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Performance and Microbial Community Analysis of Bioaugmented Activated Sludge System for Indigo Production from Indole

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Abstract

Indole is a typical nitrogen-containing aromatic pollutant in coking wastewater, and it can be used for the microbial production of indigo, one of the oldest dyestuffs. In this study, the activated sludge system bioaugmented with two indigo-producing bacterial strains, wild strain Comamonas sp. MQ and recombinant Escherichia coli (ND_IND), was constructed to investigate indigo bioproduction from indole. During the operation, the bioaugmentation could promote the production of indigo, especially in early stages, and the indigo yields gradually increased from 17.5 ± 0.4 to 44.3 ± 0.5 mg/L with the increase of influent indole (80 to 282 mg/L). Illumina MiSeq sequencing revealed that the microbial community could have a noticeable shift driven by the bioaugmentation and high indole pressure. The indigenous bacteria could be more responsible for indigo production, and the dominant genera Comamonas, Diaphorobacter, Paracoccus, Aquamicrobium, Pseudomonas, and Truepera could be the key functional taxa. Based on FAPROTAX (Functional Annotation of Prokaryotic Taxa) analysis, the nitrogen metabolism-related functional groups could play important roles in indole biotransformation and indigo biosynthesis. This study should provide insights into microbial production of indigo by microbial communities.

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References

  1. Lee, J. H., Wood, T. K., & Lee, J. (2015). Roles of indole as an interspecies and interkingdom signaling molecule. Trends in Microbiology, 23(11), 707–718.

    Article  CAS  Google Scholar 

  2. Lee, J. H., & Lee, J. (2010). Indole as an intercellular signal in microbial communities. FEMS Microbiology Reviews, 34(4), 426–444.

    Article  CAS  Google Scholar 

  3. Fetzner, S. (1998). Bacterial degradation of pyridine, indole, quinoline, and their derivatives under different redox conditions. Applied Microbiology and Biotechnology, 49(3), 237–250.

    Article  CAS  Google Scholar 

  4. Doukyu, N., & Aono, R. (1997). Biodegradation of indole at high concentration by persolvent fermentation with Pseudomonas sp. ST-200. Extremophiles, 1(2), 100–105.

    Article  CAS  Google Scholar 

  5. Lin, G. H., Chen, H. P., & Shu, H. Y. (2015). Detoxification of indole by an indole-induced flavoprotein oxygenase from Acinetobacter baumannii. PLoS One, 10(9), e0138798.

    Article  Google Scholar 

  6. Sadauskas, M., Vaitekūnas, J., Gasparavičiūtė, R., & Meškys, R. (2017). Genetic and biochemical characterization of indole biodegradation in Acinetobacter sp. strain O153. Applied and Environmental Microbiology, 83, e01453–e01417.

    Article  CAS  Google Scholar 

  7. Qu, Y., Zhang, X., Ma, Q., Ma, F., Zhang, Q., Li, X., Zhou, H., & Zhou, J. (2012). Indigo biosynthesis by Comamonas sp. MQ. Biotechnology Letters, 34(2), 353–357.

    Article  CAS  Google Scholar 

  8. Qu, Y., Xu, B., Zhang, X., Ma, Q., Zhou, H., Kong, C., Zhang, Z., & Zhou, J. (2013). Biotransformation of indole by whole cells of recombinant biphenyl dioxygenase and biphenyl-2,3-dihydrodiol-2,3-dehydrogenase. Biochemical Engineering Journal, 72, 54–60.

    Article  CAS  Google Scholar 

  9. Gray, P. H. H. (1928). The formation of indigotin from indol by soil bacteria. Proceedings of the Royal Society of London B, 102(717), 263–280.

    Article  CAS  Google Scholar 

  10. O’Connor, K. E., & Hartmans, S. (1998). Indigo formation by aromatic hydrocarbon-degrading bacteria. Biotechnology Letters, 20(3), 219–223.

    Article  Google Scholar 

  11. Pathak, H., & Madamwar, D. (2010). Biosynthesis of indigo dye by newly isolated naphthalene-degrading strain Pseudomonas sp. HOB1 and its application in dyeing cotton fabric. Applied Biochemistry and Biotechnology, 160(6), 1616–1626.

    Article  CAS  Google Scholar 

  12. Mercadal, J. P. R., Isaac, P., Siñeriz, F., & Ferrero, M. A. (2012). Indigo production by Pseudomonas sp. J26, a marine naphthalene-degrading strain. Journal of Basic Microbiology, 50, 290–293.

    Article  Google Scholar 

  13. Wang, J., Zhang, X., Fan, J., Zhang, Z., Ma, Q., & Peng, X. (2015). Indigoids biosynthesis from indole by two phenol-degrading strains, Pseudomonas sp. PI1 and Acinetobacter sp. PI2. Applied Biochemistry and Biotechnology, 176(5), 1263–1276.

    Article  CAS  Google Scholar 

  14. Fukuoka, K., Tanaka, K., Ozeki, Y., & Kanaly, R. A. (2015). Biotransformation of indole by Cupriavidus sp. strain KK10 proceeds through N-heterocyclic- and carbocyclic-aromatic ring cleavage and production of indigoids. International Biodeterioration & Biodegradation, 97, 13–14.

    Article  CAS  Google Scholar 

  15. Zhang, X., Qu, Y., Ma, Q., Zhou, H., Li, X., Kong, C., & Zhou, J. (2013). Cloning and expression of naphthalene dioxygenase genes from Comamonas sp. MQ for indigoids production. Process Biochemistry, 48(4), 581–587.

    Article  CAS  Google Scholar 

  16. Kim, J. Y., Kim, J. K., Lee, S. O., Kim, C. K., & Lee, K. (2005). Multicomponent phenol hydroxylase-catalysed formation of hydroxyindoles and dyestuffs from indole and its derivatives. Letters in Applied Microbiology, 41(2), 163–168.

    Article  CAS  Google Scholar 

  17. Kim, H. J., Jang, S., Kim, J., Yang, Y. H., Kim, Y. G., Kim, B. G., & Choi, K. Y. (2017). Biosynthesis of indigo in Escherichia coli expressing self-sufficient CYP102A from Streptomyces cattleya. Dyes and Pigments, 140, 29–35.

    Article  CAS  Google Scholar 

  18. Han, G. H., Bang, S. E., Babu, B. K., Chang, M., Shin, H. J., & Kim, S. W. (2011). Bio-indigo production in two different fermentation systems using recombinant Escherichia coli cells harboring a flavin-containing monooxygenase gene (fmo). Process Biochemistry, 46(3), 788–791.

    Article  CAS  Google Scholar 

  19. Qu, Y., Ma, Q., Liu, Z., Wang, W., Tang, H., Zhou, J., & Xu, P. (2017). Unveiling the biotransformation mechanism of indole in a Cupriavidus sp. strain. Molecular Microbiology, 106(6), 905–918.

    Article  CAS  Google Scholar 

  20. Kleerebezem, R., & van Loosdrecht, M. C. (2007). Mixed culture biotechnology for bioenergy production. Current Opinion in Biotechnology, 18(3), 207–212.

    Article  CAS  Google Scholar 

  21. Marshall, C. W., LaBelle, E. V., & May, H. D. (2013). Production of fuels and chemicals from waste by microbiomes. Current Opinion in Biotechnology, 24(3), 391–397.

    Article  CAS  Google Scholar 

  22. Qu, Y., Zhang, X., Ma, Q., Deng, J., Deng, Y., Van Nostrand, J. D., Wu, L., He, Z., Qin, Y., Zhou, J., & Zhou, J. (2015). Microbial community dynamics and activity link to indigo production from indole in bioaugmented activated sludge systems. PLoS One, 10(9), e0138455.

    Article  Google Scholar 

  23. Zhang, X., Qu, Y., Ma, Q., Zhang, Z., Li, D., Wang, J., Shen, W., Shen, E., & Zhou, J. (2015). Illumina MiSeq sequencing reveals diverse microbial communities of activated sludge systems stimulated by different aromatics for indigo biosynthesis from indole. PLoS One, 10(4), e0125732.

    Article  Google Scholar 

  24. Boon, N., Goris, J., De Vos, P., Verstraete, W., & Top, E. M. (2000). Bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading Comamonas testosteroni strain, I2gfp. Applied and Environmental Microbiology, 66(7), 2906–2913.

    Article  CAS  Google Scholar 

  25. Bai, Y., Sun, Q., Sun, R., Wen, D., & Tang, X. (2011). Bioaugmentation and adsorption treatment of coking wastewater containing pyridine and quinoline using zeolite-biological aerated filters. Environmental Science & Technology, 45(5), 1940–1948.

    Article  CAS  Google Scholar 

  26. Zhou, J., He, Z., Yang, Y., Deng, Y., Tringe, S. G., & Alvarez-Cohen, L. (2015). High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio, 6, e02288–e02214.

    Article  CAS  Google Scholar 

  27. Ma, Q., Qu, Y., Shen, W., Zhang, Z., Wang, J., Liu, Z., Li, D., Li, H., & Zhou, J. (2015). Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing. Bioresource Technology, 179, 436–443.

    Article  CAS  Google Scholar 

  28. Ma, Q., Qu, Y., Zhang, X., Liu, Z., Li, H., Zhang, Z., Wang, J., Shen, W., & Zhou, J. (2015). Systematic investigation and microbial community profile of indole degradation processes in two aerobic activated sludge systems. Scientific Reports, 5, 17674.

    Article  CAS  Google Scholar 

  29. Zhou, J., Deng, Y., Zhang, P., Xue, K., Liang, Y., Van Nostrand, J. D., Yang, Y., He, Z., Wu, L., Stahl, D. A., Hazen, T. C., Tiedje, J. M., & Arkin, A. P. (2014). Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences, 111(9), E836–E845.

    Article  CAS  Google Scholar 

  30. Zhang, J., Wen, D., Zhao, C., & Tang, X. (2014). Bioaugmentation accelerates the shift of bacterial community structure against shock load: a case study of coking wastewater treatment by zeolite-sequencing batch reactor. Applied Microbiology and Biotechnology, 98(2), 863–873.

    Article  CAS  Google Scholar 

  31. Joshi, D. R., Zhang, Y., Gao, Y., Liu, Y., & Yang, M. (2017). Biotransformation of nitrogen-and sulfur-containing pollutants during coking wastewater treatment: correspondence of performance to microbial community functional structure. Water Research, 121, 338–348.

    Article  CAS  Google Scholar 

  32. Yadav, T. C., Khardenavis, A. A., & Kapley, A. (2014). Shifts in microbial community in response to dissolved oxygen levels in activated sludge. Bioresource Technology, 165, 257–264.

    Article  CAS  Google Scholar 

  33. Tikariha, H., Pal, R. R., Qureshi, A., Kapley, A., & Purohit, H. J. (2016). In silico analysis for prediction of degradative capacity of Pseudomonas putida SF1. Gene, 591(2), 382–392.

    Article  CAS  Google Scholar 

  34. Wu, Y., Arumugam, K., Tay, M. Q. X., Seshan, H., Mohanty, A., & Cao, B. (2015). Comparative genome analysis reveals genetic adaptation to versatile environmental conditions and importance of biofilm lifestyle in Comamonas testosteroni. Applied Microbiology and Biotechnology, 99(8), 3519–3532.

    Article  CAS  Google Scholar 

  35. Srinandan, C. S., Shah, M., Patel, B., & Nerurkar, A. S. (2011). Assessment of denitrifying bacterial composition in activated sludge. Bioresource Technology, 102(20), 9481–9489.

    Article  CAS  Google Scholar 

  36. Chang, Y. C., Takada, K., Choi, D., Toyama, T., Sawada, K., & Kikuchi, S. (2013). Isolation of biphenyl and polychlorinated biphenyl-degrading bacteria and their degradation pathway. Applied Biochemistry and Biotechnology, 170(2), 381–398.

    Article  CAS  Google Scholar 

  37. Wang, F., Li, C., Wang, H., Chen, W., & Huang, Q. (2016). Characterization of a phenanthrene-degrading microbial consortium enriched from petrochemical contaminated environment. International Biodeterioration & Biodegradation, 115, 286–292.

    Article  CAS  Google Scholar 

  38. Goddard, A. D., Bali, S., Mavridou, D. A., Luque-Almagro, V. M., Gates, A. J., Dolores Roldán, M., Newstead, S., Richardson, D. J., & Ferguson, S. J. (2017). The Paracoccus denitrificans NarK-like nitrate and nitrite transporters-probing nitrate uptake and nitrate/nitrite exchange mechanisms. Molecular Microbiology, 103(1), 117–133.

    Article  CAS  Google Scholar 

  39. Zhang, H., Kallimanis, A., Koukkou, A. I., & Drainas, C. (2004). Isolation and characterization of novel bacteria degrading polycyclic aromatic hydrocarbons from polluted Greek soils. Applied Microbiology and Biotechnology, 65(1), 124–131.

    Article  CAS  Google Scholar 

  40. Singh, D., & Ramanathan, G. (2013). Biomineralization of 3-nitrotoluene by Diaphorobacter species. Biodegradation, 24(5), 645–655.

    Article  CAS  Google Scholar 

  41. Khardenavis, A. A., Kapley, A., & Purohit, H. J. (2007). Simultaneous nitrification and denitrification by diverse Diaphorobacter sp. Applied Microbiology and Biotechnology, 77(2), 403–409.

    Article  CAS  Google Scholar 

  42. Louca, S., Parfrey, L. W., & Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science, 353(6305), 1272–1277.

    Article  CAS  Google Scholar 

  43. Madsen, E. L., & Bollag, J. M. (1988). Pathway of indole metabolism by a denitrifying microbial community. Archives of Microbiology, 151(1), 71–76.

    Article  Google Scholar 

  44. Yang, Z., Zhou, J., Xu, Y., Zhang, Y., Luo, H., Chang, K., & Wang, Y. (2017). Analysis of the metabolites of indole degraded by an isolated Acinetobacter pittii L1. BioMed Research International, 2017, 2564363.

    PubMed  PubMed Central  Google Scholar 

  45. Hong, X., Zhang, X., Liu, B., Mao, Y., Liu, Y., & Zhao, L. (2010). Structural differentiation of bacterial communities in indole-degrading bioreactors under denitrifying and sulfate-reducing conditions. Research in Microbiology, 161(8), 687–693.

    Article  CAS  Google Scholar 

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Funding

This work was supported by National Natural Science Foundation of China (No. 51508068) and the Fundamental Research Funds for the Central Universities (No. DUT16RC(3)118).

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Correspondence to Yuanyuan Qu.

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Zhang, X., Qu, Y., Ma, Q. et al. Performance and Microbial Community Analysis of Bioaugmented Activated Sludge System for Indigo Production from Indole. Appl Biochem Biotechnol 187, 1437–1447 (2019). https://doi.org/10.1007/s12010-018-2879-z

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