Technological challenges to understanding the microbial ecology of deep subsurface ecosystems.

Abstract

Terrestrial subsurface geomicrobiology is a new frontier in environmental microbiology. It seeks to determine whether life can be sustained in the absence of solar radiation. Subsurface ecosystems are also intriguing astrobiological models useful in the re-creation of life in early Earth scenarios or ascertaining its possible exist- ence on other planetary bodies. Although Darwin pre- Scanning electron microscopy allows the presence of diverse mineral substrates to be correlated with identified biological structures through elemental analysis (EDAX) and morphology, but the metabolic status and the type of functional metabolism of these biological structures cannot be determined using these techniques. The adap- tation of rRN-targeted FISH (rRNA-FISH) to the study the microorganisms associated to semisolid substrates (cata- lysed reporter deposition-FISH (CARD-FISH)) was an important breakthrough in the microbial ecology study of sediments. Even though this technique has not been used intensively in the identification and quantification of micro- organisms in continental drilling projects, it is obvious that in the near future, it will play a significant role in clarifying the ambiguous results generated by more conventional techniques such as comparative sequence analysis, which, as mentioned earlier, require sample sizes and preparation methodologies that average or destroy compartmentalization. Fluorescent oligonucleotide probes were originally designed to target rRNA for identification of microorgan- isms in environmental studies. Recently, a wide range of FISH procedures have been developed targeting not only rRNA, but also mRNA or single genes (Moraru et al., 2010). It is easy to foresee that these procedures will be