Chapter Three - Contamination Control for Scientific Drilling Operations
Introduction
Exploration of deep subsurface environments relies on drilling. Many different drilling techniques are being used, the choice is mainly based on the type of sediment or rock to be penetrated and the maximum depth that has to be reached. Almost all drilling operations require the use of a drill fluid for cooling the bit, transporting cuttings out of the borehole and stabilizing the well (Kallmeyer, Mangelsdorf, Cragg, Parkes, & Horsfield, 2006). The most simple drill fluid is water, but in many cases this is not sufficient and additional compounds have to be added, e.g., clay minerals to increase specific gravity of the fluid and/or thickeners of variable composition (natural compounds such as cellulose or guar gum or synthetic polymers).
As the drilling fluid travels from the surface down to the drill bit, it comes in contact with many surfaces (holding tank, pump, pipes, etc.) and will inevitably transport some surface material down into the borehole. From a geomicrobiological or biogeochemical perspective drilling is a very dirty business, even in relatively small drilling operations, it is impossible to maintain sterile conditions or avoid contamination of the drill core with foreign compounds such as hydrocarbons. A drill core is never completely pristine but will always have at least some contamination on the outside. A drilling rig and the associated drill rods very quickly add up to a total weight of many tons. The weight of the drill string varies significantly between different diameters and wall thicknesses, as a rule of thumb a 6 m piece of drill string for a deep drilling operation weighs between 100 and 150 kg, so a kilometer of string weighs 18–25 tons. Such huge amounts of equipment are much too large and heavy to be sterilized. Even if it were possible to sterilize an entire drill string of up to several kilometers length, it would be a futile exercise because as soon as the drill string enters the drill hole it will be immediately contaminated with microbes from the surrounding sediment or rock. Due to the fact that the drilling fluid is usually an opaque mixture of water and suspended particles that are larger than microbial cells, the fluid can neither be filter-sterilized nor UV treated. In cases where only small volumes of water without any additives can be used as a drill fluid, then presterilization is indeed an option. However, this option is limited to rather small operations. In normal sized drilling operations the massive volumes of drill fluid of up to hundreds of cubic meters and flow rates of hundreds of liters per minute preclude any sterilization. At best the drilling equipment is thoroughly cleaned before use to avoid contamination with foreign hydrocarbons from the pipe grease or other chemicals, and the drill mud is prepared with clean tap water instead of well or river water. There are several ways to keep the drilling operation as clean as possible, for example, employing very strict cleaning protocols and carefully designing the operations around the drill rig with contamination avoidance in mind (Russell, Phelps, Griffin, & Sargent, 1992).
So even under the best possible conditions, drilling inevitably causes infiltration of nonsterile drilling fluid into the core, not just along cracks and fissures but also into the pore space of even undisturbed fine-grained sediments (McKinley and Colwell, 1996, Smith et al., 2000a, Smith et al., 2000b). While drill fluid contamination is problematic for many analyses, it poses particular challenges for geomicrobiological studies.
Compared to the surface, microbial cell abundances in the subsurface are several orders of magnitude lower. As an example for typical cell abundances, a coastal shallow marine or lacustrine sediment contains between 106 and 108 cells/cm3. In very organic rich sediments from upwelling areas or other eutrophic systems, cell abundances are in the 109 cells/cm3 range but can reach, or in rare cases even exceed, 1010 cells/cm3 (Andrén, Barker Jørgensen, Cotterill, Green, & the IODP expedition 347 scientific party, 2015). At the other end of the spectrum are deep subsurface sediments, which normally only have cell densities around 103–104 cells/cm3 (e.g., D'Hondt et al., 2015, Kallmeyer et al., 2012) or even less (Inagaki et al., 2015). So there are several orders of magnitude difference in cell abundance between the shallow and the deep subsurface. Thus even the slightest infiltration of drilling fluid into a deep subsurface sample (in the order of nanoliters per cubic centimeter sediment) renders the sample unsuitable for microbiological and also certain geochemical investigations (Yanagawa et al., 2013). One could argue that it should be possible to avoid any contact of the drill fluid with surface sediments, use clean but not necessarily sterile equipment, and employ strict contamination control. All these are possible and have been done in the past with various degrees of success. Still, preparation of the drill fluid is a key issue for minimizing contamination. Due to the large volumes of water that are required and the often remote location of the drill site, it is often impossible to use relatively clean tap water; instead water has to be sourced locally from wells, springs, rivers, or lakes instead. In ocean drilling the drilling liquid of choice is normally surface ocean water. However, even in the most extreme oligotrophic parts of the world's ocean cell abundance at the surface is still around 105 cells/mL (D'Hondt et al., 2011). In coastal waters or lakes, cell abundances are in the 106 cells/mL range or higher (e.g., Daley and Hobbie, 1975, Noble and Fuhrman, 1998). So even under the best possible conditions the drill fluid will have a cell concentration that is orders of magnitude higher than a deep subsurface sample, and it will inevitably infiltrate at least into the outer layers of the drill core.
Section snippets
Drilling Techniques
Drilling is an integral part of deep earth exploration. The review of Wilkins et al. (2014) provides an excellent overview of terrestrial scientific drilling operations. A recent book (Stein, Blackman, Inagaki, & Larsen, 2014) describes the state of the art and future challenges of deep life exploration in the marine realm.
Most scientists who had to deal with a large-scale drilling operation will agree that a very close collaboration between the science and drilling team a project from the
Contamination Tracers
Because contamination cannot be avoided, at least not completely, it is essential to trace contamination of the drill core to identify uncontaminated samples. To assess the degree of infiltration a tracer is added to the fluid. To attribute the detected tracer to the infiltration of drilling fluid into the sample, it is necessary that tracers (1) have no natural source, (2) are easy to detect even at extremely low concentrations, and (3) are chemically inert.
Several techniques have been used in
Concluding Remarks
Drilling is a science in itself and no bio- or geoscientist should feel bad for not being familiar with all the technical details. For the success of every scientific drilling operation, it is therefore of utmost importance to develop a drilling strategy in close collaboration with those people who will eventually run the drilling operation. Most commercial drilling companies have little to no experience working with scientist and vice versa. So it is absolutely necessary for the scientists to
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