Osborn, D., Cutter, A. & Ullah, F. in Stakeholder Forum, Commissioned by the UN Development Program. Geneva, Switzerland.
Cain, M., Bowman, W. & Hacker, S. Ecology 3rd edn. (Sinauer Associates Inc., Sunderland, 2014).
Donohue, I. et al. On the dimensionality of ecological stability. Ecol. Lett. 16, 421–429 (2013).
Hillebrand, H. et al. Decomposing multiple dimensions of stability in global change experiments. Ecol. Lett. 21, 21–30 (2018).
Briones, A. & Raskin, L. Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Curr. Opin. Biotechnol. 14, 270–276 (2003).
Wang, Q., Ding, C., Tao, G. & He, J. Analysis of enhanced nitrogen removal mechanisms in a validation wastewater treatment plant containing anammox bacteria. Appl. Microbiol. Biotechnol. 103, 1255–1265 (2019).
Zhou, J. & Ning, D. Stochastic community assembly: does it matter in microbial ecology?. Microbiol. Mol. Biol. Rev. 81, 1–32 (2017).
Santillan, E., Seshan, H., Constancias, F., Drautz-Moses, D. I. & Wuertz, S. Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities. NPJ Biofilms Microbiomes 5, 1–8 (2019).
Prosser, J. I. Replicate or lie. Environ. Microbiol. 12, 1806–1810 (2010).
Bender, E. A., Case, T. J. & Gilpin, M. E. Perturbation experiments in community ecology: theory and practice. Ecology 65, 1–13 (1984).
Shade, A. et al. Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3, 1–19 (2012).
Botton, S., van Heusden, M., Parsons, J. R., Smidt, H. & van Straalen, N. Resilience of microbial systems towards disturbances. Crit. Rev. Microbiol. 32, 101–112 (2006).
Rykiel, E. J. Towards a definition of ecological disturbance. Aust. J. Ecol. 10, 361–365 (1985).
Hu, B., Wheatley, A., Ishtchenko, V. & Huddersman, K. The effect of shock loads on SAF bioreactors for sewage treatment works. Chem. Eng. J. 166, 73–80 (2011).
Bassin, J. P. et al. Effect of increasing organic loading rates on the performance of moving-bed biofilm reactors filled with different support media: assessing the activity of suspended and attached biomass fractions. Process Saf. Environ. Prot. 100, 131–141 (2016).
Seetha, N., Bhargava, R. & Kumar, P. Effect of organic shock loads on a two-stage activated sludge-biofilm reactor. Bioresour. Technol. 101, 3060–3066 (2010).
Ketheesan, B. & Stuckey, D. C. Effects of hydraulic/organic shock/transient loads in anaerobic wastewater treatment: a review. Crit. Rev. Environ. Sci. Technol. 45, 2693–2727 (2015).
Senturk, E., Ince, M. & Onkal Engin, G. The effect of shock loading on the performance of a thermophilic anaerobic contact reactor at constant organic loading rate. J. Environ. Health Sci. Eng. 12, 1–6 (2014).
Gray, N. F. Biology of Wastewater Treatment 2nd edn, Vol. 4 (Imperial College Press, London, 2004).
Laureni, M. et al. Mainstream partial nitritation and anammox: long-term process stability and effluent quality at low temperatures. Water Res. 101, 628–639 (2016).
Wang, Q. & He, J. Newly designed high-coverage degenerate primers for nitrogen removal mechanism analysis in a partial nitrification-anammox (PN/A) process. FEMS Microbiol. Ecol. 96, fiz202 (2019).
Ma, B. et al. Suppressing nitrite-oxidizing bacteria growth to achieve nitrogen removal from domestic wastewater via anammox using intermittent aeration with low dissolved oxygen. Sci. Rep. 5, 1–9 (2015).
Sinha, B. & Annachhatre, A. P. Partial nitrification—operational parameters and microorganisms involved. Rev. Environ. Sci. Bio. Technol. 6, 285–313 (2007).
Okabe, S., Oozawa, Y., Hirata, K. & Watanabe, Y. Relationship between population dynamics of nitrifiers in biofilms and reactor performance at various C:N ratios. Water Res. 30, 1563–1572 (1996).
Ge, S. et al. Detection of nitrifiers and evaluation of partial nitrification for wastewater treatment: a review. Chemosphere 140, 85–98 (2015).
Ma, J. et al. Analysis of nitrification efficiency and microbial community in a membrane bioreactor fed with low COD/N-ratio wastewater. PLoS ONE 8, 1–10 (2013).
Tan, C., Ma, F. & Qiu, S. Impact of carbon to nitrogen ratio on nitrogen removal at a low oxygen concentration in a sequencing batch biofilm reactor. Water Sci. Technol. 67, 612–618 (2012).
Zhang, T. et al. Achieving partial nitrification in a continuous post-denitrification reactor treating low C/N sewage. Chem. Eng. J. 335, 330–337 (2018).
She, Z. et al. Partial nitrification and denitrification in a sequencing batch reactor treating high-salinity wastewater. Chem. Eng. J. 288, 207–215 (2016).
Regmi, P. et al. Control of aeration, aerobic SRT and COD input for mainstream nitritation/denitritation. Water Res. 57, 162–171 (2014).
Ge, S., Peng, Y., Qiu, S., Zhu, A. & Ren, N. Complete nitrogen removal from municipal wastewater via partial nitrification by appropriately alternating anoxic/aerobic conditions in a continuous plug-flow step feed process. Water Res. 55, 95–105 (2014).
Jiang, H. et al. A pilot-scale study on start-up and stable operation of mainstream partial nitrification-anammox biofilter process based on online pH-DO linkage control. Chem. Eng. J. 350, 1035–1042 (2018).
Pimm, S. L. The complexity and stability of ecosystems. Nature 307, 321 (1984).
Santillan, E., Constancias, F. & Wuertz, S. Press disturbance alters community structure and assembly mechanisms of bacterial taxa and functional genes in mesocosm-scale bioreactors. mSystems 5, e00471–e00420 (2020).
Nowka, B., Daims, H. & Spieck, E. Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation. Appl. Environ. Microbiol. 81, 745–753 (2015).
Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).
Okabe, S., Aoi, Y., Satoh, H. & Suwa, Y. Nitrification. In Nitrification in Wastewater Treatment (eds Ward, B. B. et al.) 405–418 (ASM Press, Washington, DC, 2011).
Blackburne, R., Yuan, Z. & Keller, J. Partial nitrification to nitrite using low dissolved oxygen concentration as the main selection factor. Biodegradation 19, 303–312 (2008).
Garrido, J. M., van Benthum, W. A. J., van Loosdrecht, M. C. M. & Heijnen, J. J. Influence of dissolved oxygen concentration on nitrite accumulation in a biofilm airlift suspension reactor. Biotechnol. Bioeng. 53, 168–178 (1997).
Almstrand, R., Daims, H., Persson, F., Sörensson, F. & Hermansson, M. New methods for analysis of spatial distribution and coaggregation of microbial populations in complex biofilms. Appl. Environ. Microbiol. 79, 5978–5987 (2013).
Law, Y. et al. High dissolved oxygen selection against nitrospira sublineage I in full-scale activated sludge. Environ. Sci. Technol. 53, 8157–8166 (2019).
Gonzalez, C., Garcia, P. A. & Munoz, R. Effect of feed characteristics on the organic matter, nitrogen and phosphorus removal in an activated sludge system treating piggery slurry. Water Sci. Technol. 60, 2145–2152 (2009).
Lydmark, P., Lind, M., Sörensson, F. & Hermansson, M. Vertical distribution of nitrifying populations in bacterial biofilms from a full-scale nitrifying trickling filter. Environ. Microbiol. 8, 2036–2049 (2006).
Okabe, S., Satoh, H. & Watanabe, Y. In situ analysis of nitrifying biofilms as determined by in situ hybridization and the use of microelectrodes. Appl. Environ. Microbiol. 65, 3182–3191 (1999).
Anthonisen, A., Loehr, R., Prakasam, T. & Srinath, E. Inhibition of nitrification by ammonia and nitrous acid. Journal (Water Pollut. Control Fed.), 835–852 (1976).
Lackner, S. et al. Full-scale partial nitritation/anammox experiences: an application survey. Water Res. 55, 292–303 (2014).
Wu, J., He, C., van Loosdrecht, M. C. M. & Pérez, J. Selection of ammonium oxidizing bacteria (AOB) over nitrite oxidizing bacteria (NOB) based on conversion rates. Chem. Eng. J. 304, 953–961 (2016).
Tchobanoglous, G. B., Franklin, L. & Stensel, H. D. Wastewater engineering: treatment and reuse 4th edn. (McGraw Hill, New York, 2003).
Smith, R. C., Elger, S. O. & Mleziva, S. Implementation of solids retention time (SRT) control in wastewater treatment. Xylem Anal. 20, 1–6 (2015).
Simsek, H., Kasi, M., Ohm, J.-B., Murthy, S. & Khan, E. Impact of solids retention time on dissolved organic nitrogen and its biodegradability in treated wastewater. Water Res. 92, 44–51 (2016).
Wu, Y.-J. et al. Impact of food to microorganism (F/M) ratio and colloidal chemical oxygen demand on nitrification performance of a full-scale membrane bioreactor treating thin film transistor liquid crystal display wastewater. Bioresour. Technol. 141, 35–40 (2013).
Meerburg, F. A. et al. High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables. Water Res. 100, 137–145 (2016).
Vuono, D. C. et al. Disturbance and temporal partitioning of the activated sludge metacommunity. ISME J. 9, 425–435 (2015).
Ballinger, S. J., Head, I. M., Curtis, T. P. & Godley, A. R. The effect of C/N ratio on ammonia oxidising bacteria community structure in a laboratory nitrification-denitrification reactor. Water Sci. Technol. 46, 543–550 (2002).
Cabrol, L. et al. Management of microbial communities through transient disturbances enhances the functional resilience of nitrifying gas-biofilters to future disturbances. Environ. Sci. Technol. 50, 338–348 (2016).
Wells, G. F. et al. Comparing the resistance, resilience, and stability of replicate moving bed biofilm and suspended growth combined nitritation–anammox reactors. Environ. Sci. Technol. 51, 5108–5117 (2017).
Pianka, E. R. R-selection and K-selection. Am. Nat. 104, 592–579 (1970).
Santillan, E., Seshan, H., Constancias, F. & Wuertz, S. Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance. Environ. Microbiol. 21, 3751–3764 (2019).
Macarthur, R. H. & Wilson, E. O. The Theory of Island Biogeography 224 (Princeton, Princeton University Press, 1967).
Blackburne, R., Vadivelu, V. M., Yuan, Z. & Keller, J. Kinetic characterisation of an enriched Nitrospira culture with comparison to Nitrobacter. Water Res. 41, 3033–3042 (2007).
Dytczak, M. A., Londry, K. L. & Oleszkiewicz, J. A. Activated sludge operational regime has significant impact on the type of nitrifying community and its nitrification rates. Water Res. 42, 2320–2328 (2008).
Huang, Z., Gedalanga, P. B., Asvapathanagul, P. & Olson, B. H. Influence of physicochemical and operational parameters on Nitrobacter and Nitrospira communities in an aerobic activated sludge bioreactor. Water Res. 44, 4351–4358 (2010).
Vuono, D. C., Munakata-Marr, J., Spear, J. R. & Drewes, J. E. Disturbance opens recruitment sites for bacterial colonization in activated sludge. Environ. Microbiol. 18, 87–99 (2016).
Jauffur, S., Isazadeh, S. & Frigon, D. Should activated sludge models consider influent seeding of nitrifiers? Field characterization of nitrifying bacteria. Water Sci. Technol. 70, 1526–1532 (2014).
Yu, L. et al. Natural continuous influent nitrifier immigration effects on nitrification and the microbial community of activated sludge systems. J. Environ. Sci. 74, 159–167 (2018).
Allison, S. D. & Martiny, J. B. H. Resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. USA 105, 11512–11519 (2008).
Shade, A. et al. Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME J. 6, 2153–2167 (2012).
Santillan, E. Disturbance-Performance-Diversity Relationships and Microbial Ecology in Bioreactors for Wastewater Treatment. Ph.D. thesis, University of California, Davis (2018).
Hesselmann, R. P. X., Werlen, C., Hahn, D., van der Meer, J. R. & Zehnder, A. J. B. Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge. Syst. Appl. Microbiol. 22, 454–465 (1999).
APHA-AWWA-WEF. Standard Methods for the Examination of Water and Wastewater 22nd edn. (AWWA, Mumbai, 2005).
Thijs, S. et al. Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys. Front. Microbiol. 8, 1–15 (2017).
Callahan, B. J. et al. DADA2: High resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Glöckner, F. O. et al. 25 years of serving the community with ribosomal RNA gene reference databases and tools. J. Biotechnol. 261, 169–176 (2017).
Chen, C., Khaleel, S. S., Huang, H. & Wu, C. H. Software for pre-processing Illumina next-generation sequencing short read sequences. Sour. Code Biol. Med. 9, 8–8 (2014).
Ilott, N. E. et al. Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling. ISME J. 10, 2389–2404 (2016).
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Huson, D. H. et al. MEGAN community edition: interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comp. Biol. 12, 1–12 (2016).
Tamames, J. & Puente-Sánchez, F. SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline. Front. Microbiol. 9 (2019).
Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457–D462 (2016).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Puente-Sánchez, F., García-García, N. & Tamames, J. SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o. BMC Bioinform. 21, 358 (2020).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. Ser. B. (Method.) 57, 289–300 (1995).
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