Culture-Dependent and Culture-Independent Characterization of Microbial Assemblages Associated with High-Temperature Petroleum Reservoirs

Abstract

ABSTRACT Recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. In this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in California. Enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90°C. Heterotrophic enrichments from all sites yielded sheathed rods ( Thermotogales ), pleomorphic rods resembling Thermoanaerobacter , and Thermococcus -like isolates. The predominant autotrophic microorganisms recovered from inorganic enrichments using H 2 , acetate, and CO 2 as energy and carbon sources were methanogens, including isolates closely related to Methanobacterium , Methanococcus , and Methanoculleus species. Two 16S rRNA gene (rDNA) libraries were generated from total community DNA collected from production wellheads, using either archaeal or universal oligonucleotide primer sets. Sequence analysis of the universal library indicated that a large percentage of clones were highly similar to known bacterial and archaeal isolates recovered from similar habitats. Represented genera in rDNA clone libraries included Thermoanaerobacter , Thermococcus , Desulfothiovibrio , Aminobacterium , Acidaminococcus , Pseudomonas , Halomonas , Acinetobacter , Sphingomonas , Methylobacterium , and Desulfomicrobium . The archaeal library was dominated by methanogen-like rDNAs, with a lower percentage of clones belonging to the Thermococcales . Our results strongly support the hypothesis that sulfur-utilizing and methane-producing thermophilic microorganisms have a widespread distribution in oil reservoirs and the potential to actively participate in the biogeochemical transformation of carbon, hydrogen, and sulfur in situ.