Metabolically Active Microbial Communities in Oilfields: A Systematic Review and Synthesis of RNA Preservation, Extraction, and Sequencing Methods
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Published:2023-10-06
Issue:4
Volume:3
Page:1144-1163
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ISSN:2673-8007
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Container-title:Applied Microbiology
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language:en
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Short-container-title:Applied Microbiology
Author:
Gomes Rosimeire Floripes1, García Glen Jasper Yupanqui2ORCID, Dutra Joyce da Cruz Ferraz1ORCID, Cardoso Mariana Santos2ORCID, Costa Eduardo Almeida3, de Abreu Waldow Vinicius4, Groposo Claudia Julia5, Akamine Rubens Nobumoto4, de Sousa Maira Paula4ORCID, Figueiredo Henrique6, Azevedo Vasco Ariston de Carvalho7ORCID, Góes-Neto Aristóteles7ORCID
Affiliation:
1. Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil 2. Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil 3. Center for Advanced and Multidisciplinary Computing, State University of Santa Cruz, Salobrinho 45662-900, Brazil 4. Petrobras Research, Development and Innovation Center Leopoldo Américo Miguez de Mello, Petrobras, Rio de Janeiro 21941-915, Brazil 5. Petrobras Research, Criciúma 88801-505, Brazil 6. Veterinary School, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil 7. Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
Abstract
Characterizing metabolically active microorganisms using RNA-based methods is a crucial tool for monitoring and mitigating operational issues, such as oil biodegradation and biocorrosion of pipelines in the oil and gas industry. Our review, a pioneering study, addresses the main methods used to preserve, isolate, and sequence RNA from oilfield samples and describes the most abundant metabolically active genera studied. Using the MEDLINE/PubMed, PubMed Central, Scopus, and Web of Science databases, 2.561 potentially eligible records were identified. After screening, 20 studies were included in our review, underscoring the scarcity of studies related to the subject. Data were extracted and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). These studies evaluated different samples, including produced water (PW), injection water (IW), solid deposits (SD), oil (OIL), and oily sludge (OS) collected from oilfields located in Australia, China, India, Mexico, and the United Arab Emirates. Environmental samples accounted for 55% of the studies, while enriched cultures and microbial consortia represented 35% and 15% of studies, respectively. PW was the most frequently studied sample, comprising 72% of all samples. Filtration and centrifugation were the only processes employed to concentrate the biomass present in samples. For RNA preservation, the most used method was a solution composed of 95:5 v/v ethanol/TRIzol, while for RNA isolation, the TRIzol reagent was the most cited. The Sanger sequencing method was used in all studies evaluating functional genes (alkB, dsrA, aprA, assA, and mcrA), and the Next-Generation Sequencing (NGS) method was employed in studies for sequencing transcripts of the 16S rRNA gene and metatranscriptomes. Pseudomonas (16S rRNA = PW: 2%; IW: 8%; metatranscriptome = PW: 20%) and Acinetobacter (16S rRNA = PW: 1%; IW: 4%; metatranscriptome = PW: 17%) were the most abundant genera. This study outlined the primary methods employed in researching metabolically active microorganisms. These data provide a foundation for future research. However, it is essential to note that we cannot yet determine the most effective method. We hope that this study will inspire further research related to the standardization of RNA preservation, extraction, and sequencing methods and significantly contribute to our understanding of active microbial communities in oilfields.
Funder
Petróleo Brasileiro S.A—Petrobras Graduate Programs of Microbiology Bioinformatics
Subject
General Earth and Planetary Sciences,General Environmental Science
Reference70 articles.
1. Salgar-Chaparro, S.J., and Machuca, L.L. (2019). Complementary DNA/RNA-based profiling: Characterization of corrosive microbial communities and their functional profiles in an oil production facility. Front. Microbiol., 10. 2. Neff, J., Lee, K., and DeBlois, E.M. (2011). Produced Water: Environmental Risks and Advances in Mitigation Technologies, Springer Science Business Media. 3. Nazina, T.N., Shestakova, N.M., Semenova, E.M., Korshunova, A.V., Kostrukova, N.K., Tourova, T.P., Liu, M., Feng, Q., and Poltaraus, A.B. (2017). Diversity of metabolically active bacteria in water-flooded high-temperature heavy oil reservoir. Front. Microbiol., 8. 4. Bisulfite reductase gene expression of thermophilic sulphate-reducing bacteria from saline connate water of oil reservoirs with high temperature;Int. Biodeterior. Biodegrad.,2016 5. Yuan, B., and Wood, D.A. (2018). Formation Damage during Improved Oil Recovery: Fundamentals and Applications, Elsevier.
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