Microbial Signatures of Two Marine Subsurface Sites in the Same Geographic Region (Eastern Equatorial Pacific)

Drilling expeditions from which marine subsurface sediment samples are obtained are extremely expensive, and thus, it is not possible to sample every location of the ocean floor extensively. As a result, estimations of the contribution of subsurface microbial communities in geochemical cycles and nutrient reservoirs are based on generalizations, which assume that subsurface microbial communities in close proximity are similar as long as there are not major chemical or physical differences in the environments. However, to date, there has been no study comparing the microbial communities in two or more highly similar and geographically close drill cores. In this study, we were fortunate to have obtained samples from two locations within the Eastern Equatorial Pacific, at sites which were both geographically close, and geochemically and lithologically very similar. Using samples from three depths at both of these sites, we are performing a molecular comparison of the microbial communities using next generation metagenomic sequencing. This comparison encompasses both phylogenetic and functional properties. In addition to the comparison between sites, we are also employing a methodology duplicate with one sample, which has rarely been done with metagenomic studies. Finally, we are also exploring the effects of whole genome amplification (WGA) on sequence analysis of extracted DNA samples, via the use of multiple WGA methods on aliquots of the same sample, with an unamplified control as a reference. Preliminary data from the first sample sequenced shows the over-amplification of archaea—particularly Thaumarchaeota—after amplification using multiple displacement amplification, as compared with the unamplified control.