Preserving Microbial Community Integrity in Oilfield Produced Water

Abstract

Determining a representative microbial signature from any given location is dependent on robust sample collection and handling. Different sampling locations and hence sample properties can vary widely; for example, soil would be collected and handled differently compared to liquid samples. In the event that sample material has a low concentration of biomass, large quantities need to be collected for microbial community analysis. This is certainly the case when investigating the microbiology of oilfield systems, wherein produced water (PW) is one of the most common sources for microbial sampling. As the detrimental effects of microbial metabolism within these industrial milieus are becoming increasingly well-established, the characterization of microbial community composition using molecular biological analyses is becoming more commonplace for accurate monitoring. As this field continues to develop, the importance for standardized operating protocols cannot be understated, so that industry can make the most informed operational decisions possible. Accurately identifying oilfield microbial communities is paramount, as improper preservation and storage following sample collection is known to lead to erroneous microbial identifications. Preserving oilfield PW can be challenging, as many locations are remote, requiring lengthy periods of time before samples can be processed and analyzed. While previous studies have characterized the effects of various preservatives on concentrated, filtered, or purified microbial samples, to the best of our knowledge, no such study has been undertaken on low biomass liquid samples. To this end, we investigated the effectiveness of nine different preservation conditions on PW collected from the same sampling location within a heavy-oil producing field, and monitored how the microbial community changed over the period of a month. Our results reveal that the choice of preservative drastically affects microbial community, and should be selected with careful consideration before sampling occurs.

Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies

“…The PW and SD sample types were the most numerous, with 155 (42.12%) and 119 (32.34%) samples, respectively, out of a total of 368. PW is one of the most common sources of microbiological samples ( Rachel & Gieg, 2020 ), mainly because it is considered a representative sample of the oil field, for having had direct contact with the oil reservoir and injection water, making it possible to predict circulating (planktonic) microorganisms in the water column, besides the logistic facilitation if compared to collections carried out directly in subsurface. On the other hand, SD allows the analysis of sessile microorganisms, which form biofilms, responsible for localized corrosion ( Carrascosa et al, 2021 ).…”

“…Literature data are heterogeneous, and it is often not possible to find a common denominator that can explain the putative driving factors that may be influencing the community dynamics of distinct microorganisms in each environment. In addition, obtaining data related to microbial communities present in industrial infrastructure is limited due to logistic difficulties of access to facilities and sample collection in pipelines, submarine, and subsurface equipment ( Rachel & Gieg, 2020 ). Furthermore, the lack of communication between different departments within the same company, particularly in large companies ( Kunsch, 2012 ), hinders the access to information by scientists and engineers.…”

Marine Microbiomes: Towards Standard Methods and Best Practices

“…Likewise, preservation with mercuric chloride Wietz et al, 2021) and formalin (Stern et al, 2015) allows ribosomal metabarcoding of microbes in autonomously collected seawater. Also the nucleic acid stabilizers RNAlater and DNAgard can preserve environmental DNA (Gray et al, 2013;Rachel and Gieg, 2020), however requiring frozen storage in stabilizer solution or the concentration of microbial biomass on filters (Ottesen et al, 2011). Both reagents have been tested as preservative in automated microbial samplings (Boeuf et al, 2019;Formel et al, 2021;Poff et al, 2021), but can lead to DNA loss and are likely unsuitable in remote regions where samples cannot be frozen immediately.…”

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

“…The existence of standardized and established protocols for nucleic acid preservation ensures that samples collected in remote areas can be successfully and consistently transported to laboratories with suitable infrastructure for RNA extraction without significantly compromising their integrity [30][31][32]. Therefore, it allows for the characterization of metabolically active microbial communities, as well as the identification of rare, less abundant species [32].…”