Phylum-targeted pyrosequencing reveals diverse planctomycete populations in a eutrophic lake

Although populations of planctomycete bacteria are nearly ubiquitous in aquatic habitats, we lack a detailed understanding of their diversity and structure. This is due to difficulty in obtaining cultured representatives, but also to low recovery rates for planctomycete 16S rRNA genes when universal PCR primers are employed for sequencing studies. In an attempt to expand re coverable planctomycete diversity, we investigated the use of primers targeting the Planctomycetes phylum. Planctomycete populations present during an algal bloom in a eutrophic lake were characterized by clone library sequencing and pyrosequencing of 16S rRNA genes, using planctomycete-targeted primers. We analyzed samples recovered from the sediment, water column, and algal mats within the lake's littoral zone. Sequences related to 9 planctomycete genera were identified within the 6287 planctomycete sequences and 1730 operational taxonomic units (OTUs) recovered. We observed variation in the specificity of the planctomycete primers, with more non-planctomycete sequences recovered through pyrosequencing than through cloning-based sequencing. Nevertheless, the results of our study suggest that phylum-targeted pyrosequencing is a useful tool for better describing the diversity of bacterial sub-populations. This methodology could be employed for future testing of hypotheses regarding spatial and temporal differences in planctomycete diversity and abundance. Candidate hypotheses arising from this preliminary study include (1) members of certain planctomycete genera (particularly Rhodopirellula) are enriched in algal mats relative to other planctomycete genera; (2) sediments harbor the most diverse planctomycete populations; and (3) most planctomycete OTUs are not shared between lake habitats.