One approach in microbial ecology is to cultivate bacteria from their natural habitat and then determine their physiology and growth rates under conditions that simulate their natural environment. The key word here is “simulate”, because of the near impossibility to adequately replicate in situ conditions of nutrient flux, community structure, and environmental variables (e.g. temperature). A second approach is to use -omics techniques to investigate the distribution, community structure, metabolic potential and gene expression of microorganisms from environmental samples. At the DSML we integrate both approaches to investigate the ecology and function of natural microbial communities in marine geothermal environments.
Our investigation of nitrate reduction at deep-sea hydrothermal vents is one example of how we integrate physiology, genomic and metagenomic approaches. Work on pure cultures of vent bacteria and archaea indicated that nitrate respiration supports chemolithoautotrophic microbial growth in deep-sea geothermal environments. The analysis of the genome sequence of these organisms allowed us to reconstruct their nitrate reduction pathways and to identify key functional genes, e.g. the gene encoding the periplasmic nitrate reductase, napA. Subsquent culture-independent analyses of the napA gene revealed that nitrate respiration is conserved and widespread in vent Epsilonproteobacteria.