Influence of molecular resolution on sequence-based discovery of ecological diversity among Synechococcus populations in an alkaline siliceous hot spring microbial mat
Melendrez MC, Lange RK, Cohan FM, Ward DM. 2011. Influence of molecular resolution on sequence-based discovery of ecological diversity among Synechococcus populations in an alkaline siliceous hot spring microbial mat. Applied and Environmental Microbiology. 77(4):1359-1367
Previous research has shown that sequences of 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions may not have enough genetic resolution to define all 30 ecologically distinct Synechococcus populations (ecotypes) inhabiting alkaline, siliceous hot spring microbial mats. To achieve higher molecular resolution, we studied sequence variation in three protein-encoding loci sampled by PCR from 60°C and 65°C sites in the Mushroom Spring mat (Yellowstone National Park, WY). Sequences were analyzed using the Ecotype Simulation (ES) and AdaptML algorithms to identify putative ecotypes. Between 4 and 14 times more 35 putative ecotypes were predicted from variation in protein-encoding loci than from variation in 16S rRNA and 16S-23S rRNA internal transcribed spacer sequences. The number of putative ecotypes predicted depended on the number of sequences sampled and the molecular resolution of the locus. Chao estimates of diversity indicated that few rare ecotypes were missed. Many ecotypes hypothesized by sequence analyses were different in their habitat specificities, 40 suggesting different adaptations to temperature or other parameters that vary along the flow channel.
- Type
- Journal Article
- Authors
- Melendrez, Melanie; Lange, Rachel; Cohan, Frederick; Ward, David
- Units
- YELL
- Keywords
- Bacteria, Hot Springs