Dataset: Middle Valley Chimney 16S Sequencing Data

Data Processing: DNA samples were sequenced using 454 pyrotag methods similar to those described previously (Dowd et al. 2008). All samples were sequenced at the Research and Testing Laboratory (Lubbock, TX) using a 454FLX instrument (Roche Inc.) with Titanium™ reagents. The resulting bacterial and archaeal 16S rRNA (bacterial V1-V3 and archaeal V3-V4 of the 16S rRNA genes; primers are shown in Table 1) as well as drsB sequences were analyzed via Mothur (Schloss et al. 2009). Sequences were trimmed, quality checked, aligned to the SILVA-compatible alignment database reference alignment (dsrB gene datasets were aligned to a dsrB gene database generated from the Ribosomal Database Project (RDP)), analyzed for chimeras, classified against the Greengenes99 database and clustered in to OTUs. Rarefaction curves were used to examine the number of OTUs as a function of sampling depth. Alpha diversity was assessed by generating values from the Chao1 richness estimators and the inverse Simpson diversity index.