Subsurface microbiology — from exploration to working tools

This specialised issue of FEMS Microbiology Ecology contains selected papers from the International Symposium on Subsurface Microbiology (ISSM02) held in Copenhagen, Denmark, 8–13 September 2002. It was the fifth in a series of symposia, the first of which was held in Orlando, Florida, USA in 1990.

The first scientific evidences of subsurface microbial life were reported in the 1930s and 1940s from investigations of deep sediment cores and waters from wells drilled for oil recovery (e.g., Issatchenko [1] and ZoBell [2]) or alpine rocks (summarized in [3]). However, 40 years later it was still discussed whether microbes are ubiquitous in the subsurface or the findings of microbes in pristine aquifers are a result of contamination from the soil surface during drilling. This was reflected at the first subsurface symposium (ISSM90) [4], where several contributions focused on how to collect undisturbed and uncontaminated samples, and on how to verify that they had not been contaminated by, e.g., drilling mud. The meeting also showed a strong need for developing new methods for studying the subsurface environment characterised by oligotrophic conditions and low numbers of microorganisms with low activity.

During the late 1970s, it was realized that the subsurface and groundwaters had often been contaminated with organic chemicals. This knowledge base was an important driving force for an increased exploration of subsurface microbiology with a hope that microorganisms may be able to degrade some of the contaminants in situ. On the other hand, it was also speculated that microbial activity could be a threat to deep subsurface deposits of nuclear waste by degrading the encapsulations and thus allowing nuclear waste to leach out. However, before these scenarios could be evaluated, it had to be verified that microorganisms were present and active in the subsurface.

The techniques for sampling and investigation of unknown life forms in the terrestrial subsurface have been useful, which inspired the exploration of other environments such as subseafloor and even extraterrestrial life, e.g., on Mars. Both topics were included in the recent ISSM conferences.

After the third Subsurface symposium in 1996, Bachofen and Ghiorse [5] concluded that the emphasis of subsurface microbiology had shifted from more technical aspects related to sampling at ISSM90 [1] and ISSM93 [6] toward more basic scientific questions within microbial ecology, biogeochemistry and geochemistry. These aspects were also in focus at the fourth and fifth subsurface symposia (ISSM99 [7] and ISSM02). However, much of the research presented at all symposia was associated with the applied problems of subsurface and groundwater pollution, oil exploration and waste disposal.

Today, subsurface microbiology has become a well-established research area and is included in many remediation strategies where insight into microbiology is important, and may provide evidence, e.g., for occurrence of natural attenuation. This understanding and the data from microbial investigations of the subsurface may provide crucial input to geochemical and hydrologic reactive models as well.

One example of the importance of microbial insight into the subsurface is the reductive dechlorination of chlorinated aliphatics. Contamination of the subsurface and groundwaters by chlorinated aliphatics is a widespread problem due to the use of these compounds in dry cleaners and as degreaser in metal shops. Under strongly reduced anaerobic conditions chlorinated aliphatics such as tetrachloroethene or trichloroethene can be reduced to dichloroethene, and via vinyl chloride to ethene. During this process chlorinated aliphatics are used as electron acceptors. However, the transformation of dichloroethene is a bottleneck, and at some sites the dechlorination stalls when this compound is formed. The ability to perform this transformation of dichloroethene seems to be limited to a specialized group of organisms, the Dehalococcoides. First of all, with this knowledge subsurface microbiology has provided insight into why the contaminant is being removed at some contaminated sites, but not at others. Secondly, molecular tools can be used to investigate if Dehalococcoides are present or not. In this way we can predict whether degradation potential is present and can be stimulated by eliminating other limiting factors such as lack of electron donors or oxidized redox conditions. Thirdly, if the redox conditions are suitable, but the dehalorespiring organisms are lacking, the contaminated site can be bioaugmented by adding cultures of these organisms enriched from contaminated soil and groundwater (e.g., [8]). However, still much needs to be learned about these organisms as discussed in the contributions of this issue.

The fifth subsurface symposium is highlighted in this issue of FEMS Microbiology Ecology. The symposium [9] covered ecology, function and diversity of microorganisms in the subsurface, under both natural and contaminated conditions. Through the presentations within the field of biodegradation, bacterial transport, natural attenuation and reduction of metals, subsurface microbiologists have gained insight into controlling processes, allowing for an improvement of remediation strategies on a scientific basis. The symposium covered various subsurface environments: the vadose zone, aquifers, extraterrestrial subsurfaces and the subseafloor. Technological advances in the field were also presented, such as emerging application for new molecular technologies, direct characterisation of microorganisms on mineral surfaces, micro flow cytometry, and other new approaches to sensing or determining microbial presence and activity for improvement of our understanding of subsurface microbiology.

We gratefully acknowledge the financial support from: Geological Survey of Denmark and Greenland (GEUS), DK; ATV Jord og Grundvand, DK; The Society of Danish Environmental Engineers (IDAmiljø), DK; Bedrock Bioremediation Center, University of New Hampshire, Durham, NH, USA; Environmental Research Group, University of New Hampshire, Durham, NH, USA; Lyondell, USA; Biological and Environmental research Program (BR), US Department of Energy, USA; Danish Technical Research Council, DK; Cowifonden, DK.

References