Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common

Abstract

Oil in subsurface reservoirs is biodegraded by resident microbial communities. Water-mediated, anaerobic conversion of hydrocarbons to methane and CO2, catalyzed by syntrophic bacteria and methanogenic archaea, is thought to be one of the dominant processes. We compared 160 microbial community compositions in ten hydrocarbon resource environments (HREs) and sequenced twelve metagenomes to characterize their metabolic potential. Although anaerobic communities were common, cores from oil sands and coal beds had unexpectedly high proportions of aerobic hydrocarbon-degrading bacteria. Likewise, most metagenomes had high proportions of genes for enzymes involved in aerobic hydrocarbon metabolism. Hence, although HREs may have been strictly anaerobic and typically methanogenic for much of their history, this may not hold today for coal beds and for the Alberta oil sands, one of the largest remaining oil reservoirs in the world. This finding may influence strategies to recover energy or chemicals from these HREs by in situ microbial processes.

Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops

“…The harsher conditions cause the microbial populations in the cliffs to be smaller than those in the rivers, as indicated by average concentrations of extracted DNA of 19.5 Ϯ 13.3 ng/g and 282 Ϯ 117 ng/g, respectively. Both of these concentrations are higher than those extracted from oil sands cores retrieved from 200 to 300 mbs, which yielded 1 ng/g (11). At an assumed average genome size of 3 ϫ 10 6 bp, these values translate into microbial numbers of approximately 6 ϫ 10 6 /g and 8 ϫ 10 7 /g for cliff and river bitumen tablets, respectively, and 3 ϫ 10 5 /g for subsurface cores.…”

“…The low fractions of Archaea were not caused by primer bias. The primer pair used detects large fractions of Archaea, when present (11).…”

“…PCR was performed using 12.5 pmol of primers 926f (AAA CTY AAA KGA ATT GRC GG) and 1392r (ACG GGC GGT GTG TRC) per 50-l reaction mixture containing 0.1 to 10 ng of DNA template as well as 2.5 units of Taq or TopTaq DNA polymerase and the other reagents prescribed by the manufacturer (either Fermentas or Qiagen). PCR was for 25 cycles of 30 s at 95°C, 45 s at 55°C, and 90 s at 72°C with a final elongation of 10 min at 72°C (11). The amplicons were purified by agarose gel electrophoresis, using SYBR green to stain the gels.…”

“…This additional step was added because it resulted in increased read lengths. Purified DNAs were subjected to pyrosequencing with a Genome Sequencer FLX instrument and a GS FLX Titanium series kit XLR70 (Roche Diagnostics Corporation) at the McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada, as described elsewhere (11).…”

“…The oil became severely biodegraded during this journey and following its placement at low depth and low temperature in the Athabasca, Cold Lake, and Peace River oil sands deposits that exist today. Biodegradation of low-molecular-weight components caused the oil to become more viscous, with the viscosity ranging from 1 cP for initially formed nondegraded light oil to 10 6 cP for heavily biodegraded, eastern Athabasca oil sands bitumen, which is currently in place (5)(6)(7)(8)(9)(10)(11). Bitumen is therefore depleted of low-molecular-weight aliphatic and aromatic hydrocarbons and enriched in polyaromatic hydrocarbons (PAHs), including alkylnaphthalenes or alkylphenanthrenes, as well as in naphthenic acids (NAs), resins, and asphaltenes (12)(13)(14).…”