The application of metagenomics in hydrocarbon resource management

Mordecai Gana , Jireh Taliya Kure and Usman Ahmadu

Abstract
The last 5-10 years has witness a new proven field of research where explanation have been provided to non-cultured microbes. This uncultured microorganisms forms the major group of organisms found in most environment of the Earth. The science of metagenomics makes it possible to investigate resources which can be used to develop new enzymes, genes and several chemical compounds for use in biotechnology. Studies of microorganisms in pure laboratory culture for over a century have led to significant advances into microbial genetics and physiology, biotechnology and molecular biology. The rapid advancement in sequencing technology has brought about drastic reduction cost of sequencing thereby leading to increasing sequencing project been undertaken. This advancement has provided the privilege for the continual use of this sequencing technology to monitor microbes in the environment which before now are not available. While metagenomic applications have been used to consistently have a better understanding of ecology and microbial diversity, it is pertinent to note that its application in environmental monitoring and application is commonly increasing and has been one of the research areas in focus. To this end this article seek to provide a general overview of what metagenmics is, its principle and application in hydrocarbon resource management.

Keywords
Metagenomics; Targeted metagenomics; Shotgun metagenomics; Petroleum; Bioremediation.

DOI
10.21472/bjbs.061310

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References
Baquiran, J. P. M. Application of metagenomics for identification of novel petroleum hydrocarbon degrading enzymes in natural asphalts from the Rancho La Brea Tar Pits. Riverside: University of Riverside, 2010. (Doctoral dissertation).

Behjati, S.; Tarpey, P. S. What is next generation sequencing? Archives of Disease in Childhood-Education and Practice, v. 98, no. 6, p. 236-238, 2013. https://doi.org/10.1136/archdischild-2013-304340

Bisht, S.; Pandey, P.; Bhargava, B.; Sharma, S.; Kumar, V.; Sharma, K. D. Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology. Brazilian Journal of Microbiology, v. 46, no. 1, p. 7-21, 2015. https://doi.org/10.1590/S1517-838246120131354

Chen, K.; Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Computational Biology, v. 1, no. 2, e24, 2005. https://doi.org/10.1371/journal.pcbi.0010024

Delmont, T. O.; Simonet, P.; Vogel, T. M. Describing microbial communities and performing global comparisons in the 'omic era. International Society of Microbial Ecology Journal, v. 6, no. 9, p. 1625-1628, 2012. https://doi.org/10.1038/ismej.2012.55

Deutschbauer, A. M.; Chivian, D.; Arkin, A. P. Genomics for environmental microbiology. Current Opinion in Biotechnology, v. 17, no. 3, p. 229-235, 2006. https://doi.org/10.1016/j.copbio.2006.04.003

Dua, M.; Singh, A.; Sethunathan, N.; Johri, A. Biotechnology and bioremediation: Successes and limitations. Applied Microbiology and Biotechnology, v. 59, no. 2/3, p. 143-152, 2002. https://doi.org/10.1007/s00253-002-1024-6

Ferrer, M.; Golyshina, O.; Beloqui, A.; Golyshin, P. N. Mining enzymes from extreme environments. Current Opinion in Microbiology, v. 10, no. 3, p. 207-214, 2007. https://doi.org/10.1016/j.mib.2007.05.004

Galvão, T. C.; Mohn, W. W.; Lorenzo, V. Exploring the microbial biodegradation and biotransformation gene pool. Trends in Biotechnology, v. 23, no. 10, p. 497-506, 2005. https://doi.org/10.1016/j.tibtech.2005.08.002

García Martín, H.; Ivanova, N.; Kunin, V.; Warnecke, F.; Barry, K. W.; McHardy, A. C.; Yeates, C.; He, S.; Salamov, A. A.; Szeto, E.; Dalin, E.; Putnam, N. H.; Shapiro, H. J.; Pangilinan, J. L.; Rigoutsos, I.; Kyrpides, N. C.; Blackall, L. L.; McMahon, K. D.; Hugenholtz, P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology, v. 24, no. 10, p. 1263, 2006. https://doi.org/10.1038/nbt1247

Grabowski, A.; Nercessian, O.; Fayolle, F.; Blanchet, D.; Jeanthon, C. Microbial diversity in production waters of a low-temperature biodegraded oil reservoir. FEMS Microbiology Ecology, v. 54, no. 3, 427-443, 2005. https://doi.org/10.1016/j.femsec.2005.05.007

Handelsman, J.; Rondon, M. R.; Brady, S. F.; Clardy, J.; Goodman, R. M. Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chemistry & Biology, v. 5, no. 10, p. R245-R249, 1998. https://doi.org/10.1016/S1074-5521(98)90108-9

Henkel, M.; Müller, M. M.; Kügler, J. H.; Lovaglio, R. B.; Contiero, J.; Syldatk, C.; Hausmann, R. Rhamnolipids as biosurfactants from renewable resources: Concepts for next-generation rhamnolipid production. Process Biochemistry, v. 47, no. 8, p. 1207-1219, 2012. https://doi.org/10.1016/j.procbio.2012.04.018

Jacques, R. J. S.; Bento, F. M.; Antoniolli, Z. I.; Camargo, F. A. D. O. Biorremediação de solos contaminados com hidrocarbonetos aromáticos policíclicos. Ciência Rural, v. 37, n. 4, p. 1192-1201, 2007. https://doi.org/10.1590/S0103-84782007000400049

Kennedy, J.; O'leary, N. D.; Kiran, G. S.; Morrissey, J. P.; O'Gara, F.; Selvin, J.; Dobson, A. D. W. Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems. Journal of Applied Microbiology, v. 111, no. 4, p. 787-799, 2011. https://doi.org/10.1111/j.1365-2672.2011.05106.x

Kuiper, I.; Lagendijk, E. L.; Bloemberg, G. V.; Lugtenberg, B. J. Rhizoremediation: A beneficial plant-microbe interaction. Molecular Plant-Microbe Interactions, v. 17, no. 1, p. 6-15, 2004. https://doi.org/10.1094/MPMI.2004.17.1.6

Kure, J. T.; Gana, M.; Emmanuel, A.; Isah, R. M.; Ukubuiwe, C. C. Bacteria associated with heavy metal bioremediation: A review. International Journal of Applied Biological Research, v. 9, no. 1, p. 134-148, 2018.

Li, H.; Yang, S. Z.; Mu, B. Z.; Rong, Z. F.; Zhang, J. Molecular analysis of the bacterial community in a continental high-temperature and water-flooded petroleum reservoir. FEMS Microbiology Letters, v. 257, no. 1, p. 92-98, 2006. https://doi.org/ 10.1111/j.1574-6968.2006.00149.x

Marcos, M. S.; Lozada, M.; Dionisi, H. M. Aromatic hydrocarbon degradation genes from chronically polluted Subantarctic marine sediments. Letters in Applied Microbiology, v. 49, no. 5, p. 602-608, 2009. https://doi.org/10.1111/j.1472-765X.2009.02711.x

Morikawa, M.; Ito, M.; Imanaka, T. Isolation of a new surfactin producer Bacillus pumilus A-1, and cloning and nucleotide sequence of the regulator gene, psf-1. Journal of Fermentation and Bioengineering, v. 74, no. 5, p. 255-261, 1992. https://doi.org/10.1016/0922-338X(92)90055-Y

Ollivier, B.; Magot, M. (Eds.). Petroleum microbiology. Washington, DC: ASM Press, 2005.

Ono, A.; Miyazaki, R.; Sota, M.; Ohtsubo, Y.; Nagata, Y.; Tsuda, M. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Applied Microbiology and Biotechnology, v. 74, no. 2, p. 501-510, 2007. https://doi.org/10.1007/s00253-006-0671-4

Paul, D.; Pandey, G; Pandey, J; Jain, R. K. Accessing microbial diversity for bioremediation and environmental restoration. Trends in Biotechnology, v. 23, no. 3, p. 135-142, 2005. https://doi.org/10.1016/j.tibtech.2005.01.001

Rabus, R.; Kube, M.; Heider, J.; Beck, A.; Heitmann, K.; Widdel, F.; Reinhardt, R. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Archives of Microbiology, v. 183, no. 1, p. 27-36, 2005. https://doi.org/10.1007/s00203-004-0742-9

Rahman, M. E. A. Biodegradation of crude oil by bacteria isolated from produced formation water of an onshore oil field in Sudan. Khartoum: University of Khartoum, 2011. (Doctoral dissertation).

Riesenfeld, C. S.; Schloss, P. D.; Handelsman, J. Metagenomics: Genomic analysis of microbial communities. Annual Reviews of Genetics, v. 38, p. 525-552, 2004. https://doi.org/10.1146/annurev.genet.38.072902.091216

Roy, A. A review on the biosurfactants: Properties, types and its applications. Journal of Fundamental Renewable Energy Application, 8:1, 2017. https://doi.org/10.4172/2090-4541.1000248

Salanitro, J. P. Bioremediation of petroleum hydrocarbons in soil. Advances in Agronomy, v. 72, no. 53, p. 105, 2001.

Satpute, S. K.; Banat, I. M.; Dhakephalkar, P. K.; Banpurkar, A. G.; Chopade, B. A. Biosurfactants, bioemulsifiers and exopolysaccharides from marine microorganisms. Biotechnology Advances, v. 28, no. 4, p. 436-450, 2010. https://doi.org/10.1016/j.biotechadv.2010.02.006

Sierra-García, I. N.; Alvarez, J. C.; Vasconcellos, S. P.; Souza, A. P.; Santos Neto, E. V.; Oliveira, V. M. New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. PLoS ONE, v. 9, p. 2, e90087, 2014. https://doi.org/10.1371/journal.pone.0090087

Simon, C.; Daniel, R. Metagenomic analyses: Past and future trends. Applied and Environmental Microbiology, v. 77, no. 4, 1153-1161, 2011. https://doi.org/10.1128/AEM.02345-10

Suenaga, H.; Ohnuki, T.; Miyazaki, K. Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environmental Microbiology, v. 9, no. 9, 2289-2297, 2007. https://doi.org/10.1111/j.1462-2920.2007.01342.x

Techtmann, S. M.; Hazen, T. C. Metagenomic applications in environmental monitoring and bioremediation. Journal of Industrial Microbiology & Biotechnology, v. 43, no. 10, p. 1345-1354, 2016. https://doi.org/10.1007/s10295-016-1809-8

Thomas, T.; Gilbert, J.; Meyer, F. Metagenomics: A guide from sampling to data analysis. Microbial Informatics and Experimentation, 2:3, 2012. https://doi.org/10.1186/2042-5783-2-3

Van Hamme, J. D.; Singh, A.; Ward, O. P. Recent advances in petroleum microbiology. Microbiology and Molecular Biology Reviews, v. 67, no. 4, p. 503-549, 2003. https://doi.org/10.1128/mmbr.67.4.503-549.2003

Vieites, J. M.; Guazzaroni, M.-E.; Beloqui, A.; Golyshin, P. N.; Ferrer, M. Metagenomics approaches in systems microbiology. FEMS Microbiology Reviews, v. 33, no. 1, p. 236-255, 2008. https://doi.org/10.1111/j.1574-6976.2008.00152.x

Wang, J.; Ma, T.; Zhao, L.; Lv, J.; Li, G.; Liang, F.; Liu, R. PCR-DGGE method for analyzing the bacterial community in a high temperature petroleum reservoir. World Journal of Microbiology and Biotechnology, v. 24, no. 9, p. 1981-1987, 2008. https://doi.org/10.1007/s11274-008-9694-6

Wexler, M.; Bond, P. L.; Richardson, D. J.; Johnston, A. W. A wide host-range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase. Environmental Microbiology, v. 7, no. 12, p. 1917-1926, 2005. https://doi.org/10.1111/j.1462-2920.2005.00854.x

Williams, W.; Trindade, M. Metagenomics for the discovery of novel biosurfactants. In: Charles, T.; Liles, M.; Sessitsch, A. (Eds.). Functional metagenomics: Tools and applications. Cham: Springer, 2017. p. 95-117. https://doi.org/10.1007/978-3-319-61510-3_6

Xiong, M.; Zhao, Z.; Arnold, J.; Yu, F. Next-generation sequencing. BioMedical Research International, v. 2010, Article ID 370710, 2010. https://doi.org/10.1155/2010/370710

Yoshida, N.; Yagi, K.; Sato, D.; Watanabe, N.; Kuroishi, T.; Nishimoto, K.; Tani, Y. Bacterial communities in petroleum oil in stockpiles. Journal of Bioscience and Bioengineering, v. 99, no. 2, p. 143-149, 2005. https://doi.org/10.1263/jbb.99.143



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