Identifying the core bacterial microbiome of hydrocarbon degradation and a shift of dominant methanogenesis pathways in the oil and aqueous phases of petroleum reservoirs of different temperatures from China

Abstract

Abstract. Microorganisms in petroleum reservoirs play significant roles in hydrocarbon degradation, and through the terminal electron-accepting process of methanogenesis, they also contribute to microbially enhanced oil recovery (MEOR) worldwide, with great economic and environmental benefits. Here, a molecular investigation, using the 16S rRNA and mcrA gene profiles based on MiSeq sequencing and clone library construction methods, was conducted on oil and water (aqueous) phases of samples of high (82–88 ∘C), moderate (45–63 ∘C), and low temperatures (21–32 ∘C) from seven petroleum reservoirs in China. A core bacterial microbiome with a small proportion of shared operational taxonomic unit (OTU) values, but a high proportion of sequences among all reservoirs was discovered, including aerobic degraders, sulfate- and nitrate-reducing bacteria, fermentative bacteria, and sulfur-oxidizing bacteria distributed mainly in Proteobacteria, Bacteroidetes, Deferribacteres, Deinococcus–Thermus, Firmicutes, Spirochaetes, and Thermotogae. Their prevalence in the previously reported petroleum reservoirs and successive enrichment cultures suggests their common roles and functions involved in aliphatic and aromatic hydrocarbon degradation. The methanogenic process generally shifts from the dominant hydrogenotrophic pathway in the aqueous phase to the acetoclastic pathway in the oil phase in high-temperature reservoirs, but the opposite was true for low-temperature reservoirs. No difference was detected between the two phases in moderate temperature reservoirs. Physicochemical factors, including pH; temperature; phase conditions; and nitrate, Mn2+, and Mg2+ concentrations were the main factors correlated to the microbial compositional and functional profiles significantly. Linear discriminant analysis (LDA) effect size (LEfSe) analysis shows distribution differences of microbial groups towards pH, temperature, and the oil and aqueous phases. Using the software Tax4Fun for functional profiling indicated functional metabolism differences between the two phases, including amino acids, hydrocarbons in the oil phase, and carbohydrates in the aqueous phase.

Microbial Degradation Rates of Natural Bitumen

“…A possible explanation are fermenters, which are present in numerous oil reservoirs and play an important role in the overall hydrocarbon degradation. Fermenters often belong to the most abundant microorganisms after incubation of oil, heavy oil, or water from oil reservoirs. ,− Among others, several members of the phylum Chloroflexi , the order Desulfobacterales , the family Deferribacteraceae , or the genus Thermovirga were present in our communities. These microorganisms are either known fermenters or possess at least the ability for hydrocarbons fermentation in oil reservoirs. ,− ,− In addition, many sulfate reducers present in oil reservoirs can also ferment in the absence of sulfate or when sulfate reduction is inhibited .…”

On Enrichment Culturing and Transferring Technique

“…A specific chemical of choice shall be a source of carbon and energy for the microorganisms in the enrichment culture to utilize it for population growth when the chosen concentration is obviously below the toxicity level (Gu, 2020b). For many environmental pollutants, water solubility of them is a major limiting factor to allow high concentration achieved in cultural media (Ji et al,2020a;2020b;2020b;Zhou et al, 2019), and, as a result, bioaccumulation in organisms and animals, and biomagnification through the food chain transfer are often observed (Gu, 2019). The specific concentration used in cultural media is far exceeding the solubility of them in water in many publications (Ma et al, 2020;Zhang et al, 2021) and the determination of concen- tration during incubation becomes less reliable or inaccurate to show the indicative degradation as claimed.…”

pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs

“…Until February 2022, literature retrieval was conducted through the Web of Science database, and the published papers on “petroleum” and “microbial communities” were retrieved ( Lenchi et al, 2013 ; Gao P. et al, 2015 ; Gao et al, 2016 ; Mand et al, 2016 ; Shelton et al, 2016 ; Li et al, 2017a ; Aurepatipan et al, 2018 ; Nazina et al, 2019 ; Phetcharat et al, 2019 ; Zhou et al, 2019 , 2020 ; Santos et al, 2020 ; de Sousa Pires et al, 2021 ). Samples of petroleum or produced water that are closely related to petroleum reservoirs were manually selected.…”

“…Microorganisms are the core drivers of the biogeochemistry of important elements (especially C, N, and S) in petroleum reservoirs and have received extensive attention for their ability to enhance the recovery of energy materials such as petroleum ( Brown, 2010 ; Nazina et al, 2019 ; Zhou et al, 2020 ). The distribution characteristics of microbial populations in global petroleum reservoirs have been extensively reported in the past decade ( Aurepatipan et al, 2018 ; Zhou et al, 2019 , 2020 ; de Sousa Pires et al, 2021 ). In addition, a variety of C-N-S related functional microorganisms, including sulfate reducers, fermentative bacteria, acidogens, and methanogens ( Magot et al, 2000 ; Li et al, 2017b ; Santos et al, 2020 ), have been widely detected in petroleum reservoirs.…”