Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring

Dutta, Avishek; Smith, Ben; Goldman, Thomas; Walker, Leanne; Streets, Matthew; Eden, Bob; Dirmeier, Reinhard; Bowman, Jeff S.

doi:10.3389/fmicb.2020.585943

Cited by 9 publications

(7 citation statements)

References 58 publications

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“…SRBs exist both in a planktonic state and in a sessile state as biofilms ( 12 , 13 ), and it is generally accepted that biofilms are the main driver of oil field biosouring. In previous work ( 10 ), we observed shifts in the structure of the planktonic community after successful H 2 S suppression with nitrate addition in ex situ experiments. However, in that work, the state of the sessile community and potential elimination of biofilm-forming SRBs from the system during and after nitrate treatment was not known.…”

Section: Introductionmentioning

confidence: 63%

“…Injection of nitrate salts in oil reservoirs is one of the most effective ways for mitigate biosouring ( 5 – 9 ). In previous work ( 10 ), we observed prominent microbial community shifts when nitrate salts were added to a microcosm representation of a biosouring system. The addition of nitrate salts to a souring system facilitates the growth of heterotrophic nitrate-reducing bacteria (hNRBs).…”

Section: Introductionmentioning

confidence: 73%

“…Although an increase in NRB populations in effluents can be used as an indicator for the successful mitigation of biosouring, it does not necessarily mean eradication of biofilm-forming SRBs from the system. SRBs can change their metabolic lifestyle ( 5 , 10 , 14 ) and still persist after nitrate treatments. The persistence of SRBs in biofilms can lead to faster rebound sulfidogenesis once the nitrate treatment is stopped.…”

Section: Discussionmentioning

confidence: 99%

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Detection of Sulfate-Reducing Bacteria as an Indicator for Successful Mitigation of Sulfide Production

Dutta

Valle²,

Goldman³

et al. 2021

Appl Environ Microbiol

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Sulfate-reducing bacteria (SRB) are one of the main sources of biogenic H 2 S generation in oil reservoirs. Excess H 2 S production in these systems leads to oil biosouring, which causes operational risks, health hazards and can increase the cost of refining crude oil. Nitrate salts are often added to the system to suppress sulfidogenesis. Because SRB populations can persist in biofilms even after nitrate treatment, identifying shifts in the sessile community is crucial for successful mitigation. However, sampling the sessile community is hampered by its inaccessibility. Here we use the results of a long-term (148 days) ex situ experiment to identify particular sessile community members from observations of the sample waste stream. Microbial community structure was determined for 731 samples across twenty bioreactors using 16S rRNA gene sequencing. By associating microbial community structure with specific steps in the mitigation process, we could distinguish between taxa associated with H 2 S production and mitigation. After initiation of nitrate treatment, certain SRB populations increased in the planktonic community during critical time points, indicating the dissociation of SRBs from the biofilm. Predicted relative abundances of the dissimilatory sulfate reduction pathway also increased during the critical time points. Here, by analyzing the planktonic community structure, we describe a general method that uses high-throughput amplicon sequencing, metabolic inferences, and cell abundance data to identify successful biofilm mitigation. We anticipate that our approach is also applicable to other systems where biofilms must be mitigated but cannot be easily sampled. Importance Microbial biofilms are commonly present in many industrial processes and can negatively impact performance and safety. Within the oil industry, subterranean biofilms cause biosouring with implications for oil quality, cost, occupational health, and the environment. Because these biofilms cannot be directly sampled, methods are needed to indirectly assess the success of mitigation measures. This study demonstrates how the planktonic microbial community can be used to assess the dissociation of SRB-containing biofilms. We found that an increase in the abundance of a specific SRB population in the effluent after nitrate treatment can be used as a potential indicator for the successful mitigation of biofilm-forming SRBs. Moreover, a method for determining critical time points for detecting potential indicators is suggested. This study expands our knowledge in improving mitigation strategies for biosouring and could have broader implications in other systems where biofilms lead to adverse consequences.

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Section: Introductionmentioning

confidence: 63%

Section: Introductionmentioning

confidence: 73%

Section: Discussionmentioning

confidence: 99%

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Detection of Sulfate-Reducing Bacteria as an Indicator for Successful Mitigation of Sulfide Production

Dutta

Valle²,

Goldman³

et al. 2021

Appl Environ Microbiol

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“…This may result from the ubiquity of SRBs in the sulfidogenic and mitigation phases, in contrast to the much greater abundance of NRBs in the mitigation phase. The presence of NRBs is evidence of suppressed sulfidogenesis, but the presence of SRBs does not necessarily indicate enhanced sulfidogenesis since, under limiting conditions, SRBs can switch from sulfate reduction to fermentation or even nitrate reduction depending on their genomic repertoire ( 3 , 9 , 26 ).…”

Section: Discussionmentioning

confidence: 99%

Machine Learning Predicts Biogeochemistry from Microbial Community Structure in a Complex Model System

Dutta

Goldman²,

Keating³

et al. 2022

Microbiol Spectr

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“…In Bowman and Ducklow (2015) , paprica was used to infer microbial metabolism and results were comparable to other common metabolic inference pipelines such as PICRUSt ( Langille et al, 2013 ). Paprica has been used to understand the temporal dynamics of bacterial and archaeal community structure in coastal ecosystems ( Wilson et al, 2021 ), the microbial diversity of hypersaline lakes ( Klempay et al, 2021 ), and the microbial dynamics in up-flow bioreactors ( Dutta et al, 2020 ). Paprica offers a framework to bridge the gap between taxonomy and marker gene studies, which are economical but indirectly linked to community function, and potential metabolism, which is costly and can be labor intensive to analyze but is directly linked to function ( Bowman and Ducklow, 2015 ).…”

Section: Before You Beginmentioning

confidence: 99%

From microbial community structure to metabolic inference using paprica

2021

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Summary Microbial taxonomic marker gene studies using 16S rRNA gene amplicon sequencing provide an understanding of microbial community structure and diversity; however, it can be difficult to infer the functionality of microbes in the ecosystem from these data. Here, we show how to predict metabolism from phylogeny using the paprica pipeline. This approach allows resolution at the strain and species level for select regions on the prokaryotic phylogenetic tree and provides an estimate of gene and metabolic pathway abundance. For complete details on the use and execution of this protocol, please refer to Erazo and Bowman (2021) .

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Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring

Cited by 9 publications

References 58 publications

Detection of Sulfate-Reducing Bacteria as an Indicator for Successful Mitigation of Sulfide Production

Detection of Sulfate-Reducing Bacteria as an Indicator for Successful Mitigation of Sulfide Production

Machine Learning Predicts Biogeochemistry from Microbial Community Structure in a Complex Model System

From microbial community structure to metabolic inference using paprica

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