UC San Diego
Metagenomic Characterization of a Hypersaline Microbial Ecosystem /
- Author(s): Ugalde, Juan A.
- et al.
The use of metagenomic approximations to study natural microbial communities has allowed us to understand the phylogenetic and functional composition of these communities. Gene fragments, derived from the sequence reads, can be phylogenetically classified by binning methods, and compared against reference databases for functional assignments. However, these classifications are limited by the availability of reference genomes in the databases. One way to overcome such limitations, is through the use of assembly-based metagenomics, where the de novo sequence assembly, which does not rely on external reference sequences, can allow us to identify novel organisms that are present in the community. The work presented here, shows the results of the assembly-based metagenomic characterization of a hypersaline microbial community, from Lake Tyrrell, Australia. The main objective was the reconstruction of the most abundant members of this microbial community using the sequence information, and generate a set of habitat-specific genomes that can be used for future studies. The assembly and characterization of this metagenomic dataset allowed the discovery of a novel archaeal Class, the Nanohaloarchaea (Chapter 2), an ubiquitous lineage late found to be present in other hypersaline environments. The work on the Nanohaloarchaea, led to the discovery a novel type of rhodopsin protein, Xenorhodopsins (Chapter 3), that is present on the genomes of members of this group. Phylogenetic analysis indicates that this new rhodopsin has been horizontally transferred between Bacteria and Archaea. The complete assembly analysis of the metagenome dataset, allowed the description of the most abundante members present in this microbial community (Chapter 4), allowing estimations of relative abundance, phylogenetic and functional diversity. With the availability of habitat -specific genomes, it is possible to study not only the phylogenetic and functional diversity, but also the fine- scale genetic diversity of the members of the community. Deep sampling of four samples from the Lake Tyrrell microbial community, using high-throughput sequencing, and the availability of habitat-specific genomes allowed the characterization of this genetic diversity (Chapter 5). This information was used to compare the genetic diversity between populations, and identify signatures of environmental adaptation at the sequence level