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Journal of Environmental Science and Health, Part A
Toxic/Hazardous Substances and Environmental Engineering
Volume 57, 2022 - Issue 8
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Research Article

Insight into bacterial community profiles of oil shale and sandstone in ordos basin by culture-dependent and culture-independent methods

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Pages 723-735 | Received 31 Jan 2022, Accepted 19 Jul 2022, Published online: 29 Jul 2022

References

  • Guo, R.; Zhao, Y.; Wang, W.; Hu, X.; Zhou, X.; Hao, L.; Ma, X.; Ma, D.; Li, S. Application of Rare-Earth Elements and Comparison to Molecular Markers in Oil-Source Correlation of Tight Oil: A Case Study of Chang 7 of the Upper Triassic Yanchang Formation in Longdong Area, Ordos Basin, China. ACS Omega 2020, 5, 22140–22156. DOI: 10.1021/acsomega.0c02233.
  • Jia, C.; Zheng, M.; Zhang, Y. Unconventional Hydrocarbon Resources in China and the Prospect of Exploration and Development. Pet. Explor. Dev. 2012, 39, 139–146. DOI: 10.1016/S1876-3804(12)60026-3.
  • Yang, H.; Li, S.; Liu, X. Characteristics and Resource Prospects of Tight Oil in Ordos Basin, China. Petroleum Res. 2016, 1, 27–38. DOI: 10.1016/S2096-2495(17)30028-5.
  • Liu, X.; Kang, Y.; Li, J.; Chen, Z.; Ji, A.; Xu, H. Percolation Characteristics and Fluid Movability Analysis in Tight Sandstone Oil Reservoirs. ACS Omega 2020, 5, 14316–14323. DOI: 10.1021/acsomega.0c00569.
  • Fu, J. H.; Deng, X. Q.; Chu, M. J.; Zhang, H. F.; Li, S. X. Features of Deepwater Lithofcies, Yanchang Formation in Ordos Basin and Its Petroleum Significance. Acta Sedimentologica Sinica 2013, 31, 929–938.
  • Zhang, X.; He, J.; Zhao, Y.; Wu, H.; Ren, Z. Geochemical Characteristics and Origins of the Crude Oil of Triassic Yanchang Formation in Southwestern Yishan Slope, Ordos Basin. Int. J. Anal. Chem. 2017, 2017, 6953864. DOI: 10.1155/2017/6953864.
  • Mukhina, E.; Cheremisin, A.; Khakimova, L.; Garipova, A.; Dvoretskaya, E.; Zvada, M.; Kalacheva, D.; Prochukhan, K.; Kasyanenko, A.; Cheremisin, A. Enhanced Oil Recovery Method Selection for Shale Oil Based on Numerical Simulations. ACS Omega 2021, 6, 23731–23741. DOI: 10.1021/acsomega.1c01779.
  • Phetcharat, T.; Dawkrajai, P.; Chitov, T.; Mhuantong, W.; Champreda, V.; Bovonsombut, S. Biosurfactant-Producing Capability and Prediction of Functional Genes Potentially Beneficial to Microbial Enhanced Oil Recovery in Indigenous Bacterial Communities of an Onshore Oil Reservoir. Curr. Microbiol. 2019, 76, 382–391. DOI: 10.1007/s00284-019-01641-8.
  • Nikolova, C.; Gutierrez, T. Use of Microorganisms in the Recovery of Oil from Recalcitrant Oil Reservoirs: current State of Knowledge, Technological Advances and Future Perspectives. Front Microbiol. 2019, 10, 2996.
  • Brown, L. R. Microbial Enhanced Oil Recovery (MEOR). Curr. Opin. Microbiol. 2010, 13, 316–320. DOI: 10.1016/j.mib.2010.01.011.
  • Sen, R. Biotechnology in Petroleum Recovery: The Microbial EOR. Prog. Energy Combust. Sci. 2008, 34, 714–724. DOI: 10.1016/j.pecs.2008.05.001.
  • Ghilamicael, A. M.; Budambula, N. L. M.; Anami, S. E.; Mehari, T.; Boga, H. I. Evaluation of Prokaryotic Diversity of Five Hot Springs in Eritrea. BMC Microbiol. 2017, 17, 203. DOI: 10.1186/s12866-017-1113-4.
  • Lewis, W. H.; Tahon, G.; Geesink, P.; Sousa, D. Z.; Ettema, T. J. G. Innovations to Culturing the Uncultured Microbial Majority. Nat. Rev. Microbiol. 2021, 19, 225–240. DOI: 10.1038/s41579-020-00458-8.
  • Su, C.; Lei, L.; Duan, Y.; Zhang, K. Q.; Yang, J. Culture-Independent Methods for Studying Environmental Microorganisms: methods, Application, and Perspective. Appl. Microbiol. Biotechnol. 2012, 93, 993–1003. DOI: 10.1007/s00253-011-3800-7.
  • Yarza, P.; Yilmaz, P.; Pruesse, E.; Glockner, F. O.; Ludwig, W.; Schleifer, K. H.; Whitman, W. B.; Euzeby, J.; Amann, R.; Rossello-Mora, R. Uniting the Classification of Cultured and Uncultured Bacteria and Archaea Using 16S rRNA Gene Sequences. Nat. Rev. Microbiol. 2014, 12, 635–645. DOI: 10.1038/nrmicro3330.
  • Xiong, L.; An, L.; Zong, Y.; Wang, M.; Wang, G.; Li, M. Luteimonas Gilva sp. nov., Isolated from Farmland Soil. Int. J. Syst. Evol. Microbiol. 2020, 70, 3462–3467. DOI: 10.1099/ijsem.0.004197.
  • Sinclair, L.; Osman, O. A.; Bertilsson, S.; Eiler, A. Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: evaluating the Illumina Platform. PLoS One 2015, 10, e0116955. DOI: 10.1371/journal.pone.0116955.
  • Frank, J. A.; Reich, C. I.; Sharma, S.; Weisbaum, J. S.; Wilson, B. A.; Olsen, G. J. Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes. Appl. Environ. Microbiol. 2008, 74, 2461–2470. DOI: 10.1128/AEM.02272-07.
  • Haas, B. J.; Gevers, D.; Earl, A. M.; Feldgarden, M.; Ward, D. V.; Giannoukos, G.; Ciulla, D.; Tabbaa, D.; Highlander, S. K.; Sodergren, E.; Human Microbiome Consortium.; et al. Chimeric 16S rRNA Sequence Formation and Detection in Sanger and 454-Pyrosequenced PCR Amplicons. Genome Res. 2011, 21, 494–504. DOI: 10.1101/gr.112730.110.
  • Wang, Q.; Garrity, G. M.; Tiedje, J. M.; Cole, J. R. Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl. Environ. Microbiol. 2007, 73, 5261–5267. DOI: 10.1128/AEM.00062-07.
  • Quast, C.; Pruesse, E.; Yilmaz, P.; Gerken, J.; Schweer, T.; Yarza, P.; Peplies, J.; Glockner, F. O. The SILVA Ribosomal RNA Gene Database Project: improved Data Processing and Web-Based Tools. Nucleic Acids Res. 2013, 41, D590–596. DOI: 10.1093/nar/gks1219.
  • Gao, P.; Tian, H.; Li, G.; Sun, H.; Ma, T. Microbial Diversity and Abundance in the Xinjiang Luliang Long-Term Water-Flooding Petroleum Reservoir. Microbiologyopen 2015, 4, 332–342. DOI: 10.1002/mbo3.241.
  • Li, L.; Huang, B.; Tan, Y.; Deng, X.; Li, Y.; Zheng, H. Geometric Heterogeneity of Continental Shale in the Yanchang Formation, Southern Ordos Basin, China. Sci. Rep. 2017, 7, 6006. DOI: 10.1038/s41598-017-05144-z.
  • Qiu, X.; Liu, C.; Mao, G.; Deng, Y.; Wang, F.; Wang, J. Major, Trace and Platinum-Group Element Geochemistry of the Upper Triassic Nonmarine Hot Shales in the Ordos Basin, Central China. Appl. Geochem. 2015, 53, 42–52. DOI: 10.1016/j.apgeochem.2014.11.028.
  • Dopson, M.; Holmes, D. S. Metal Resistance in Acidophilic Microorganisms and Its Significance for Biotechnologies. Appl. Microbiol. Biotechnol. 2014, 98, 8133–8144. DOI: 10.1007/s00253-014-5982-2.
  • Falagan, C.; Johnson, D. B. The Significance of pH in Dictating the Relative Toxicities of Chloride and Copper to Acidophilic Bacteria. Res. Microbiol. 2018, 169, 552–557. DOI: 10.1016/j.resmic.2018.07.004.
  • Si, Y.; Wang, X.; Yang, G.; Yang, T.; Li, Y.; Ayala, G. J.; Li, X.; Wang, H.; Su, J. Crystal Structures of Pyrophosphatase from acinetobacter baumannii: snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate. Int. J. Mol. Sci. 2019, 20, 4394.
  • Feng, X.; Guo, J.; Zhang, R.; Liu, W.; Cao, Y.; Xian, M.; Liu, H. An Aminotransferase from enhydrobacter aerosaccus to Obtain Optically Pure Beta-Phenylalanine. ACS Omega 2020, 5, 7745–7750. DOI: 10.1021/acsomega.9b03416.
  • Gao, S.; Su, Y.; Zhao, L.; Li, G.; Zheng, G. Characterization of a (R)-Selective Amine Transaminase from fusarium oxysporum. Process Biochem. 2017, 63, 130–136. DOI: 10.1016/j.procbio.2017.08.012.
  • Wongwilaiwalin, S.; Mhuantong, W.; Champreda, V.; Tangphatsornruang, S.; Panichnumsin, P.; Ratanakhanokchai, K.; Tachaapaikoon, C. Structural and Metabolic Adaptation of Cellulolytic Microcosm in co-Digested Napier Grass-Swine Manure and Its Application in Enhancing Thermophilic Biogas Production. RSC Adv. 2018, 8, 29806–29815. DOI: 10.1039/c8ra05616a.
  • Meng, Q.; Wang, X.; Liao, Y.; Lei, Y.; Yin, J.; Liu, P.; Shi, B. The Effect of Slight to Moderate Biodegradation on the Shale Soluble Organic Matter Composition of the Upper Triassic Yanchang Formation, Ordos Basin, China. Mar. Pet. Geol. 2021, 128, 105021. DOI: 10.1016/j.marpetgeo.2021.105021.
  • Yang, S.; Huang, L. H.; Zhao, X. H.; Xing, M. Y.; Shao, L. W.; Zhang, M. Y.; Shao, R. Y.; Wei, J. H.; Gao, C. H. Using the Delphi Method to Establish Nursing-Sensitive Quality Indicators for ICU Nursing in China. Res. Nurs. Health 2019, 42, 48–60. DOI: 10.1002/nur.21925.
  • Zou, C.; Zhu, R.; Chen, Z.-Q.; Ogg, J. G.; Wu, S.; Dong, D.; Qiu, Z.; Wang, Y.; Wang, L.; Lin, S.; et al. Organic-Matter-Rich Shales of China. Earth. Sci. Rev. 2019, 189, 51–78. DOI: 10.1016/j.earscirev.2018.12.002.
  • Brown, L.; A, V.; Stephens, J. O. Slowing Production Decline and Extending the Economic Life of an Oil Field: New MEOR Technology. SPE Reserv. Eval. Eng. 2002, 5, 33–41. DOI: 10.2118/75355-PA.
  • Phetcharat, T.; Dawkrajai, P.; Chitov, T.; Wongpornchai, P.; Saenton, S.; Mhuantong, W.; Kanokratana, P.; Champreda, V.; Bovonsombut, S. Effect of Inorganic Nutrients on Bacterial Community Composition in Oil-Bearing Sandstones from the Subsurface Strata of an Onshore Oil Reservoir and Its Potential Use in Microbial Enhanced Oil Recovery. PLoS One 2018, 13, e0198050. DOI: 10.1371/journal.pone.0198050.
  • Choe, Y. H.; Kim, M.; Lee, Y. K. Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert. Front Microbiol. 2020, 11, 607396.
  • Guo, J.; Kang, Y. Characterization of Sulfate-Reducing Bacteria Anaerobic Sludge Granulation Enhanced by Chitosan. J. Environ. Manage. 2020, 253, 109648. DOI: 10.1016/j.jenvman.2019.109648.
  • Zhou, K.; Qiao, K.; Edgar, S.; Stephanopoulos, G. Distributing a Metabolic Pathway among a Microbial Consortium Enhances Production of Natural Products. Nat. Biotechnol. 2015, 33, 377–383. DOI: 10.1038/nbt.3095.
  • Li, Y.; Zheng, B.; Yang, Y.; Chen, K.; Chen, X.; Huang, X.; Wang, X. Soil Microbial Ecological Effect of Shale Gas Oil-Based Drilling Cuttings Pyrolysis Residue Used as Soil Covering Material. J. Hazard Mater. 2022, 436, 129231. DOI: 10.1016/j.jhazmat.2022.129231.
  • Jiang, B.; Zhang, B.; Li, L.; Zhao, Y.; Shi, Y.; Jiang, Q.; Jia, L. Analysis of Microbial Community Structure and Diversity in Surrounding Rock Soil of Different Waste Dump Sites in Fushun Western Opencast Mine. Chemosphere 2021, 269, 128777. DOI: 10.1016/j.chemosphere.2020.128777.
  • Vikram, A.; Lipus, D.; Bibby, K. Metatranscriptome Analysis of Active Microbial Communities in Produced Water Samples from the Marcellus Shale. Microb. Ecol. 2016, 72, 571–581. DOI: 10.1007/s00248-016-0811-z.
  • Lipus, D.; Vikram, A.; Ross, D.; Bain, D.; Gulliver, D.; Hammack, R.; Bibby, K. Predominance and Metabolic Potential of Halanaerobium Spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells. Appl. Environ. Microbiol. 2017, 83, e02659-02616. DOI: 10.1128/AEM.02659-16.
  • Rizoulis, A.; Elliott, D. R.; Rolfe, S. A.; Thornton, S. F.; Banwart, S. A.; Pickup, R. W.; Scholes, J. D. Diversity of Planktonic and Attached Bacterial Communities in a Phenol-Contaminated Sandstone Aquifer. Microb. Ecol. 2013, 66, 84–95. DOI: 10.1007/s00248-013-0233-0.
  • Sadauskas, M.; Vaitekūnas, J.; Gasparavičiūtė, R.; Meškys, R. Indole Biodegradation in Acinetobacter sp. Strain O153: Genetic and Biochemical Characterization. Appl. Environ. Microbiol. 2017, 83, e01453-01417. DOI: 10.1128/AEM.01453-17.
  • Liu, Y.; Wang, W.; Shah, S. B.; Zanaroli, G.; Xu, P.; Tang, H. Phenol Biodegradation by Acinetobacter radioresistens APH1 and Its Application in Soil Bioremediation. Appl. Microbiol. Biotechnol. 2020, 104, 427–437. DOI: 10.1007/s00253-019-10271-w.
  • Van Dexter, S.; Boopathy, R. Biodegradation of Phenol by Acinetobacter tandoii Isolated from the Gut of the Termite. Environ. Sci. Pollut. Res. Int. 2019, 26, 34067–34072. DOI: 10.1007/s11356-018-3292-4.
  • Jiang, Y.; Zhang, Z.; Zhang, X. Co-Biodegradation of Pyrene and Other PAHs by the Bacterium Acinetobacter johnsonii. Ecotoxicol. Environ. Saf. 2018, 163, 465–470. DOI: 10.1016/j.ecoenv.2018.07.065.
  • Amobonye, A.; Bhagwat, P.; Singh, S.; Pillai, S. Plastic Biodegradation: Frontline Microbes and Their Enzymes. Sci. Total Environ. 2021, 759, 143536. DOI: 10.1016/j.scitotenv.2020.143536.
  • Singh Jadaun, J.; Bansal, S.; Sonthalia, A.; Rai, A. K.; Singh, S. P. Biodegradation of Plastics for Sustainable Environment. Bioresour. Technol. 2022, 347, 126697. DOI: 10.1016/j.biortech.2022.126697.
  • Tang, P.; Xie, W.; Tiraferri, A.; Zhang, Y.; Zhu, J.; Li, J.; Lin, D.; Crittenden, J. C.; Liu, B. Organics Removal from Shale Gas Wastewater by Pre-Oxidation Combined with Biologically Active Filtration. Water Res. 2021, 196, 117041. DOI: 10.1016/j.watres.2021.117041.
  • Miao, Y.; Heintz, M. B.; Bell, C. H.; Johnson, N. W.; Polasko, A. L.; Favero, D.; Mahendra, S. Profiling Microbial Community Structures and Functions in Bioremediation Strategies for Treating 1,4-Dioxane-Contaminated Groundwater. J. Hazard Mater. 2021, 408, 124457. DOI: 10.1016/j.jhazmat.2020.124457.
  • Kawamura, Y.; Fujiwara, N.; Naka, T.; Mitani, A.; Kubota, H.; Tomida, J.; Morita, Y.; Hitomi, J. Genus Enhydrobacter Staley et al. 1987 Should Be Recognized as a Member of the Family Rhodospirillaceae within the Class Alphaproteobacteria. Microbiol. Immunol. 2012, 56, 21–26.
  • Baek, S. H.; Im, W. T.; Oh, H. W.; Lee, J. S.; Oh, H. M.; Lee, S. T. Brevibacillus ginsengisoli sp. nov., a Denitrifying Bacterium Isolated from Soil of a Ginseng Field. Int. J. Syst. Evol. Microbiol. 2006, 56, 2665–2669. DOI: 10.1099/ijs.0.64382-0.
  • Premalatha, N.; Gopal, N. O.; Jose, P. A.; Anandham, R.; Kwon, S. W. Optimization of Cellulase Production by Enhydrobacter sp. ACCA2 and Its Application in Biomass Saccharification. Front Microbiol. 2015, 6, 1046.
  • Wang, M.; Wang, C.; Yang, C.; Peng, L.; Xie, Q.; Zheng, R.; Dai, Y.; Liu, S.; Peng, X. Effects of Lactobacillus plantarum C7 and Staphylococcus warneri S6 on Flavor Quality and Bacterial Diversity of Fermented Meat Rice, a Traditional Chinese Food. Food Res. Int. 2021, 150, 110745. DOI: 10.1016/j.foodres.2021.110745.
  • Shen, L. D.; He, Z. F.; Wu, H. S.; Gao, Z. Q. Nitrite-Dependent Anaerobic Methane-Oxidising Bacteria: unique Microorganisms with Special Properties. Curr. Microbiol. 2015, 70, 562–570. DOI: 10.1007/s00284-014-0762-x.
  • Elumalai, P.; P, P.; Huang, M.; Muthukumar, B.; Cheng, L.; Govarthanan, M.; Rajasekar, A. Enhanced Biodegradation of Hydrophobic Organic Pollutants by the Bacterial Consortium: Impact of Enzymes and Biosurfactants. Environ. Pollut. 2021, 289, 117956. DOI: 10.1016/j.envpol.2021.117956.
  • Mai, Z.; W, L.; Li, Q.; Sun, Y.; Zhang, S. Biodegradation and Metabolic Pathway of Phenanthrene by a Newly Isolated Bacterium Gordonia sp. SCSIO19801. Biochem. Biophys. Res. Commun. 2021, 585, 42–47. DOI: 10.1016/j.bbrc.2021.10.069.
  • Shintani, M.; S, K.; Sakurai, T.; Yamada, K.; Kimbara, K. Biodegradation of A-Fuel Oil in Soil Samples with Bacterial Mixtures of Rhodococcus and Gordonia Strains under Low Temperature Conditions. 2018, 127, 197–200.
  • Shrestha, R.; Černoušek, T.; Stoulil, J.; Kovářová, H.; Sihelská, K.; Špánek, R.; Ševců, A.; Steinová, J. Anaerobic Microbial Corrosion of Carbon Steel under Conditions Relevant for Deep Geological Repository of Nuclear Waste. Sci. Total Environ. 2021, 800, 149539. DOI: 10.1016/j.scitotenv.2021.149539.
  • Yang, J.; Wang, J.; Li, A.; Li, G.; Zhang, F. Disturbance, Carbon Physicochemical Structure, and Soil Microenvironment Codetermine Soil Organic Carbon Stability in Oilfields. Environ. Int. 2020, 135, 105390. DOI: 10.1016/j.envint.2019.105390.
  • Chukwuma, O. B.; Rafatullah, M.; Tajarudin, H. A.; Ismail, N. Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential. Life (Basel) 2021, 11, 493. DOI: 10.3390/life11060493.
  • Henry, C. S.; Bernstein, H. C.; Weisenhorn, P.; Taylor, R. C.; Lee, J. Y.; Zucker, J.; Song, H. S. Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction. J. Cell Physiol. 2016, 231, 2339–2345. DOI: 10.1002/jcp.25428.
  • Bhatt, P.; Bhatt, K.; Sharma, A.; Zhang, W.; Mishra, S.; Chen, S. Biotechnological Basis of Microbial Consortia for the Removal of Pesticides from the Environment. Crit. Rev. Biotechnol. 2021, 41, 317–338. DOI: 10.1080/07388551.2020.1853032.
  • Qian, X.; Chen, L.; Sui, Y.; Chen, C.; Zhang, W.; Zhou, J.; Dong, W.; Jiang, M.; Xin, F.; Ochsenreither, K. Biotechnological Potential and Applications of Microbial Consortia. Biotechnol. Adv. 2020, 40, 107500. DOI: 10.1016/j.biotechadv.2019.107500.
  • Lin, Z.; Pang, S.; Zhou, Z.; Wu, X.; Li, J.; Huang, Y.; Zhang, W.; Lei, Q.; Bhatt, P.; Mishra, S.; Chen, S. Novel Pathway of Acephate Degradation by the Microbial Consortium ZQ01 and Its Potential for Environmental Bioremediation. J. Hazard Mater. 2022, 426, 127841. DOI: 10.1016/j.jhazmat.2021.127841.
  • Wittebolle, L.; Marzorati, M.; Clement, L.; Balloi, A.; Daffonchio, D.; Heylen, K.; De Vos, P.; Verstraete, W.; Boon, N. Initial Community Evenness Favours Functionality under Selective Stress. Nature 2009, 458, 623–626. DOI: 10.1038/nature07840.
  • Puentes-Tellez, P. E.; Falcao Salles, J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. Microb. Ecol. 2018, 76, 419–429. DOI: 10.1007/s00248-017-1141-5.

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