Concluding Remarks and Outlook

Principles for an Ecological Engineering of Nutrient Removal in Granular Sludge Processes

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Engineering Granular Microbiomes

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Abstract

Granular sludge reduces costs for biological nutrient removal (BNR) from wastewater. The microbial resource is managed in granular sludge using principles of microbial ecology, biofilm gradients, and process engineering. Microbial selection phenomena were elucidated in the microbiome of BNR granular sludge. A rational wet-lab and dry-lab biomolecular methodology was used to profile microbiomes with fast analytical throughput and high taxonomic and temporal resolutions. The conceptual ecosystem model of BNR granular sludge was built to foster functional analyses and microbial community engineering. Granulation mechanisms and granule architectures rely on predominant phylotypes and their physiologies. Biomass wash-out drives rapid granulation but affects the microbiome balance. Controlling the organic loading rate, the anaerobic contact time, and the starvation phase length is the key for selecting for polyphosphate-accumulating organism (PAOs) and promoting a stable granulation and EBPR, while out-selecting bulking bacteria and preventing process failures. A careful design of the anaerobic selector is necessary to fully remove organics prior to switching on aeration. Hydraulic-biokinetic modeling supports the design of the anaerobic up-flow feeding selector. A slightly alkaline pH selects for the PAO “Candidatus Accumulibacter” over glycogen-accumulating competitors. Fractions of active PAOs and the EBPR potential of sludge can be rapidly measured in an electrical-conductivity-based metabolic batch test and a polyphosphatase enzymatic assay. The robustness of the biosystem relies on feed-forward and feed-back controls in function of operational variations, granule size distributions, bed volume, and biochemical conversions. An applied methodology is proposed to guide an ecological engineering of BNR granular sludge. Although granules and flocs differ in density, metrics and gradients, the last 100 years of activated sludge research should not be forgotten when designing granular sludge technologies.

Bacterial resource management: the seed for granular sludge.

(This study)

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Notes

  1. 1.

    Royal HaskoningDHV (status 2022) https://nereda.royalhaskoningdhv.com/.

  2. 2.

    Swiss Confederation, 814.201 Waters Protection Ordinance 1998 (status 1st January 2021). https://www.fedlex.admin.ch/eli/cc/1998/2863_2863_2863/en.

  3. 3.

    Delft student team WaterSkins won the Bio-based Innovation Student Challenge Europe with artificial leather made out of Kaumera® https://www.tudelft.nl/en/2021/tnw/making-artificial-leather-while-processing-wastewater.

  4. 4.

    Kaumera Nereda® Gum, a biomaterial extracted from Nereda® granules https://kaumera.com/.

  5. 5.

    de Kreuk and Weissbrodt (conference chairs), International Water Association, Biofilms Specialist Group, “IWA Biofilms: Granular Sludge Conference 2018”, Delft, The Netherlands. www.granularsludgeconference.org.

References

  • Adav SS, Lee DJ, Lai JY (2010) Microbial community of acetate utilizing denitrifiers in aerobic granules. Appl Microbiol Biotechnol 85(3):753–762

    Article  CAS  PubMed  Google Scholar 

  • Adiba S, Nizak C, van Baalen M, Denamur E, Depaulis F (2010) From grazing resistance to pathogenesis: the coincidental evolution of virulence factors. PLoS ONE 5(8):e11882

    Article  PubMed  PubMed Central  Google Scholar 

  • Adler A, Holliger C (2020) Multistability and reversibility of aerobic granular sludge microbial communities upon changes from simple to complex synthetic wastewater and back. Front Microbiol 11:574361

    Google Scholar 

  • Adler A, Poirier S, Pagni M, Maillard J, Holliger C (2022) Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. Environ Microbiol 24(4):2136–2156

    Google Scholar 

  • Agrawal S, Seuntjens D, Cocker P, Lackner S, Vlaeminck SE (2018) Success of mainstream partial nitritation/anammox demands integration of engineering, microbiome and modeling insights. Curr Opin Biotechnol 50:214–221

    Google Scholar 

  • Aguado D, Montoya T, Ferrer J, Seco A (2006) Relating ions concentration variations to conductivity variations in a sequencing batch reactor operated for enhanced biological phosphorus removal. Environ Model Softw 21(6):845–851

    Google Scholar 

  • Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH (2013a) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31(6):533–538

    Article  CAS  PubMed  Google Scholar 

  • Albertsen M, Saunders AM, Nielsen KL, Nielsen PH (2013b) Metagenomes obtained by ‘deep sequencing’—what do they tell about the enhanced biological phosphorus removal communities? Water Sci Technol 68(9):1959–1968

    Article  CAS  PubMed  Google Scholar 

  • Albertsen M, Karst SM, Ziegler AS, Kirkegaard RH, Nielsen PH (2015) Back to basics—the influence of DNA extraction and primer choice on phylogenetic analysis of activated sludge communities. PLoS ONE 10(7):e0132783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ali M, Wang Z, Salam KW, Hari AR, Pronk M, van Loosdrecht MCM, Saikaly PE (2019) Importance of species sorting and immigration on the bacterial assembly of different-sized aggregates in a full-scale aerobic granular sludge plant. Environ Sci Technol 53(14):8291–8301

    Google Scholar 

  • Alpkvist E, Klapper I (2007) A multidimensional multispecies continuum model for heterogeneous biofilm development. Bull Math Biol 69(2):765–789

    Article  PubMed  Google Scholar 

  • Amorim CL, Maia AS, Mesquita RBR, Rangel AOSS, van Loosdrecht MCM, Tiritan ME, Castro PML (2014) Performance of aerobic granular sludge in a sequencing batch bioreactor exposed to ofloxacin, norfloxacin and ciprofloxacin. Water Res 50:101–113

    Google Scholar 

  • Amorim de Carvalho C, Ferreira dos Santos A, Tavares Ferreira TJ, Sousa Aguiar Lira VN, Mendes Barros AR, Bezerra dos Santos A (2021) Resource recovery in aerobic granular sludge systems: is it feasible or still a long way to go? Chemosphere 274:129881

    Google Scholar 

  • Andersen KS, Kirkegaard RH, Karst SM, Albertsen M (2018) ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. bioRxiv 299537

    Google Scholar 

  • Aqeel H, Basuvaraj M, Hall M, Neufeld JD, Liss SN (2016) Microbial dynamics and properties of aerobic granules developed in a laboratory-scale sequencing batch reactor with an intermediate filamentous bulking stage. Appl Microbiol Biotechnol 100(1):447–460

    Article  CAS  PubMed  Google Scholar 

  • Aqeel H, Weissbrodt DG, Cerruti M, Wolfaardt GM, Wilén B-M, Liss SN (2019) Drivers of bioaggregation from flocs to biofilms and granular sludge. Environ Sci Water Res Technol 5:2072–2089

    Article  Google Scholar 

  • Avila I, Freedman D, Johnston J, Wisdom B, McQuarrie J (2021) Inducing granulation within a full-scale activated sludge system to improve settling. Water Sci Technol 84(2):302–313

    Article  CAS  PubMed  Google Scholar 

  • Baeten JE, van Loosdrecht MCM, Volcke EIP (2018) Modelling aerobic granular sludge reactors through apparent half-saturation coefficients. Water Res 146:134–145

    Article  CAS  PubMed  Google Scholar 

  • Baeten JE, Batstone DJ, Schraa OJ, van Loosdrecht MCM, Volcke EIP (2019) Modelling anaerobic, aerobic and partial nitritation-anammox granular sludge reactors—a review. Water Res 149:322–341

    Article  CAS  PubMed  Google Scholar 

  • Baeten JE, van Dijk EJH, Pronk M, van Loosdrecht MCM, Volcke EIP (2021) Potential of off-gas analyses for sequentially operated reactors demonstrated on full-scale aerobic granular sludge technology. Sci Total Environ 787:147651

    Google Scholar 

  • Bagchi S, Lamendella R, Strutt S, van Loosdrecht MCM, Saikaly PE (2016) Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor. Sci Rep 6:28327

    Google Scholar 

  • Ballance S, Holtan S, Aarstad OA, Sikorski P, Skjåk-Braek G, Christensen BE (2005) Application of high-performance anion-exchange chromatography with pulsed amperometric detection and statistical analysis to study oligosaccharide distributions—a complementary method to investigate the structure and some properties of alginates. J Chromatogr A 1093(1–2):59–68

    Google Scholar 

  • Barnard JL, Dunlap P, Steichen M (2017) Rethinking the mechanisms of biological phosphorus removal. Water Environ Res 89(11):2043–2054

    Article  CAS  PubMed  Google Scholar 

  • Barr JJ (2010) The microbial ecology of granular sludge in enhanced biological phosphorus removal. PhD thesis, The University of Queensland

    Google Scholar 

  • Barr JJ, Slater FR, Fukushima T, Bond PL (2010) Evidence for bacteriophage activity causing community and performance changes in a phosphorus-removal activated sludge. FEMS Microbiol Ecol 74(3):631–642

    Article  CAS  PubMed  Google Scholar 

  • Barr JJ, Hastie ML, Fukushima T, Plan MR, Gorman JJ, Tyson GW, Bond PL (2011) Metaproteomic analysis of laboratory scale phophorus removal reactors reveals functional insights of aerobic granular sludge. In: Qi Z (ed) IWA biofilm specialist conference 2011: processes in biofilms. Tongji University, Shanghai, China

    Google Scholar 

  • Barr JJ, Dutilh BE, Skennerton CT, Fukushima T, Hastie ML, Gorman JJ, Tyson GW, Bond PL (2015) Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm. Environ Microbiol 18(1):273–287

    Google Scholar 

  • Barrios-Hernández ML, Bettinelli C, Mora-Cabrera K, Vanegas-Camero M-C, Garcia H, van de Vossenberg J, Prats D, Brdjanovic D, van Loosdrecht MCM, Hooijmans CM (2021) Unravelling the removal mechanisms of bacterial and viral surrogates in aerobic granular sludge systems. Water Res 195:116992

    Article  CAS  PubMed  Google Scholar 

  • Bassin JP, Winkler MKH, Kleerebezem R, Dezotti M, van Loosdrecht MCM (2012) Improved phosphate removal by selective sludge discharge in aerobic granular sludge reactors. Biotechnol Bioeng 109(8):1919–1928

    Article  CAS  PubMed  Google Scholar 

  • Bellini MI, Kumaresan D, Tarlera S, Murrell JC, Fernández-Scavino A (2017) Identification of active denitrifiers by DNA-stable isotope probing and amplicon sequencing reveals Betaproteobacteria as responsible for attenuation of nitrate contamination in a low impacted aquifer. FEMS Microbiol Ecol 94(2):fix181

    Google Scholar 

  • Beloin C, Ghigo J-M (2005) Finding gene-expression patterns in bacterial biofilms. Trends Microbiol 13(1):16–19

    Article  CAS  PubMed  Google Scholar 

  • Bernstein HC (2019) Reconciling ecological and engineering design principles for building microbiomes. mSystems 4(3):e00106–19

    Google Scholar 

  • Beun JJ, Hendriks A, van Loosdrecht MCM, Morgenroth E, Wilderer PA, Heijnen JJ (1999) Aerobic granulation in a sequencing batch reactor. Water Res 33(10):2283–2290

    Article  CAS  Google Scholar 

  • Bhattacharjee AS, Choi J, Motlagh AM, Mukherji ST, Goel R (2015) Bacteriophage therapy for membrane biofouling in membrane bioreactors and antibiotic-resistant bacterial biofilms. Biotechnol Bioeng 112(8):1644–1654

    Article  CAS  PubMed  Google Scholar 

  • Bock E, Koops H-P, Muller U, Rudert M (1990) A new facultatively nitrite oxidizing bacterium, Nitrobacter vulgaris sp. nov. Arch Microbiol 153(2):105–110

    Google Scholar 

  • Boleij M, Kleikamp H, Pabst M, Neu TR, van Loosdrecht MCM, Lin Y (2020) Decorating the anammox house: sialic acids and sulfated glycosaminoglycans in the extracellular polymeric substances of anammox granular sludge. Environ Sci Technol 54(8):5218–5226

    Google Scholar 

  • Bossier P, Verstraete W (1996) Triggers for microbial aggregation in activated sludge? Appl Microbiol Biotechnol 45(1–2):1–6

    Article  CAS  Google Scholar 

  • Bradford LM, Vestergaard G, Táncsics A, Zhu B, Schloter M, Lueders T (2018) Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into microaerobic pollutant-degrading aquifer microbiota. Front Microbiol 9:2696

    Article  PubMed  PubMed Central  Google Scholar 

  • Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T (2011) Bacterial community assembly based on functional genes rather than species. Proc Nat Acad Sci USA 108(34):14288–14293

    Google Scholar 

  • Calderón-Franco D, Sarelse R, Christou S, Pronk M, van Loosdrecht MCM, Abeel T, Weissbrodt DG (2022) Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant. Water Res 219:118571

    Google Scholar 

  • Calero-Cáceres W, Muniesa M (2016) Persistence of naturally occurring antibiotic resistance genes in the bacteria and bacteriophage fractions of wastewater. Water Res 95:11–18

    Google Scholar 

  • Caluwé M, Dobbeleers T, D’Aes J, Miele S, Akkermans V, Daens D, Geuens L, Kiekens F, Blust R, Dries J (2017) Formation of aerobic granular sludge during the treatment of petrochemical wastewater. Bioresour Technol 238:559–567

    Google Scholar 

  • Caluwé M, Goossens K, Seguel Suazo K, Tsertou E, Dries J (2022) Granulation strategies applied to industrial wastewater treatment: from lab to full-scale. Water Sci Technol 85(9):2761–2771

    Google Scholar 

  • Cerruti M, Guo B, Delatolla R, de Jonge N, Hommes-de Vos van Steenwijk A, Kadota P, Lawson CE, Mao T, Oosterkamp MJ, Sabba F, Stokholm-Bjerregaard M, Watson I, Frigon D, Weissbrodt DG (2021) Plant-wide systems microbiology for the wastewater industry. Environ Sci Water Res Technol 7(10):1687–1706

    Google Scholar 

  • Choi J, Kotay SM, Goel R (2011) Bacteriophage-based biocontrol of biological sludge bulking in wastewater. Bioeng Bugs 2(4):214–217

    Article  CAS  PubMed  Google Scholar 

  • Christensen BB, Sternberg C, Andersen JB, Palmer RJ Jr, Nielsen AT, Givskov M, Molin S (1999) Molecular tools for study of biofilm physiology. Methods Enzymol 310:20–42

    Article  CAS  PubMed  Google Scholar 

  • Close K, Marques R, Carvalho VCF, Freitas EB, Reis MAM, Carvalho G, Oehmen A (2021) The storage compounds associated with Tetrasphaera PAO metabolism and the relationship between diversity and P removal. Water Res 204:117621

    Article  CAS  PubMed  Google Scholar 

  • Comeau Y, Hall KJ, Hancock REW, Oldham WK (1986) Biochemical model for enhanced biological phosphorus removal. Water Res 20(12):1511–1521

    Article  CAS  Google Scholar 

  • Conthe M, Kuenen JG, Kleerebezem R, van Loosdrecht MCM (2018) Exploring microbial N2O reduction: a continuous enrichment in nitrogen free medium. Environ Microbiol Rep 10(1):102–107

    Google Scholar 

  • Costa E, Pérez J, Kreft J-U (2006) Why is metabolic labour divided in nitrification? Trends Microbiol 14(5):213–219

    Article  CAS  PubMed  Google Scholar 

  • Cydzik-Kwiatkowska A, de Jonge N, Poulsen JS, Nielsen JL (2022) Unravelling gradient layers of microbial communities, proteins, and chemical structure in aerobic granules. Sci Total Environ 829:154253

    Google Scholar 

  • Daigger GT (2011) Changing paradigms: from wastewater treatment to resource recovery. Proc Water Environ Fed 2011(6):942–957

    Article  Google Scholar 

  • Daigger GT (2017) Flexibility and adaptability: essential elements of the WRRF of the future. Water Pract Technol 12(1):156–165

    Article  Google Scholar 

  • Daigger GT, Redmond E, Downing L (2018) Enhanced settling in activated sludge: design and operation considerations. Water Sci Technol 78(2):247–258

    Article  CAS  PubMed  Google Scholar 

  • Daims H, Nielsen PH, Nielsen JL, Juretschko S, Wagner M (2000) Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: diversity and in situ physiology. Water Sci Technol 41(4–5):85–90

    Article  CAS  Google Scholar 

  • Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, Bergen MV, Rattei T, Bendinger B, Nielsen PH, Wagner M (2015) Complete nitrification by Nitrospira bacteria. Nature 528(7583):504–509

    Google Scholar 

  • de Bruin LMM, de Kreuk MK, van der Roest HFR, Uijterlinde C, van Loosdrecht MCM (2004) Aerobic granular sludge technology: an alternative to activated sludge? Water Sci Technol 49(11–12):1–7

    Article  PubMed  Google Scholar 

  • De Clippeleir H, Han M, Al-Omari A, Bott C, Wett B, Murthy S (2014) From nitrite shunt to mainstream deammonification strategy: pilot-scale demonstration. In: WEF (ed) Water environment federation’s annual technical exhibition and conference (WEFTEC), New Orleans, LA

    Google Scholar 

  • de Graaff DR, Felz S, Neu TR, Pronk M, van Loosdrecht MCM, Lin Y (2019) Sialic acids in the extracellular polymeric substances of seawater-adapted aerobic granular sludge. Water Res 155:343–351

    Article  CAS  PubMed  Google Scholar 

  • de Graaff DR, van Dijk EJH, van Loosdrecht MCM, Pronk M (2020a) Strength characterization of full-scale aerobic granular sludge. Environ Technol 41(13):1637–1647

    Article  CAS  PubMed  Google Scholar 

  • de Graaff DR, van Loosdrecht MCM, Pronk M (2020b) Stable granulation of seawater-adapted aerobic granular sludge with filamentous Thiothrix bacteria. Water Res 175:115683

    Google Scholar 

  • de Kreuk MK, van Loosdrecht MCM (2004) Selection of slow growing organisms as a means for improving aerobic granular sludge stability. Water Sci Technol 49(11–12):9–17

    Article  PubMed  Google Scholar 

  • de Kreuk MK, van Loosdrecht MCM (2006) Formation of aerobic granules with domestic sewage. J Environ Eng ASCE 132(6):694–697

    Article  Google Scholar 

  • de Kreuk MK, Heijnen JJ, van Loosdrecht MCM (2005) Simultaneous COD, nitrogen, and phosphate removal by aerobic granular sludge. Biotechnol Bioeng 90(6):761–769

    Article  PubMed  Google Scholar 

  • de Kreuk MK, Kishida N, Tsuneda S, van Loosdrecht MCM (2010) Behavior of polymeric substrates in an aerobic granular sludge system. Water Res 44(20):5929–5938

    Article  PubMed  Google Scholar 

  • De Vleeschauwer F, Caluwé M, Dobbeleers T, Stes H, Dockx L, Kiekens F, D’Aes J, Copot C, Dries J (2019) Performance and stability of a dynamically controlled EBPR anaerobic/aerobic granular sludge reactor. Bioresour Technol 280:151–157

    Article  CAS  PubMed  Google Scholar 

  • Derlon N, Peter-Varbanets M, Scheidegger A, Pronk W, Morgenroth E (2012) Predation influences the structure of biofilm developed on ultrafiltration membranes. Water Res 46(10):3323–3333

    Article  CAS  PubMed  Google Scholar 

  • Derlon N, Wagner J, da Costa RHR, Morgenroth E (2016) Formation of aerobic granules for the treatment of real and low-strength municipal wastewater using a sequencing batch reactor operated at constant volume. Water Res 105:341–350

    Article  CAS  PubMed  Google Scholar 

  • Derlon N, Garcia Villodres M, Kovács R, Brison A, Layer M, Takács I, Morgenroth E (2022) Modelling of aerobic granular sludge reactors: the importance of hydrodynamic regimes, selective sludge removal and gradients. Water Sci Technol 86(3):410–431

    Article  CAS  PubMed  Google Scholar 

  • Ding K, Xu L, Chen Y, Li W, Chai X, Dai X, Wu B (2023) Mechanistic insights into polyhydroxyalkanoate-enhanced denitrification capacity of microbial community: evolution of community structure and intracellular electron transfer of nitrogen metabolism. Sci Total Environ 856(Pt 1):159147

    Google Scholar 

  • Dobbeleers T, D’aes J, Miele S, Caluwé M, Akkermans V, Daens D, Geuens L, Dries J (2017) Aeration control strategies to stimulate simultaneous nitrification-denitrification via nitrite during the formation of aerobic granular sludge. Appl Microbiol Biotechnol 101(17):6829–6839

    Article  CAS  PubMed  Google Scholar 

  • Dobbeleers T, Caluwé M, Daens D, Geuens L, Dries J (2018) Evaluation of two start-up strategies to obtain nitrogen removal via nitrite and examination of the nitrous oxide emissions for different nitritation levels during the treatment of slaughterhouse wastewater. J Chem Technol Biotechnol 93(2):569–576

    Article  CAS  Google Scholar 

  • Downing L, Redmond E, Avila I (2022) When density is desirable. Water Online, September 9, 2022

    Google Scholar 

  • Dueholm MKD, Nierychlo M, Andersen KS, Rudkjøbing V, Knutsson S, Arriaga S, Bakke R, Boon N, Bux F, Christensson M, Chua ASM, Curtis TP, Cytryn E, Erijman L, Etchebehere C, Fatta-Kassinos D, Frigon D, Garcia-Chaves MC, Gu AZ, Horn H, Jenkins D, Kreuzinger N, Kumari S, Lanham A, Law Y, Leiknes TO, Morgenroth E, Muszyński A, Petrovski S, Pijuan M, Pillai SB, Reis MAM, Rong Q, Rossetti S, Seviour R, Tooker N, Vainio P, van Loosdrecht M, Vikraman R, Wanner J, Weissbrodt D, Wen X, Zhang T, Nielsen PH, Albertsen M, Nielsen PH, MiDAS GC (2022) MiDAS 4: a global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants. Nat Commun 13(1):1908

    Google Scholar 

  • Dueholm MKD, Besteman M, Zeuner EJ, Riisgaard-Jensen M, Nielsen ME, Vestergaard SZ, Heidelbach S, Bekker NS, Nielsen PH (2023) Genetic potential for exopolysaccharide synthesis in activated sludge bacteria uncovered by genome-resolved metagenomics. Water Res 229:119485

    Google Scholar 

  • Dulekgurgen E, Artan N, Orhon D, Wilderer PA (2008) How does shear affect aggregation in granular sludge sequencing batch reactors? Relations between shear, hydrophobicity, and extracellular polymeric substances. Water Sci Technol 58(2):267–276

    Article  CAS  PubMed  Google Scholar 

  • Durrenmatt DJ, Wanner O (2008) Simulation of the wastewater temperature in sewers with TEMPEST. Water Sci Technol 57(11):1809–1815

    Article  CAS  PubMed  Google Scholar 

  • Dutch Water Sector (2019) World’s first waste water treatment plant to produce biopolymer. Kaumera Water & Technology, Netherlands

    Google Scholar 

  • Ebrahimi S, Gabus S, Rohrbach-Brandt E, Hosseini M, Rossi P, Maillard J, Holliger C (2010) Performance and microbial community composition dynamics of aerobic granular sludge from sequencing batch bubble column reactors operated at 20 °C, 30 °C, and 35 °C. Appl Microbiol Biotechnol 87(4):1555–1568

    Article  CAS  PubMed  Google Scholar 

  • Eggen RI, Hollender J, Joss A, Schärer M, Stamm C (2014) Reducing the discharge of micropollutants in the aquatic environment: the benefits of upgrading wastewater treatment plants. Environ Sci Technol 48(14):7683–7689

    Article  CAS  PubMed  Google Scholar 

  • Eikelboom DH, Geurkink B (2002) Filamentous micro-organisms observed in industrial activated sludge plants. Water Sci Technol 46(1–2):535–542

    Article  CAS  Google Scholar 

  • Ekholm J, Persson F, de Blois M, Modin O, Pronk M, van Loosdrecht MCM, Suarez C, Gustavsson DJI, Wilén B-M (2022) Full-scale aerobic granular sludge for municipal wastewater treatment—granule formation, microbial succession, and process performance. Environ Sci Water Res Technol 8(12):3138–3154

    Article  CAS  Google Scholar 

  • Elahinik A, Haarsma M, Abbas B, Pabst M, Xevgenos D, van Loosdrecht MCM, Pronk M (2022) Glycerol conversion by aerobic granular sludge. Water Res 227:119340

    Google Scholar 

  • Elawwad A, Matta M, Abo-Zaid M, Abdel-Halim H (2019) Plant-wide modeling and optimization of a large-scale WWTP using BioWin’s ASDM model. J Water Process Eng 31:100819

    Google Scholar 

  • Erguder TH, Boon N, Vlaeminck SE, Verstraete W (2008) Partial nitrification achieved by pulse sulfide doses in a sequential batch reactor. Environ Sci Technol 42(23):8715–8720

    Google Scholar 

  • Falås P, Wick A, Castronovo S, Habermacher J, Ternes TA, Joss A (2016) Tracing the limits of organic micropollutant removal in biological wastewater treatment. Water Res 95:240–249

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Felz S, Al-Zuhairy S, Aarstad OA, van Loosdrecht MCM, Lin YM (2016) Extraction of structural extracellular polymeric substances from aerobic granular sludge. J vis Exp 115:e54534

    Article  CAS  Google Scholar 

  • Felz S, Vermeulen P, van Loosdrecht MCM, Lin YM (2019) Chemical characterization methods for the analysis of structural extracellular polymeric substances (EPS). Water Res 157:201–208

    Article  CAS  PubMed  Google Scholar 

  • Feng C, Welles L, Zhang X, Pronk M, de Graaff D, van Loosdrecht M (2020) Stress-induced assays for polyphosphate quantification by uncoupling acetic acid uptake and anaerobic phosphorus release. Water Res 169:115228

    Article  CAS  PubMed  Google Scholar 

  • Fernando EY, McIlroy SJ, Nierychlo M, Herbst F-A, Petriglieri F, Schmid MC, Wagner M, Nielsen JL, Nielsen PH (2019) Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman–FISH. ISME J 13(8):1933–1946

    Google Scholar 

  • Filali A (2011) Analyse et modélisation du traitement de l’azote dans un procédé de granulation aérobie hybride. PhD thesis, INSA

    Google Scholar 

  • Filali A, Bessiere Y, Sperandio M (2012) Effects of oxygen concentration on the nitrifying activity of an aerobic hybrid granular sludge reactor. Water Sci Technol 65(2):289–295

    Google Scholar 

  • Finkmann W, Altendorf K, Stackebrandt E, Lipski A (2000) Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. Int J Syst Evol Microbiol 50(1):273–282

    Google Scholar 

  • Fitzgerald CM, Camejo P, Oshlag JZ, Noguera DR (2015) Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen. Water Res 70:38–51

    Article  CAS  PubMed  Google Scholar 

  • Freitag A, Rudert M, Bock E (1987) Growth of Nitrobacter by dissimilatoric nitrate reduction. FEMS Microbiol Lett 48(1–2):105–109

    Google Scholar 

  • Frigon D, Wells G (2019) Microbial immigration in wastewater treatment systems: analytical considerations and process implications. Curr Opin Biotechnol 57:151–159

    Google Scholar 

  • Fumasoli A, Keller A, Gubser N, Weissbrodt DG (2022) DNA-analyse im belebtschlamm. Aqua Gas 1:2–8

    Google Scholar 

  • Gao R, Peng Y, Li J, Liu Y, Deng L, Li W, Kao C (2022) Mainstream partial denitrification-anammox (PD/A) for municipal sewage treatment from moderate to low temperature: reactor performance and bacterial structure. Sci Total Environ 806:150267

    Google Scholar 

  • Giesen A, Niermans R, van Loosdrecht MCM (2012) Aerobic granular biomass: the new standard for domestic and industrial wastewater treatment? Water 21(4):28–30

    Google Scholar 

  • Gilbride KA, Lee DY, Beaudette LA (2006) Molecular techniques in wastewater: understanding microbial communities, detecting pathogens, and real-time process control. J Microbiol Methods 66(1):1–20

    Article  CAS  PubMed  Google Scholar 

  • Goel R, Mino T, Satoh H, Matsuo T (1998) Intracellular storage compounds, oxygen uptake rates and biomass yield with readily and slowly degradable substrates. Water Sci Technol 38(8–9):85–93

    Google Scholar 

  • Goel R, Kotay SM, Butler CS, Torres CI, Mahendra S (2011) Molecular biological methods in environmental engineering. Water Environ Res 83(10):927–955

    Article  CAS  Google Scholar 

  • Gonzalez-Gil G, Holliger C (2011) Dynamics of microbial community structure and enhanced biological phosphorus removal of propionate- and acetate-cultivated aerobic granules. Appl Environ Microbiol 77:8041–8051

    Google Scholar 

  • Gonzalez-Gil G, Holliger C (2014) Aerobic granules: microbial landscape and architecture, stages, and practical implications. Appl Environ Microbiol 80(11):3433–3441

    Google Scholar 

  • Grau P, de Gracia M, Vanrolleghem PA, Ayesa E (2007) A new plant-wide modelling methodology for WWTPs. Water Res 41(19):4357–4372

    Article  CAS  PubMed  Google Scholar 

  • Gruber W, von Känel L, Vogt L, Luck M, Biolley L, Feller K, Moosmann A, Krähenbühl N, Kipf M, Loosli R, Vogel M, Morgenroth E, Braun D, Joss A (2021) Estimation of countrywide N2O emissions from wastewater treatment in Switzerland using long-term monitoring data. Water Res X 13:100122

    Google Scholar 

  • Gruber W, Magyar PM, Mitrovic I, Zeyer K, Vogel M, von Känel L, Biolley L, Werner RA, Morgenroth E, Lehmann MF, Braun D, Joss A, Mohn J (2022) Tracing N2O formation in full-scale wastewater treatment with natural abundance isotopes indicates control by organic substrate and process settings. Water Res X 15:100130

    Google Scholar 

  • Gu AZ, Nerenberg R, Sturm BM, Chul P, Goel R (2010) Molecular methods in biological systems. Water Environ Res 82(10):908–930

    Article  CAS  Google Scholar 

  • Guest JS, Skerlos SJ, Barnard JL, Beck MB, Daigger GT, Hilger H, Jackson SJ, Karvazy K, Kelly L, Macpherson L, Mihelcic JR, Pramanik A, Raskin L, van Loosdrecht MCM, Yeh D, Love NG (2009) A new planning and design paradigm to achieve sustainable resource recovery from wastewater. Environ Sci Technol 43(16):6126–6130

    Google Scholar 

  • Guimarães LB, Gubser NR, Lin Y, Pronk M, Welles L, Albertsen M, Daudt GC, Geleijnse MAA, da Costa RHR, Nielsen PH, van Loosdrecht MCM, Weissbrodt DG (2016) Exopolysaccharides biorefining from used water: an enterprise in the microbiome of granular sludge. In: van Loosdrecht MCM et al (eds) 13th IWA leading edge conference on water and wastewater technologies: evaluating impacts of innovation. International Water Association, Jerez de la Fontera, Spain

    Google Scholar 

  • Guimarães LB, Gubser NR, Lin Y, Zlopasa J, Albertsen M, Akaboci TRV, da Costa RHR, Nielsen PH, van Loosdrecht MCM, Weissbrodt DG (2017a) Alginate-like exopolymer recovery from granular sludge biofilm reactor under conditions selecting for slow-growing PAOs. In: Casey et al (eds) 10th international conference on biofilm reactors. International Water Association, Dublin, Ireland

    Google Scholar 

  • Guimarães LB, Wagner J, Akaboci TRV, Daudt GC, Nielsen PH, van Loosdrecht MCM, Weissbrodt DG, da Costa RHR (2017b) From failures to successful granular sludge process: hints for real wastewater treatment under coastal warm climate. In: Alvarez et al (eds) 14th IWA leading edge conference on water and wastewater technologies: evaluating impacts of innovation. International Water Association, Florianopolis, Brazil

    Google Scholar 

  • Guimarães LB, Wagner J, Akaboci TRV, Daudt GC, Nielsen PH, van Loosdrecht MCM, Weissbrodt DG, da Costa RHR (2018) Elucidating performance failures in use of granular sludge for nutrient removal from domestic wastewater in a warm coastal climate region. Environ Technol 41(15):1896–1911

    Article  CAS  PubMed  Google Scholar 

  • Gujer W (2010) Nitrification and me—a subjective review. Water Res 44(1):1–19

    Article  CAS  PubMed  Google Scholar 

  • Gunathilaka GU, Tahlan V, Mafiz AI, Polur M, Zhang Y (2017) Phages in urban wastewater have the potential to disseminate antibiotic resistance. Int J Antimicrob Agents 50(5):678–683

    Article  CAS  PubMed  Google Scholar 

  • Gunther S, Trutnau M, Kleinsteuber S, Hause G, Bley T, Roske I, Harms H, Muller S (2009) Dynamics of polyphosphate-accumulating bacteria in wastewater treatment plant microbial communities detected via DAPI (4′,6′-diamidino-2-phenylindole) and tetracycline labeling. Appl Environ Microbiol 75(7):2111–2121

    Google Scholar 

  • Guo B, Liu C, Gibson C, Frigon D (2019) Wastewater microbial community structure and functional traits change over short timescales. Sci Total Environ 662:779–785

    Article  CAS  PubMed  Google Scholar 

  • Haaksman VA, Mirghorayshi M, van Loosdrecht MCM, Pronk M (2020) Impact of aerobic availability of readily biodegradable COD on morphological stability of aerobic granular sludge. Water Res 187:116402

    Google Scholar 

  • Hahn MW, Höfle MG (2001) Grazing of protozoa and its effect on populations of aquatic bacteria. FEMS Microbiol Ecol 35(2):113–121

    Google Scholar 

  • Hanada S, Liu WT, Shintani T, Kamagata Y, Nakamura K (2002) Tetrasphaera elongata sp. nov., a polyphosphate-accumulating bacterium isolated from activated sludge. Int J Syst Evol Microbiol 52(Pt 3):883–887

    Google Scholar 

  • Hawley AK, Brewer HM, Norbeck AD, Paša-Tolić L, Hallam SJ (2014) Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. Proc Natl Acad Sci USA 111(31):11395–11400

    Google Scholar 

  • He Q, Zhang J, Gao S, Chen L, Lyu W, Zhang W, Song J, Hu X, Chen R, Wang H, Yu J (2019) A comprehensive comparison between non-bulking and bulking aerobic granular sludge in microbial communities. Bioresour Technol 294:122151

    Google Scholar 

  • Heijnen JJ, Van’t Riet K (1984) Mass transfer, mixing and heat transfer phenomena in low viscosity bubble column reactors. Chem Eng J 28(2):B21–B42

    Article  CAS  Google Scholar 

  • Heijnen JJ, van Loosdrecht MCM, Mulder A, Tijhuis L (1992) Formation of biofilms in a biofilm air-lift suspension reactor. Water Sci Technol 26(3–4):647–654

    Article  CAS  Google Scholar 

  • Henriet O, Meunier C, Henry P, Mahillon J (2016) Improving phosphorus removal in aerobic granular sludge processes through selective microbial management. Bioresour Technol 211:298–306

    Google Scholar 

  • Henriet O, Meunier C, Henry P, Mahillon J (2017) Filamentous bulking caused by Thiothrix species is efficiently controlled in full-scale wastewater treatment plants by implementing a sludge densification strategy. Sci Rep 7(1):1430

    Google Scholar 

  • Henze M, Gujer W, Mino T, van Loosdrecht MCM (2000) Activated sludge models ASM1, ASM2, ASM2d and ASM3. IWA Publishing, London

    Google Scholar 

  • Herbst FA, Dueholm MS, Wimmer R, Nielsen PH (2019) The proteome of Tetrasphaera elongata is adapted to changing conditions in wastewater treatment plants. Proteomes 7(2):16

    Google Scholar 

  • Hoekstra M, Geilvoet SP, Hendrickx TLG, van Erp Taalman Kip CS, Kleerebezem R, van Loosdrecht MCM (2019) Towards mainstream anammox: lessons learned from pilot-scale research at WWTP Dokhaven. Environ Technol 40(13):1721–1733

    Google Scholar 

  • Hofman-Bang J, Zheng D, Westermann P, Ahring BK, Raskin L (2003) Molecular ecology of anaerobic reactor systems. Adv Biochem Eng Biotechnol 81:151–203

    CAS  PubMed  Google Scholar 

  • Holmes DE, Dang Y, Smith JA (2019) Nitrogen cycling during wastewater treatment. Adv Appl Microbiol 106:113–192

    Article  CAS  PubMed  Google Scholar 

  • Huisman JL, Krebs P, Gujer W (2003) Integral and unified model for the sewer and wastewater treatment plant focusing on transformations. Water Sci Technol 47(12):65–71

    Article  CAS  PubMed  Google Scholar 

  • Hupfer M, Glöss S, Schmieder P, Grossart HP (2008) Methods for detection and quantification of polyphosphate and polyphosphate accumulating microorganisms in aquatic sediments. Int Rev Hydrobiol 93(1):1–30

    Google Scholar 

  • Huws SA, McBain AJ, Gilbert P (2005) Protozoan grazing and its impact upon population dynamics in biofilm communities. J Appl Microbiol 98(1):238–244

    Article  CAS  PubMed  Google Scholar 

  • Jehmlich N, Schmidt F, von Bergen M, Richnow H-H, Vogt C (2008) Protein-based stable isotope probing (protein-SIP) reveals active species within anoxic mixed cultures. ISME J 2(11):1122–1133

    Article  CAS  PubMed  Google Scholar 

  • Jenkins D, Wanner J (eds) (2014) Activated sludge—100 years and counting. London

    Google Scholar 

  • Jetten MSM (2008) The microbial nitrogen cycle. Environ Microbiol 10(11):2903–2909

    Article  CAS  PubMed  Google Scholar 

  • Joss A, Derlon N, Cyprien C, Burger S, Szivak I, Traber J, Siegrist H, Morgenroth E (2011) Combined nitritation-anammox: advances in understanding process stability. Environ Sci Technol 45(22):9735–9742

    Article  CAS  PubMed  Google Scholar 

  • Kampschreur MJ, Temmink H, Kleerebezem R, Jetten MS, van Loosdrecht MC (2009) Nitrous oxide emission during wastewater treatment. Water Res 43(17):4093–4103

    Article  CAS  PubMed  Google Scholar 

  • Karst SM, Albertsen M, Kirkegaard RH, Dueholm MS, Nielsen PH (2016) Molecular methods. In: van Loosdrecht MCM, Nielsen PH, Lopez-Vazquez CM, Brdjanovic D (eds) Experimental methods in wastewater treatment. IWA Publishing, London, pp 285–323

    Google Scholar 

  • Kehrein P, van Loosdrecht M, Osseweijer P, Garfí M, Dewulf J, Posada J (2020a) A critical review of resource recovery from municipal wastewater treatment plants—market supply potentials, technologies and bottlenecks. Environ Sci Water Res Technol 6(4):877–910

    Article  CAS  Google Scholar 

  • Kehrein P, van Loosdrecht M, Osseweijer P, Posada J, Dewulf J (2020b) The SPPD-WRF framework: a novel and holistic methodology for strategical planning and process design of water resource factories. Sustainability 12(10):4168

    Article  Google Scholar 

  • Khan MA, Satoh H, Mino T (2006) Occurrence and significance of bacteriophages in biological wastewater treatment processes. In: Reclaiming the desert: towards a sustainable environment in arid lands. Proceedings of the 3rd UAE-Japan symposium on sustainable GCC environment and water resources, EWR 2006, pp 295–303

    Google Scholar 

  • Kim NK, Mao N, Lin R, Bhattacharyya D, van Loosdrecht MCM, Lin Y (2020) Flame retardant property of flax fabrics coated by extracellular polymeric substances recovered from both activated sludge and aerobic granular sludge. Water Res 170:115344

    Google Scholar 

  • Kirkland CM, Krug JR, Vergeldt FJ, van den Berg L, Velders AH, Seymour JD, Codd SL, van As H, de Kreuk MK (2020) Characterizing the structure of aerobic granular sludge using ultra-high field magnetic resonance. Water Sci Technol 82(4):627–639

    Article  CAS  PubMed  Google Scholar 

  • Kleerebezem R, Lücker S (2021) Cyclic conversions in the nitrogen cycle. Front Microbiol 12:622504

    Google Scholar 

  • Kleerebezem R, van Loosdrecht MC (2007) Mixed culture biotechnology for bioenergy production. Curr Opin Biotechnol 18(3):207–212

    Article  CAS  PubMed  Google Scholar 

  • Kleikamp HBC, Lin Y, McMillan DGG, Geelhoed JS, Naus-Wiezer SNH, van Baarlen P, Saha C, Louwen R, Sorokin DY, van Loosdrecht MCM, Pabst M (2020) Tackling the chemical diversity of microbial nonulosonic acids—a universal large-scale survey approach. Chem Sci 11:3074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kleikamp HBC, Pronk M, Tugui C, Guedes da Silva L, Abbas B, Lin YM, van Loosdrecht MCM, Pabst M (2021) Database-independent de novo metaproteomics of complex microbial communities. Cell Syst 12(5):375–383.e5

    Google Scholar 

  • Kleikamp HBC, Grouzdev D, Schaasberg P, van Valderen R, van der Zwaan R, van de Wijgaart R, Lin Y, Abbas B, Pronk M, van Loosdrecht MCM, Pabst M (2022) Comparative metaproteomics demonstrates different views on the complex granular sludge microbiome. bioRxiv 2022.03.07.483319

    Google Scholar 

  • Kleiner M, Kouris A, Jensen M, Liu Y, McCalder J, Strous M (2021) Ultra-sensitive protein-SIP to quantify activity and substrate uptake in microbiomes with stable isotopes. Microbiome 11:24

    Google Scholar 

  • Koch H, Lucker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H (2015) Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proc Natl Acad Sci USA 112(36):11371–11376

    Google Scholar 

  • Kornberg A (1995) Inorganic polyphosphate: toward making a forgotten polymer unforgettable. J Bacteriol 177(3):491–496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kotay SM, Datta T, Choi J, Goel R (2011) Biocontrol of biomass bulking caused by Haliscomenobacter hydrossis using a newly isolated lytic bacteriophage. Water Res 45(2):694–704

    Google Scholar 

  • Koton-Czarnecka M, Chrost RJ (2002) Measurement of protozoan grazing on bacteria by means of [3H-thymidine]—labeled natural assemblages of lake bacteria. Pol J Environ Stud 11(4):385–393

    CAS  Google Scholar 

  • Kristiansen R, Nguyen HTT, Saunders AM, Nielsen JL, Wimmer R, Le VQ, McIlroy SJ, Petrovski S, Seviour RJ, Calteau A, Nielsen KL, Nielsen PH (2013) A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal. ISME J 7(3):543–554

    Google Scholar 

  • Kuba T, van Loosdrecht MCM, Heijnen JJ (1996) Phosphorus and nitrogen removal with minimal COD requirement by integration of denitrifying dephosphatation and nitrification in a two-sludge system. Water Res 30(7):1702–1710

    Article  CAS  Google Scholar 

  • Kuypers MMM, Marchant HK, Kartal B (2018) The microbial nitrogen-cycling network. Nat Rev Microbiol 16(5):263–276

    Article  CAS  PubMed  Google Scholar 

  • Lackner S, Terada A, Horn H, Henze M, Smets BF (2010) Nitritation performance in membrane-aerated biofilm reactors differs from conventional biofilm systems. Water Res 44(20):6073–6084

    Article  CAS  PubMed  Google Scholar 

  • Lackner S, Gilbert EM, Vlaeminck SE, Joss A, Horn H, van Loosdrecht MCM (2014) Full-scale partial nitritation/anammox experiences—an application survey. Water Res 55:292–303

    Article  CAS  PubMed  Google Scholar 

  • Lajoie CA, Layton AC, Gregory IR, Sayler GS, Don ET, Meyers AJ (2000) Zoogleal clusters and sludge dewatering potential in an industrial activated-sludge wastewater treatment plant. Water Environ Res 72(1):56–64

    Article  CAS  Google Scholar 

  • Lalumière A (2016) Le PEX StaRRE: un nouveau programme destiné aux ouvrages d’assainissement des eaux usées. Vecteur Environ Mars 58–59

    Google Scholar 

  • Landreau M, Byson SJ, You H, Stahl DA, Winkler MKH (2020) Effective nitrogen removal from ammonium-depleted wastewater by partial nitritation and anammox immobilized in granular and thin layer gel carriers. Water Res 183:116078

    Google Scholar 

  • Larsen P, von Ins M (2010) The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index. Scientometrics 84(3):575–603

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laureni M, Weissbrodt DG, Villez K, Robin O, de Jonge N, Rosenthal A, Wells G, Nielsen JL, Morgenroth E, Joss A (2019) Biomass segregation between biofilm and flocs improves the control of nitrite-oxidizing bacteria in mainstream partial nitritation and anammox processes. Water Res 154:104–116

    Article  CAS  PubMed  Google Scholar 

  • Lawson CE, Lücker S (2018) Complete ammonia oxidation: an important control on nitrification in engineered ecosystems? Curr Opin Biotechnol 50:158–165

    Article  CAS  PubMed  Google Scholar 

  • Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Löffler FE, O’Malley MA, García Martín H, Pfleger BF, Raskin L, Venturelli OS, Weissbrodt DG, Noguera DR, McMahon KD (2019) Common principles and best practices for engineering microbiomes. Nat Rev Microbiol 17:725–741

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Layer M, Adler A, Reynaert E, Hernandez A, Pagni M, Morgenroth E, Holliger C, Derlon N (2019) Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge. Water Res X 4:100033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Layer M, Villodres MG, Hernandez A, Reynaert E, Morgenroth E, Derlon N (2020) Limited simultaneous nitrification-denitrification (SND) in aerobic granular sludge systems treating municipal wastewater: mechanisms and practical implications. Water Res X 7:100048

    Google Scholar 

  • Layer M, Brison A, Villodres MG, Stähle M, Házi F, Takács I, Morgenroth E, Derlon N (2022) Microbial conversion pathways of particulate organic substrate conversion in aerobic granular sludge systems: limited anaerobic conversion and the essential role of flocs. Environ Sci Water Res Technol 8(6):1236–1251

    Google Scholar 

  • Le T, Peng B, Su C, Massoudieh A, Torrents A, Al-Omari A, Murthy S, Wett B, Chandran K, deBarbadillo C, Bott C, De Clippeleir H (2019) Nitrate residual as a key parameter to efficiently control partial denitrification coupling with anammox. Water Environ Res 91(11):1455–1465

    Google Scholar 

  • Lee CO, Boe-Hansen R, Musovic S, Smets B, Albrechtsen HJ, Binning P (2014) Effects of dynamic operating conditions on nitrification in biological rapid sand filters for drinking water treatment. Water Res 64:226–236

    Google Scholar 

  • Lekunberri I, Villagrasa M, Balcázar JL, Borrego CM (2017) Contribution of bacteriophage and plasmid DNA to the mobilization of antibiotic resistance genes in a river receiving treated wastewater discharges. Sci Total Environ 601–602:206–209

    Article  CAS  PubMed  Google Scholar 

  • Li DC, Gao JF, Zhang SJ, Gao YQ, Sun LX (2020) Emergence and spread patterns of antibiotic resistance genes during two different aerobic granular sludge cultivation processes. Environ Int 137:105540

    Article  CAS  PubMed  Google Scholar 

  • Limpiyakorn T, Sonthiphand P, Rongsayamanont C, Polprasert C (2011) Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants. Bioresour Technol 102(4):3694–3701

    Article  CAS  PubMed  Google Scholar 

  • Lin Y, de Kreuk MK, van Loosdrecht MCM, Adin A (2010) Characterization of alginate-like exopolysaccharides isolated from aerobic granular sludge in pilot-plant. Water Res 44(11):3355–3364

    Article  CAS  PubMed  Google Scholar 

  • Lin YM, Nierop KGJ, Girbal-Neuhauser E, Adriaanse M, van Loosdrecht MCM (2015) Sustainable polysaccharide-based biomaterial recovered from waste aerobic granular sludge as a surface coating material. Sustain Mater Technol 4:24–29

    Article  CAS  Google Scholar 

  • Lindemann SR, Bernstein HC, Song H-S, Fredrickson JK, Fields MW, Shou W, Johnson DR, Beliaev AS (2016) Engineering microbial consortia for controllable outputs. ISME J 10(9):2077–2084

    Google Scholar 

  • Liu Y, Liu Q-S (2006) Causes and control of filamentous growth in aerobic granular sludge sequencing batch reactors. Biotechnol Adv 24(1):115–127

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Tay J-H (2002) The essential role of hydrodynamic shear force in the formation of biofilm and granular sludge. Water Res 36(7):1653–1665

    Google Scholar 

  • Liu WT, Nielsen AT, Wu JH, Tsai CS, Matsuo Y, Molin S (2001) In situ identification of polyphosphate- and polyhydroxyalkanoate-accumulating traits for microbial populations in a biological phosphorus removal process. Environ Microbiol 3(2):110–122

    Google Scholar 

  • Lochmatter S, Holliger C (2014) Optimization of operation conditions for the startup of aerobic granular sludge reactors biologically removing carbon, nitrogen, and phosphorous. Water Res 59:58–70

    Google Scholar 

  • Lochmatter S, Gonzalez-Gil G, Holliger C (2013) Optimized aeration strategies for nitrogen and phosphorus removal with aerobic granular sludge. Water Res 47(16):6187–6197

    Google Scholar 

  • Lochmatter S, Maillard J, Holliger C (2014) Nitrogen removal over nitrite by aeration control in aerobic granular sludge sequencing batch reactors. Int J Environ Res Public Health 11(7):6955

    Article  PubMed  PubMed Central  Google Scholar 

  • Lopez-Vazquez CM, Oehmen A, Hooijmans CM, Brdjanovic D, Gijzen HJ, Yuan Z, van Loosdrecht MCM (2009) Modeling the PAO-GAO competition: effects of carbon source, pH and temperature. Water Res 43(2):450–462

    Article  CAS  PubMed  Google Scholar 

  • Lucker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Damste JSS, Spieck E, Le Paslier D, Daims H (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci USA 107(30):13479–13484

    Google Scholar 

  • Luiz de Sousa Rollemberg S, Queiroz de Oliveira L, Nascimento de Barros A, Igor Milen Firmino P, Bezerra dos Santos A (2020) Pilot-scale aerobic granular sludge in the treatment of municipal wastewater: optimizations in the start-up, methodology of sludge discharge, and evaluation of resource recovery. Bioresour Technol 311:123467

    Google Scholar 

  • Mahendra S, Gedalanga P, Kotay SM, Torres CI, Butler CS, Goel R (2012) Advancements in molecular techniques and applications in environmental engineering. Water Environ Res 84(10):814–844

    Article  CAS  Google Scholar 

  • Mannina G, Ekama G, Caniani D, Cosenza A, Esposito G, Gori R, Garrido-Baserba M, Rosso D, Olsson G (2016) Greenhouse gases from wastewater treatment—a review of modelling tools. Sci Total Environ 551–552:254–270

    Article  CAS  PubMed  Google Scholar 

  • Margot J, Lochmatter S, Barry DA, Holliger C (2016) Role of ammonia-oxidizing bacteria in micropollutant removal from wastewater with aerobic granular sludge. Water Sci Technol 73(3):564–575 

    Article  CAS  PubMed  Google Scholar 

  • Marques R, Santos J, Nguyen H, Carvalho G, Noronha JP, Nielsen PH, Reis MAM, Oehmen A (2017) Metabolism and ecological niche of Tetrasphaera and Ca. Accumulibacter in enhanced biological phosphorus removal. Water Res 122:159–171

    Article  CAS  PubMed  Google Scholar 

  • Martins AMP, Heijnen JJ, van Loosdrecht MCM (2004a) Bulking sludge in biological nutrient removal systems. Biotechnol Bioeng 86(2):125–135

    Article  CAS  PubMed  Google Scholar 

  • Martins AMP, Pagilla K, Heijnen JJ, van Loosdrecht MCM (2004b) Filamentous bulking sludge—a critical review. Water Res 38(4):793–817

    Article  CAS  PubMed  Google Scholar 

  • Marzorati M, Read S, Arends JB, Verstraete W, Boon N (2011) Microbial resource management (MRM): theory and practical tools to exploit bacterial capabilities. Commun Agric Appl Biol Sci 76(2):27–29

    PubMed  Google Scholar 

  • Maszenan AM, Seviour RJ, Patel BKC, Schumann P, Burghardt J, Tokiwa Y, Stratton HM (2000) Three isolates of novel polyphosphate-accumulating Gram-positive cocci, obtained from activated sludge, belong to a new genus, Tetrasphaera gen. nov., and description of two new species, Tetrasphaera japonica sp. nov. and Tetrasphaera australiensis sp. nov. Int J Syst Evol Microbiol 50(2):593–603

    Google Scholar 

  • Mathieu J, Yu P, Zuo P, Da Silva MLB, Alvarez PJJ (2019) Going viral: emerging opportunities for phage-based bacterial control in water treatment and reuse. Acc Chem Res 52(4):849–857 

    Google Scholar 

  • Matz C, Kjelleberg S (2005) Off the hook—how bacteria survive protozoan grazing. Trends Microbiol 13(7):302–307

    Article  CAS  PubMed  Google Scholar 

  • Maurer M, Gujer W (1995) Monitoring of microbial phosphorus release in batch experiments using electric conductivity. Water Res 29(11):2613–2617

    Article  CAS  Google Scholar 

  • McDaniel EA, Wahl SA, Si I, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH (2021) Prospects for multi-omics in the microbial ecology of water engineering. Water Res 205:117608

    Article  CAS  PubMed  Google Scholar 

  • McIlroy SJ, Saunders AM, Albertsen M, Nierychlo M, McIlroy B, Hansen AA, Karst SM, Nielsen JL, Nielsen PH (2015) MiDAS: the field guide to the microbes of activated sludge. Database 2015:bav062

    Google Scholar 

  • McMahon KD, Gu AZ, Nerenberg R, Sturm BM (2009) Molecular methods in biological systems. Water Environ Res 81(10):986–1002

    Article  CAS  Google Scholar 

  • McMahon KD, He S, Oehmen A (2010) The microbiology of phosphorus removal. In: Seviour RJ, Nielsen PH (eds) Microbial ecology of activated sludge. IWA Publishing, London, pp 281–320

    Google Scholar 

  • Meunier C, Henriet O, Schroonbroodt B, Boeur JM, Mahillon J, Henry P (2016) Influence of feeding pattern and hydraulic selection pressure to control filamentous bulking in biological treatment of dairy wastewaters. Bioresour Technol 221:300–309

    Article  CAS  PubMed  Google Scholar 

  • Miłobedzka A, Ferreira C, Vaz-Moreira I, Calderón-Franco D, Gorecki A, Purkrtova S, Jan B, Dziewit L, Singleton CM, Nielsen PH, Weissbrodt DG, Manaia CM (2021) Monitoring antibiotic resistance genes in wastewater environments: the challenges of filling a gap in the one-health cycle. J Hazard Mater 424:127407

    Google Scholar 

  • Mino T, Satoh H (2006) Wastewater genomics. Nat Biotechnol 24(10):1229–1230

    Article  CAS  PubMed  Google Scholar 

  • Miyake M, Hasebe Y, Furusawa K, Shiomi H, Inoue D, Ike M (2023) Pilot-scale demonstration of aerobic granular sludge augmentation applied to continuous-flow activated sludge process for the treatment of low-strength municipal wastewater. J Water Process Eng 51(1):103392

    Google Scholar 

  • Montoya T, Borrás L, Aguado D, Ferrer J, Seco A (2008) Detection and prevention of enhanced biological phosphorus removal deterioration caused by Zoogloea overabundance. Environ Technol 29(1):35–42

    Google Scholar 

  • Morgenroth E, Milferstedt K (2009) Biofilm engineering: linking biofilm development at different length and time scales. Rev Environ Sci Biotechnol 8(3):203–208

    Google Scholar 

  • Morgenroth E, Wilderer PA (1998) Sequencing batch reactor technology: concepts, design and experiences. J Chart Inst Water Environ Manag 12(5):314–321

    Google Scholar 

  • Morgenroth E, Wilderer PA (1999) Controlled biomass removal—the key parameter to achieve enhanced biological phosphorus removal in biofilm systems. Water Sci Technol 39(7):33–40

    Article  CAS  Google Scholar 

  • Moser-Engeler R, Udert KM, Wild D, Siegrist H (1998) Products from primary sludge fermentation and their suitability for nutrient removal. Water Sci Technol 38(1):265–273

    Article  CAS  Google Scholar 

  • Mosquera-Corral A, de Kreuk MK, Heijnen JJ, van Loosdrecht MCM (2005) Effects of oxygen concentration on N-removal in an aerobic granular sludge reactor. Water Res 39(12):2676–2686

    Article  CAS  PubMed  Google Scholar 

  • Mosquera-Corral A, Arrojo B, Figueroa M, Campos JL, Mendez R (2011) Aerobic granulation in a mechanical stirred SBR: treatment of low organic loads. Water Sci Technol 64(1):155–161

    Article  CAS  PubMed  Google Scholar 

  • Motlagh AM, Bhattacharjee AS, Goel R (2016) Biofilm control with natural and genetically-modified phages. World J Microbiol Biotechnol 32(4):1–10

    Article  CAS  Google Scholar 

  • Muñoz-Palazon B, Rodriguez-Sanchez A, Castellano-Hinojosa A, Gonzalez-Lopez J, van Loosdrecth MCM, Vahala R, Gonzalez-Martinez A (2018) Quantitative and qualitative studies of microorganisms involved in full-scale autotrophic nitrogen removal performance. AIChE J 64(2):457–467

    Article  CAS  Google Scholar 

  • Muyzer G, Ramsing NB (1995) Molecular methods to study the organization of microbial communities. Water Sci Technol 32:1–9

    Article  CAS  Google Scholar 

  • Narayanasamy S, Muller EE, Sheik AR, Wilmes P (2015) Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities. Microb Biotechnol 8(3):363–368

    Article  PubMed  PubMed Central  Google Scholar 

  • Nguyen HTT, Le VQ, Hansen AA, Nielsen JL, Nielsen PH (2011) High diversity and abundance of putative polyphosphate-accumulating Tetrasphaera-related bacteria in activated sludge systems. FEMS Microbiol Ecol 76(2):256–267

    Article  CAS  PubMed  Google Scholar 

  • Nguyen HTT, Nielsen JL, Nielsen PH (2012) “Candidatus Halomonas phosphatis”, a novel polyphosphate-accumulating organism in full-scale enhanced biological phosphorus removal plants. Environ Microbiol 14(10):2826–2837

    Google Scholar 

  • Nguyen HT, Kristiansen R, Vestergaard M, Wimmer R, Nielsen PH (2015) Intracellular accumulation of glycine in polyphosphate-accumulating organisms in activated sludge, a novel storage mechanism under dynamic anaerobic-aerobic conditions. Appl Environ Microbiol 81(14):4809–4818

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen Quoc B, Wei S, Armenta M, Bucher R, Sukapanpotharam P, Stahl DA, Stensel HD, Winkler MKH (2021) Aerobic granular sludge: impact of size distribution on nitrification capacity. Water Res 188:116445

    Google Scholar 

  • Niba ETE, Naka Y, Nagase M, Mori H, Kitakawa M (2007) A genome-wide approach to identify the genes involved in biofilm formation in E. coli. DNA Res 14(6):237–246

    Google Scholar 

  • Nielsen PH, McMahon KD (2014) Microbiology and microbial ecology of the activated sludge process. In: Jenkins D, Wanner J (eds) Activated sludge—100 years and counting. IWA Publishing, London, p 464

    Google Scholar 

  • Nielsen PH, Raunkjaer K, Norsker NH, Jensen NA, Hvitved-Jacobsen T (1992) Transformation of wastewater in sewer systems—a review. Water Sci Technol 25(6):17–31

    Google Scholar 

  • Nielsen PH, Thomsen TR, Nielsen JL (2004) Bacterial composition of activated sludge—importance for floc and sludge properties. Water Sci Technol 49(10):51–58

    Article  CAS  PubMed  Google Scholar 

  • Nielsen PH, Mielczarek AT, Kragelund C, Nielsen JL, Saunders AM, Kong Y, Hansen AA, Vollertsen J (2010) A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. Water Res 44(17):5070–5088

    Google Scholar 

  • Nielsen JL, Nguyen H, Meyer RL, Nielsen PH (2012a) Identification of glucose-fermenting bacteria in a full-scale enhanced biological phosphorus removal plant by stable isotope probing. Microbiology 158(7):1818–1825

    Article  CAS  PubMed  Google Scholar 

  • Nielsen PH, Saunders AM, Hansen AA, Larsen P, Nielsen JL (2012b) Microbial communities involved in enhanced biological phosphorus removal from wastewater—a model system in environmental biotechnology. Curr Opin Biotechnol 23(3):452–459

    Google Scholar 

  • Nielsen JL, Seviour RJ, Nielsen PH (2016) Microscopy. In: van Loosdrecht MCM, Nielsen PH, Lopez-Vazquez CM, Brdjanovic D (eds) Experimental methods in wastewater treatment. IWA Publishing, London, pp 263–284

    Google Scholar 

  • Nogueira R, Melo LF (2006) Competition between Nitrospira spp. and Nitrobacter spp. in nitrite-oxidizing bioreactors. Biotechnol Bioeng 95(1):169–175

    Google Scholar 

  • Oehmen A, Lemos PC, Carvalho G, Yuan Z, Keller J, Blackall LL, Reis MAM (2007) Advances in enhanced biological phosphorus removal: from micro to macro scale. Water Res 41:2271–2300

    Google Scholar 

  • Oehmen A, Carvalho G, Lopez-Vazquez CM, van Loosdrecht MCM, Reis MAM (2010a) Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms. Water Res 44(17):4992–5004

    Article  CAS  PubMed  Google Scholar 

  • Oehmen A, Lopez-Vazquez CM, Carvalho G, Reis MAM, van Loosdrecht MCM (2010b) Modelling the population dynamics and metabolic diversity of organisms relevant in anaerobic/anoxic/aerobic enhanced biological phosphorus removal processes. Water Res 44(15):4473–4486

    Article  CAS  PubMed  Google Scholar 

  • Ofiteru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA, Sloan WT (2010) Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci USA 107(35):15345–15350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oishi R, Hirooka K, Otawa K, Tada C, Nakai Y (2012) Ammonia-oxidizing Archaea in laboratory-scale activated sludge systems for wastewater of low- or high-ammonium concentration. Anim Sci J 83(7):571–576

    Google Scholar 

  • Onda S, Takii S (2002) Isolation and characterization of a Gram-positive polyphosphate-accumulating bacterium. J Gen Appl Microbiol 48(3):125–133

    Article  CAS  PubMed  Google Scholar 

  • Onuki M, Satoh H, Mino T, Matsuo T (2000) Application of molecular methods to microbial community analysis of activated sludge. Water Sci Technol 42:17–22

    Article  Google Scholar 

  • Oshiki M, Onuki M, Satoh H, Mino T (2008) PHA-accumulating microorganisms in full-scale wastewater treatment plants. Water Sci Technol 58(1):13–20

    Article  CAS  PubMed  Google Scholar 

  • Páez-Watson T, van Loosdrecht MCM, Wahl SA (2023) Predicting the impact of temperature on metabolic fluxes using resource allocation modelling: application to polyphosphate accumulating organisms. Water Res 228(Pt A):119365

    Article  CAS  PubMed  Google Scholar 

  • Pallares-Vega R, Hernandez Leal L, Fletcher BN, Vias-Torres E, van Loosdrecht MCM, Weissbrodt DG, Schmitt H (2021) Annual dynamics of antimicrobials and resistance determinants in flocculent and aerobic granular sludge treatment systems. Water Res 190:116752

    Article  CAS  PubMed  Google Scholar 

  • Palomo A, Pedersen AG, Fowler SJ, Dechesne A, Sicheritz-Pontén T, Smets BF (2018) Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira. ISME J 12(7):1779–1793

    Article  PubMed  PubMed Central  Google Scholar 

  • Perez J, Costa E, Kreft JU (2009) Conditions for partial nitrification in biofilm reactors and a kinetic explanation. Biotechnol Bioeng 103(2):282–295

    Article  CAS  PubMed  Google Scholar 

  • Perez J, Lotti T, Kleerebezem R, Picioreanu C, van Loosdrecht MC (2014) Outcompeting nitrite-oxidizing bacteria in single-stage nitrogen removal in sewage treatment plants: a model-based study. Water Res 66:208–218

    Article  CAS  PubMed  Google Scholar 

  • Pérez J, Laureni M, van Loosdrecht MCM, Persson F, Gustavsson DJI (2020) The role of the external mass transfer resistance in nitrite oxidizing bacteria repression in biofilm-based partial nitritation/anammox reactors. Water Res 186:116348

    Google Scholar 

  • Pernthaler J, Posch T, Simek K, Vrba J, Amann R, Psenner R (1997) Contrasting bacterial strategies to coexist with a flagellate predator in an experimental microbial assemblage. Appl Environ Microbiol 63(2):596–601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pessi IS, Viitamäki S, Virkkala A-M, Eronen-Rasimus E, Delmont TO, Marushchak ME, Luoto M, Hultman J (2022) In-depth characterization of denitrifier communities across different soil ecosystems in the tundra. Environ Microbiome 17(1):30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Picioreanu C, van Loosdrecht MCM, Heijnen JJ (2000) A theoretical study on the effect of surface roughness on mass transport and transformation in biofilms. Biotechnol Bioeng 68(4):355–369

    Article  CAS  PubMed  Google Scholar 

  • Poot V, Hoekstra M, Geleijnse MAA, van Loosdrecht MCM, Pérez J (2016) Effects of the residual ammonium concentration on NOB repression during partial nitritation with granular sludge. Water Res 106:518–530

    Article  CAS  PubMed  Google Scholar 

  • Posch T, Simek K, Vrba J, Pernthaler J, Nedoma J, Sattler B, Sonntag B, Psenner R (1999) Predator-induced changes of bacterial size-structure and productivity studied on an experimental microbial community. Aquat Microb Ecol 18(3):235–246

    Article  Google Scholar 

  • Prata JC, Ribeiro AI, Rocha-Santos T (2022) Chapter 1—An introduction to the concept of One Health. In: Prata JC, Ribeiro AI, Rocha-Santos T (eds) One Health. Academic Press, pp 1–31

    Google Scholar 

  • Price DJdS (1963) Little science, big science. The impact of the explosive growth of science on the wolrd we live in. Columbia University Press, New York

    Google Scholar 

  • Pronk M, Abbas B, Al-Zuhairy SH, Kraan R, Kleerebezem R, van Loosdrecht MC (2015a) Effect and behaviour of different substrates in relation to the formation of aerobic granular sludge. Appl Microbiol Biotechnol 99(12):5257–5268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pronk M, de Kreuk MK, de Bruin B, Kamminga P, Kleerebezem R, van Loosdrecht MCM (2015b) Full scale performance of the aerobic granular sludge process for sewage treatment. Water Res 84:207–217

    Article  CAS  PubMed  Google Scholar 

  • Pronk M, van Dijk EJH, van Loosdrecht MCM (2020) Aerobic granular sludge. In: Chen GH, van Loosdrecht MCM, Ekama GA, Brdjanovic D (eds) Biological wastewater treatment: principles, modelling and design, 2nd edn. IWA Publishing, London

    Google Scholar 

  • Radauer A, Rivoire L, Eparvier P, Schwanbeck H (2012) Presenting the (economic) value of patents nominated for the European Inventor Award 2012—inventor file Mark van Loosdrecht. Technopolis Group Austria, Vienna, pp 1–10

    Google Scholar 

  • Regmi P, DeBarbadillo C, Weissbrodt DG (2017) Biofilm reactor technology and design. In: Krause TL et al (eds) Design of water resource recovery facilities—MOP 8. WEF manual of practice No. 8, ASCE manuals and reports on engineering practice No. 76, 6th edn. Water Environment Federation, American Society of Civil Engineers and Environmental and Water Resources Institute, McGraw-Hill Education, Alexandria VA, Reston VA, New York

    Google Scholar 

  • Regmi P, Sturm B, Hiripitiyage D, Keller N, Murthy S, Jimenez J (2022) Combining continuous flow aerobic granulation using an external selector and carbon-efficient nutrient removal with AvN control in a full-scale simultaneous nitrification-denitrification process. Water Res 210:117991

    Google Scholar 

  • Reino C, Suárez-Ojeda ME, Pérez J, Carrera J (2016) Kinetic and microbiological characterization of aerobic granules performing partial nitritation of a low-strength wastewater at 10 °C. Water Res 101:147–156

    Article  CAS  PubMed  Google Scholar 

  • Rodríguez E, García-Encina PA, Stams AJM, Maphosa F, Sousa DZ (2015) Meta-omics approaches to understand and improve wastewater treatment systems. Rev Environ Sci Biotechnol 14(3):385–406

    Article  CAS  Google Scholar 

  • Rodríguez-Ramos JA, Borton MA, McGivern BB, Smith GJ, Solden LM, Shaffer M, Daly RA, Purvine SO, Nicora CD, Eder EK, Lipton M, Hoyt DW, Stegen JC, Wrighton KC (2022) Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments. mSystems 7(4):e00516–e00522

    Google Scholar 

  • Rombouts JL, Mos G, Weissbrodt DG, Kleerebezem R, van Loosdrecht MCM (2019) Diversity and metabolism of xylose and glucose fermenting microbial communities in sequencing batch or continuous culturing. FEMS Microbiol Ecol 95(2):fiz233

    Google Scholar 

  • Ronn R, McCaig AE, Griffiths BS, Prosser JI (2002) Impact of protozoan grazing on bacterial community structure in soil microcosms. Appl Environ Microbiol 68(12):6094–6105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rubio-Rincon FJ, Lopez-Vazquez CM, Welles L, van Loosdrecht MC, Brdjanovic D (2017) Sulphide effects on the physiology of Candidatus Accumulibacter phosphatis type I. Appl Microbiol Biotechnol 101(4):1661–1672

    Article  CAS  PubMed  Google Scholar 

  • Rubio-Rincon FJ, Weissbrodt DG, Lopez-Vazquez CM, Welles L, Abbas B, Albertsen M, Nielsen PH, van Loosdrecht MCM, Brdjanovic D (2019) “Candidatus Accumulibacter delftensis”: a clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate. Water Res 161:136–151

    Google Scholar 

  • Sabri NA, van Holst S, Schmitt H, van der Zaan BM, Gerritsen HW, Rijnaarts HHM, Langenhoff AAM (2020) Fate of antibiotics and antibiotic resistance genes during conventional and additional treatment technologies in wastewater treatment plants. Sci Total Environ 741:140199

    Article  CAS  PubMed  Google Scholar 

  • Santorio S, Couto AT, Amorim CL, Val del Rio A, Arregui L, Mosquera-Corral A, Castro PML (2021) Sequencing versus continuous granular sludge reactor for the treatment of freshwater aquaculture effluents. Water Res 201:117293

    Google Scholar 

  • Sauder LA, Peterse F, Schouten S, Neufeld JD (2012) Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant. Environ Microbiol 14(9):2589–2600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD (2017) Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME J 11(5):1142–1157

    Google Scholar 

  • Sauer K (2003) The genomics and proteomics of biofilm formation. Genome Biol 4(6):219

    Article  PubMed  PubMed Central  Google Scholar 

  • Schambeck CM, Magnus BS, de Souza LCR, Leite WRM, Derlon N, Guimaraes LB, da Costa RHR (2020) Biopolymers recovery: dynamics and characterization of alginate-like exopolymers in an aerobic granular sludge system treating municipal wastewater without sludge inoculum. J Environ Manage 263:110394

    Article  CAS  PubMed  Google Scholar 

  • Schwarzenbeck N, Erley R, Wilderer PA (2004) Aerobic granular sludge in an SBR-system treating wastewater rich in particulate matter. Water Sci Technol 49(11–12):41–46

    Article  CAS  PubMed  Google Scholar 

  • Sepúlveda-Mardones M, Campos JL, Magrí A, Vidal G (2019) Moving forward in the use of aerobic granular sludge for municipal wastewater treatment: an overview. Rev Environ Sci Biotechnol 18(4):741–769

    Article  CAS  Google Scholar 

  • Seviour RJ, Mino T, Onuki M (2003) The microbiology of biological phosphorus removal in activated sludge systems. FEMS Microbiol Rev 27(1):99–127

    Article  CAS  PubMed  Google Scholar 

  • Seviour T, Yuan Z, van Loosdrecht MCM, Lin Y (2012) Aerobic sludge granulation: a tale of two polysaccharides? Water Res 46(15):4803–4813

    Article  CAS  PubMed  Google Scholar 

  • Seviour T, Derlon N, Dueholm MS, Flemming H-C, Girbal-Neuhauser E, Horn H, Kjelleberg S, van Loosdrecht MCM, Lotti T, Malpei MF, Nerenberg R, Neu TR, Paul E, Yu H, Lin Y (2019) Extracellular polymeric substances of biofilms: suffering from an identity crisis. Water Res 151:1–7

    Article  CAS  PubMed  Google Scholar 

  • Shapiro OH, Kushmaro A (2011) Bacteriophage ecology in environmental biotechnology processes. Curr Opin Biotechnol 22(3):449–455

    Article  CAS  PubMed  Google Scholar 

  • Shapiro OH, Kushmaro A, Brenner A (2010) Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater. ISME J 4(3):327–336

    Article  PubMed  Google Scholar 

  • Shaw A, Takacs I, Pagilla K, Riffat R, DeClippeleir H, Wilson C, Murthy S (2015) Toward universal half-saturation coefficients: describing extant Ks as a function of diffusion. Water Environ Res 87(5):387–391

    Google Scholar 

  • Siegrist H, Brack T, Koch G, Nussbaumer A, Gujer W (2000) Optimization of nutrient removal in the WWTP Zurich-Werholzli. Water Sci Technol 41(9):63–71

    Article  CAS  Google Scholar 

  • Singleton CM, Petriglieri F, Kristensen JM, Kirkegaard RH, Michaelsen TY, Andersen MH, Kondrotaite Z, Karst SM, Dueholm MS, Nielsen PH, Albertsen M (2021) Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing. Nat Commun 12(1):2009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singleton CM, Petriglieri F, Wasmund K, Nierychlo M, Kondrotaite Z, Petersen JF, Peces M, Dueholm MS, Wagner M, Nielsen PH (2022) The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide. ISME J 16(6):1605–1616

    Google Scholar 

  • Soler-Jofra A, Wang R, Kleerebezem R, van Loosdrecht MCM, Pérez J (2019) Stratification of nitrifier guilds in granular sludge in relation to nitritation. Water Res 148:479–491

    Google Scholar 

  • Solon K, Flores-Alsina X, Kazadi Mbamba C, Ikumi D, Volcke EIP, Vaneeckhaute C, Ekama G, Vanrolleghem PA, Batstone DJ, Gernaey KV, Jeppsson U (2017) Plant-wide modelling of phosphorus transformations in wastewater treatment systems: impacts of control and operational strategies. Water Res 113:97–110

    Google Scholar 

  • Sperandio M, Masse A, Espinosa-Bouchot MC, Cabassud C (2005) Characterization of sludge structure and activity in submerged membrane bioreactor. Water Sci Technol 52(10–11):401–408

    Article  CAS  PubMed  Google Scholar 

  • Stokholm-Bjerregaard M (2016) Control of GAOs in wastewater treatment plants with enhanced biological phosphorus removal. PhD thesis, Aalborg University

    Google Scholar 

  • Stokholm-Bjerregaard M, McIlroy SJ, Nierychlo M, Karst SM, Albertsen M, Nielsen PH (2017) A critical assessment of the microorganisms proposed to be important to enhanced biological phosphorus removal in full-scale wastewater treatment systems. Front Microbiol 8:718

    Article  PubMed  PubMed Central  Google Scholar 

  • Stokholm-Bjerregaard MA, Hansen AA, Strandbæk H, Vølund I, Thornberg D, Hughes L, Nielsen PH (2021) Intelligent and dynamic control of optimal WWTP operation from microbial sequencing. In: IWA (ed) IWA world water congress & exhibition, Copenhagen, Denmark. IWA Publishing

    Google Scholar 

  • Strubbe L, Pennewaerde M, Baeten JE, Volcke EIP (2022) Continuous aerobic granular sludge plants: better settling versus diffusion limitation. Chem Eng J 428(4):131427

    Google Scholar 

  • Subirats J, Sànchez-Melsió A, Borrego CM, Balcázar JL, Simonet P (2016) Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes. Int J Antimicrob Agents 48(2):163–167

    Article  CAS  PubMed  Google Scholar 

  • Sun Y, Angelotti B, Brooks M, Wang ZW (2021) Feast/famine ratio determined continuous flow aerobic granulation. Sci Total Environ 750:141467

    Google Scholar 

  • Tavares Ferreira TJ, Luiz de Sousa Rollemberg S, Nascimento de Barros A, Machado de Lima JP, Bezerra dos Santos A (2021) Integrated review of resource recovery on aerobic granular sludge systems: possibilities and challenges for the application of the biorefinery concept. J Environ Manage 291:112718

    Google Scholar 

  • Temudo MF (2008) Directing product formation by mixed culture fermentation. PhD thesis, Delft University of Technology

    Google Scholar 

  • Temudo MF, Muyzer G, Kleerebezem R, van Loosdrecht MCM (2008) Diversity of microbial communities in open mixed culture fermentations: impact of the pH and carbon source. Appl Microbiol Biotechnol 80(6):1121–1130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas MP (2008) The secret to achieving reliable biological phosphorus removal. Water Sci Technol 58(6):1231–1236

    Article  CAS  PubMed  Google Scholar 

  • Tijhuis L, Rekswinkel E, van Loosdrecht MCM, Heijnen JJ (1994) Dynamics of population and biofilm structure in the biofilm airlift suspension reactor for carbon and nitrogen removal. Water Sci Technol 29(10–11):377–384

    Article  CAS  Google Scholar 

  • Toja Ortega S, van den Berg L, Pronk M, de Kreuk MK (2022) Hydrolysis capacity of different sized granules in a full-scale aerobic granular sludge (AGS) reactor. Water Res X 16:100151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tomás-Martínez S, Kleikamp HBC, Neu TR, Pabst M, Weissbrodt DG, van Loosdrecht MCM, Lin Y (2021) Production of nonulosonic acids in the extracellular polymeric substances of “Candidatus Accumulibacter phosphatis”. Appl Microbiol Biotechnol 105(8):3327–3338

    Google Scholar 

  • Tomás-Martínez S, Chen LM, Neu TR, Weissbrodt DG, van Loosdrecht MCM, Lin Y (2022a) Catabolism of sialic acids in an environmental microbial community. FEMS Microbiol Ecol 98(5):fiac047

    Google Scholar 

  • Tomás-Martínez S, Chen LM, Pabst M, Weissbrodt DG, van Loosdrecht MCM, Lin Y (2022b) Enrichment and application of extracellular nonulosonic acids containing polymers of Accumulibacter. Appl Microbiol Biotechnol 107(2-3):931–941

    Article  PubMed  Google Scholar 

  • Tomás-Martínez S, Zwolsman EJ, Merlier F, Pabst M, Lin Y, van Loosdrecht MCM, Weissbrodt DG (2022c) Turnover of the extracellular polymeric matrix in an EBPR microbial community. Appl Microbiol Biotechnol 107(5-6):1997–2009

    Google Scholar 

  • Val del Rio A, Winkler MKH, Volcke EI, Meunier C, Baeten J, Henriet O, Del Moro G, Suárez-Ojeda ME, De Sanctis M, Dries J, Castro P, Weissbrodt DG, Di Iaconi C (2016) Aerobic granular sludge reactors: from fundamentals to full application In: Lema et al (eds) Water 2020. IWA Publishing, London

    Google Scholar 

  • van den Berg L, Kirkland CM, Seymour JD, Codd SL, van Loosdrecht MCM, de Kreuk MK (2020) Heterogeneous diffusion in aerobic granular sludge. Biotechnol Bioeng 117(12):3809–3819

    Google Scholar 

  • van den Berg L, van Loosdrecht MCM, de Kreuk MK (2021) How to measure diffusion coefficients in biofilms: a critical analysis. Biotechnol Bioeng 118(3):1273–1285

    Article  CAS  PubMed  Google Scholar 

  • van der Roest HF, van Loosdrecht MCM (2012) Water purification, the new standard: purely based on character Delft outlook. Magazine of Delft University of Technology. TU Delft, Delft, pp 6–11

    Google Scholar 

  • van der Roest H, van Loosdrecht M, Langkamp EJ, Uijterlinde C (2015) Recovery and reuse of alginate from granular Nereda sludge. Water 21:48

    Google Scholar 

  • van Dijk EJH, Pronk M, van Loosdrecht MCM (2020) A settling model for full-scale aerobic granular sludge. Water Res 186:116135

    Google Scholar 

  • van Dijk EJH, van Loosdrecht MCM, Pronk M (2021) Nitrous oxide emission from full-scale municipal aerobic granular sludge. Water Res 198:117159

    Google Scholar 

  • van Dijk EJH, Haaksman VA, van Loosdrecht MCM, Pronk M (2022) On the mechanisms for aerobic granulation—model based evaluation. Water Res 216:118365

    Google Scholar 

  • van Groenestijn J, Zuidema M, van de Worp JJM, Deinema MH, Zehnder AJB (1989) Influence of environmental parameters on polyphosphate accumulation in Acinetobacter sp. Anton Van Leeuw Int J Gen Mol Microbiol 55(1):67–82

    Google Scholar 

  • van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lucker S (2015) Complete nitrification by a single microorganism. Nature 528(7583):555–559

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van Lier JB, van der Zee FP, Frijters CT, Ersahin ME (2016) Development of anaerobic high-rate reactors, focusing on sludge bed technology. Adv Biochem Eng Biotechnol 156:363–395

    Google Scholar 

  • van Loosdrecht MCM, Brdjanovic D (2014) Anticipating the next century of wastewater treatment. Science 344(6191):1452–1453

    Article  PubMed  Google Scholar 

  • van Loosdrecht MCM, Hooijmans CM, Brdjanovic D, Heijnen JJ (1997) Biological phosphate removal processes. Appl Microbiol Biotechnol 48(3):289–296

    Google Scholar 

  • van Loosdrecht MCM, Martins AM, Ekama GA (2020) Bulking sludge. In: Henze M, van Loosdrecht MCM, Ekama GA, Brdjanovic D (eds) Biological wastewater treatment: principles, modelling and design, 2nd edn. IWA Publishing, London, pp 475–496

    Google Scholar 

  • van Niekerk AM, Jenkins D, Richard MG (1987) The competitive growth of Zoogloea ramigera and type 021N in activated sludge and pure culture—a model for low F:M bulking. J Water Pollut Control Fed 59(5):262–273

    Google Scholar 

  • Vanrolleghem P (2015) Les StaRRE de type conventionnel: une bonne option pour éliminer beaucoup d’azote. Vecteur Environ Janvier 56

    Google Scholar 

  • Vanwonterghem I, Jensen PD, Rabaey K, Tyson GW (2016) Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environ Microbiol 18(9):3144–3158 

    Article  CAS  PubMed  Google Scholar 

  • Verstraete W, Wittebolle L, Heylen K, Vanparys B, de Vos P, van de Wiele T, Boon N (2007) Microbial resource management: the road to go for environmental biotechnology. Eng Life Sci 7(2):117–126

    Article  CAS  Google Scholar 

  • Vlaeminck SE, De Clippeleir H, Verstraete W (2012) Microbial resource management of one-stage partial nitritation/anammox. Microb Biotechnol 5(3):433–448

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wagner M, Nielsen PH, Loy A, Nielsen JL, Daims H (2006) Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr Opin Biotechnol 17(1):83–91

    Article  CAS  PubMed  Google Scholar 

  • Wagner J, Weissbrodt DG, Manguin V, Ribeiro da Costa RH, Morgenroth E, Derlon N (2015) Effect of particulate organic substrate on aerobic granulation and operating conditions of sequencing batch reactors. Water Res 85:158–166

    Article  CAS  PubMed  Google Scholar 

  • Wang X, Hu M, **a Y, Wen X, Ding K (2012) Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Appl Environ Microbiol 78(19):7042–7047

    Google Scholar 

  • Wang D, Meng Y, Meng F (2022) Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia. Water Res 224:119062 

    Article  CAS  PubMed  Google Scholar 

  • Wanner O, Panagiotidis V, Clavadetscher P, Siegrist H (2005) Effect of heat recovery from raw wastewater on nitrification and nitrogen removal in activated sludge plants. Water Res 39(19):4725–4734

    Article  CAS  PubMed  Google Scholar 

  • Warwick C, Guerreiro A, Wood E, Kitson J, Robinson J, Soares A (2014) A molecular imprinted polymer based sensor for measuring phosphate in wastewater samples. Water Sci Technol 69(1):48–54

    Article  CAS  PubMed  Google Scholar 

  • Weber SD, Ludwig W, Schleifer KH, Fried J (2007) Microbial composition and structure of aerobic granular sewage biofilms. Appl Environ Microbiol 73(19):6233–6240

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei SP, Stensel HD, Nguyen Quoc B, Stahl DA, Huang X, Lee PH, Winkler MKH (2020) Flocs in disguise? High granule abundance found in continuous-flow activated sludge treatment plants. Water Res 179:115865

    Google Scholar 

  • Weissbrodt DG (2018) StaRRE—stations de récupération des ressources de l’eau. Aqua Gas 1:20–24

    Google Scholar 

  • Weissbrodt DG (2019) Engineering the microbiome of EBPR granular sludge for nutrient removal and biorefinery. In: WEF (ed) WEF forum 2019: James Barnard research conference on emerging themes in biological phosphorus removal and recovery. Water Environment Federation, Austin, TX

    Google Scholar 

  • Weissbrodt DG (2022) Microbial ecology principles for urban circular economies—polyphosphate-accumulating organisms: nutrient cycling and beyond. In: ISME (ed) 18th international symposium on microbial ecology (ISME18), Lausanne, Switzerland

    Google Scholar 

  • Weissbrodt DG, Holliger C (2013) Intensification du traitement biologique des eaux usées: technologie à boues granulaires et Gestion des ressources bactériennes. Bull l’ARPEA J Romand L’environ 256:12–22

    Google Scholar 

  • Weissbrodt DG, Holliger C (2014) Towards management of the bacterial resource for nutrient removal in granular sludge biofilm systems. In: Fatone et al (eds) Keynote lecture at the 2nd IWA specialized conference on ecotechnologies for wastewater treatment. University of Verona, Italy

    Google Scholar 

  • Weissbrodt DG, Winkler MKH, Barr JJ (2011) Microbial diversity of aerobic granules: is it different from activated sludge? In: Qi Z (ed) IWA biofilm conference 2011: processes in biofilms. Tongji University, Shanghai

    Google Scholar 

  • Weissbrodt DG, Lochmatter S, Ebrahimi S, Rossi P, Maillard J, Holliger C (2012a) Bacterial selection during the formation of early-stage aerobic granules in wastewater treatment systems operated under wash-out

    Google Scholar 

  • Weissbrodt DG, Shani N, Sinclair L, Lefebvre G, Rossi P, Maillard J, Rougemont J, Holliger C (2012b) PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data. BMC Microbiol 12:306

    Google Scholar 

  • Weissbrodt DG, Neu TR, Kuhlicke U, Rappaz Y, Holliger C (2013a) Assessment of bacterial and structural dynamics in aerobic granular biofilms. Front Microbiol 4:175

    Article  PubMed  PubMed Central  Google Scholar 

  • Weissbrodt DG, Schneiter GS, Fürbringer JM, Holliger C (2013b) Identification of trigger factors selecting for polyphosphate- and glycogen-accumulating organisms in aerobic granular sludge sequencing batch reactors. Water Res 47(19):7006–7018

    Article  CAS  PubMed  Google Scholar 

  • Weissbrodt DG, Derlon N, Morgenroth E, Holliger C (2014a) A consolidated approach of flocculent and granular sludge systems under the perspective of bacterial resource management. Proc Water Environ Fed 2014(19):5008–5009

    Google Scholar 

  • Weissbrodt DG, Maillard J, Brovelli A, Chabrelie A, May J, Holliger C (2014b) Multilevel correlations in the biological phosphorus removal process: from bacterial enrichment to conductivity-based metabolic batch tests and polyphosphatase assays. Biotechnol Bioeng 111(12):2421–2435

    Google Scholar 

  • Weissbrodt DG, Shani N, Holliger C (2014c) Linking bacterial population dynamics and nutrient removal in the granular sludge biofilm ecosystem engineered for wastewater treatment. FEMS Microbiol Ecol 88(3):579–595

    Google Scholar 

  • Weissbrodt DG, Morgenroth E, Wells GF, Goel RK, Nielsen PH, van Loosdrecht MCM (2015) How far can genetic signatures be used to anticipate and trigger the behavior of environmental biotechnology systems in the water engineering domain? Proc Water Environ Fed 2015(10):6170–6170

    Google Scholar 

  • Weissbrodt DG, Holliger C, Morgenroth E (2017) Modeling hydraulic transport and anaerobic uptake by PAOs and GAOs during wastewater feeding in EBPR granular sludge reactors. Biotechnol Bioeng 114(8):1688–1702

    Google Scholar 

  • Weissbrodt DG, Laureni M, van Loosdrecht MCM, Comeau Y (2020a) Basic microbiology and metabolism. In: Chen GH, van Loosdrecht MCM, Ekama GA, Brdjanovic D (eds) Biological wastewater treatment: principles, modelling and design, 2nd edn. IWA Publishing, London

    Google Scholar 

  • Weissbrodt DG, Winkler MKH, Wells GF (2020b) Responsible science, engineering and education for water resource recovery and circularity. Environ Sci Water Res Technol 6(8):1952–1966 

    Article  Google Scholar 

  • Welles L, Lopez-Vazquez CM, Hooijmans CM, van Loosdrecht MC, Brdjanovic D (2014) Impact of salinity on the anaerobic metabolism of phosphate-accumulating organisms (PAO) and glycogen-accumulating organisms (GAO). Appl Microbiol Biotechnol 98(17):7609–7622

    Article  CAS  PubMed  Google Scholar 

  • Welles L, Lopez-Vazquez CM, Hooijmans CM, van Loosdrecht MC, Brdjanovic D (2015) Impact of salinity on the aerobic metabolism of phosphate-accumulating organisms. Appl Microbiol Biotechnol 99(8):3659–3672

    Article  CAS  PubMed  Google Scholar 

  • Wey JK, Scherwass A, Norf H, Arndt H, Weitere M (2008) Effects of protozoan grazing within river biofilms under semi-natural conditions. Aquat Microb Ecol 52(3):283–296

    Google Scholar 

  • Wilderer PA, McSwain BS (2004) The SBR and its biofilm application potentials. Water Sci Technol 50(10):1–10

    Google Scholar 

  • Wilén BM, Lumley D, Mattsson A, Mino T (2008) Relationship between floc composition and flocculation and settling properties studied at a full scale activated sludge plant. Water Res 42(16):4404–4418

    Google Scholar 

  • Wilén B-M, Liébana R, Persson F, Modin O, Hermansson M (2018) The mechanisms of granulation of activated sludge in wastewater treatment, its optimization, and impact on effluent quality. Appl Microbiol Biotechnol 102(12):5005–5020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilmes P, Heintz-Buschart A, Bond PL (2015) A decade of metaproteomics: where we stand and what the future holds. Proteomics 15(20):3409–3417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Winkler MKH, Bassin JP, Kleerebezem R, de Bruin LMM, van den Brand TPH, van Loosdrecht MCM (2011) Selective sludge removal in a segregated aerobic granular biomass system as a strategy to control PAO-GAO competition at high temperatures. Water Res 45(11):3291–3299

    Google Scholar 

  • Winkler MKH, Bassin JP, Kleerebezem R, Sorokin DY, van Loosdrecht MCM (2012a) Unravelling the reasons for disproportion in the ratio of AOB and NOB in aerobic granular sludge. Appl Microbiol Biotechnol 94(6):1657–1666

    Google Scholar 

  • Winkler MKH, Bassin JP, Kleerebezem R, van der Lans RGJM, van Loosdrecht MCM (2012b) Temperature and salt effect on settling velocity in granular sludge technology. Water Res 46(12):3897–3902

    Google Scholar 

  • Winkler MKH, Kleerebezem R, de Bruin LMM, Verheijen PJT, Abbas B, Habermacher J, van Loosdrecht MCM (2012c) Microbial diversity differences within aerobic granular sludge and activated sludge flocs. Appl Microbiol Biotechnol 97(16):7447–7458

    Google Scholar 

  • Winkler MKH, Meunier C, Henriet O, Mahillon J, Suarez-Ojeda ME, Del Moro G, De Sanctis M, Di Iaconi C, Weissbrodt DG (2018) An integrative review of granular sludge for the biological removal of nutrients and of recalcitrant organic matter from wastewater. Chem Eng J 336:489–502

    Article  CAS  Google Scholar 

  • Winkler M-KH, van Loosdrecht MCM (2022) Intensifying existing urban wastewater. Science 375(6579):377–378

    Article  CAS  PubMed  Google Scholar 

  • Withey S, Cartmell E, Avery LM, Stephenson T (2005) Bacteriophages—potential for application in wastewater treatment processes. Sci Total Environ 339(1–3):1–18

    Article  CAS  PubMed  Google Scholar 

  • Wuertz S, Okabe S, Hausner M (2004) Microbial communities and their interactions in biofilm systems: an overview. Water Sci Technol 49(11–12):327–336

    Google Scholar 

  • Wunderlin P, Mohn J, Joss A, Emmenegger L, Siegrist H (2012) Mechanisms of N2O production in biological wastewater treatment under nitrifying and denitrifying conditions. Water Res 46(4):1027–1037

    Google Scholar 

  • Wunderlin P, Siegrist H, Joss A (2013) Online N2O measurement: the next standard for controlling biological ammonia oxidation? Environ Sci Technol 47(17):9567–9568

    Google Scholar 

  • Xu D, Li J, Liu J, Qu X, Ma H (2022) Advances in continuous flow aerobic granular sludge: a review. Process Saf Environ Prot 163:27–35

    Google Scholar 

  • Yan JL, Cui YW, Huang JL (2021) Continuous flow reactors for cultivating aerobic granular sludge: configuration innovation, principle and research prospect. J Chem Technol Biotechnol 96(10):2721–2734

    Article  CAS  Google Scholar 

  • Ye L, Zhang T (2011) Ammonia-oxidizing bacteria dominates over ammonia-oxidizing archaea in a saline nitrification reactor under low DO and high nitrogen loading. Biotechnol Bioeng 108(11):2544–2552

    Article  CAS  PubMed  Google Scholar 

  • Yilmaz G, Lemaire R, Keller J, Yuan Z (2008) Simultaneous nitrification, denitrification, and phosphorus removal from nutrient-rich industrial wastewater using granular sludge. Biotechnol Bioeng 100(3):529–541

    Article  CAS  PubMed  Google Scholar 

  • Yoon S, Song B, Phillips RL, Chang J, Song MJ (2019) Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems. FEMS Microbiol Ecol 95(6):fiz066

    Google Scholar 

  • Young B, Banihashemi B, Forrest D, Kennedy K, Stintzi A, Delatolla R (2016) Meso and micro-scale response of post carbon removal nitrifying MBBR biofilm across carrier type and loading. Water Res 91:235–243

    Article  CAS  PubMed  Google Scholar 

  • Zare M, Heidari MH, Pouresmaeili F, Niyyati M, Moradi M (2012) Introducing a novel facultative nitrifying bacterium, Nitrobacter hamadaniensis. Afr J Microbiol Res 6(24):5126–5133

    CAS  Google Scholar 

  • Zeng RJ, Yuan Z, Keller J (2006) Effects of solids concentration, pH and carbon addition on the production rate and composition of volatile fatty acids in prefermenters using primary sewage sludge. Water Sci Technol 53(8):263–269

    Article  CAS  PubMed  Google Scholar 

  • Zhang D, Vahala R, Wang Y, Smets BF (2016) Microbes in biological processes for municipal landfill leachate treatment: community, function and interaction. Int Biodeterior Biodegrad 113:88–96

    Article  CAS  Google Scholar 

  • Zhang S, Zhang Z, **a S, Ding N, Long X, Wang J, Chen M, Ye C, Chen S (2020) Combined genome-centric metagenomics and stable isotope probing unveils the microbial pathways of aerobic methane oxidation coupled to denitrification process under hypoxic conditions. Bioresour Technol 318:124043

    Article  CAS  PubMed  Google Scholar 

  • Ziliani A, Bovio-Winkler P, Cabezas A, Etchebehere C, Garcia HA, López-Vázquez CM, Brdjanovic D, van Loosdrecht MCM, Rubio-Rincón FJ (2023) Putative metabolism of Ca. Accumulibacter via the utilization of glucose. Water Res 229:119446

    Google Scholar 

  • Zima BE, Diez L, Kowalczyk W, Delgado A (2007) Sequencing batch reactor (SBR) as optimal method for production of granular activated sludge (GAS)—fluid dynamic investigations. Water Sci Technol 55(8–9):151–158

    Article  CAS  PubMed  Google Scholar 

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Weissbrodt, D.G. (2024). Concluding Remarks and Outlook. In: Engineering Granular Microbiomes. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-031-41009-3_12

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