Autotrophic bacteria in groundwater systems

Current knowledge suggests that heterotrophic bacteria mediate the majority of biogeochemical transformations in groundwater ecosystems. What is less known, however, is the significance of autotrophic processes in the subsurface, although groundwater systems are frequently depleted in organic carbon. Carbon dioxide is, therefore, the sole source of readily available carbon. Carbon dioxide fixation in chemolithoautotrophic bacteria generally occurs via the Calvin-BensonBassham cycle, with ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) as the principal enzyme for the assimilation of carbon dioxide. As a highly conserved molecule, the RubisCO large subunit gene provides a very useful phylogenetic marker for the analysis of autotrophic bacteria. The first objective of our proposed research is to determine the carbon dioxide fixation potential and capabilities of chemolithoautotrophic bacteria based on detailed analysis of diversity and distribution of RubisCO genes in selected subsurface systems. We are especially interested to examine the differences between particle-associated and free-living autotrophic bacteria, because we anticipate significant compositional and potential functional differences between autotrophic microorganisms suspended in the groundwater and those attached to the substrate. We also expect to gain information whether the RubisCO diversity encountered corresponds to ecologically distinct units within the autotrophic microbial assemblages. Another principal objective of this study is to measure RubisCO gene expression by quantitative PCR-based techniques. This allows us to determine whether the gene encoded enzyme function for carbon dioxide fixation is operational in a particular aquifer environment or not. Finally, the data retrieved from the RubisCO sequence diversity analysis will be used to design specific genetic markers to examine distribution, relative abundances and activity of individual populations in different groundwater habitats, ultimately providing a better understanding of the forces and conditions affecting the carbon fixation potential and population dynamics of chemolithoautotrophic bacteria in subsurface systems.

Current knowledge suggests that heterotrophic bacteria mediate the majority of biogeochemical transformations in groundwater ecosystems. What is less known, however, is the significance of autotrophic processes in the subsurface, although groundwater systems are frequently depleted in organic carbon. Carbon dioxide is, therefore, the sole source of readily available carbon. Carbon dioxide fixation in chemolithoautotrophic bacteria generally occurs via the Calvin-BensonBassham cycle, with ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) as the principal enzyme for the assimilation of carbon dioxide. As a highly conserved molecule, the RubisCO large subunit gene provides a very useful phylogenetic marker for the analysis of autotrophic bacteria. The first objective of our proposed research is to determine the carbon dioxide fixation potential and capabilities of chemolithoautotrophic bacteria based on detailed analysis of diversity and distribution of RubisCO genes in selected subsurface systems. We are especially interested to examine the differences between particle-associated and free-living autotrophic bacteria, because we anticipate significant compositional and potential functional differences between autotrophic microorganisms suspended in the groundwater and those attached to the substrate. We also expect to gain information whether the RubisCO diversity encountered corresponds to ecologically distinct units within the autotrophic microbial assemblages. Another principal objective of this study is to measure RubisCO gene expression by quantitative PCR-based techniques. This allows us to determine whether the gene encoded enzyme function for carbon dioxide fixation is operational in a particular aquifer environment or not. Finally, the data retrieved from the RubisCO sequence diversity analysis will be used to design specific genetic markers to examine distribution, relative abundances and activity of individual populations in different groundwater habitats, ultimately providing a better understanding of the forces and conditions affecting the carbon fixation potential and population dynamics of chemolithoautotrophic bacteria in subsurface systems.