Principles for quorum sensing-based exogeneous denitrifier enhancement of nitrogen removal in biofilm: a review

References

• Albright, M. B. N., Louca, S., Winkler, D. E., Feeser, K. L., Haig, S. J., Whiteson, K. L., Emerson, J. B., & Dunbar, J. (2022). Solutions in microbiome engineering: prioritizing barriers to organism establishment. The ISME Journal, 16(2), 331–338.
   PubMedGoogle Scholar
• Andalib, M., Nakhla, G., McIntee, E., & Zhu, J. (2011). Simultaneous denitrification and methanogenesis (SDM): Review of two decades of research. Desalination, 279(1-3), 1–14. https://doi.org/10.1016/j.desal.2011.06.018
   Google Scholar
• Banihani, Q., Sierra-Alvarez, R., & Field, J. A. (2009). Nitrate and nitrite inhibition of methanogenesis during denitrification in granular biofilms and digested domestic sludges. Biodegradation, 20(6), 801–812.
   PubMedGoogle Scholar
• Batchelor, S. E., Cooper, M., Chhabra, S. R., Glover, L. A., Stewart, G., Williams, P., & Prosser, J. (1997). Cell density-regulated recovery of starved biofilm populations of ammonia-oxidizing bacteria. Applied and Environmental Microbiology, 63(6), 2281–2286.
   PubMedGoogle Scholar
• Beardmore, R. E., Gudelj, I., Lipson, D. A., & Hurst, L. D. (2011). Metabolic trade-offs and the maintenance of the fittest and the flattest. Nature, 472(7343), 342–346.
   PubMedGoogle Scholar
• Bettenworth, V., van Vliet, S., Turkowyd, B., Bamberger, A., Wendt, H., McIntosh, M., Steinchen, W., Endesfelder, U., & Becker, A. (2022). Frequency modulation of a bacterial quorum sensing response. Nature Communications, 13(1), 2772.
   PubMedGoogle Scholar
• Brislawn, C. J., Graham, E. B., Dana, K., Ihardt, P., Fansler, S. J., Chrisler, W. B., Cliff, J. B., Stegen, J. C., Moran, J. J., & Bernstein, H. C. (2019). Forfeiting the priority effect: turnover defines biofilm community succession. The ISME Journal, 13(7), 1865–1877.
   PubMedGoogle Scholar
• Burmølle, M., Webb, J. S., Rao, D., Hansen, L. H., Sorensen, S. J., & Kjelleberg, S. (2006). Enhanced biofilm formation and increased resistance to antimicrobial agents and bacterial invasion are caused by synergistic interactions in multispecies biofilms. Applied and Environmental Microbiology, 72(6), 3916–3923.
   PubMed Web of Science ®Google Scholar
• Burton, E. O., Read, H. W., Pellitteri, M. C., & Hickey, W. J. (2005). Identification of acyl-homoserine lactone signalling molecules produced by Nitrosomonas europaea strain Schmidt. Applied and Environmental Microbiology, 71(8), 4906–4909. https://doi.org/10.1128/AEM.71.8.4906-4909.2005
   PubMedGoogle Scholar
• Carvalho, J. C., Cardoso, P., Borges, P. A. V., Schmera, D., & Podani, J. (2013). Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches. Oikos, 122(6), 825–834. https://doi.org/10.1111/j.1600-0706.2012.20980.x
   Google Scholar
• Chen, M., Wang, W., Feng, Y., Zhu, X., Zhou, H., Tan, Z., & Li, X. (2014). Impact resistance of different factors on ammonia removal by heterotrophic nitrification-aerobic denitrification bacterium Aeromonas sp HN-02. Bioresource Technology, 167, 456–461.
   PubMed Web of Science ®Google Scholar
• Cheng, Y., Zhang, Y., Shen, Q., Gao, J., Zhuang, G., & Zhuang, X. (2017). Effects of exogenous short-chain N-acyl homoserine lactone on denitrifying process of Paracoccus denitrificans. Journal of Environmental Sciences, 54, 33–39. https://doi.org/10.1016/j.jes.2016.05.019
   Google Scholar
• Cheong, W. S., Kim, S. R., Oh, H. S., Lee, S. H., Yeon, K. M., Lee, C. H., & Lee, J. K. (2014). Design of quorum quenching microbial vessel to enhance cell viability for biofouling control in membrane bioreactor. Journal of Microbiology and Biotechnology, 24(1), 97–105.
   PubMed Web of Science ®Google Scholar
• Condon, C., Liveris, D., Squires, C., Schwartz, I., & Squires, C. L. (1995). rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn nactivation. Journal of Bacteriology, 177(14), 4152–4156. https://doi.org/10.1128/jb.177.14.4152-4156.1995
   PubMedGoogle Scholar
• Cornforth, D., & Foster, K. (2013). Competition sensing: the social side of bacterial stress responses. Nature Reviews Microbiology, 11(4), 285–293. https://doi.org/10.1038/nrmicro2977
   PubMed Web of Science ®Google Scholar
• Craig, L., Forest, K. T., & Maier, B. (2019). Type IV pili: dynamics, biophysics and functional consequences. Nature Reviews Microbiology, 17(7), 429–440. https://doi.org/10.1038/s41579-019-0195-4
   PubMed Web of Science ®Google Scholar
• Cui, X., Ruan, X., Yin, J., Wang, M., Li, N., & Shen, D. (2021). Regulation of las and rhl quorum sensing on aerobic denitrification in Pseudomonas aeruginosa PAO1. Current Microbiology, 78(2), 659–667. https://doi.org/10.1007/s00284-020-02338-z
   PubMed Web of Science ®Google Scholar
• Cui, Y. X., Biswal, B. K., Guo, G., Deng, Y. F., Huang, H., Chen, G. H., & Wu, D. (2019). Biological nitrogen removal from wastewater using sulphur-driven autotrophic denitrification. Applied Microbiology and Biotechnology, 103(15), 6023–6039. https://doi.org/10.1007/s00253-019-09935-4
   PubMed Web of Science ®Google Scholar
• De Roy, K., Marzorati, M., Negroni, A., Thas, O., Balloi, A., Fava, F., Verstraete, W., Daffonchio, D., & Boon, N. (2013). Environmental conditions and community evenness determine the outcome of biological invasion. Nature Communications, 4, 1383.
   PubMedGoogle Scholar
• Debray, R., Herbert, R. A., Jaffe, A. L., Crits-Christoph, A., Power, M. E., & Koskella, B. (2022). Priority effects in microbiome assembly. Nature Reviews. Microbiology, 20(2), 109–121. https://doi.org/10.1038/s41579-021-00604-w
   PubMed Web of Science ®Google Scholar
• Dietrich, L. E. P., Price-Whelan, A., Petersen, A., Whiteley, M., & Newman, D. K. (2006). The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa. Molecular Microbiology, 61(5), 1308–1321.
   PubMed Web of Science ®Google Scholar
• Dolinšek, J., Ramoneda, J., & Johnson, D. R. (2022). Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability. ISME Communications, 2(1), 1–9. https://doi.org/10.1038/s43705-022-00160-1
   Google Scholar
• Doucette, C. D., Schwab, D. J., Wingreen, N. S., & Rabinowitz, J. D. (2011). α-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition. Nature Chemical Biology, 7(12), 894–901.
   PubMed Web of Science ®Google Scholar
• Dufrêne, Y. F., & Persat, A. (2020). Mechanomicrobiology: how bacteria sense and respond to forces. Nature Reviews. Microbiology, 18(4), 227–240.
   PubMedGoogle Scholar
• Freilich, S., Zarecki, R., Eilam, O., Segal, E. S., Henry, C. S., Kupiec, M., Gophna, U., Sharan, R., & Ruppin, E. (2011). Competitive and cooperative metabolic interactions in bacterial communities. Nature Communications, 2, 589–596.
   PubMed Web of Science ®Google Scholar
• Fu, S., Fan, H., Liu, S., Liu, Y., & Liu, Z. (2009). A bioaugmentation failure caused by phage infection and weak biofilm formation ability. Journal of Environmental Science, 21(8), 1153–1161. https://doi.org/10.1016/S1001-0742(08)62396-7
   Google Scholar
• Fukami, T., Dickie, I. A., Paula Wilkie, J., Paulus, B. C., Park, D., Roberts, A., Buchanan, P. K., & Allen, R. B. (2010). Assembly history dictates ecosystem functioning: Evidence from wood decomposer communities. Ecology Letters, 13(6), 675–684. https://doi.org/10.1111/j.1461-0248.2010.01465.x
   PubMed Web of Science ®Google Scholar
• Fukami, T., & Nakajima, M. (2011). Community assembly: alternative stable states or alternative transient states? Ecology Letters, 14(10), 973–984. https://doi.org/10.1111/j.1461-0248.2011.01663.x
   PubMed Web of Science ®Google Scholar
• Ganusova, E. E., Vo, L. T., Abraham, P. E., Yoder, L. O., Hettich, R. L., & Alexandre, G. (2021). The Azospirillum brasilense core chemotaxis proteins CheA1 and CheA4 link chemotaxis signaling with nitrogen metabolism. mSystems, 6(1), e01354-20. https://doi.org/10.1128/mSystems.01354-20
   PubMedGoogle Scholar
• Gonzalez-Martinez, A., Munoz-Palazon, B., Maza-Marquez, P., Rodriguez-Sanchez, A., Gonzalez-Lopez, J., & Vahala, R. (2018). Performance and microbial community structure of a polar Arctic circle aerobic granular sludge system operating at low temperature. Bioresource Technology, 256, 22–29.
   PubMedGoogle Scholar
• Gosztolai, A., Schumacher, J., Behrends, V., Bundy, J. G., Heydenreich, F., Bennett, M. H., Buck, M., & Barahona, M. (2017). Glnk facilitates the dynamic regulation of bacterial nitrogen assimilation. Biophysical Journal, 112(10), 2219–2230.
   PubMedGoogle Scholar
• Gralka, M., Szabo, R., Stocker, R., & Cordero, O. X. (2020). Trophic interactions and the drivers of microbial community assembly. Current Biology, 30(19), R1176–R1188. https://doi.org/10.1016/j.cub.2020.08.007
   PubMedGoogle Scholar
• Gudelj, I., Weitz, J. S., Ferenci, T., Horner-Devine, M. C., Marx, C. J., Meyer, J. R., & Forde, S. E. (2010). An integrative approach to understanding microbial diversity: From intracellular mechanisms to community structure. Ecology Letters, 13(9), 1073–1084.
   PubMedGoogle Scholar
• Ha, J., Hauk, P., Cho, K., Eo, Y., Ma, X., Stephens, K., Cha, S., Jeong, M., Suh, J.-Y., Sintim, H. O., Bentley, W. E., & Ryu, K.-S. (2018). Evidence of link between quorum sensing and sugar metabolism in Escherichia coli revealed via cocrystal structures of LsrK and HPr. Science Advances, 4(6), eaar7063. https://doi.org/10.1126/sciadv.aar7063
   PubMed Web of Science ®Google Scholar
• Hallin, A., Philippot, L., Loffler, F. E., Sanford, R. A., & Jones, C. M. (2018). Genomics and ecology of novel N2O-reducing microorganisms. Trends in Microbiology, 26(1), 43–55.
   PubMed Web of Science ®Google Scholar
• Harper, C. J., Hayward, D., Kidd, M., Wiid, I., & van Helden, P. (2010). Glutamate dehydrogenase and glutamine synthetase are regulated in response to nitrogen availability in Myocbacterium smegmatis. BMC Microbiology, 10(1), 138.
   PubMedGoogle Scholar
• Hayastu, M., Tago, K., & Saito, M. (2008). Various players in the nitrogen cycle: Diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Science and Plant Nutrition, 54, 33–45.
   Google Scholar
• He, X., Tian, Y., Guo, L., Lux, R., Zusman, D. R., & Shi, W. (2010). Oral-derived bacterial flora defends its domain by recognizing and killing intruders-a molecular analysis using Escherichia coli as a model intestinal bacterium. Microbial Ecology, 60(3), 655–664. https://doi.org/10.1007/s00248-010-9708-4
   PubMedGoogle Scholar
• Herrero, M., & Stuckey, D. C. (2015). Bioaugmentation and its application in wastewater treatment: A review. Chemosphere, 140, 119–128.
   PubMed Web of Science ®Google Scholar
• Heylen, K., & Keltjens, J. (2012). Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus. Frontiers in Microbiology, 3(371), 327–371.
   PubMedGoogle Scholar
• Houry, A., Gohar, M., Deschamps, J., Tischenko, E., Aymerich, S., Gruss, A., & Briandet, R. (2012). Bacterial swimmers that infiltrate and take over the biofilm matrix. Proceedings of the National Academy of Sciences of the United States of America, 109(32), 13088–13093.
   PubMed Web of Science ®Google Scholar
• Høyland-Kroghsbo, N. M., Paczkowski, J., Mukherjee, S., Broniewski, J., Westra, E., Bondy-Denomy, J., & Bassler, B. L. (2017). Quorum sensing controls the Pseudomonas aeruginosa CRISPR–Cas adaptive immune system. Proceedings of the National Academy of Sciences of the United States of America, 114(1), 131–135.
   PubMed Web of Science ®Google Scholar
• Hu, H., He, J., Liu, J., Yu, H., & Zhang, J. (2016). Biofilm activity and sludge characteristics affected by exogenous N-acyl homoserine lactones in biofilm reactors. Bioresource Technology, 211, 339–347.
   PubMedGoogle Scholar
• Huang, S., Zhang, H., Ng, T. C. A., Xu, B., Shi, X., & Ng, H. Y. (2020). Analysis of N-Acy-L-homoserine lactones (AHLs) in wastewater treatment systems using SPE-LLE with LC-MS/MS. Water Research, 177, 115756. https://doi.org/10.1016/j.watres.2020.115756
   PubMedGoogle Scholar
• Huang, T., Zhou, S., Zhang, H., Bai, S., He, X., & Yang, X. (2015). Nitrogen removal characteristics of a newly isolated indigenous aerobic denitrifier from oligotrophic drinking water reservoir, Zoogloea sp N299. International Journal of Molecular Sciences, 16(5), 10038–10060.
   PubMedGoogle Scholar
• Huergo, L. F., & Dixon, R. (2015). The emergence of 2-oxoglutarate as a master regulator metabolite. Microbiology and Molecular Biology Reviews : MMBR, 79(4), 419–435.
   PubMed Web of Science ®Google Scholar
• Ikeda-Ohtsubo, W., Miyahara, M., Kim, S. W., Yamada, T., Matsuoka, M., Watanabe, A., Fushinobu, S., Wakagi, T., Shoun, H., Miyauchi, K., & Endo, G. (2013). Bioaugmentation of a wastewater bioreactor system with the nitrous oxide-reducing denitrifier Pseudomonas stutzeri strain TR2. Journal of Bioscience and Bioengineering, 115(1), 37–42.
   PubMed Web of Science ®Google Scholar
• Jahangir, M. M. R., Richards, K. G., Healy, M. G., Gill, L., Müller, C., Johnston, P., & Fenton, O. (2016). Carbon and nitrogen dynamics and greenhouse gas emissions in constructed wetlands treating wastewater: A review. Hydrology and Earth System Sciences, 20(1), 109–123. https://doi.org/10.5194/hess-20-109-2016
   Google Scholar
• Jia, Y., Zhou, M., Chen, Y., Hu, Y., & Luo, J. (2020). Insight into short-cut of simultaneous nitrification and denitrification process in moving bed biofilm reactor: Effects of carbon to nitrogen ratio. Chemical Engineering Journal, 400, 125905. https://doi.org/10.1016/j.cej.2020.125905
   Web of Science ®Google Scholar
• Jiang, L., Brady, L., & Tan, J. (2011). Species diversity, invasion, and alternative community states in sequentially assembled communities. The American Naturalist, 178(3), 411–418.
   PubMedGoogle Scholar
• Jiang, M., Zheng, X., & Chen, Y. (2020). Enhancement of denitrification performance with reduction of nitrite accumulation and N2O emission by Shewanella oneidensis MR-1 in microbial denitrifying process. Water Research, 169, 115242. https://doi.org/10.1016/j.watres.2019.115242
   PubMedGoogle Scholar
• Joo, H. S., Hirai, M., & Shoda, M. (2005). Characteristics of ammonium removal by heterotrophic nitrification-aerobic denitrification by Alcaligenes faecalis no. 4. Journal of Bioscience and Bioengineering, 100(2), 184–191.
   PubMed Web of Science ®Google Scholar
• Kang, Y., Goo, E., Kim, J., & Hwang, I. (2017). Critical role of quorum sensing-dependent glutamate metabolism in homeostatic osmolality and outer membrane vesiculation in Burkholderia glumae. Scientific Reports, 7, 44195.
   PubMedGoogle Scholar
• Karanasios, K. A., Vasiliadou, I. A., Pavlou, S., & Vayenas, D. V. (2010). Hydrogenotrophic denitrification of potable water: A review. Journal of Hazardous Materials, 180(1-3), 20–37.
   PubMed Web of Science ®Google Scholar
• Kassinger, S. J., & van Hoek, M. L. (2020). Biofilm architecture: An emerging synthetic biology target. Synthetic and Systems Biotechnology, 5(1), 1–10. https://doi.org/10.1016/j.synbio.2020.01.001
   PubMedGoogle Scholar
• Keegstra, J. M., Carrara, F., & Stocker, R. (2022). The ecological roles of bacterial chemotaxis. Nature Reviews Microbiology, 20(8), 491–504. https://doi.org/10.1038/s41579-022-00709-w
   PubMedGoogle Scholar
• Kim, J., Darlington, A., Salvador, M., Utrilla, J., & Jimenez, J. I. (2020). Trade-offs between gene expression, growth and phenotypic diversity in microbial populations. Current Opinion in Biotechnology, 62, 29–37.
   PubMedGoogle Scholar
• Kinnunen, M., Dechesne, A., Proctor, C., Hammes, F., Johnson, D., Quintela-Baluja, M., Graham, D., Daffonchio, D., Fodelianakis, S., Hahn, N., Boon, N., & Smets, B. F. (2016). A conceptual framework for invasion in microbial communities. The ISME Journal, 10(12), 2773–2775.
   PubMedGoogle Scholar
• Kraft, B., Tegetmeyer, H. E., Sharma, R., Klotz, M. G., Ferdelman, T. G., Hettich, R. L., Geelhoed, J. S., & Strous, M. (2014). The environmental controls that govern the end product of bacterial nitrate respiration. Science (New York, N.Y.), 345(6197), 676–679.
   PubMedGoogle Scholar
• Kuypers, M. M. M., Marchant, H. K., & Kartal, B. (2018). The microbial nitrogen-cycling network. Nature Reviews. Microbiology, 16(5), 263–276.
   PubMed Web of Science ®Google Scholar
• Ladau, J., & Eloe-Fadrosh, E. A. (2019). Spatial, temporal, and phylogenetic scales of Microbial Ecology. Trends in Microbiology, 27(8), 662–669.
   PubMed Web of Science ®Google Scholar
• Larkin, J. W., Zhai, X., Kikuchi, K., Redford, S. E., Prindle, A., Liu, J., Greenfield, S., Walczak, A. M., Garcia-Ojalvo, J., Mugler, A., & Suel, G. M. (2018). Signal percolation within a bacterial community. Cell Systems, 7(2), 137–145.e3.
   PubMedGoogle Scholar
• Lawson, C. E., Harcombe, W. R., Hatzenpichler, R., Lindemann, S. R., Löffler, F. E., O’Malley, M. A., Martín, H. G., Pfleger, B. F., Raskin, L., Venturelli, O. S., Weissbrodt, D. G., Noguera, D. R., & McMahon, K. D. (2019). Common principles and best practices for engineering microbiomes. Nature Reviews Microbiology, 17(12), 725–741. https://doi.org/10.1038/s41579-019-0255-9
   PubMed Web of Science ®Google Scholar
• Leadbetter, J. R., & Greenberg, E. P. (2000). Metabolism of acyl-homoserine lactone quorum-sensing signals by Variovorax paradoxus. Journal of Bacteriology, 182(24), 6921–6926.
   PubMed Web of Science ®Google Scholar
• Lennon, J. T., Aanderud, Z. T., Lehmkuhl, B. K., & Schoolmaster, D. R. (2012). Mapping the niche space of soil microorganisms using taxonomy and traits. Ecology, 93(8), 1867–1879.
   PubMedGoogle Scholar
• Ley, R., Peterson, D., & Gordon, J. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell, 124(4), 837–848.
   PubMed Web of Science ®Google Scholar
• Li, M., Su, Y., Chen, Y., Wan, R., Zheng, X., & Liu, K. (2016). The effects of fulvic acid on microbial denitrification: Promotion of NADH generation, electron transfer, and consumption. Applied Microbiology and Biotechnology, 100(12), 5607–5618.
   PubMedGoogle Scholar
• Li, X., Peng, Y., Zhang, J., & Du, R. (2022). Multiple roles of complex organics in polishing THP-AD filtrate with double-line anammox: Inhibitory relief and bacterial selection. Water Research, 216, 118373. https://doi.org/10.1016/j.watres.2022.118373
   PubMedGoogle Scholar
• Li, Y., Pan, X., Cao, J., Song, X., Fang, F., Tong, Z., Li, W., & Yu, H. (2017). Augmentation of acyl homoserine lactones-producing and -quenching bacterium into activated sludge for its granulation. Water Research, 125, 309–317.
   PubMedGoogle Scholar
• Liang, W., & Huang, S. (2016). Isolation of a thermophilic aerobic denitrifier and characterization for its denitrification performance. Desalination and Water Treatment, 57(45), 21455–21462. https://doi.org/10.1080/19443994.2015.1119750
   Web of Science ®Google Scholar
• Liébana, R., Modin, O., Persson, F., Szabó, E., Hermansson, M., & Wilén, B.-M. (2019). Combined eterministic and stochastic processes control microbial succession in replicate granular biofilm reactors. Environmental Science & Technology, 53(9), 4912–4921. https://doi.org/10.1021/acs.est.8b06669
   PubMedGoogle Scholar
• Lilja, E. E., & Johnson, D. R. (2016). Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates. The ISME Journal, 10(7), 1568–1578.
   PubMedGoogle Scholar
• Liu, Q., Schumacher, J., Wan, X., Lou, C., & Wang, B. (2018). Orthogonality and burdens of heterologous and gate gene circuits in E. coli. ACS Synthetic Biology, 7(2), 553–564. https://doi.org/10.1021/acssynbio.7b00328
   PubMedGoogle Scholar
• Lozupone, C., & Knight, R. (2007). Global patterns in bacterial diversity. Proceedings of the National Academy of Sciences of the United States of America, 104(27), 11436–11440.
   PubMed Web of Science ®Google Scholar
• Lu, H. J., Chandran, K., & Stensel, D. (2014). Microbial ecology of denitrification in biological wastewater treatment. Water Research, 64, 237–254.
   PubMed Web of Science ®Google Scholar
• Lycus, P., Lovise Bothun, K., Bergaust, L., Peele Shapleigh, J., Reier Bakken, L., & Frostegard, A. (2017). Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy. The ISME Journal, 11(10), 2219–2232.
   PubMedGoogle Scholar
• Ma, H., Zhao, Y., Yang, K., Wang, Y., Zhang, C., & Ji, M. (2022). Application oriented bioaugmentation processes: Mechanism, performance improvement and scale-up. Bioresource Technology, 344(Pt B), 126192.
   PubMedGoogle Scholar
• Ma, Y., Zheng, X., Fang, Y., Xu, K., He, S., & Zhao, M. (2020). Autotrophic denitrification in constructed wetlands: Achievements and challenges. Bioresource Technology, 318, 123778.
   PubMedGoogle Scholar
• Mallon, C. A., van Elsas, J. D., & Salles, J. F. (2015). Microbial invasions: The process, patterns, and mechanisms. Trends in Microbiology, 23(11), 719–729.
   PubMed Web of Science ®Google Scholar
• Mangalea, M. R., Plumley, B. A., & Borlee, B. R. (2017). Nitrate sensing and metabolism inhibit biofilm formation in the opportunistic pathogen Burkholderia pseudomallei by reducing the intracellular concentration of c-di-GMP. Frontiers in Microbiology, 8, 1353. https://doi.org/10.3389/fmicb.2017.01353
   PubMedGoogle Scholar
• Martiny, J. B. H., Jones, S. E., Lennon, J. T., & Martiny, A. C. (2015). Microbiomes in light of traits: A phylogenetic perspective. Science, 350(6261), aac9323. https://doi.org/10.1126/science.aac9323
   PubMedGoogle Scholar
• Mauri, M., & Klumpp, S. (2014). A model for sigma factor competition in bacterial cells. PLoS Computational Biology, 10(10), e1003845. https://doi.org/10.1371/journal.pcbi.1003845
   PubMedGoogle Scholar
• Mellbye, B., & Schuster, M. (2014). Physiological framework for the regulation of quorum sensingdependent public goods in Pseudomonas aeruginosa. Journal of Bacteriology, 196(6), 1155–1164.
   PubMedGoogle Scholar
• Mellbye, B. L., Giguere, A. T., Bottomley, P. J., & Sayavedra-Soto, L. A. (2016). Quorum quenching of Nitrobacter winogradskyi suggests that quorum sensing regulates fluxes of nitrogen oxide(s) during nitrification. Mbio, 7(5), e01753–01716. https://doi.org/10.1128/mBio.01753-16
   PubMedGoogle Scholar
• Morgan-Sagastume, F., Boon, N., Dobbelaere, S., Defoirdt, T., & Verstraete, W. (2005). Production of acylated homoserine lactones by Aeromonas and Pseudomonas strains isolated from municipal activated sludge. Canadian Journal of Microbiology, 51(11), 924–933.
   PubMed Web of Science ®Google Scholar
• Mukherjee, S., & Bassler, B. L. (2019). Bacterial quorum sensing in complex and dynamically changing environments. Nature Reviews Microbiology, 17(6), 371–382. https://doi.org/10.1038/s41579-019-0186-5
   PubMed Web of Science ®Google Scholar
• Muro-Pastor, A., & Hess, W. (2020). Regulatory RNA at the crossroads of carbon and nitrogen metabolism in photosynthetic cyanobacteria. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, 1863(1), 194477.
   PubMedGoogle Scholar
• Nadell, C. D., Drescher, K., Wingreen, N. S., & Bassler, B. L. (2015). Extracellular matrix structure governs invasion resistance in bacterial biofilms. The ISME Journal, 9(8), 1700–1709.
   PubMedGoogle Scholar
• Nelson, E. M., Kurz, V., Perry, N., Kyrouac, D., & Timp, G. (2014). Biological noise abatement: coordinating the responses of autonomous bacteria in a synthetic biofilm to a fluctuating environment using a stochastic bistable switch. ACS Synthetic Biology, 3(5), 286–297. https://doi.org/10.1021/sb400052f
   PubMedGoogle Scholar
• Nemergut, D., Knelman, J., Ferrenberg, S., Bilinski, T., Melbourne, B., Jiang, L., Violle, C., Darcy, J. L., Prest, T., Schmidt, S. K., & Townsend, A. R. (2016). Decreases in average bacterial community rRNA operon copy number during succession. The ISME Journal, 10(5), 1147–1156.
   PubMedGoogle Scholar
• Ngraham, J., & Stokes, J. (1959). Psychrophilic bacteria. Bacteriological Reviews, 23(3), 97–108.
   PubMedGoogle Scholar
• Niederdorfer, R., Besemer, K., Battin, T. J., & Peter, H. (2017). Ecological strategies and metabolic trade-offs of complex environmental biofilms. NPJ Biofilms and Microbiomes, 3(21), 21. https://doi.org/10.1038/s41522-017-0029-y
   PubMedGoogle Scholar
• Niu, C., Clemmer, K. M., Bonomo, R. A., & Rather, P. N. (2008). Isolation and characterization of an autoinducer synthase from Acinetobacter baumannii. Journal of Bacteriology, 190(9), 3386–3392.
   PubMed Web of Science ®Google Scholar
• O'Loughlin, C. T., Miller, L. C., Siryaporn, A., Drescher, K., Semmelhack, M. F., & Bassler, B. L. (2013). A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation. Proceedings of the National Academy of Sciences of the United States of America, 110(44), 17981–17986.
   PubMed Web of Science ®Google Scholar
• Ochiai, S., Morohoshi, T., Kurabeishi, A., Shinozaki, M., Fujita, H., Sawada, I., & Ikeda, T. (2013). Production and degradation of N-acylhomoserine lactone quorum sensing signalling molecules in bacteria isolated from activated sludge. Bioscience Biotechnology and Biochemistry, 77(12), 2436–2440. https://doi.org/10.1271/bbb.130553
   PubMed Web of Science ®Google Scholar
• Ochiai, S., Yasumoto, S., Morohoshi, T., & Ikeda, T. (2014). AmiE, a novel N-acylhomoserine lactone acylase belonging to the Amidase family, from the activated-sludge isolate Acinetobacter sp. strain Ooi24. Applied and Environmental Microbiology, 80(22), 6919–6925. https://doi.org/10.1128/AEM.02190-14
   PubMedGoogle Scholar
• Paczia, N., Nilgen, A., Lehmann, T., Gätgens, J., Wiechert, W., & Noack, S. (2012). Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms. Microbial Cell Factories, 11(1), 122.
   PubMedGoogle Scholar
• Pandey, C. B., Kumar, U., Kaviraj, M., Minick, K. J., Mishra, A. K., & Singh, J. S. (2020). DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems. The Science of the Total Environment, 738, 139710.
   PubMedGoogle Scholar
• Papenfort, K., & Bassler, B. (2016). Quorum sensing signal–response systems in Gram-negative bacteria. Nature Reviews Microbiology, 14(9), 576–588. https://doi.org/10.1038/nrmicro.2016.89
   PubMed Web of Science ®Google Scholar
• Park, D., Lee, D. S., Kim, Y. M., & Park, J. M. (2008). Bioaugmentation of cyanide-degrading microorganisms in a full-scale cokes wastewater treatment facility. Bioresource Technology, 99(6), 2092–2096. https://doi.org/10.1016/j.biortech.2007.03.027
   PubMed Web of Science ®Google Scholar
• Parsek, M. R., & Greenberg, E. P. (2005). Sociomicrobiology: the connections between quorum sensing and biofilms. Trends in Microbiology, 13(1), 27–33.
   PubMed Web of Science ®Google Scholar
• Pessi, I. S., Viitamaki, S., Virkkala, A. M., Eronen-Rasimus, E., Delmont, T. O., Marushchak, M. E., Luoto, M., & Hultman, J. (2022). In-depth characterization of denitrifier communities across different soil ecosystems in the tundra. Environmental Microbiome, 17(1), 17–30.
   PubMedGoogle Scholar
• Pfeiffer, T., Schuster, S., & Bonhoeffer, S. (2001). Cooperation and competition in the evolution of ATP-producing pathways. Science (New York, N.Y.), 292(5516), 504–507.
   PubMed Web of Science ®Google Scholar
• Pfluger-Grau, K., & Gorke, B. (2010). Regulatory roles of the bacterial nitrogen-related phosphotransferase system. Trends in Microbiology, 18(5), 205–214.
   PubMedGoogle Scholar
• Piccardi, P., Vessman, B., & Mitri, S. (2019). Toxicity drives facilitation between 4 bacterial species. Proceedings of the National Academy of Sciences of the United States of America, 116(32), 15979–15984.
   PubMed Web of Science ®Google Scholar
• Prescott, R. D., & Decho, A. W. (2020). Flexibility and adaptability of quorum sensing in nature. Trends in Microbiology, 28(6), 436–444.
   PubMedGoogle Scholar
• Rawls, J., Mahowald, M., Ley, R., & Gordon, J. (2006). Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell, 127(2), 423–433.
   PubMed Web of Science ®Google Scholar
• Robertson, L., & Kuenen, J. (1984). Aerobic denitrification: A controversy revived. Archives of Microbiology, 139(4), 351–354. https://doi.org/10.1007/BF00408378
   Google Scholar
• Røder, H. L., Olsen, N. M. C., Whiteley, M., & Burmølle, M. (2020). Unravelling interspecies interactions across heterogeneities in complex biofilm communities. Environmental Microbiology, 22(1), 5–16.
   PubMed Web of Science ®Google Scholar
• Rumbaugh, K. P., & Sauer, K. (2020). Biofilm dispersion. Nature Reviews Microbiology, 18(10), 571–586. https://doi.org/10.1038/s41579-020-0385-0
   PubMed Web of Science ®Google Scholar
• Saavedra, S., & Stouffer, D. (2013). “Disentangling nestedness” disentangled. Nature, 500(7463), E1–E2.
   PubMedGoogle Scholar
• Saleh-Lakha, S., Shannon, K., Henderson, S., Goyer, C., Trevors, J., Zebarth, B., & Burton, D. (2009). Effect of pH and temperature on denitrification gene expression and activity in Pseudomonas mandelii. Applied and Environmental Microbiology, 75(12), 3903–3911.
   PubMed Web of Science ®Google Scholar
• Saxena, G., & Gupta, P. K. (2020). Microbial metabolism of xenobiotic compounds. Integrated Environmental Assessment and Management, 16(5), 797–798.
   Google Scholar
• Schmidt, A., Kochanowski, K., Vedelaar, S., Ahrne, E., Volkmer, B., Callipo, L., Knoops, K., Bauer, M., Aebersold, R., & Heinemann, M. (2016). The quantitative and condition-dependent Escherichia coli proteome. Nature Biotechnology, 34(1), 104–110. https://doi.org/10.1038/nbt.3418
   PubMed Web of Science ®Google Scholar
• Schuster, M., Hawkins, A. C., Harwood, C. S., & Greenberg, E. P. (2004). The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing. Molecular Microbiology, 51(4), 973–985.
   PubMedGoogle Scholar
• Schutte, C. A., Teske, A., MacGregor, B. J., Salman-Carvalho, V., Lavik, G., Hach, P., & de Beer, D. (2018). Filamentous giant Beggiatoaceae from the Guaymas Basin are capable of both denitrification and dissimilatory nitrate reduction to ammonium. Applied and Environmental Microbiology, 84(15), e02860–17. https://doi.org/10.1128/AEM.02860-17
   PubMedGoogle Scholar
• Sepehri, A., & Sarrafzadeh, M. (2018). Effect of nitrifiers community on fouling mitigation and nitrification efficiency in a membrane bioreactor. Chemical Engineering and Processing-Process Intensification, 128, 10–18. https://doi.org/10.1016/j.cep.2018.04.006
   Web of Science ®Google Scholar
• Simon, J., Einsle, O., Kroneck, P. M. H., & Zumft, W. G. (2004). The unprecedented nos gene cluster of Wolinella succinogenes encodes a novel respiratory electron transfer pathway to cytochrome c nitrous oxide reductase. FEBS Letters, 569(1-3), 7–12.
   PubMedGoogle Scholar
• Singh, R., Paul, D., & Jain, R. K. (2006). Biofilms: implications in bioremediation. Trends in Microbiology, 14(9), 389–397.
   PubMed Web of Science ®Google Scholar
• Starkenburg, S. R., Chain, P. S. G., Sayavedra-Soto, L. A., Hauser, L., Land, M. L., Larimer, F. W., Malfatti, S. A., Klotz, M. G., Bottomley, P. J., Arp, D. J., & Hickey, W. J. (2006). Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Applied and Environmental Microbiology, 72(3), 2050–2063.
   PubMedGoogle Scholar
• Steinberg, N., Keren-Paz, A., Hou, Q., Doron, S., Yanuka-Golub, K., Olender, T., Hadar, R., Rosenberg, G., Jain, R., Cámara-Almirón, J., Romero, D., van Teeffelen, S., & Kolodkin-Gal, I. (2020). The extracellular matrix protein TasA is a developmental cue that maintains a motile subpopulation within Bacillus subtilis biofilms. Science Signaling, 13(632), 632. https://doi.org/10.1126/scisignal.aaw8905
   Google Scholar
• Surajit Das, V. (2022). Genetic regulation, biosynthesis and applications of extracellular polysaccharides of the biofilm matrix of bacteria. Carbohydrate Polymers, 291, 119536.
   PubMedGoogle Scholar
• Tan, C. H., Koh, K. S., Xie, C., Zhang, J., Tan, X. H., Lee, G. P., Zhou, Y., Ng, W. J., Rice, S. A., & Kjelleberg, S. (2015). Community quorum sensing signalling and quenching: microbial granular biofilm assembly. NPJ Biofilms and Microbiomes, 1, 15006.
   PubMed Web of Science ®Google Scholar
• Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J. T., Mirarab, S., Zech Xu, Z., Jiang, L., … Knight, R. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), 457–463.
   PubMed Web of Science ®Google Scholar
• Toyofuku, M., Nomura, N., Fujii, T., Takaya, N., Maseda, H., Sawada, I., Nakajima, T., & Uchiyama, H. (2007). Quorum sensing regulates denitrification in Pseudomonas aeruginosa PAO1. Journal of Bacteriology, 189(13), 4969–4972.
   PubMed Web of Science ®Google Scholar
• Tian, T., & Yu, H. (2020). Denitrification with non-organic electron donor for treating low C/N ratio wastewaters. Bioresource Technology, 299, 122686. https://doi.org/10.1016/j.biortech.2019.122686
   PubMed Web of Science ®Google Scholar
• Tugtas, A. E., & Pavlostathis, S. G. (2007). Inhibitory effects of nitrogen oxides on a mixed methanogenic culture. Biotechnology and Bioengineering, 96(3), 444–455.
   PubMedGoogle Scholar
• Ueda, A., & Wood, T. K. (2009). Connecting quorum sensing, c-di-GMP, pel polysaccharide, and biofilm formation in Pseudomonas aeruginosa through tyrosine phosphatase Tpba (PA3885). PLoS Pathogens, 5(6), e1000483. https://doi.org/10.1371/journal.ppat.1000483
   PubMed Web of Science ®Google Scholar
• Van Wolferen, M., Orell, A., & Albers, S. V. (2018). Archaeal biofilm formation. Nature Reviews. Microbiology, 16(11), 699–713. https://doi.org/10.1038/s41579-018-0058-4
   PubMedGoogle Scholar
• Vellend, M. (2010). Conceptual synthesis in community ecology. The Quarterly Review of Biology, 85(2), 183–206.
   PubMed Web of Science ®Google Scholar
• Wadhwa, N., & Berg, H. C. (2022). Bacterial motility: Machinery and mechanisms. Nature Reviews. Microbiology, 20(3), 161–173.
   PubMed Web of Science ®Google Scholar
• Wang, J., Ding, L., Li, K., Schmieder, W., Geng, J., Xu, K., Zhang, Y., & Ren, H. (2017). Development of an extraction method and LC–MS analysis for N-acylated-L-homoserine lactones (AHLs) in wastewater treatment biofilms. Journal of Chromatography B, 1041, 37–44.
   PubMedGoogle Scholar
• Wang, J., Liu, Q., Ma, S., Hu, H., Wu, B., Zhang, X-x., & Ren, H. (2019). Distribution characteristics of N-acyl homoserine lactones during the moving bed biofilm reactor biofilm development process: Effect of carbon/nitrogen ratio and exogenous quorum sensing signals. Bioresource Technology, 289, 121591. https://doi.org/10.1016/j.biortech.2019.121591
   PubMedGoogle Scholar
• Wang, J., Quan, C., Wang, X., Zhao, P., & Fan, X. (2011). Extraction, purification and identification of bacterial signal molecules based on N-acyl homoserine lactones. Microbial Biotechnology, 4(4), 479–490. https://doi.org/10.1111/j.1751-7915.2010.00197.x
   PubMedGoogle Scholar
• Wang, Y., Niu, Q., Zhang, X., Liu, L., Wang, Y., Chen, Y., Negi, M., Figeys, D., Li, Y., & Zhang, T. (2019). Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics. Microbiome, 7(1), 122. https://doi.org/10.1186/s40168-019-0730-6
   PubMedGoogle Scholar
• Waqas, S., Bilad, M. R., Man, Z., Wibisono, Y., Jaafar, J., Indra Mahlia, T. M., Khan, A. L., & Aslam, M. (2020). Recent progress in integrated fixed-film activated sludge process for wastewater treatment: A review. Journal of Environmental Management, 268, 110718.
   PubMedGoogle Scholar
• Whiteley, M., Diggle, S., & Greenberg, E. (2017). Progress in and promise of bacterial quorum sensing research. Nature, 551(7680), 313–320.
   PubMed Web of Science ®Google Scholar
• Wosten, M. (1998). Eubacterial sigma-factors. FEMS Microbiology Reviews, 22(3), 127–150.
   PubMedGoogle Scholar
• Wu, L., Ding, X., Lin, Y., Lu, X., Lv, H., Zhao, M., & Yu, R. (2022). Nitrogen removal by a novel heterotrophic nitrification and aerobic denitrification bacterium Acinetobacter calcoaceticus TY1 under low temperatures. Bioresource Technology, 353, 127148. https://doi.org/10.1016/j.biortech.2022.127148
   PubMedGoogle Scholar
• Xiong, F., Zhao, X., Wen, D., & Li, Q. (2020). Effects of N-acyl-homoserine lactones-based quorum sensing on biofilm formation, sludge characteristics, and bacterial community during the start-up of bioaugmented reactors. The Science of the Total Environment, 735, 139449. https://doi.org/10.1016/j.scitotenv.2020.139449
   PubMed Web of Science ®Google Scholar
• Yan, L., Liu, S., Liu, Q., Zhang, M., Liu, Y., Wen, Y., Chen, Z., Zhang, Y., & Yang, Q. (2019). Improved performance of simultaneous nitrification and denitrification via nitrite in an oxygen-limited SBR by alternating the DO. Bioresource Technology, 275, 153–162. https://doi.org/10.1016/j.biortech.2018.12.054
   PubMed Web of Science ®Google Scholar
• Yan, X., Zheng, S., Huo, Z., Shi, B., Huang, J., Yang, J., Ma, J., Han, Y., Wang, Y., Cheng, K., Feng, J., & Sun, J. (2020). Effects of exogenous N-acyl-homoserine lactones on nutrient removal, sludge properties and microbial community structures during activated sludge process. Chemosphere, 255, 126945. https://doi.org/10.1016/j.chemosphere.2020.126945
   PubMedGoogle Scholar
• Yao, S., Ni, J., Ma, T., & Li, C. (2013). Heterotrophic nitrification and aerobic denitrification at low temperature by a newly isolated bacterium, Acinetobacter sp HA2. Bioresource Technology, 139, 80–86.
   PubMed Web of Science ®Google Scholar
• Yawata, Y., Cordero, O. X., Menolascina, F., Hehemann, J. H., Polz, M. F., & Stocker, R. (2014). Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations. Proceedings of the National Academy of Sciences of the United States of America, 111(15), 5622–5627. https://doi.org/10.1073/pnas.1318943111
   PubMedGoogle Scholar
• Zhang, J., Wu, P., Hao, B., & Yu, Z. (2011). Heterotrophic nitrification and aerobic denitrification by the bacterium Pseudomonas stutzeri YZN-001. Bioresource Technology, 102(21), 9866–9869.
   PubMed Web of Science ®Google Scholar
• Zhang, J., Li, J., Zhao, B., Zhang, Y., Wang, X., & Chen, G. (2019). Long-term effects of N-acyl-homoserine lactone-based quorum sensing on the characteristics of anammox granules in high-loaded gnomic for reactors. Chemosphere, 218, 632–642. https://doi.org/10.1016/j.chemosphere.2018.11.170
   PubMed Web of Science ®Google Scholar
• Zhang, L., Narita, Y., Gao, L., Ali, M., Oshiki, M., Ishii, S., & Okabe, S. (2017a). Microbial competition among anammox bacteria in nitrite-limited bioreactors. Water Research, 125, 249–258.
   PubMed Web of Science ®Google Scholar
• Zhang, Q., Yang, G., Zhang, L., Zhang, Z., Tian, G., & Jin, R. (2017b). Bioaugmentation as a useful strategy for performance enhancement in biological wastewater treatment undergoing different stresses: Application and mechanisms. Critical Reviews in Environmental Science and Technology, 47(19), 1877–1899. https://doi.org/10.1080/10643389.2017.1400851
   Web of Science ®Google Scholar
• Zhang, Y., Shi, Z., Chen, M., Dong, X., & Zhou, J. (2015). Evaluation of simultaneous nitrification and denitrification under controlled conditions by an aerobic denitrifier culture. Bioresource Technology, 175, 602–605.
   PubMedGoogle Scholar
• Zheng, Z., Li, W., Wang, Y., Zhang, D., Wen, Q., & Zhao, Y. (2021). Application of glucose for improving NH4+-N removal in micro-polluted source water by immobilized heterotrophic nitrifiers at low temperature. Chemosphere, 278, 130459. https://doi.org/10.1016/j.chemosphere.2021.130459
   PubMedGoogle Scholar