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Week 2 - Methanotrophes and NSF site visit fun

My second week at CMOP has largely been an interest-driven, rather than project-focused week. Because I am still patiently awaiting the Mt. Erebus metagenomic sequences to arrive, I have continued work on the hydrothermal vent data trying to learn more about the metabolic potential of microbes in deep-sea hydrothermal environments. I began my week searching through the literature to learn about the metabolic pathways involved in methane oxidation as well as the principal genes involved. I was interested in methanotrophy because of the importance of methane as a greenhouse gas, in global carbon and methane cycles, and its use in bioremediation.

Methanotrophic bacteria are extremely interesting! They are able to derive energy from methane by using the enzyme methane monooxygenase (MMO) to oxidize methane to methanol. Methane monooxygenase is present in two forms, a particulate (pMMO) and soluble form (sMMO), of which the particulate form is present in all known methanotrophes and the soluble form only present in some groups (Semrau et al. 1995). pMMO has been annotated in a gene cluster of three subunits (pmoCAB) in many bacterial species (Stolyar et al. 1999) and provided the basis for my research on the IMG database for potentially homologous genes. Upon compiling a database of known methanotrophic bacteria containing annotated pmoA genes, I used the same method as last week to identify and extract homologous sequences in the metagenomic database. The hydrothermal vent metagenome produced a considerable amount of "hits" to many well-known methanotrophs and enzyme/proteins involved in methane oxidation, and high similarity to the pmoA gene sequence.

Thursday was the 2012 NSF site visit, where CMOP was evaluated on their progress and future goals by three members of the NSF staff and a site review team of five scientists from universities around the country. Myself and the other interns watched the presentations remotely via webcam and had the opportunity to have lunch with the site visit team. Although it was a long day of presentations, it was great to learn more about the type of research that goes in other labs and how it relates to the goals of CMOP. What really struck me was how diverse the research is at CMOP, while staying relevant to issues relating to the management of the Columbia River. It was great to hear presenters discuss how their science is actually being used by management people and native tribes to make more informed decisions about this shared resource.

Semrau, JD (1995) Particulate methane monooxygenase genes in methanotrophs. Journal of bacteriology 177: 3071.

Stolyar, S (1999) Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath. Microbiology 145:1235.