Quorum sensing between Gram-negative bacteria responsible for methane production in a complex waste sewage sludge consortium

Abstract

Quorum sensing (QS) plays a key role in activating bacterial functions through small molecules called autoinducers. In this study, the QS of Gram-negative bacteria in waste sewage sludge (WSS) was downregulated by adding the quorum quenching enzyme, AiiM lactonase, which cleaved the acyl-homoserine lactone (AHL) autoinducer signals from Gram-negative bacteria, and subsequently methane production was inhibited by over 400%. The pH was lowered after 2 days in the anaerobic fermentation whereas protease activity at the hydrolysis step was almost the same with or without AiiM. The production of acetic acid significantly increased during the fermentation in the presence of AiiM. The bacterial community at day 2 indicated that the population of Gram-positive bacteria increased in the presence of AiiM, and the percentage of Gram-negative bacteria decreased in the WSS containing AiiM. The change in the bacterial community in the presence of AiiM may be due to the different antimicrobial agents produced in the WSS because some of the Gram-positive bacteria were killed by adding the solid-phase extraction (SPE) fraction from the WSS without AiiM. In contrast, the SPE fraction with AiiM had reduced bactericidal activity against Gram-negative bacteria. Thus, bacterial signaling between Gram-negative bacteria is critical for methane production by the microbial consortia.

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References

  1. Ahring BK, Sandberg M, Angelidaki I (1995) Volatile fatty acids as indicators of process imbalance in anaerobic digestors. Appl Microbiol Biotechnol 43(3):559–565

    CAS  Article  Google Scholar 

  2. Ananou S, Gálvez A, Martínez-Bueno M, Maqueda M, Valdivia E (2005) Synergistic effect of enterocin AS-48 in combination with outer membrane permeabilizing treatments against Escherichia coli O157: H7. J Appl Microbiol 99(6):1364–1372

    CAS  PubMed  Article  Google Scholar 

  3. Antunes LCM, Queiroz Ferreira L, Oliveira Ferreira E, Rodrigues Miranda K, Eliane Santos Avelar K, Pilotto MC, Domingues R, Candida de Souza Ferreira M (2005) Bacteroides species produce Vibrio harveyi autoinducer 2-related molecules. Anaerobe 11(5):295–301

    CAS  PubMed  Article  Google Scholar 

  4. Appels L, Baeyens J, Degrève J, Dewil R (2008) Principles and potential of the anaerobic digestion of waste-activated sludge. Prog Energy Combust Sci 34(6):755–781

    CAS  Article  Google Scholar 

  5. Barbosa MJ, Rocha JM, Tramper J, Wijffels RH (2001) Acetate as a carbon source for hydrogen production by photosynthetic bacteria. J Biotechnol 85(1):25–33

    CAS  PubMed  Article  Google Scholar 

  6. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP (2016) Taxonomy, physiology, and natural products of Actinobacteria. Microbiol Mol Biol Rev 80(1):1–43

    PubMed  Article  Google Scholar 

  7. Borriss R, Danchin A, Harwood CR, Médigue C, Rocha E, Sekowska A, Vallenet D (2017) Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement. Microb Biotechnol 11(1):3–17

    PubMed Central  Article  Google Scholar 

  8. Burgess JG, Jordan EM, Bregu M, Mearns-Spragg A, Boyd KG (1999) Microbial antagonism: a neglected avenue of natural products research. J Biotechnol 70(1):27–32

    CAS  PubMed  Article  Google Scholar 

  9. Chau HTC, Kadokami K, Ifuku T, Yoshida Y (2017) Development of a comprehensive screening method for more than 300 organic chemicals in water samples using a combination of solid-phase extraction and liquid chromatography-time-of-flight-mass spectrometry. Environ Sci Pollut R 24(34):26396–26409

    CAS  Article  Google Scholar 

  10. Cheong WS, Lee CH, Moon YH, Oh HS, Kim SR, Lee SH, Lee CH, Lee JK (2013) Isolation and identification of indigenous quorum quenching bacteria, Pseudomonas sp. 1A1, for biofouling control in MBR. Ind Eng Chem Res 52(31):10554–10560

    CAS  Article  Google Scholar 

  11. Dhall P, Kumar R, Kumar A (2012) Biodegradation of sewage wastewater using autochthonous bacteria. Sci World J

  12. Dong YH, Xu JL, Li XZ, Zhang LH (2000) AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc Natl Acad Sci 97(7):3526–3531

    CAS  PubMed  Article  Google Scholar 

  13. Dubuis C, Keel C, Haas D (2007) Dialogues of root-colonizing biocontrol pseudomonads. Eur J Plant Pathol 119(3):311–328

    Article  Google Scholar 

  14. Duerkop BA, Varga J, Chandler JR, Peterson SB, Herman JP, Churchill ME, Parsek MR, Nierman WC, Greenberg EP (2009) Quorum-sensing control of antibiotic synthesis in Burkholderia thailandensis. J Bacteriol 191(12):3909–3918

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. El-Bestawy E, El-Masry MH, Nawal E (2005) The potentiality of free gram-negative bacteria for removing oil and grease from contaminated industrial effluents. World J Microbiol Biotechnol 21(6-7):815–822

    CAS  Article  Google Scholar 

  16. Fukuzaki S, Nishio N, Shobayashi M, Nagai S (1990) Inhibition of the fermentation of propionate to methane by hydrogen, acetate, and propionate. Appl Environ Microbiol 56(3):719–723

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Galloway WRJD, Hodgkinson JT, Bowden SD, Welch M, Spring DR (2011) Quorum sensing in gram-negative bacteria: small-molecule modulation of AHL and AI-2 quorum sensing pathways. Chem Rev 111(1): 28-67.

  18. Gerardi MH (2006) Wastewater bacteria (Vol. 5): John Wiley & Sons

  19. Grandclément C, Tannières M, Moréra S, Dessaux Y, Faure D (2015) Quorum quenching: role in nature and applied developments. FEMS Microbiol Rev 40(1):86–116

    PubMed  Article  CAS  Google Scholar 

  20. Guendouze A, Plener L, Bzdrenga J, Jacquet P, Rémy B, Elias M, Lavigne JP, Daudé D, Chabrière E (2017) Effect of quorum quenching lactonase in clinical isolates of Pseudomonas aeruginosa and comparison with quorum sensing inhibitors. Front Microbiol 8:227

    PubMed  PubMed Central  Article  Google Scholar 

  21. Huang J, Shi Y, Zeng G, Gu Y, Chen G, Shi L, Hu Y, Tang B, Zhou J (2016) Acyl-homoserine lactone-based quorum sensing and quorum quenching hold promise to determine the performance of biological wastewater treatments: an overview. Chemosphere 157:137–151

    CAS  PubMed  Article  Google Scholar 

  22. Ivanov V, Stabnikov V, Zhuang W, Tay J, Tay S (2005) Phosphate removal from the returned liquor of municipal wastewater treatment plant using iron-reducing bacteria. J Appl Microbiol 98(5):1152–1161

    CAS  PubMed  Article  Google Scholar 

  23. Jarvik T, Smillie C, Groisman EA, Ochman H (2010) Short-term signatures of evolutionary change in the Salmonella enterica serovar Typhimurium 14028 genome. J Bacteriol 192(2):560–567

    CAS  PubMed  Article  Google Scholar 

  24. Jiang W, Xia S, Liang J, Zhang Z, Hermanowicz SW (2013) Effect of quorum quenching on the reactor performance, biofouling and biomass characteristics in membrane bioreactors. Water Res 47(1):187–196

    CAS  PubMed  Article  Google Scholar 

  25. Kato T, Inuzuka L, Kondo M, Matsuda T (2001) Growth of nisin-producing lactococci in cooked rice supplemented with soybean extract and its application to inhibition of Bacillus subtilis in rice miso. Biosci Biotechnol Biochem 65(2):330–337

    CAS  PubMed  Article  Google Scholar 

  26. Kaufmann GF, Sartorio R, Lee SH, Rogers CJ, Meijler MM, Moss JA, Clapham B, Brogan AP, Dickerson TJ, Janda KD (2005) Revisiting quorum sensing: discovery of additional chemical and biological functions for 3-oxo-N-acylhomoserine lactones. Proc Natl Acad Sci 102(2):309–314

    CAS  PubMed  Article  Google Scholar 

  27. Kim JH, Choi DC, Yeon KM, Kim SR, Lee CH (2011) Enzyme-immobilized nanofiltration membrane to mitigate biofouling based on quorum quenching. Environ Sci Technol 45(4):1601–1607

    CAS  PubMed  Article  Google Scholar 

  28. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41(1):e1–e1

    CAS  PubMed  Article  Google Scholar 

  29. Kurokawa T, Tanisho S (2005) Effects of formate on fermentative hydrogen production by Enterobacter aerogenes. Mar Biotechnol 7(2):112–118

    CAS  PubMed  Article  Google Scholar 

  30. Lay JJ, Li YY, Noike T (1998) The influence of pH and ammonia concentration on the methane production in high-solids digestion processes. Water Environ Res 70(5):1075–1082

    CAS  Article  Google Scholar 

  31. Lee JH, Wood TK, Lee J (2015) Roles of indole as an interspecies and interkingdom signaling molecule. Trends Microbiol 23(11):707–718

    CAS  PubMed  Article  Google Scholar 

  32. Lowry OHRN, Farr AL, Randall RJ (1951) Protein measurement with the folin phenol reagent. J Biol Chem 193:265–275

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Luo ZQ, Su S, Farrand SK (2003) In situ activation of the quorum-sensing transcription factor TraR by cognate and noncognate acyl-homoserine lactone ligands: kinetics and consequences. J Bacteriol 185(19):5665–5672

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  34. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66(3):506–577. https://doi.org/10.1128/mmbr.66.3.506-577.2002

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  35. Maeda T, García-Contreras R, Pu M, Sheng L, Garcia LR, Tomás M, Wood TK (2012) Quorum quenching quandary: resistance to antivirulence compounds. ISME J 6(3):493–501. https://doi.org/10.1038/ismej.2011.122

    CAS  PubMed  Article  Google Scholar 

  36. Maeda T, Yoshimura T, García-Contreras R, Ogawa HI (2011) Purification and characterization of a serine protease secreted by Brevibacillus sp. KH3 for reducing waste activated sludge and biofilm formation. Bioresour Technol 102(22):10650–10656

    CAS  PubMed  Article  Google Scholar 

  37. Mayer C, Romero M, Muras A, Otero A (2015) Aii20J, a wide-spectrum thermostable N-acylhomoserine lactonase from the marine bacterium Tenacibaculum sp. 20J, can quench AHL-mediated acid resistance in Escherichia coli. Appl Microbiol Biotechnol 99(22):9523–9539

    CAS  PubMed  Article  Google Scholar 

  38. McAnulty MJ, Poosarla VG, Li J, Soo VW, Zhu F, Wood TK (2017) Metabolic engineering of Methanosarcina acetivorans for lactate production from methane. Biotechnol Bioeng 114(4):852–861

    CAS  PubMed  Article  Google Scholar 

  39. McClean KH, Winson MK, Fish L, Taylor A, Chhabra SR, Camara M, Daykin M, Lamb JH, Swift S, Bycroft BW, Stewart GS, Williams P (1997) Quorum sensing and Chromobacterium violaceum: exploitation of violacein production and inhibition for the detection of N-acylhomoserine lactones. Microbiol 143(12):3703–3711

    CAS  Article  Google Scholar 

  40. Migiyama Y, Kaneko Y, Yanagihara K, Morohoshi T, Morinaga Y, Nakamura S, Miyazaki T, Hasegawa H, Izumikawa K, Kakeya H, Kohrogi H (2013) Efficacy of AiiM, an N-acylhomoserine lactonase, against Pseudomonas aeruginosa in a mouse model of acute pneumonia. Antimicrob Agents Chemother: AAC. 00456–00413

  41. Mikkelsen LH, Keiding K (2002) Physico-chemical characteristics of full scale sewage sludges with implications to dewatering. Water Res 36(10):2451–2462

    CAS  PubMed  Article  Google Scholar 

  42. Mohd Yasin NH, Maeda T, Hu A, Yu C-P, Wood TK (2015) CO2 sequestration by methanogens in activated sludge for methane production. Appl Energy 142:426–434

    CAS  Article  Google Scholar 

  43. Mohd Yusoff MZ, Maeda T, Sanchez-Torres V, Ogawa HI, Shirai Y, Hassan MA, Wood TK (2012) Uncharacterized Escherichia coli proteins YdjA and YhjY are related to biohydrogen production. Int J Hydrogen Energy 37(23):17778–17787

    CAS  Article  Google Scholar 

  44. Morohoshi T, Tokita K, Ito S, Saito Y, Maeda S, Kato N, Ikeda T (2013) Inhibition of quorum sensing in gram-negative bacteria by alkylamine-modified cyclodextrins. J Biosci Bioeng 116(2):175–179

    CAS  PubMed  Article  Google Scholar 

  45. Mustapha NA, Hu A, Yu C-P, Sharuddin SS, Ramli N, Shirai Y, Maeda T (2018) Seeking key microorganisms for enhancing methane production in anaerobic digestion of waste sewage sludge. Appl Microbiol Biotechnol 102(12):5323–5334

    CAS  PubMed  Article  Google Scholar 

  46. Mustapha NA, Sakai K, Shirai Y, Maeda T (2016) Impact of different antibiotics on methane production using waste-activated sludge: mechanisms and microbial community dynamics. Appl Microbiol Biotechnol 100(21):9355–9364

    CAS  PubMed  Article  Google Scholar 

  47. Mustapha NA, Sharuddin SS, Mohd Zainudin MH, Ramli N, Shirai Y, Maeda T (2017) Inhibition of methane production by the palm oil industrial waste phospholine gum in a mimic enteric fermentation. J Clean Prod 165:621–629

    CAS  Article  Google Scholar 

  48. Nguyen MT, Maeda T, Yusoff MZM, Ogawa HI (2014) Effect of azithromycin on enhancement of methane production from waste activated sludge. J Ind Microbiol Biotechnol 41(7):1051–1059

    CAS  PubMed  Article  Google Scholar 

  49. Oh HS, Kim SR, Cheong WS, Lee CH, Lee JK (2013) Biofouling inhibition in MBR by Rhodococcus sp. BH4 isolated from real MBR plant. Appl Microbiol Biotechnol 97(23):10223–10231

    CAS  PubMed  Article  Google Scholar 

  50. Peixoto RJM, Miranda KR, Ferreira EO, de Paula GR, Rocha ER, Lobo LA, Domingues RMCP (2014) Production of AI-2 is mediated by the S-ribosylhomocystein lyase gene luxS in Bacteroides fragilis and Bacteroides vulgatus. J Basic Microbiol 54(7):644–649

    CAS  PubMed  Article  Google Scholar 

  51. Regueiro L, Veiga P, Figueroa M, Alonso-Gutierrez J, Stams AJM, Lema JM, Carballa M (2012) Relationship between microbial activity and microbial community structure in six full-scale anaerobic digesters. Microbiol Res 167(10):581–589

    CAS  PubMed  Article  Google Scholar 

  52. Rutherford ST, Bassler BL (2012) Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harb Perspect Med 2(11):a012427

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  53. Smaoui S, Elleuch L, Bejar W, Karray-Rebai I, Ayadi I, Jaouadi B, Mathieu F, Chouayekh H, Bejar S, Mellouli L (2010) Inhibition of fungi and gram-negative bacteria by bacteriocin BacTN635 produced by Lactobacillus plantarum sp. TN635 Appl Biochem Biotechnol 162(4):1132–1146

    CAS  PubMed  Article  Google Scholar 

  54. Sturme MHJ, Kleerebezem M, Nakayama J, Akkermans ADL, Vaughan EE, de Vos WM (2002) Cell to cell communication by autoinducing peptides in gram-positive bacteria. Antonie Van Leeuwenhoek 81(1):233–243

    CAS  PubMed  Article  Google Scholar 

  55. Tan CH, Koh KS, Xie C, Zhang J, Tan XH, Lee GP, Zhou Y, Ng WJ, Rice SA, Kjelleberg S (2015) Community quorum sensing signalling and quenching: microbial granular biofilm assembly. NPJ Biofilms Microbiomes 1:15006

    PubMed  PubMed Central  Article  Google Scholar 

  56. Ungerfeld EM (2015) Shifts in metabolic hydrogen sinks in the methanogenesis-inhibited ruminal fermentation: a meta-analysis. Front Microbiol 6:37. https://doi.org/10.3389/fmicb.2015.00037

    PubMed  PubMed Central  Article  Google Scholar 

  57. Venkiteshwaran K, Bocher B, Maki J, Zitomer D (2015) Relating anaerobic digestion microbial community and process function: supplementary issue: water microbiology. Microbiol Insights 8s2:MBI.S33593

    Article  Google Scholar 

  58. Wang WZ, Morohoshi T, Ikenoya M, Someya N, Ikeda T (2010) AiiM, a novel class of N-Acylhomoserine lactonase from the leaf-associated bacterium Microbacterium testaceum. Appl Environ Microbiol 76(8):2524–2530

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  59. Zielińska M, Rusanowska P, Jarząbek J, Nielsen JL (2016) Community dynamics of denitrifying bacteria in full-scale wastewater treatment plants. Environ Technol 37(18):2358–2367

    PubMed  Article  CAS  Google Scholar 

  60. Ziemiński K, Frąc M (2012) Methane fermentation process as anaerobic digestion of biomass: transformations stages and microorganisms. Afr J Biotechnol 11(18):4127–4139

    Google Scholar 

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Acknowledgements

The authors wish to thank Dr. Tomohiro Morohoshi for providing a plasmid harboring an AHL lactonase.

Funding

This study was supported by Kitakyushu City as a research grant.

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Correspondence to Toshinari Maeda.

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Nguyen, P.D.T., Mustapha, N.A., Kadokami, K. et al. Quorum sensing between Gram-negative bacteria responsible for methane production in a complex waste sewage sludge consortium. Appl Microbiol Biotechnol 103, 1485–1495 (2019). https://doi.org/10.1007/s00253-018-9553-9

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Keywords

  • Anaerobic digestion
  • Waste sewage sludge
  • Quorum sensing
  • AHL lactonase
  • Gram-negative bacteria