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Metabolically Active Microbial Communities in Oilfields: A Systematic Review and Synthesis of RNA Preservation, Extraction, and Sequencing Methods

Authors :
Rosimeire Floripes Gomes
Glen Jasper Yupanqui García
Joyce da Cruz Ferraz Dutra
Mariana Santos Cardoso
Eduardo Almeida Costa
Vinicius de Abreu Waldow
Claudia Julia Groposo
Rubens Nobumoto Akamine
Maira Paula de Sousa
Henrique Figueiredo
Vasco Ariston de Carvalho Azevedo
Aristóteles Góes-Neto
Source :
Applied Microbiology, Vol 3, Iss 4, Pp 1144-1163 (2023)
Publication Year :
2023
Publisher :
MDPI AG, 2023.

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.

Details

Language :
English
ISSN :
26738007
Volume :
3
Issue :
4
Database :
Directory of Open Access Journals
Journal :
Applied Microbiology
Publication Type :
Academic Journal
Accession number :
edsdoj.194dd22b61c1405aa1311c6b30f12e72
Document Type :
article
Full Text :
https://doi.org/10.3390/applmicrobiol3040079