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Week 1 - Having a BLAST

WOW! How do I even begin to summarize one full week of CMOP-interning into one blog entry!?

Well…my first week at CMOP has had its fair share of obstacles but has been rewarding nonetheless. On day one I became completely CMOP-oriented along with several other interns and finally had the opportunity to meet my frontline mentor, Rick Davis. Rick brought me up to speed on some of the particulars of my project and left me with some literature to parse through for the rest of the day. I quickly started to delve deeper into this new and exciting world of research. My project, which is entitled "The Microbial Diversity of Dark Antarctic Ice Caves," will be focused on constructing a metagenomic database from ice cave samples taken from Mt. Erebus (Antarctica) on a previous field trip by Rick and other members of the Tebo Lab. Specifically, I will (1) construct a database of potential chemoautotrophic metabolic pathways (e.g., carbon and nitrogen fixation) and (2) query the metagenomic database to learn about the metabolic potential of microbial communities within these caves.

This week, however, my project was pulled a slightly different direction because the Mt. Erebus ice cave samples were still awaiting sequencing. So…I began constructing a library of carbon monoxide metabolic genes from known carbon monoxide oxidizing bacteria (using the Integrated Microbial Genomes database, IMG) and used it to query metagenomic samples collected from a hydrothermal vent near the Hawaiian Islands on a previous research cruise. I hoped to identify how significant carbon monoxide (CO) metabolism is to these systems and the relative phylogenetic placement of the metagenomic samples to described CO-oxidizing species. Upon reading a review on aerobic CO-oxidizing bacteria by King and Weber (2007), I learned that there are significant gaps in the scientific knowledge of the diversity of organisms that utilize CO for growth, even though CO is a ubiquitous chemical in many biotic and abiotic processes. Because there is currently a lack of knowledge on this subject, I really felt my research might uncover new insights into how diverse CO-oxidation is in the microbial world. 

After a long week of toiling through the arduous process of building the CO-metabolism IMG database, identifying and extracting the potentially homologous sequences in the metagenomic database, and constructing contiguous reference sequences from the fragments, I was able to identify a sequence in the database with strong correlations to well described CO-oxidizing bacteria using a BLASTx search (Basic Local Alignment Search Tool; Because many of the bacteria isolated from the hydrothermal vents are either unculturable through modern methods or have never had there complete genomes sequenced, the metagenomic sequences identified and the matches found in the BLAST search likely have very loose phylogenetic ties...

Thus far, my project relates to the broader CMOP/EBS research goals in that, in order to gain a more complete understanding of the biotic and abiotic processes mediating global biogeochemical nutrient cycling, it will be necessary to identify what organisms are potential sinks and sources of nutrients important for human, ecosystem, and global atmospheric health. Because microbes are often the foundation and most basal members of the food chain, they are instrumental in global biogeochemical cycling. A more comprehensive understanding of the metabolic potential of microbes found in deep sea hydrothermal systems as well as in fumarolic ice caves will provide insights into the nutrient cycling in dark oligotrophic, deep subsurface environments.

King GM, Carolyn WF (2007) Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nature Reviews Microbiology 5: 107-18