The archaeal diversity in a shallow geothermal well on Vulcano Island, Italy was characterized using culture-independent 16S rDNA sequence analysis. Environmental DNA was extracted from 56 °C well water, and the 16S ribosomal RNA gene was amplified with archaea-specific primers. Restriction fragment length polymorphism (RFLP) analysis of ∼250 clones revealed 35 unique patterns, which were sequenced and analyzed. These yielded 17 operational taxonomic units, of which 13, 3, and 1 were unique cren-, eury-, and korarchaeotal sequences, respectively. The majority of the crenarchaeotal phylotypes formed a novel, deeply-branching clade that includes sequences from other hydrothermal environments, but no cultured representatives. Three phylotypes represent novel lineages in the Thermoproteales and two phylotypes represent a novel genus of Euryarchaeota. One euryarchaeotal phylotype was nearly identical (99%) to Palaeococcus helgesonii, an aerotolerant, hyperthermophilic fermenter previously isolated from the same well. To place this diverse archaeal community in the geochemical framework of this ecosystem, we calculate values of Gibbs free energy of 145 organic and inorganic redox reactions at in situ conditions. Energy yields ranged from 0 to 125 kJ per mole of electrons transferred. The most exergonic organic reactions were organic carbon oxidation with O2 (>100 kJ/mol e−), followed by oxidation with (61–93 kJ/mol e−), Fe(III) (43–60 kJ/mol e−), and S0/ (6–27 kJ/mol e−) as terminal electron acceptors. Overall, energy yields from inorganic reactions were similar to those of the organic reactions considered, but were less systematic with respect to terminal electron acceptor. The oxidation of methane coupled with Fe(III) reduction yielded the most energy (123 kJ/mol e−). However, the most exergonic inorganic reactions were predominantly O2, , or reduction. Reduction of , S0, CO2, and CO yielded significantly less energy (0–18 kJ/mol e−). Metabolisms of the cultured organisms identified in the Pozzo Istmo archaeal clone library were exergonic. However, most of the archaeal diversity remains uncultured and energetic calculations reveal an extensive suite of potential lithotrophic and heterotrophic metabolisms that could be exploited by these novel organisms.
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