Hydrogen and energy flow as “sensed” by molecular genetics

Perhaps just a quick whiff of the rarified air in Yellowstone Park might lead one to the apparently wrong conclusion; namely, that this is a sulfur-driven ecosystem. With all of that smelly hydrogen sulfide emanating from the hot water, it is easy for a microbiologist to leap to the conclusion that sulfur must dominate this ecosystem. Perhaps even more so since the discovery of the deep sea hydrothermal vents and their remarkable symbiotically driven ecosystems (1, 2), we have become accustomed to the notion of microbial systems powered by sulfide and/or sulfur oxidation and expect them to be operating here. For this reason, it was somewhat surprising to read the conclusion of the Spear et al. (3) in a recent issue of PNAS, who reported that these smelly boiling pools were in fact running on hydrogen rather than sulfide metabolism. The implications of this work go beyond this apparently straightforward conclusion.

The ability to identify and classify microbes by using molecular genetics techniques (16S rRNA sequence analysis) ushered in a new era in microbiology, making it possible for the first time to assess “who's there” even when the organisms could not be cultivated (4–6). Based on previously published results showing that members of the Aquificales were abundant (7–11), the authors suspected that hydrogen and not sulfur should be the important nutrient. This logic comes from the knowledge that cultivated members of the Aquificales use hydrogen either exclusively or preferentially. To test this hypothesis, Spear et al. (3) examined the populations in a variety of Yellowstone ponds, with levels of sulfides ranging from nondetectable to >200 μM. They also measured several key chemical variables, including sulfate, hydrogen, oxygen, pH, …