OLI Grant: Studies of Gene Expression and Identification of Active Members of Hydrothermal Vent Microbial Communities: Instrument Development for In Situ Preservation of RNA in Deep-Sea Sediment Samples

Stefan Sievert, Biology Department

Grant Funded: 2003

Proposed Research

Abstract
Present day molecular studies of the ecology and diversity of prokaryotic and eukaryotic microorganisms in the marine environment have heavily emphasized approaches based upon quantification and sequencing of DNA. Though DNA can provide information on the presence and diversity of microorganisms in the environment, one is not able to infer activity or even viability of the population. RNA, on the other hand, can overcome this limitation by virtue of the fact that it represents actively transcribed genes in organisms that are responding to changing environmental conditions. Only actively growing cells maintain messenger RNA (mRNA) and ribosome copy numbers at detectable levels. RNA-based approaches provide insights into metabolic interactions between microbial groups and the environmental factors that affect microbial activity. A major challenge for rRNA based community analyses and for studies looking at gene expression based on mRNA is the rapid degradation of rRNA and especially mRNA once the cells become inactive or die. In addition, assessment of microbial community composition and the activity of specific groups can be dramatically affected when samples are removed from their natural habitat. The remoteness of the deep ocean and the length of time between sampling and retrieval greatly exacerbate this problem. We propose work towards the design of a device that will permit the rapid in situ preservation of RNA in deep ocean sediment cores. Rapidly preserved samples will significantly advance our ability to understand the microbial ecology of remote environments and in particular the active functional microbial groups by making possible the analyses of mRNA as an indicator of gene expression.