Current rates for sequencing microbial genomes are far outpacing the capacity to understand the corresponding biological complexity encoded in the DNA. Much attention is focused on in silico methods for extracting insights into biological function. However, it is becoming clear that “low throughput” efforts are needed to complement the “high throughput” capabilities associated with systems biology. In fact, a critical challenge now is how to balance modern and classical approaches to obtain new insights into the relationship between genotype and phenotype.

In our laboratory, we use functional genomics approaches to study extremely thermophilic microorganisms. Our model microorganisms include archaea, such as Pyrococcus furiosus (T_opt 98-100°C), Metallosphaera sedula (T_opt 73°C, pH_opt 2.0), and Sulfolobus solfataricus (T_opt 80°C, pH_opt 3.0) and bacteria, such as Thermotoga maritima (T_opt 80°C) and Caldicellulosiruptor saccharolyticus (T_opt 70°C). These microorganisms have significant biotechnological potential as sources of thermostable biocatalysts, as biohydrogen producers, for recovery of base and precious metals, and for unique metabolic characteristics. Using genome sequence information, transcriptional response analysis, biochemical characterization of specific proteins, and microbiological assays, we have uncovered numerous leads with biotechnological relevance. In addition, this has enabled us to provide definitive annotation of many ORFs that otherwise would remain as “hypothetical” or “conserved hypothetical” proteins in our model systems. Discussed here is how modern and classical methods are being used to study extreme thermophiles, an approach that can be extended to less extremophilic microorganisms and cells. Examples provided will include biocatalyst discovery, metagenomics, interspecies interactions, metabolic pathway identification, secretome analysis, and comparative bioenergetics.