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Title: Metabolic capability and in situ activity of microorganisms in an oil reservoir

Abstract

Background: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. Results: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondarymore » recovery. Conclusion: Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.« less

Authors:
 [1];  [2];  [3];  [2];  [4];  [3];  [5]
  1. Chinese Academy of Sciences (CAS), Shanghai (China). Shanghai Inst. of Ceramics, Key Lab. for Bioreactor Engineering and Inst. of Applied Chemistry; Univ. of California, San Diego, CA (United States). Dept. of Pediatrics
  2. Univ. of California, San Diego, CA (United States). Dept. of Pediatrics
  3. Chinese Academy of Sciences (CAS), Shanghai (China). Shanghai Inst. of Ceramics, Key Lab. for Bioreactor Engineering and Inst. of Applied Chemistry; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai (China)
  4. Univ. of Hong Kong (China). School of Biological Sciences
  5. Univ. of California, San Diego, CA (United States). Dept. of Pediatrics and Center for Microbiome Innovation,
Publication Date:
Research Org.:
Univ. of California, San Diego, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1510971
Grant/Contract Number:  
SC0012586
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Auxotrophy; Hydrocarbon degradation; Metagenomics and metatranscriptomics; Microbial community; Oil reservoir

Citation Formats

Liu, Yi-Fan, Galzerani, Daniela Domingos, Mbadinga, Serge Maurice, Zaramela, Livia S., Gu, Ji-Dong, Mu, Bo-Zhong, and Zengler, Karsten. Metabolic capability and in situ activity of microorganisms in an oil reservoir. United States: N. p., 2018. Web. doi:10.1186/s40168-017-0392-1.
Liu, Yi-Fan, Galzerani, Daniela Domingos, Mbadinga, Serge Maurice, Zaramela, Livia S., Gu, Ji-Dong, Mu, Bo-Zhong, & Zengler, Karsten. Metabolic capability and in situ activity of microorganisms in an oil reservoir. United States. doi:10.1186/s40168-017-0392-1.
Liu, Yi-Fan, Galzerani, Daniela Domingos, Mbadinga, Serge Maurice, Zaramela, Livia S., Gu, Ji-Dong, Mu, Bo-Zhong, and Zengler, Karsten. Fri . "Metabolic capability and in situ activity of microorganisms in an oil reservoir". United States. doi:10.1186/s40168-017-0392-1. https://www.osti.gov/servlets/purl/1510971.
@article{osti_1510971,
title = {Metabolic capability and in situ activity of microorganisms in an oil reservoir},
author = {Liu, Yi-Fan and Galzerani, Daniela Domingos and Mbadinga, Serge Maurice and Zaramela, Livia S. and Gu, Ji-Dong and Mu, Bo-Zhong and Zengler, Karsten},
abstractNote = {Background: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. Results: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery. Conclusion: Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.},
doi = {10.1186/s40168-017-0392-1},
journal = {Microbiome},
issn = {2049-2618},
number = 1,
volume = 6,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
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Cited by: 13 works
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Figures / Tables:

Fig. 1 Fig. 1: Taxonomic analysis of metagenomes evaluated from unassembled reads by MetaPhlAn2 and Metaxa2 and from assembled 16S rRNA gene sequences. Bar graph is showing the percent abundance of the different members at order level, and only members with more than 0.1% abundance in either sample is showed here. Archaealmore » members are marked in gray. To get a better visualization, relative abundances of archaeal members are normalized to total number of archaeal members« less

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      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.