Week 8 - Sulfur oxidation?

This week I have been trying to identify the potential for sulfur oxidation within the community. Because I did not find either soxA or soxB genes (Week 7), I began my research on the sox-independent pathway of sulfur oxidation. A key enzyme in this pathways is APS reductase which catalyzes the conversion of APS --> AMP + sulfite. The gene, aprA, which encodes APS reductase was used to screen the metagenome. Assembly of the homologous sequences found, yielded five high quality contigs representing 5319 sequences in the metagenome. This was quite a surprise, because the potential for sulfur-oxidation within these caves is supposed to be nonexistent due to a lack of abundant substrate. This finding led me to build a phylogenetic tree to learn about the phylogenetic placement of the aprA genes in Warren Cave to aprA genes found elsewhere. The tree included cultured representatives from all clades of proteobacteria, sulfur-oxidizing archaeal species, and uncultured prokaryotes. Phylogenetic analysis revealed that ~79% of the sequences were most closely related to archaeal species, ~13% to gamma/beta-proteobacteria, and the remaining ~8% to alpha-proteobacteria. These results were also quite surprising since no archaeal species were found within Warren Cave. The similarity of archaeal aprA genes to aprA genes in the metagenome could be to instances of lateral gene transfer, where an Archaea transferred genetic material to a bacterium in Warren Cave through a variety of mechanisms (e.g. gene transfer agents, transformation).

With only two weeks left, a few interns had their final presentations today and it looks like most of the projects are wrapping up. Over the past eight weeks I have really become fascinated with the field of metagenomics and the use of bioinformatics to solve otherwise unanswerable questions pertaining to microbial ecology. I have really had an invaluable experience at CMOP so far and am so greatful for this opportunity.