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.

Figure 1

(I) Dendrogram for 160 amplicon libraries from 10 HREs (Table 1), generated using the UPMGA algorithm with the distance between communities calculated using the Bray–Curtis coefficient in the Mothur software package. Libraries with more than 72% sequence similarity were collapsed into the same clade; the number is indicated in parentheses. Clades with samples used for metagenome analysis are indicated (red solid star). Note that three samples in clade 18 were used for metagenome sequencing. (II) Presence of orders from Network A (red, predominantly anaerobic), Network B (blue, predominantly aerobic), and Group C (green), indicated in Figure 2. The R-score indicates the degree to which communities in each clade vary from strictly anaerobic (R = 1.00) to strictly aerobic (R = −1.00).

Figure 2

Positive co-occurrence analysis of taxonomic orders present as ≥0.1% of total pyrosequencing reads using a threshold of 0.5 for the Spearman coefficient in the OTU association function of Mothur. The corresponding networks were visualized with Cytoscape. The size of a circle (node) is proportional to the number of samples in which the order was observed. The thickness of a connection (edge) is proportional to the correlation value. Network A consists of 19 orders with mostly strictly anaerobic genera. Network B consists of 11 orders with genera/species which are either strictly aerobic or facultative. Group C consists of 11 non-co-occurring orders in the α-, β-, and γ-Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Planctomycetes, listed in Table S5.

Figure 3

Microbial community variation in oil sands core FB11 as a function of vertical distance. (I) Depiction of the core and its location in the subsurface (m below surface); the position of samples, representing 5-cm sections, is indicated. (II) Proportions of the microbial community that were in Network A (predominantly anaerobic), Network B (predominantly aerobic), indicated in Figure 2, and of Group C (predominantly aerobic). (III) Genus-level diversity of methanogenic Archaea in the indicated core sections. The bars represent fractions (%) of sequence reads. The R-score indicates the degree to which communities are strictly anaerobic (R = 1.00) or strictly aerobic (R = −1.00).