequencing is an effective method for surveying microbial communities, and this is often performed with short 16S rDNA sequences from the prokaryotic component.  Eukaryotic communities can be effectively sequenced using 18S ribosomal regions, though this has been performed much less often.  We present analysis of the combination of these two dataset types from a diatomaceous geothermal biological soil crust in Yellowstone National Park, WY, USA.  Samples were taken from the epipedon of two different soil types, and across a photic depth gradient. Aspects of rarefaction and beta-diversity assessments are emphasized.  

Results/Conclusions

Microbial communities were significantly different between soil types and along a photic depth gradient, consistent with visible color banding in the surface layers of soil.  Several ecologically-important prokaryotic groups, such as Cyanobacteria, Planctomycetes, and Verrucomicrobia, differed strongly with both gradients, but the dominant eukaryotic group, diatoms, showed more nuanced partitioning.  From an analysis standpoint, results depended on relative rarefaction of 16S and 18S sequences, though surprisingly few sequences per sample were needed to effectively detect beta-diversity patterns. Our analysis is unique in that we were able to capture both major components of the soil microbial community in a single analysis.