Ancestors in the Extreme: A Genomics View of Microbial Diversity in Hypersaline Aquatic Environments.

Abstract

The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.