In the past decade, knowledge of microbial diversity of heat ecosystems has expanded substantially. This increased knowledge is essentially thanks to the appliance of molecular phylogenetic techniques to microbial ecology, especially the analysis of phylogenetically informative macromolecules like small subunit rDNA (16S rDNA) genes. For example, analysis of the archaeal and bacterial diversity of Obsidian Pool, Yellowstone park (YNP), yielded a plethora of novel sequence types (‘phylotypes’), which substantially expanded the crenarchaeal and bacterial 16S rDNA sequence database and led to the proposal of a 3rd kingdom within the archaeal domain. Similarly, the phylogenetic diversity of the conspicuous pink filamentous community associated with the outflow of Octopus Pool, YNP was determined. This organism had intrigued researchers for many years, and attempts by independent researchers to enrich for this organism were unsuccessful. Phylogenetic analysis of the pink filamentous organism (EM17) revealed it to be an in depth relative of the organisms in culture, Aquifex pyrophilus and Hydrogenobacter thermophilus, and it had been identified in situ using fluorescent oligonucleotide probes (FISH). Thermocrinis ruber, an in depth relative of EM17 (98.7%), subsequently was isolated from Octopus Spring. Additionally, studies of white and yellow filamentous sulfur mats in Icelandic and Japanese thermal springs detected several phylotypes within the Aquificales that were closely related to organisms detected in YNP geothermal springs.  

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