Drilling and Sampling Technologies and the Potential for Contamination
BIOLOGICAL CONTAMINANT DETECTION
The detection of whole cells has traditionally relied on a variety of techniques including culture-based methods in which different media are used to grow organ-isms from a sample that can then be counted microscopically or as colonies on plates.
These techniques are limited in scope because only those organisms capable of grow-ing on a particular media formulation can be cultured, and these may constitute only a small fraction of the total community (Kämpfer et al. 1996). Microscopic counts of spores have also been used as proxies of bacteria (see Potential for Testing and Assess-Potential for Testing and Assess-ing Contamination: Experiences from Interplanetary Research). An important set of techniques for counting intact cells is the use of fluorescent dyes such as SYBR Gold, 4’,6-diamidino-2-phenylindole (DAPI), and acridine orange (AO). These methods use epifluorescence microscopy or flow cytometry to quantify the fluorescent-stained cells, and they are appropriate to the ongoing analysis of Antarctic glacial ice and drilling fluids for environmental monitoring and management. Application of this approach
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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 phylo-genetic 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 docu-ment 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.
CONCLUSIONS
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 environ-ment. 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 contamina-tion 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-0 EXPLORATION OF ANTARCTIC SUBGLACIAL AQUATIC ENVIRONMENTS
nitude of contamination from each of these sources will be highly specific to the type of drilling and sampling operation.
Biological contamination of subglacial aquatic environments can come from a vari-ety of sources that contain not only microorganisms but also the substrates they use for growth (Alekhina et al. 2007). Drilling fluids may contain both microbiota and growth substrates. The release of this inoculum plus growth medium into the relatively warm (by comparison with the ice hole and surface environment), liquid-water conditions of a subglacial lake could result in a short-term phase of increased metabolism and growth. It is of critical importance to minimize the introduction of living exogenous microbes, and even of exogenous nucleic acids, to prevent changes in native microbial composition and to allow for proper investigation of the native microbial community (and not contaminants).
A variety of allochthonous microbes (“contaminants”) could be introduced into subglacial aquatic environments from microorganisms native to the surface environ-ment or from humans or equipenviron-ment brought to the sampling area. Microbes could be transferred deeper into the system through sampling and could potentially grow (e.g., in meltwaters produced during hot-water drilling). Microbes immured in glacial ice for long periods of time might conceivably proliferate once they are released back into the modern-day biosphere through natural melting processes or research activities.
In subglacial lakes, large differences in chemical properties among liquid-water strata are possible, including the presence of anoxia at depth in the water column and in the sediments. Releases of water during sample removal could enrich or inhibit communities in the water column or overlying ice. As in lakes elsewhere, the sediments underlying subglacial lakes are likely to contain orders-of-magnitude higher concen-trations of microbes, nutrients, and metals. The benthic microbial communities also are likely to have a very different phylogenetic composition than those in the water column, and transfers during sampling could compromise subsequent measurements of water and ice samples (e.g., DNA clone library analysis).
In addition, research activities targeting one component of the environment may have the potential to cause contamination or damage of another. Once contamination reaches the aquatic environment, a variety of hydrodynamic circulation processes are likely to operate in the subglacial waters, and these localized inputs of contamination could be widely dispersed. This is particularly important for subglacial aquatic envi-ronments that are connected via subglacial hydrological networks. However, protocols or codes of environmental conduct may be developed to include specific measures to minimize or avoid such effects on the aquatic microbial ecosystems of these environ-ments. If downstream sites are the initial targets of investigation, this may reduce the potential risk of contamination to other environments along a specific flow path.
Molecular biological and genomics approaches have made it routine to sample the presence and diversity of microbial communities from many environments throughout the biosphere. Of particular importance to these sampling regimes, especially those taking place in areas where biomass is predicted to be low, is the prevention of con-tamination of the environment and subsequent samples with exogenous life or nucleic acids. These precautions should seek to preserve both the subglacial aquatic environ-ment and the integrity of the scientific samples.
Most protocols, that focus on preventing contamination of the environments and protecting the integrity of samples extracted from the environment have employed advancements in drilling technology to obtain the necessary depths and allow the
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use of sterile liners and other sterile devices for obtaining sample cores (for solids) or liquids. Most protocols for sample cores recommend further processing of the core under sterile conditions and removing interior portions for actual microbiological analysis. The inclusion of tracer studies to complement and track possible contamina-tion during any deep-biosphere sampling is also an extremely important step in most protocols examined.
Current levels of cleanliness associated with planetary protection standards are not feasible for the exploration of subglacial aquatic environments. Although it may be possible to control the initial number of cells associated with drilling and sampling equipment using current technologies, it is not possible to prevent the transfer and distribution of cells between different strata in the borehole during the drilling and sampling processes. Drilling and sampling equipment can be cleaned prior to entering the ice, but the extreme depths achieved during drilling and the fact that the drilling hardware is inaccessible for subsequent cleaning make stringent bacterial cleanliness requirements such as those implemented in space research unrealistic.
The hydrodynamic nature of subglacial aquatic environments facilitates cell trans-fer from any object that may find its way into liquid water. If the lake has unique biological ecosystems, transfer may also occur as a robotic sampling device moves from ecosystem to ecosystem. In general, requirements for cleanliness will have to be addressed in terms of (1) cleaning hardware (quantification of bacterial levels and bacterial diversity present) prior to penetration, (2) maintaining hardware cleanliness as much as possible during penetration, and (3) designing research techniques that mini-mize the possibility of cell transfer between different levels in the ice and the lake bed itself. Specific decontamination techniques need to be developed for any instruments Specific decontamination techniques need to be developed for any instruments deployed in a subglacial aquatic environment. The current decontamination approaches include sterilization by heat (autoclave) and/or chemical treatment (peroxide). The instrument packages must be robust to maintain their operational specifications fol-lowing these decontamination protocols.
A critical aspect of subglacial lake exploration and technology development is test-ing, verification, and monitoring of potential contamination during all phases of the scientific program. There must be deliberate and careful scrutiny of the methodologies employed, from ice drilling to sample recovery, from both an environmental steward-ship and a scientific standpoint. Stewardsteward-ship issues include providing the maximum possible protection of subglacial lake environments by ensuring minimal alteration or change due to the planned scientific studies. From a scientific standpoint, it is essential that uncompromised samples be provided for study and that the presence of human-made devices does not bias the data collected. There is also concern that unusual or previously unknown biological agents be properly handled upon retrieval to avoid an unwanted release to the environment.
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