Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria

Abstract

Oil field bacteria were characterized by cloning and sequencing of PCR-amplified 16S rRNA genes. A variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family Desulfovibrionaceae and 8 members of the family Desulfobacteriaceae). In contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one Clostridium sp., one Eubacterium sp., and one Synergistes sp.). Potential sulfide oxidizers and/or microaerophiles (Thiomicrospira, Arcobacter, Campylobacter, and Oceanospirillum spp.) were also detected. The first two were prominently amplified from uncultured production water DNA and represented 28 and 47% of all clones, respectively. Growth on media containing sulfide as the electron donor and nitrate as the electron acceptor and designed for the isolation of Thiomicrospira spp. gave only significant enrichment of the Campylobacter sp., which was shown to be present in different western Canadian oil fields. This newly discovered sulfide oxidizer may provide a vital link in the oil field sulfur cycle by reoxidizing sulfide formed by microbial sulfate or sulfur reduction.

The microbial communities in two apparently physically separated deep subsurface oil reservoirs show extensive DNA sequence similarities

“…Because of the challenges associated with access to uncontaminated samples and low rates of successful cultivations, these communities are still poorly understood. So far, community studies have been performed primarily by cultivations (Magot et al, 2000;Youssef et al, 2009) or 16S rRNA gene sequencing (Voordouw et al, 1996;Orphan et al, 2000;Brakstad et al, 2008), but recently, we reported a high-coverage metagenomic sequencing study (Well I) (Kotlar et al, 2011) that indicated the presence of many different species (e.g. sulphate-reducing bacteria, methanogenic archaeal species and fermentative bacterial species) in a community of an oil reservoir on the Norwegian Continental Shelf (NCS).…”

Microbial diversity in production waters of a low-temperature biodegraded oil reservoir

“…The resident anaerobic bacteria include sulfate-reducers [4][5][6][7][8], fermentative bacteria [9][10][11][12][13][14][15], iron reducers [16][17][18], acetogens [19,20] and methanogens [21][22][23][24][25][26] (for a review, see [27]). Recent applications of molecular techniques allowed more complete characterizations of the microbial assemblages inhabiting a low-temperature waterflooded Canadian reservoir [28] and high-temperature, sulfur-rich oil-bearing formations in California and in Siberia [15,29]. The latter studies have extended our view of microbial communities in reservoirs and suggested the potential for closely coupled biogeochemical cycling of carbon and sulfur in these saline petroleum systems.…”

Molecular characterization of a sulfate-reducing consortium which mineralizes benzene

“…Hydrothermal vents such as the one where the original inoculum for this culture was collected [25] are known to contain large numbers of the genus Thiomicrospira, and not all sul¢de oxidizers are strict aerobes [32]. In addition, investigations of the microbial community in anaerobic production waters at oil ¢elds have found signi¢cant numbers of sul¢de oxidizers [12,33].…”

“…The technique of cloning and sequencing the 16S rRNA genes ampli¢ed from environmental samples to study the composition of microbial communities has become well established during the past 10 years (for review, see [35]). Variations of these techniques have been used to study the microbial communities in hot springs [36], marine bacterioplankton [37], soils [38], marine sediments [39], oil ¢elds [12], activated sludge [40], and freshwater lakes [41]. The information gained by phylogenetically identifying the members of a consortium can be used to make inferences about the microbially mediated processes occurring in an environment [12,33] or to design isolation schemes for speci¢c bacteria [13].…”

“…Given all these reasons, alternative methods to examine the microorganisms would be useful and molecular tools can provide information about the organisms that we would not otherwise be able to determine. The approach of using 16S rRNA gene sequences has been applied to characterize the sulfate-reducing communities present at oil ¢elds [12] and to identify bacteria present in a co-culture capable of reducing sulfate after exposure to oxygen [13]. In the latter study, the information from analyses of 16S rRNA genes was used to devise an isolation scheme which successfully separated the two strains.…”