Testing of a Downhole Sampler Incubator (DSI) for the Uncontaminated and Exogenous DNA-Free Sampling of Crustal Fluids from Deep-Sea Bore Holes

Craig Taylor, Biology

DOEI Project Funded: 2004

Proposed Research

What are the primary questions you are trying to address with this research?
The object of this project is to test a non-contaminating microbial sampling apparatus being developed under NSF SGER funding, a Downhole Sampler / Incubator (DSI), for sampling subsurface hydrothermal fluids accessed via Ocean Drilling Program (ODP) boreholes.

What is the significance of this research for others working in this field of inquiry and for the broader scientific community?
The study of the ecology, diversity and function of microbes in the marine or subsurface biosphere requires the marriage between culture independent, molecular techniques of DNA

sequencing and manipulation to determine the important players and culture-dependent approaches to understand their physiology and functioning. In either case it is essential that samples be obtained that are free from cross-contamination by microbes and microbial DNA from locations other than the site of sampling.

When and where will this investigation be conducted?
This study will be conducted at the WHOI dock using an apparatus simulating the casing of an ODP borehole (see figure to the right) to prove that the newly developed DSI is able to obtain contamination free samples.

What are the key tools or instruments needed to conduct this research? The DSI and the apparatus illustrated in the figure. The Borehole Simulating Apparatus injects a microbial tracer into a flowing stream of filtered seawater (shaded area in pipe). The DSI is to be lowered through the water that is purposely “contaminated” with a tracer organism into the tracer organism-free region and a sample taken. Successful operation of the instrument will reveal “no” tracer organisms in the sample.What are the greatest challenges – physical or intellectual – to conducting this investigation?
The biggest challenge will be the design and construction of the DSI so that it will fit within the 4” ID casing of an ODP borehole. The DSI will need to possess an OD no greater than 3”, which will be a miniaturization engineering challenge. The objective of “this” project is a straightforward test of the ability of the DSI to obtain contamination-free samples, the results of which will serve as part of the technical foundation for acquiring funding for the study of sub-seafloor microbiology.

Is this research part of a larger project or program? A group of us [J.P. Cowen (U. Hawaii), F. Kenig (U. Illinois, Chicago), C.D. Taylor (WHOI) and S.J. Giovannoni (Oregon State U.)] had submitted a 5 yr. proposal to the Microbial Observatories and Microbial Interactions and Processes program at NSF entitled “Microbial metabolic activity, genetic and physiological diversity and biomass within aging (off axis) ocean crustal fluids: ODP Borehole Observatories” to study the microbes of this subsurface environment. A component of that proposal was development of the DSI for the in situ sampling of the deep borehole fluids to provide uncontaminated material for proposed microbial studies. Both the Panel and Reviewers praised the proposal as a “pioneer attempt to explore the biosphere present in the subseafloor.” However, they were also concerned that the success of the project rested too much on the successful development of novel sampling instrumentation capable of obtaining “contamination-free” samples of crustal fluids. Once the DSI is developed (NSF SGER) and tested (this project) we will have addressed reviewer concerns and will proceed with the Microbial Observatory project.

If you have conducted previous/similar work on this subject, please suggest any web links or citations that might help others better understand the background to your line of research. If appropriate and readily available, please suggest or provide photographs, illustrations, tables, and charts, as well. See attached photos.

Biographical information
Craig Taylor is an Associate Scientist in the Biology Department. He grew up on a wheat farm in N.E. Oregon where he acquired a fair share of the hands-on technical skills he uses today in the laboratory and during cruises. In a steady march eastward he acquired a Masters degree in Biology at Portland State University followed by a Masters and PhD in Microbiology at the University of Illinois; ultimately joining the Scientific Staff at WHOI via a postdoc in the laboratory Holger Jannasch. Throughout his career at WHOI he has maintained an interest in the microbiology of remote environments and the development of autonomous technologies for studying their in situ activity.