Comparative genomic analyses of Yellowstone hot spring microbial mat Synechococcus spp.

Abstract

The question of "What is a microbial species?" has been a highly debated issue in the field of microbiology. Many have accepted a molecular species demarcation approach, that any two organisms with a high enough 16S rRNA sequence similarity are members of the same species. However, the Ward lab has shown that there are many ecologically distinct Synechococcus spp. inhabiting hot springs of the Lower Geyser Basin in Yellowstone National Park, WY, that would be defined as members of the same species using the molecular demarcation approach. Using a theory-based species demarcation approach with a conserved photosystem gene (psaA), evidence of the existence of putative ecotypes, or predicted ecologically distinct species, has been found in the microbial mat, distributed along both temperature and light gradients. Isolates representative of these ecologically distinct populations have also been shown to have distinct temperature adaptations and light adaptations. I obtained the genomes of these isolates, which include representatives of populations with different temperature distributions and different vertical distributions, and replicate isolates within individual putative ecotypes. Using these genome sequences, I compared the psaA gene phylogeny and multi-locus sequence phylogenies with a phylogeny created using genes shared among the genomes to explore the effects of recombination on phylogenies of closely-related organisms. I then explored the underlying genetic mechanisms of the niche adaptations of these ecotypes by (i) comparing the isolate gene content, diel transcription patterns, and positive selection evidence of putative ecotypes with different vertical distributions in the mat and different light adaptations, (ii) comparing the gene content and evidence of positive selection among isolates representative of populations with different temperature distributions, and (iii) comparing the gene content and evidence of positive selection among replicate isolates within individual putative ecotypes. I found that, while recombination may have caused the inaccurate demarcation of genetically distinct isolates into a single PE, there is genomic evidence that species of Synechococcus that are ecologically distinct from one another exist, along both temperature and vertical gradients. Members of a species are ecologically homogenous, though there is evidence of some genetic heterogeneity within a species.