Advertisement

Denitrifying Microbial Community Structure and bamA Gene Diversity of Phenol Degraders in Soil Contaminated from the Coking Process

  • Yanan Li
  • Jing Li
  • Di Wang
  • Guoying WangEmail author
  • Xiuping Yue
  • Xin Kong
  • Lily Young
  • Weilin Huang
Article
  • 44 Downloads

Abstract

Phenolic compounds are the dominant pollutants in soils contaminated by the coking industry. Ring opening by the hydroxylase gene (bamA) is the key step in the benzoyl-CoA degradation pathway under anaerobic conditions, and a broad spectrum of microorganisms possesses this functional gene, including denitrifiers. The present study analyzed the community structure of denitrifying bacteria and the diversity of the bamA gene for mixed cultures enriched from soil collected at a coking industrial site and then grown under nitrate-reducing conditions on phenol or p-hydroxybenzoate (4HBA), a key intermediate product of anaerobic phenol degradation. Illumina sequencing of the 16S rRNA gene showed different bacterial compositions between the two cultures. The dominant phyla were Proteobacteria, Armatimonadetes, and Planctomycetes in the phenol culture and Proteobacteria and Bacteroidetes in the 4HBA culture. Phylogenetic analysis further demonstrated that bamA genes were associated with four clusters of bacteria, three of known bacteria and one of uncultured bacteria. The diversity of the bamA gene differed from that reported in anaerobic aromatic degradation cultures, suggesting that these enriched cultures may contain new strains unique to coking-contaminated soils. The present study further validates the potential application of this functional gene as a marker for anaerobic biodegradation processes in enrichment cultures from contaminated soil.

Keywords

Azoarcus bamA gene Denitrifiers Illumina sequencing p-Hydroxybenzoate Phenol 

Notes

Acknowledgments

Jianwei Wang is acknowledged for the helpful discussion in the design of the study and for the help with culture setting up. Jin Liu and Jingyi Fu are both thanked for collecting soil samples from the coking plant.

Funding Information

This study was supported by the Science and Technology Planning Project of Guangdong Province (No. 2017B030314092), Open Fund of Key Laboratory of Eco-geochemistry, Ministry of Natural Resources (No. ZSDHJJ201804), Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi (No. 2016146, 201802026), the Scientific and Technological Project of Shanxi Province (No. 2015021119), and the National Natural Science Foundation of China (No. 51378330, 51408396).

Compliance with Ethical Standards

Competing Interests

The authors declare that they have no competing interests.

Supplementary material

12010_2019_3144_MOESM1_ESM.docx (14 kb)
ESM 1 (DOCX 13 kb)

References

  1. 1.
    Ahmed, S., Rasul, M. G., Brown, R., & Hashib, M. A. (2011). Influence of parameters on the heterogeneous photocatalytic degradation of pesticides and phenolic contaminants in wastewater: a short review. Journal of Environmental Management, 92(3), 311–330.PubMedCrossRefPubMedCentralGoogle Scholar
  2. 2.
    Schie, P. M. V., & Young, L. Y. (1998). Isolation and characterization of phenol-degrading denitrifying bacteria. Applied and Environmental Microbiology, 64(7), 2432–2438.PubMedPubMedCentralGoogle Scholar
  3. 3.
    Schink, B., Philipp, B., & Müller, J. (2000). Anaerobic degradation of phenolic compounds. Naturwissenschaften, 87(1), 12–23.PubMedCrossRefPubMedCentralGoogle Scholar
  4. 4.
    Baek, S. H., Kim, K. H., Yin, C. R., Jeon, C. O., Im, W. T., Kim, K. K., & Lee, S. T. (2003). Isolation and characterization of bacteria capable of degrading phenol and reducing nitrate under low-oxygen conditions. Current Microbiology, 47(6), 462–466.PubMedCrossRefPubMedCentralGoogle Scholar
  5. 5.
    Li, Z., Suzuki, D., Zhang, C., Yang, S., Nan, J., & Yoshida, N. (2014). Anaerobic 4-chlorophenol mineralization in an enriched culture under iron-reducing conditions. Journal of Bioscience and Bioengineering, 118(5), 529–532.PubMedCrossRefPubMedCentralGoogle Scholar
  6. 6.
    Narmandakh, A., Gad’On, N., Drepper, F., Knapp, B., Haehnel, W., & Fuchs, G. (2006). Phosphorylation of phenol by phenylphosphate synthase: role of histidine phosphate in catalysis. Journal of Bacteriology, 188(22), 7815–7822.PubMedPubMedCentralCrossRefGoogle Scholar
  7. 7.
    Schmeling, S., Narmandakh, A., Schmitt, O., Gad’On, N., Schühle, K., & Fuchs, G. (2004). Phenylphosphate synthase: a new phosphotransferase catalyzing the first step in anaerobic phenol metabolism in Thauera aromatica. Journal of Bacteriology, 186(23), 8044–8057.PubMedPubMedCentralCrossRefGoogle Scholar
  8. 8.
    Schuhle, K., & Fuchs, G. (2004). Phenylphosphate carboxylase: a new C-C lyase involved in anaerobic phenol metabolism in Thauera aromatica. Journal of Bacteriology, 186(14), 4556–4567.PubMedPubMedCentralCrossRefGoogle Scholar
  9. 9.
    Kuntze, K., Shinoda, Y., Moutakki, H., Mcinerney, M. J., Vogt, C., & Richnow, H. H. (2008). 6-oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes. Environmental Microbiology, 10(6), 1547–1556.PubMedCrossRefPubMedCentralGoogle Scholar
  10. 10.
    Harwood, C. S., Burchhardt, G., Herrmann, H., & Fuchs, G. (1998). Anaerobic metabolism of aromatic compounds via the benzoyl-coA pathway. FEMS Microbiology Reviews, 22(5), 439–458.CrossRefGoogle Scholar
  11. 11.
    Boll, M., Löffler, C., Morris, B. E. L., & Kung, J. W. (2014). Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes. Environmental Microbiology, 16(3), 612–627.PubMedCrossRefPubMedCentralGoogle Scholar
  12. 12.
    Porter, A. W., & Young, L. Y. (2013). The bamA gene for anaerobic ring fission is widely distributed in the environment. Frontiers in Microbiology, 4, 302.PubMedPubMedCentralCrossRefGoogle Scholar
  13. 13.
    Higashioka, Y., Kojima, H., & Fukui, M. (2011). Temperature-dependent differences in community structure of bacteria involved in degradation of petroleum hydrocarbons under sulfate-reducing conditions. Journal of Applied Microbiology, 110(1), 314–322.PubMedCrossRefGoogle Scholar
  14. 14.
    Kuntze, K., Vogt, C., Richnow, H. H., & Boll, M. (2011). Combined application of PCR-based functional assays for the detection of aromatic-compound-degrading anaerobes. Applied and Environmental Microbiology, 77(14), 5056–5061.PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Staats, M., Braster, M., & Röling, W. F. M. (2011). Molecular diversity and distribution of aromatic hydrocarbon-degrading anaerobes across a landfill leachate plume. Environmental Microbiology, 13(5), 1216–1227.PubMedCrossRefPubMedCentralGoogle Scholar
  16. 16.
    Li, Y. N., Porter, A. W., Mumford, A., Zhao, X. H., & Young, L. Y. (2012). Bacterial community structure and bamA gene diversity in anaerobic degradation of toluene and benzoate under denitrifying conditions. Journal of Applied Microbiology, 112(2), 269–279.PubMedCrossRefPubMedCentralGoogle Scholar
  17. 17.
    Porter, A. W., & Young, L. Y. (2014). Benzoyl-CoA, a universal biomarker for anaerobic degradation of aromatic compounds. Advances in Applied Microbiology, 88, 167–203.PubMedCrossRefPubMedCentralGoogle Scholar
  18. 18.
    Sun, W., Sun, X., & Cupples, A. M. (2014). Presence, diversity and enumeration of functional genes (bssA and bamA) relating to toluene degradation across a range of redox conditions and inoculum sources. Biodegradation, 25(2), 189–203.PubMedCrossRefPubMedCentralGoogle Scholar
  19. 19.
    Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., & Knight, R. (2011). Global patterns of 16s rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, 108(Suppl 1), 4516–4522.CrossRefGoogle Scholar
  20. 20.
    Evans, P. J., Mang, D. T., Kim, K. S., & Young, L. Y. (1991). Anaerobic degradation of toluene by a denitrifying bacterium. Applied and Environmental Microbiology, 57(4), 1139–1145.PubMedPubMedCentralGoogle Scholar
  21. 21.
    Lane, D. J. (1991). Nucleic acid techniques in bacterial systematic (16S/23S rRNA sequencing) (Vol. 2, pp. 115–175). Chichester: Wiley.Google Scholar
  22. 22.
    Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797.PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). Fasttree 2 – approximately maximum-likelihood trees for large alignments. Plos One, 5, e9490.PubMedPubMedCentralCrossRefGoogle Scholar
  24. 24.
    Na, J. G., Lee, M. K., Yun, Y. M., Moon, C., Kim, M. S., & Kim, D. H. (2016). Microbial community analysis of anaerobic granules in phenol-degrading UASB by next generation sequencing. Biochemical Engineering Journal, 112, 241–248.CrossRefGoogle Scholar
  25. 25.
    Cheng, C., Zhou, Z., Niu, T., An, Y., Shen, X., Pan, W., Chen, Z. H., & Liu, J. (2017). Effects of side-stream ratio on sludge reduction and microbial structures of anaerobic side-stream reactor coupled membrane bioreactors. Bioresource Technology, 234, 380–388.PubMedCrossRefPubMedCentralGoogle Scholar
  26. 26.
    van Teeseling, M. C., Mesman, R. J., Kuru, E., Espaillat, A., Cava, F., Brun, Y. V., VanNieuwenhze, M. S., Kartal, B., & van Niftrik, L. (2015). Anammox planctomycetes have a peptidoglycan cell wall. Nature Communications, 6(6878), 6878.PubMedPubMedCentralCrossRefGoogle Scholar
  27. 27.
    Ma, Q., Qu, Y., Shen, W., Zhang, Z., Wang, J., Liu, Z., Li, D., Li, H., & Zhou, J. (2014). Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing. Bioresource Technology, 179, 436–443.PubMedCrossRefPubMedCentralGoogle Scholar
  28. 28.
    Ren, L. F., Chen, R., Zhang, X. F., Shao, J. H., & He, Y. L. (2017). Phylotypes belonging to the Bacteroidetes are known to be physiologically diverse and are found in a wide range of environments, e.g. soil, freshwater, ocean and the human gastrointestinal tract. Bioresource Technology, 244, 1121–1128.PubMedCrossRefPubMedCentralGoogle Scholar
  29. 29.
    Ibarbalz, F. M., Figuerola, E. L., & Erijman, L. (2013). Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks. Water Research, 47(11), 3854–3864.PubMedCrossRefPubMedCentralGoogle Scholar
  30. 30.
    Manefield, M., Griffiths, R. I., Leigh, M. B., Fisher, R., & Whiteley, A. S. (2005). Functional and compositional comparison of two activated sludge communities remediating coking effluent. Environmental Microbiology, 7(5), 715–722.PubMedCrossRefPubMedCentralGoogle Scholar
  31. 31.
    Mechichi, T., Stackebrandt, E., Gad’On, N., & Fuchs, G. (2002). Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckelii sp. nov. Archives of Microbiology, 178(1), 26–35.PubMedCrossRefPubMedCentralGoogle Scholar
  32. 32.
    Morgan-Sagastume, F., Nielsen, J. L., & Nielsen, P. H. (2008). Substrate-dependent denitrification of abundant probe-defined denitrifying bacteria in activated sludge. FEMS Microbiology Ecology, 66(2), 447–461.PubMedCrossRefPubMedCentralGoogle Scholar
  33. 33.
    Lee, D. J., Wong, B. T., & Adav, S. S. (2014). Azoarcus taiwanensis, sp. nov. a denitrifying species isolated from a hot spring. Applied Microbiology and Biotechnology, 98(3), 1301–1307.PubMedCrossRefPubMedCentralGoogle Scholar
  34. 34.
    Vedler, E., Heinaru, E., Jutkina, J., Viggor, S., Koressaar, T., Remm, M., & Heinaru, A. (2013). Limnobacter spp. as newly detected phenol-degraders among Baltic Sea surface water bacteria characterised by comparative analysis of catabolic genes. Systematic and Applied Microbiology, 36(8), 525–532.PubMedCrossRefPubMedCentralGoogle Scholar
  35. 35.
    Sass, A. M., Schmerk, C., Agnoli, K., Norville, P. J., Eberl, L., Valvano, M. A., & Mathenthiralingam, E. (2013). The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia. The ISME Journal, 7(8), 1568–1581.PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Mi, W., Zhao, J., Ding, X., Ge, G., & Zhao, R. (2017). Treatment performance, nitrous oxide production and microbial community under low-ammonium wastewater in a CANON process. Water Science and Technology, 76(12), 3468–3477.PubMedCrossRefPubMedCentralGoogle Scholar
  37. 37.
    Wang, Z., Yang, Y. Y., Dai, Y., & Xie, S. G. (2015). Anaerobic biodegradation of nonylphenol in river sediment under nitrate- or sulfate-reducing conditions and associated bacterial community. Journal of Hazardous Materials, 286, 306–314.PubMedCrossRefPubMedCentralGoogle Scholar
  38. 38.
    Bai, N. (2018) Microbiological study on the formation of black and smelly water in typical areas. Master thesis, Capital University of Economics and Business, Beijing, China.Google Scholar
  39. 39.
    Andreoni, V., Cavalca, L., Rao, M. A., Nocerino, G., Bernasconi, S., Dell’Amico, E., Colombo, M., & Gianfreda, L. (2004). Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere, 57(5), 401–412.PubMedCrossRefPubMedCentralGoogle Scholar
  40. 40.
    Huang, Y., Hou, X., Liu, S., & Ni, J. (2016). Correspondence analysis of bio-refractory compounds degradation and microbiological community distribution in anaerobic filter for coking wastewater treatment. Chemical Engineering Journal, 304, 864–872.CrossRefGoogle Scholar
  41. 41.
    Sampaio, D. S., Almeida, J. R. B., Jesus, H. E. D., Rosado, A. S., & Jurelevicius, D. (2017). Distribution of anaerobic hydrocarbon-degrading bacteria in soils from King George island, Maritime Antarctica. Microbial Ecology, 74(24), 1–11.Google Scholar
  42. 42.
    Ruan, M. Y., Liang, B., Mbadinga, S. M., Zhou, L., Wang, L. Y., Liu, J. F., Gu, J. D., & Mu, B. Z. (2016). Molecular diversity of bacterial bamA gene involved in anaerobic degradation of aromatic hydrocarbons in mesophilic petroleum reservoirs. International Biodeterioration & Biodegradation, 114, 122–128.CrossRefGoogle Scholar
  43. 43.
    Lahme, S., Harder, J., & Rabus, R. (2012). Anaerobic degradation of 4-methylbenzoate by a newly isolated denitrifying bacterium, strain pmbn1. Applied and Environmental Microbiology, 78(5), 1606–1610.PubMedPubMedCentralCrossRefGoogle Scholar
  44. 44.
    Wirth, B., Krebs, M., & Andert, J. (2015). Anaerobic degradation of increased phenol concentrations in batch assays. Environmental Science and Pollution Research, 22(23), 19048–19059.PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Yanan Li
    • 1
  • Jing Li
    • 1
  • Di Wang
    • 1
  • Guoying Wang
    • 1
    Email author
  • Xiuping Yue
    • 1
  • Xin Kong
    • 1
  • Lily Young
    • 3
  • Weilin Huang
    • 2
    • 3
  1. 1.College of Environmental Science and EngineeringTaiyuan University of TechnologyTaiyuanChina
  2. 2.Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and ManagementGuangdong Institute of Eco-environmental Sciences & TechnologyGuangzhouChina
  3. 3.Department of Environmental SciencesRutgers, The State University of New JerseyNew BrunswickUSA

Personalised recommendations