Estudio de la microbiota degradadora de hidrocarburos en suelos mediante técnica metagenómica
DOI:
https://doi.org/10.18041/2323-0320/microciencia..2023.12603Palabras clave:
Hidrocarburos, Metagenómica, Biorremediación, Biología molecularResumen
A través de los años, los hidrocarburos han sido una de las principales fuentes de energía del planeta, por lo tanto, existe un alto riesgo de que el medio ambiente se vea contaminado por ellos. Una de las estrategias usadas para lidiar con esta problemática es la biorremediación; en la cual se hace uso de microorganismos con la capacidad de degradar estos contaminantes en compuestos menos tóxicos. Esto ha hecho necesario que se empleen técnicas para la identificación de estos microorganismos que presentan la capacidad de degradar hidrocarburos para su posterior uso en ensayos de biorremediación. Este artículo de revisión tiene como objeto actualizar el conocimiento sobre técnicas para la determinación de organismos que trabajan en consorcio para degradar hidrocarburos en suelos contaminados, utilizando técnicas moleculares de metagenómica y presentar los marcadores moleculares más utilizados; además, se hará una revisión de las enzimas producidas por estor organismos con potencial degradador y se abordará el papel de la bioinformática en los estudios metagenómicos. Basados en fuentes bibliográficas, se mostrarán los microorganismos comúnmente identificados en estos estudios.
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1. Koshlaf, E., Shahsavari, E., Haleyur, N., Mark Osborn, A., & Ball, A. (2019). Effect of biostimulation on the distribution and composition of the microbial community of a polycyclic aromatic hydrocarboncontaminated landfill soil during bioremediation. Geoderma, 338, 216-225.
2. Elangovan, S., Pandian, S., S. J., G., & Joshi, S. (2019). Polychlorinated Biphenyls (PCBs): Environmental Fate, Challenges and Bioremediation. Microorganisms For Sustainability, 165-188.
3. . Košnář, Z., Částková, T., Wiesnerová, L., Praus, L., Jablonský, I., Koudela, M., & Tlustoš, P. (2019). Comparing the removal of polycyclic aromatic hydrocarbons in soil after different bioremediation approaches in relationto the extracellular enzyme activities. Journal Of Environmental Sciences, 76, 249- 258.
4 Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6), 745-755.
5. Napp, A., Pereira, J., Oliveira, J., SilvaPortela, R., Agnez-Lima, L., & Peralba, M. et al. (2018). Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste. Chemosphere, 209,7-16.
6. Breitwieser, F. P., Lu, J., & Salzberg, S. L. (2019). A review of methods and databases for metagenomic classification and assembly. Briefings in bioinformatics, 20(4), 1125- 1136.
7. Zafra, G., Taylor, T., Absalón, A., & Cortés-Espinosa, D. (2016). Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium. Journal Of Hazardous Materials, 318, 702-710.
8. Chang, C. Y., Li, Y. C., Chen, N. C., Huang, X. X., & Lu, Y. C. (2016, November). A special processor design for nucleotide basic local alignment search tool with a new banded two-hit method. In 2016 IEEE Nordic Circuits and Systems Conference (NORCAS) (pp. 1-5). IEEE.
9. Bao, Y., Xu, Z., Li, Y., Yao, Z., Sun, J., & Song, H. (2017). High-throughput metagenomic analysis of petroleumcontaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism. Journal Of Environmental Sciences, 56, 25-35.
10. Kamble, A., Sawant, S., & Singh, H. (2020). 16S ribosomal RNA gene-based metagenomics: A review. Biomedical Research Journal, 7(1), 5.
11. Fajarningsih, N. D. (2016). Internal Transcribed Spacer (ITS) as Dna Barcoding to Identify Fungal Species: A Review. Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology, 11(2), 37.
12. DeLong EF (1992). Archaea in coastal marine environments. Proceedings of the National Academy of Sciences of the United States of America;89(12):5685-5689.
13. Covacevich, F. (2012). First archaeal rDNA sequences from Argentine coastal waters: Unexpected PCR characterization using eukaryotic primers. Ciencias Marinas, 38(2), 427-439.
14. Nejstgaard, J., Frischer, M., Raule, C., Gruebel, R., Kohlberg, K., & Verity, P. (2003). Molecular detection of algal prey in copepod guts and fecal pellets. Limnology And Oceanography: Methods, 1(1), 29-38.
15. Martin, Kendall & Rygiewicz, Paul. (2005). Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC microbiology. 5. 28.
16. . Varjani, S. J., &;Upasani, V. N. (2013). Comparative studies on bacterial consortia for hydrocarbon degradation. Screening, 2(10), 5377-5383.
17. Kale, S. K., &;Deshmukh, A. G. (2016). 3D structure prediction of lignolytic enzymes lignin peroxidase and manganese peroxidase based on homology modelling. Journal of BioScience& Biotechnology, 5(1).
18. Kües, U. (2015). Fungal enzymes for environmental management. Current Opinion In Biotechnology, 33, 268-278
19. Ghosh, A., Dastidar, M.G., Sreekrishnan, T.R., 2017. Bioremediation of chromium complex dyes and treatment of sludge generated during the process. Int. Biodeterior. Biodegrad. 119, 448-460
20. Upadhyay, P., Shrivastava, R., & Agrawal, P. (2016). Bioprospecting and biotechnological applications of fungal laccase. 3 Biotech, 6(1).
21. Sharma, B., Dangi, A. K., & Shukla, P. (2018). Contemporary enzyme based technologies for bioremediation: A review. Journal of Environmental Management, 210, 10–22.
22. Abdel-Shafy, H. I., & Mansour, M. S. M. (2016, March 1). A review on polycyclic aromatic hydrocarbons: Source, environmental impact, effect on human health and remediation. Egyptian Journal of Petroleum. Egyptian Petroleum Research Institute.
23. Escobar-Zepeda, A., Vera-Ponce de León, A., & Sanchez-Flores, A. (2015). MoghThe road to metagenomics: from microbiology to DNA sequencing technologies and bioinformatics. Frontiers in genetics, 6, 348.
24. . Raggi, L., García-Guevara, F., GodoyLozano, E. E., Martínez-Santana, A., - Zepeda, A., Gutierrez-Rios, R. M., Loza, A., Merino, E., Sanchez-Flores, A., LiceaNavarro, A., Pardo-Lopez, L., Segovia, L., & Juarez, K. (2020). Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico. Frontiers in microbiology, 11, 1825.
25. van Aerle, R., & van der Giezen, M. (2017). Next-generation sequencing, bioinformatics, and infectious diseases. Genetics and Evolution of Infectious Diseases, 405.
26. Moghimi, H., Heidary Tabar, R., & Hamedi, J. (2017). Assessing the biodegradation of polycyclic aromatic hydrocarbons and laccase production by new fungus Trematophoma sp. UTMC 5003. World Journal Of Microbiology And Biotechnology, 33(7).
27. Moreno-Ulloa, A., Diaz, V., TejedaMora, J., Macias Contreras, M., Díaz Castillo, F., & Guerrero, A. et al. (2019). Metabolic and metagenomic profiling of hydrocarbondegrading microorganisms obtained from the deep biosphere of the Gulf of México.
28. Mukherjee, A., Chettri, B., Langpoklakpam, J. S., Basak, P., Prasad, A., Mukherjee, A. K.& Chattopadhyay, D. (2017). Bioinformatic approaches including predictive metagenomic profiling reveal characteristics of bacterial response to petroleum hydrocarbon contamination in diverse environments. Scientific reports, 7(1), 1-22.
29. Hernández-León R, I VelázquezSepúlveda, MC Orozco-Mosqueda, G Santoyo. (2010). Metagenómica de suelos: grandes desafíos y nuevas oportunidades biotecnológicas. FYTON ISSN 0031 9457, (2010) 79: 133-139
30. Martínez Álvarez, L. M., Lo Balbo, A., Mac Cormack, W. P., & Ruberto, L. A. M. (2015). Bioremediation of a petroleum hydrocarbon-contaminated Antarctic soil: Optimization of a biostimulation strategy using response-surface methodology (RSM). Cold Regions Science and Technology, 119, 61–67.
31. Bharagava, R. N., Purchase, D., Saxena, G., &; Mulla, S. I. (2019). Applications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup. In Microbial diversity in the genomic era (pp. 459-477). Academic Press
32. Yu, Y., Yin, H., Huang, W., Peng, H., Lu, G., &; Dang, Z. (2020). Cellular changes of microbial consortium GY1 during decabromodiphenyl ether(BDE-209) biodegradation and identification of strains responsible for BDE-209 degradation in GY1. Chemosphere, 249, 126205.
33. Prenafeta-Boldú, F., de Hoog, G., & Summerbell, R. (2018). Fungal Communities in Hydrocarbon Degradation. Microbial Communities Utilizing Hydrocarbons And Lipids: Members, Metagenomics And Ecophysiology, 1-36.
34. Bhatt, P., Pathak, V. M., Joshi, S., Bisht, T. S., Singh, K., &; Chandra, D. (2019). Major metabolites after degradation of xenobiotics and enzymes involved in these pathways. Smart Bioremediation Technologies, 205–215.
35. Mojiri, A., Zhou, J. L., Ohashi, A., Ozaki, N., &; Kindaichi, T. (2019). Comprehensive review of polycyclic aromatic hydrocarbons in wáter sources, their effects and treatments. Science of The Total Environment, 133971.
36. Rodríguez-Couto S. (2019) Fungal Laccase: A Versatile Enzyme for Biotechnological Applications. In: Yadav A., Mishra S., Singh S., Gupta A. (eds) Recent Advancement in White Biotechnology Through Fungi. Fungal Biology. Springer, Cham.
37. Sarkar, P., Roy, A., Pal, S., Mohapatra, B., Kazy, S., Maiti, M., & Sar, P. (2017). Enrichment and characterization of hydrocarbon-degrading bacteria from petroleum refinery waste as potent bioaugmentation agent for in situ bioremediation. Bioresource Technology, 242, 15-27.
38. Saxena, R., Dhakan, D., Mittal, P., Waiker, P., Chowdhury, A., Ghatak, A., & Sharma, V. (2017). Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Frontiers In Microbiology, 7.
39. Khudur, L. S., Shahsavari, E., Webster, G. T., Nugegoda, D., &; Ball, A. S. (2019). The impact of lead co-contamination on ecotoxicity and the bacterial community during the bioremediation of total petroleum hydrocarbon-contaminated soils. Environmental Pollution.
40. Tan, B., Jane Fowler, S., Laban, N., Dong, X., Sensen, C., Foght, J., & Gieg, L. (2015). Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. The ISME Journal, 9(9), 2028-2045.
41. Toth, C., Berdugo-Clavijo, C., O’Farrell, C., Jones, G., Sheremet, A., Dunfield, P., & Gieg, L. (2018). Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms, 6(3), 65.
42. Imam, A., Suman, S. K., Ghosh, D., &Kanaujia, P. K. (2019). Analytical approaches used in monitoring the bioremediation of hydrocarbons in petroleum-contaminated soil and sludge. TrACTrends in Analytical Chemistry.
43. Yadav, T. C., Pal, R. R., Shastri, S., Jadeja, N. B., & Kapley, A. (2015). Comparative metagenomics demonstrating different degradative capacity of activated biomass treating hydrocarbon contaminated wastewater. Bioresource Technology, 188, 24–32.
44. Ivshina, I. B., Kuyukina, M. S., &; Krivoruchko, A. V.(2017). HydrocarbonOxidizingBacteria and Their Potential in EcoBiotechnology and Bioremediation. Microbial Resources, 121–148.
45. Zhang, S., Hu, Z., & Wang, H. (2019). Metagenomic analysis exhibited the cometabolism of polycyclic aromatic hydrocarbons by bacterial community from estuarine sediment. Environment International, 129, 308-319.
46. Hazim, R. N., &; Al-Ani, M. A. (2019). Effect of Petroleum Hydrocarbons Contamination on Soil Microorganisms and Biodegradation. Rafidain Journal of Science, 28(1), 13-22.
47. Fritz, A., Hofmann, P., Majda, S. et al. (2019) CAMISIM: simulating metagenomes and microbial communities. Microbiome 7, 17
48. Ruiz, O. N., Brown, L. M., Radwan, O., Bowen, L. L., Gunasekera, T. S., Mueller, S. S., ... & Striebich, R. C. (2021). Metagenomic characterization reveals complex association of soil hydrocarbon-degrading bacteria. International Biodeterioration & Biodegradation, 157, 105161.
49. Eze, M. O., Hose, G. C., George, S. C., & Daniel, R. (2021). Diversity and metagenome analysis of a hydrocarbondegrading bacterial consortium from asphalt lakes located in Wietze, Germany. AMB Express, 11(1), 1-12.
50. Jurelevicius, D., Pereira, R. D. S., da Mota, F. F., Cury, J. C., de Oliveira, I. C., Rosado, A. S., ... & Seldin, L. (2022). Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon‐contaminated soils in King George Island, Maritime Antarctica. Geobiology, 20(1), 98-111
