Project: Discovering pathways for organic matter breakdown in deep subsurface sediments using detailed gene homologue analysis of metagenomes

Heterotrophy supports much of the energy-starved life in the deep biosphere, yet we know almost nothing about the pathways by which organic matter (OM) is remineralized in the deep subseafloor. The microbes responsible for OM breakdown in the subsurface are taxonomically diverse, but their lack of resemblance to well-characterized lab cultures makes it impossible to use taxonomy alone to predict the nature of their interactions with OM. Even when metagenomes or metatranscriptomes are available to provide functional information, common analysis tools only categorize annotated genes into general classes that do not distinguish between degradative, synthetic, or housekeeping processes. We propose to develop detailed gene homologue analyses to unlock hidden details about OM degradation pathways in subsurface metagenomes from a range of OM types and amounts in the Peru Margin deep biosphere. This will allow us to describe the intricate landscape of biological remineralization of OM in the marine subsurface. Finally, we will develop an open-source software tool that replicates our analysis methods (freely available to the community via web-interface or as source code from a public repository such as GitHub) to allow other researchers to perform this analysis automatically.

Reference:

Lloyd, K.G., Schreiber, L., Petersen, D.G., Kjeldsen, K.U., Lever, M.A., Steen, A.D., Stepanauskas, R., Richter, M., Kleindienst, S., Lenk, S., Schramm, A., Jørgensen, B.B. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature 496, 215–218. C-DEBI Contribution 177. Publisher’s Link