. "4 Drilling and Sampling Technologies and the Potential for Contamination." Exploration of Antarctic Subglacial Aquatic Environments: Environmental and Scientific Stewardship. Washington, DC: The National Academies Press, 2007.
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Exploration of Antarctic Subglacial Aquatic Environments: Environmental and Scientific Stewardship
to samples from the lower strata of Vostok glacial ice has given counts of the order of 102 DNA-containing cells per milliliter of melted ice (Christner et al. 2006, Figure 2A), and this forms the basis for the committee’s Recommendation 7.
Molecular biological and genomic approaches offer a suite of tools that that can be complemented with culture-based techniques and biochemical methods to provide new and powerful strategies not only for gaining fundamentally new insights into the diversity of microbial life in subglacial aquatic environments but also for detection of exogenous cells and nucleic acids. A variety of molecular-based methods already exist and have been used extensively since at least the mid 1990’s for surveys of microbial diversity and community structure (denaturing gradient gel electrophoresis [DGGE], terminal restriction fragment length polymorphism [T-RFLP], fluorescence in situ hybridization [FISH], clone libraries) that rely on the identification of nucleic acids and circumvent culturing biases. Of particular importance has been the construction of clone libraries of genetic markers that can be sequenced and analyzed using phylogenetic methods to assess microbial diversity using 16S rRNA (for prokaryotes) and 18S rRNA (for eukaryotes) gene sequences. For a review of the techniques discussed in this paragraph see Spiegelman et al. (2005). In the future, the use of other genetic markers or the use of multiple genetic markers should also be considered. There is no universal protocol for performing any of these techniques. Investigators should document their methods and results carefully, utilize appropriate controls, and work toward developing standardized protocols for contaminant detection and documentation.
Biology continues to undergo a revolution with the advent of new genomic, post genomic, and culturing techniques (Handelsman 2004; Page et al. 2004; Xu 2006). These rapidly progressing areas of science not only can be applied to studying microbial diversity and their functional roles in the environment but also hold great promise in providing rapid and sensitive methods for detecting and identifying the introduction of exogenous microbiota or nucleic acids. The ongoing development and application of these technologies with the goal of producing standardized protocols of methods and documentation of results should be strongly encouraged in the arena of biological contaminant detection.
The problem of how to penetrate and sample subglacial aquatic environments in the cleanest manner possible remains a challenge because any form of invasive sampling of a subglacial aquatic system will result in some level of perturbation to the environment. Current drilling technologies are not sterile and it is not possible to guarantee that subglacial aquatic environments will not be contaminated during drilling, sampling, and monitoring. Drilling approaches that result in freezing subglacial water inside the borehole have worked well to keep the drilling fluids in the borehole (Byrd and EPICA DML boreholes in Antarctica and the NGRIP borehole in Greenland), but contamination of the core recovered by redrilling was evident.
During penetration and exploration of a subglacial aquatic environment, chemical contaminants could enter the water as liquid constituents of the drilling fluid and as solutes or particulates in that fluid. Direct contamination could also occur from the drilling and sampling apparatus, for example, from water-soluble oils used in metal working during the fabrication of the instruments and equipment or from phthalate ester additives that are used extensively in the plastics industry. The nature and mag-