Microbial diversity assessment of polychlorinated biphenyl–contaminated soils and the biostimulation and bioaugmentation processes

  • Elsa Cervantes-GonzálezEmail author
  • Mariela Anelhayet Guevara-García
  • Jaime García-Mena
  • Víctor Manuel Ovando-Medina


The aim of this study was to know the biodiversity of total microorganisms contained in two polychlorinated biphenyl-contaminated aged soils and evaluate the strategies of bioaugmentation and biostimulation to biodegrade the biphenyls. Besides, the aerobic cultivable microorganisms were isolated and their capacity to biodegrade a commercial mixture of six congeners of biphenyls was evaluated. Biodiversity of contaminated soils was dominated by Actinobacteria (42.79%) and Firmicutes (42.32%) phyla, and others in smaller proportions such as Proteobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes. At the genus level, the majority of the population did not exceed 7% of relative abundance, including Bacillus, Achromobacter, Clostridium, and Pontibacter. Furthermore, four autochthonous bacterial cultures were possible isolates from the soils, which were identified by partial sequencing of the 16S rRNA gene, as Bacillus sp., Achromobacter sp., Pseudomonas stutzeri, and Bacillus subtilis, which were used for the bioaugmentation process. The bioaugmentation and biostimulation strategies achieved a biodegradation of about 60% of both soils after 8 weeks of the process; also, the four isolates were used as mixed culture to biodegrade a commercial mix of six polychlorinated biphenyl congeners; after 4 weeks of incubation, the concentration decreased from 0.5 mg/L to 0.23 mg/L.


Autochthonous microbial communities Bioaugmentation Biostimulation DNA sequencing Polychlorinated biphenyls 



The authors sincerely thank Dra. Elvira Rios Leal for her support in the analysis of samples by GC-ECD, and the Biologist Alberto Piña Escobedo for his help in the massive sequencing, both from Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional.

Funding information

This research was funded by CONACyT-163235 INFR-2011-01.


  1. Ahmed, M., & Focht, D. D. (1973). Degradation of polychlorinated biphenyls by two species of Achromobacter. Canadian Journal of Microbiology, 19(1), 47–52.Google Scholar
  2. Al-Amoudi, S., Razali, R., Essack, M., Amini, M. S., Bougouffa, S., Archer, J. A., Lafi, F. F., & Bajic, V. B. (2016). Metagenomics as a preliminary screen for antimicrobial bioprospecting. Gene, 594(2), 248–258.Google Scholar
  3. Bray, R. H., & Kurtz, L. T. (1945). Determination of total, organic and available form of phosphorus in soil. Soil Science., 59(1), 360–361.Google Scholar
  4. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung, M., Reeder, J., Sevinsky, J. R., Turnbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko, T., Zaneveld, J., & Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335–336.Google Scholar
  5. Chen, F., Hao, S., Qu, J., Ma, J., & Zhang, S. (2015). Enhanced biodegradation of polychlorinated biphenyls by defined bacteria-yeast consortium. Annals of Microbiology, 65(4), 1847–1854.Google Scholar
  6. Correa, P. A., Lin, L., Just, C. L., Hu, D., Hornbuckle, K. C., Schnoor, J. L., & Van Aken, B. (2010). The effects of individual PCB congeners on the soil bacterial community structure and the abundance of biphenyl dioxygenase genes. Environment International, 36(8), 901–906.Google Scholar
  7. De, J., Ramaiah, N., & Sarkar, A. (2006). Aerobic degradation of highly chlorinated polychlorobiphenyls by a marine bacterium, Pseudomonas CH07. World Journal of Microbiology and Biotechnology, 22(12), 1321–1327.Google Scholar
  8. Delgado-Baquerizo, M., Reich, P. B., Khachane, A. N., Campbell, C. D., Thomas, N., Freitag, T. E., Al-Soud, W. A., Sørensen, S., Bardgett, R. D., & Singh, B. K. (2017). It is elemental: soil nutrient stoichiometry drives bacterial diversity. Environmental Microbiology, 19(3), 1176–1188.Google Scholar
  9. Dubey, S. K., Tripathi, A. K., & Upadhyay, S. N. (2006). Exploration of soil bacterial communities for their potential as bioresource. Bioresource Technology, 97(17), 2217–2224.Google Scholar
  10. Dudasova, H., Derco, J., Sumegova, L., Dercova, K., & Laszlova, K. (2017). Removal of polychlorinated biphenyl congeners in mixture Delor 103 from wastewater by ozonation vs/and biological method. Journal of Hazardous Materials, 321, 54–61.Google Scholar
  11. Dudášová, H., Lukáčová, L., Murínová, S., Puškárová, A., Pangallo, D., & Dercová, K. (2012). Bacterial strains isolated from PCB-contaminated sediments and their use for bioaugmentation strategy in microcosms. Journal of Basic Microbiology, 54(4), 253–260.Google Scholar
  12. Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460–2461.Google Scholar
  13. Egorova, D. O., Demakov, V. A., & Plotnikova, E. G. (2011). Destruction of mixture of tri-hexa-chlorinated biphenyls by Rhodococcus genus strains. Applied Biochemistry and Microbiology, 47(6), 599–606.Google Scholar
  14. Fagervold, S. K., Watts, J. E., May, H. D., & Sowers, K. R. (2011). Effects of bioaugmentation on indigenous PCB dechlorinating activity in sediment microcosms. Water Research, 45(13), 3899–3907.Google Scholar
  15. Faroon, O., Keith, L., Smith-Simon, C., & De Rosa, C. (2003). Polychlorinated biphenyls: human health aspects. In Concise International Chemical Assessment Document 55, (pp. 1-58). World Health Organization.Google Scholar
  16. Fava, F., Bertin, L., Fedi, S., & Zannon, D. (2003). Methyl-beta-cyclodextrin enhanced solubilization and aerobic biodegradation of polychlorinated biphenyls in two aged-contaminated soils. Biotechnology and Bioengineering, 81(4), 381–390.Google Scholar
  17. Fernández Linares, L. C., Rojas Avelizapa, N. G., Roldán Carrillo, T.G., Ramírez Islas, M.E., Zegarra Martínez, H. G., Uribe Hernández, R., & Arce Ortega, J. M. (2006). Manual de técnicas de análisis de suelos aplicadas a la remediación de sitios contaminados. Secretaría de Medio Ambiente y Recursos Naturales, Instituto Nacional de Ecología, Instituto Mexicano del Petróleo. México.Google Scholar
  18. Field, J. A., & Sierra-Alvarez, R. (2008). Microbial transformation and degradation of polychlorinated biphenyls. Environmental Pollution, 155(1), 1–12.Google Scholar
  19. Fierer, N., Hamady, M., Lauber, C. L., & Knight, R. (2008). The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proceedings of the National Academy of Sciences of the United States, 105(46), 17994–17999.Google Scholar
  20. Hatamian-Zarmi, A., Shojaosadati, S. A., Vasheghani-Farahani, E., Hosseinkhani, E., & Emamzadeh, A. (2009). Extensive biodegradation of higly chlorinated biphenyl and Aroclor 1242 by Pseudomonas aeruginosa TMU56 isolated from contaminated soils. International Biodeterioration and Biodegradation, 63(6), 788–794.Google Scholar
  21. Hembree, D. M., Smyrl, N. R., Davis, W. E., & Williams, D. M. (1993). Isomeric characterization of polychlorinated biphenyls using gas chromatography-Fourier transform infrared/gas chromatography-mass spectrometry. Analyst, 118(3), 249–252.Google Scholar
  22. Hong, Q., Dong, X., He, L., Jiang, X., & Li, S. (2009). Isolation of a biphenyl-degrading bacterium, Achromobacter sp. BP3, and cloning of the bph gene cluster. International Biodeterioration and Biodegradation, 63(4), 365–370.Google Scholar
  23. Kjeldahl, J. (1883). Neue Methode zur bestimmung des stickstoffs in organischen Körpern. Fresenius Journal of Analytical Chemistry, 22(1), 366–382.Google Scholar
  24. Lehtinen, T., Mikkonen, A., Sigfusson, B., Ólafsdóttir, K., Ragnarsdóttir, K. V., & Guicharnaud, R. (2014). Bioremediation trial on aged PCB-polluted soils—a bench study in Iceland. Environmental Science and Pollution Research, 21(3), 1759–1768.Google Scholar
  25. Lunt, D., & Evans, W. C. (1970). The microbial metabolism of biphenyl. Biochemical Journal, 118(3), 54–55.Google Scholar
  26. Luo, W., D'Angelo, E. M., & Coyne, M. (2007). Plant secondary metabolites, biphenyl, and hydroxypropyl-beta-cyclodextrin effects on aerobic polychlorinated biphenyl removal and microbial community structure in soils. Soil Biology and Biochemistry, 39(3), 735–743.Google Scholar
  27. Macedo, A. J., Timmis, K. N., & Abraham, W. R. (2007). Widespread capacity to metabolize polychlorinated biphenyls by diverse microbial communities in soils with no significant exposure to PCB contamination. Environmental Miicrobiology, 9(8), 1890–1897.Google Scholar
  28. Mackova, M., Uhlik,O., Lovecka, P., Viktorova, J., Demnerova, K., Sylvestre, M., & Macek, T. (2010). Bacterial degradation of polychlorinated biphenyls. Geomicrobiology. Molecular and Environmental Perspective. 347–366.Google Scholar
  29. Manickam, N., Singh, N. K., Bajaj, A., Kumar, R. M., Kaur, G., Kaur, N., Bala, M., Kumar, A., & Mayilraj, S. (2014). Bacillus mesophilum sp. nov., strain IITR-54T, a novel 4-chlorobiphenyl dechlorinating bacterium. Archives of Microbiology, 196(7), 517–523.Google Scholar
  30. Matturro, B., Ubaldi, C., Grenni, P., Caracciolo, A. B., & Rossetti, S. (2015). Polychlorinated biphenyl (PCB) anaerobic degradation in marine sediments: microcosm study and role of autochthonous microbial communities. Environmental Science and Pollution Research, 23(13), 12613–12623.Google Scholar
  31. Murínová, S., Dercová, K., & Dudášová, H. (2014). Degradation of polychlorinated biphenyls (PCBs) by four bacterial isolates obtained from the PCB-contaminated soil and PCB-contaminated sediment. International Biodeterioration and Biodegradation, 91, 52–59.Google Scholar
  32. Passatore, L., Rossetti, S., Juwarkar, A. A., & Massacci, A. (2014). Phytoremediation and bioremediation of polychlorinated biphenyls (PCBs): state of knowledge and research perspectives. Journal of Hazardous Materials, 278, 189–202.Google Scholar
  33. Petric, I., Hrsak, D., Fingler, S., Udikovic-Kolić, N., Bru, D., & Martin-Laurent, F. (2011). Insight in the PCB-degrading functional community in long term contaminated soil under bioremediation. Journal of Soils and Sediments, 11(2), 290–300.Google Scholar
  34. Petrik, J., Drobna, B., Pavuk, M., Jursa, S., Wimmerova, S., & Chovancova, J. (2006). Serum PCBs and organochlorine pesticides in Slovakia: age, gender, and residence as determinants of organochlorine concentrations. Chemosphere, 65(3), 410–418.Google Scholar
  35. Pieper, D. H. (2005). Aerobic degradation of polychlorinated biphenyls. Applied Microbiology and Biotechnology, 67, 170–191.Google Scholar
  36. Qian, Y., Meng, G., Huang, Q., Zhu, C., Huang, Z., Sun, K., & Chen, B. (2014). Flexible membranes of Ag-nanosheet-grafted polyamide-nanofibers as effective 3D SERS substrates. Nanoscale, 6(9), 4781–4788.Google Scholar
  37. Romero-Torres, T., Cortinas de Nava, C., & Gutiérrez-Avedoy V. (2009) Diagnóstico nacional sobre la situación de los contaminantes orgánicos persistentes en México. Secretaría de Medio Ambiente y Recursos Naturales, Instituto Nacional de Ecología.Google Scholar
  38. Sharma, J. K., Gautam, R. K., Nanekar, S. V., Weber, R., Singh, B. K., Singh, S. K., & Juwarkar, A. A. (2017). Advances and perspective in bioremediation of polychlorinated biphenyl-contaminated soils. Environmental Science and Pollution Research, 17, 16355–16375.Google Scholar
  39. Skaare, J., Larsen, H. J., Lie, E., Bernhoft, A., Derocher, A. E., & Norstrom, R. (2012). Ecological risk assessment of persistent organic pollutants in the arctic. Toxicology, 181, 193–197.Google Scholar
  40. Stella, T., Covino, S., Burianová, E., Filipová, A., Křesinová, Z., Voříšková, J., Větrovský, T., Baldrian, P., & Cajthaml, T. (2015). Chemical and microbiological characterization of an aged PCB-contaminated soil. Science of Total Environmental, 533, 177–186.Google Scholar
  41. Stella, T., Covino, S., Čvančarová, M., Filipová, A., Petruccioli, M., D’Annibale, A., & Cajthaml, T. (2017). Bioremediation of long-term PCB-contaminated soil by white-rot fungi. Journal of Hazardous Materials, 324, 701–710.Google Scholar
  42. Su, X., Zhang, Q., Hu, J., Hashmi, M. Z., Ding, L., & Shen, C. (2015). Enhanced degradation of biphenyl from PCB-contaminated sediments: the impact of extracellular organic matter from Micrococcus luteus. Applied Microbiology and Biotechnology, 99(4), 1989–2000.Google Scholar
  43. Tandlich, R., Brežná, B., & Dercová, K. (2001). The effect of terpenes on the biodegradation of polychlorinated biphenyls by Pseudomonas stutzeri. Chemosphere, 44(7), 1547–1555.Google Scholar
  44. Tang, X., Qiao, J., Chen, C., Chen, L., Yu, C., Shen, C., & Chen, Y. (2013). Bacterial communities of polychlorinated biphenyls polluted soil around an e-waste recycling workshop. Soil and Sediment Contamination: An International Journal, 22(5), 562–573.Google Scholar
  45. Tu, C., Teng, Y., Luo, Y., Li, X., Sun, X., Li, Z., & Christie, P. (2011). Potential for biodegradation of polychlorinated biphenyls (PCBs) by Sinorhizobium meliloti. Journal of Hazardous Materials, 186(2), 1438–1444.Google Scholar
  46. Vrana, B., Dercova, K., Baláž, Š., & Ševčíková, A. (1996). Effect of chlorobenzoates on the degradation of polychlorinated biphenyls (PCB) by Pseudomonas stutzeri. World Journal of Microbiology and Biotechnology, 12(4), 323–326.Google Scholar
  47. Walkley, A., & Black, I. A. (1934). An examination of Degtjareff method for determining soil organic matter and a proposed modification of the chromic acid titration method. Soil Science, 37(1), 29–37.Google Scholar
  48. Wan, C., Du, M., Lee, D. J., Yang, X., Ma, W., & Zheng, L. (2011). Electrokinetic remediation and microbial community shift of β-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil. Applied Microbiology and Biotechnology, 89(6), 2019–2025.Google Scholar
  49. Wardle, D. A. (2006). The influence of biotic interactions on soil biodiversity. Ecology Letters, 9, 870–886.Google Scholar
  50. Whiteley, A. S., Jenkins, S., Waite, I., Kresoje, N., Payne, H., Mullan, B., Allcock, R., & O’Donnell, A. (2012). Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. Journal of Microbiological Methods, 91(1), 80–88.Google Scholar
  51. Wiegel, J., & Wu, Q. (2000). Microbial reductive dehalogenation of polychlorinated biphenyls. FEMS Microbiology Ecology, 32(1), 1–15.Google Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Chemical EngineeringUniversidad Autónoma de San Luis Potosí, Coordinación Académica Región AltiplanoMatehuala CityMexico
  2. 2.Department of Genetic and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalUnidad ZacatencoMexico City D.F.Mexico

Personalised recommendations