Sóley Ruth Islin:
Mining hot springs for biodiversity and novel enzymes

Date: 09-08-2016    Supervisor: Xu Peng

The existence of microbial life at extreme environments, such as hot springs, has been known for a few decades. The remarkable ability of microorganisms to withstand the extreme conditions of their habitats, has astounded scientist and pushed the limits of what was considered possible. Thermophilic organisms have proven to be a great source of novel enzymes that are valuable in a variety of industrial processes. We set out to search for novel thermophilic hydrolytic enzymes by taking samples from thermal environments around the world. We employed several different methods in achieving this, both culture-dependent as well as culture-independent methods.

Each hot spring sample was enriched on various polymeric substrates at high temperatures in the search of thermophilic microorganism with the ability to degrade the substrate. Enzymatic activity of the cultures was confirmed, the most promising ones were sequenced and available for in silico screening. A search for novel viruses from cultures grown in rich medium was also performed and several novel virus like particles were observed. Total genomic DNA was extracted directly from a few environmental samples allowing us to assess the biodiversity within the environment. By comparing several metagenomic data sets from hot spring from around the world, we could analyze community structures of cellular microorganisms as well as the biodiversity of viral sequences. We found that crenarchaeal viruses are dominant in these environments and that several crenarchaeal families were present in all samples. We discovered several novel viral genomes allowing us to do comparative genomics with known viruses, not previously possible. Because each metagenome contained both cellular and viral sequences we were able to direct link viral genomes to their hosts, based on the CRISPR sequences within the metagenomes.

Such metagenomic data contains incredible wealth of information and can be used to answer several questions. We found several homologs to the only known crenarchaeal viral DNA polymerase based on sequence similarity using BLASTp. The polymerase activity of one of the homologs was confirmed and could have potential use in applications that require e.g. amplification of large DNA fragments.

Another gene was found tandemly repeated, with high sequence variability and conserved intergenic regions, on several contigs in the metagenomes. We speculate on the function of the protein and hypothesize a bifunctional role.