Jayathilake PG, Jana S, Rushton S, Swailes D, Bridgens B, Curtis T, et al. Extracellular polymeric substance production and aggregated bacteria colonization influence the competition of microbes in biofilms. Front Microbiol. 2017;8:1865.
Google Scholar
Flemming H-C, Neu TR, Wingender J (eds). The Perfect Slime: Microbial Extracellular Polymeric Substances (EPS). IWA Publishing, London, 2016.
Morales-García AL, Bailey RG, Jana S, Burgess JG. The role of polymers in cross-kingdom bioadhesion. Philos Trans R Soc Lond B Biol Sci. 2019;374:20190192.
Google Scholar
Davey ME, O’Toole GA. Microbial biofilms: From ecology to molecular genetics. Microbiol Mol. 2000;64:847–67.
Google Scholar
Peters BM, Jabra-Rizk MA, O’May GA, Costerton JW, Shirtliff ME. Polymicrobial interactions: Impact on pathogenesis and human disease. Clin Microbiol Rev. 2012;25:193–213.
Google Scholar
Karygianni L, Ren Z, Koo H, Thurnheer T. Biofilm matrixome: Extracellular components in structured microbial communities. Trends Microbiol. 2020;28:668–81.
Google Scholar
Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C. Microbial syntrophy: Interaction for the common good. FEMS Microbiol Rev. 2013;37:384–406.
Google Scholar
Decho AW, Gutierrez T. Microbial extracellular polymeric substances (EPSs) in ocean systems. Front Microbiol. 2017;8:922.
Google Scholar
Boleij M, Seviour T, Wong LL, van Loosdrecht MCM, Lin Y. Solubilization and characterization of extracellular proteins from anammox granular sludge. Water Res. 2019;164:114952.
Google Scholar
Kim D, Barraza JP, Arthur RA, Hara A, Lewis K, Liu Y, et al. Spatial mapping of polymicrobial communities reveals a precise biogeography associated with human dental caries. Proc Natl Acad Sci USA. 2020;117:12375–86.
Google Scholar
Sadiq FA, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, et al. Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms. Crit Rev Microbiol. 2021;47:338–58.
Google Scholar
Liu W, Jacquiod S, Brejnrod A, Russel J, Burmølle M, Sørensen SJ. Deciphering links between bacterial interactions and spatial organization in multispecies biofilms. ISME J. 2019;13:3054–66.
Google Scholar
Bridier A, Le Coq D, Dubois-Brissonnet F, Thomas V, Aymerich S, Briandet R. The spatial architecture of Bacillus subtilis biofilms deciphered using a surface-associated model and in situ imaging. PLOS One. 2011;6:e16177.
Google Scholar
Lee KWK, Periasamy S, Mukherjee M, Xie C, Kjelleberg S, Rice SA. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm. ISME J. 2014;8:894–907.
Google Scholar
Myszka K, Czaczyk K. Characterization of adhesive exopolysaccharide (EPS) produced by Pseudomonas aeruginosa under starvation conditions. Curr Microbiol. 2009;58:541–6.
Google Scholar
Harimawan A, Ting YP. Investigation of extracellular polymeric substances (EPS) properties of P. aeruginosa and B. subtilis and their role in bacterial adhesion. Colloids Surf B. 2016;146:459–67.
Google Scholar
Yang X-R, Li H, Nie S-A, Su J-Q, Weng B-S, Zhu G-B, et al. Potential contribution of anammox to nitrogen loss from paddy soils in Southern China. Appl Environ Microbiol. 2015;81:938–47.
Google Scholar
Kartal B, van Niftrik L, Keltjens JT, Op den Camp HJM, Jetten MSM Chapter 3 – Anammox—Growth physiology, cell biology, and metabolism. In: Poole RK, editor. Adv Microb Physiol. 60: Academic Press; 2012. p. 211–62.
Lu Y, Natarajan G, Nguyen TQN, Thi SS, Arumugam K, Seviour TW, et al. Species level enrichment of AnAOB and associated growth morphology under the effect of key metabolites. bioRxiv. 2020. 2020.02.04.934877
Gonzalez-Gil G, Sougrat R, Behzad AR, Lens PN, Saikaly PE. Microbial community composition and ultrastructure of granules from a full-scale anammox reactor. Micro Ecol. 2015;70:118–31.
Google Scholar
Kindaichi T, Yuri S, Ozaki N, Ohashi A. Ecophysiological role and function of uncultured Chloroflexi in an anammox reactor. Water Sci Technol. 2012;66:2556–61.
Google Scholar
Qin Y, Han B, Cao Y, Wang T. Impact of substrate concentration on anammox-UBF reactors start-up. Bioresour Technol. 2017;239:422–9.
Google Scholar
Chen Z, Meng Y, Sheng B, Zhou Z, Jin C, Meng F. Linking exoproteome function and structure to anammox biofilm development. Environ Sci Technol. 2019;53:1490–500.
Google Scholar
Ali M, Shaw DR, Albertsen M, Saikaly PE. Comparative genome-centric analysis of freshwater and marine ANAMMOX cultures suggests functional redundancy in nitrogen removal processes. Front Microbiol. 2020;11:1637.
Google Scholar
Jia F, Yang Q, Liu X, Li X, Li B, Zhang L, et al. Stratification of extracellular polymeric substances (EPS) for aggregated anammox microorganisms. Environ Sci Technol. 2017;51:3260–8.
Google Scholar
Hou X, Liu S, Zhang Z. Role of extracellular polymeric substance in determining the high aggregation ability of anammox sludge. Water Res. 2015;75:51–62.
Google Scholar
Feng C, Lotti T, Lin Y, Malpei F. Extracellular polymeric substances extraction and recovery from anammox granules: Evaluation of methods and protocol development. Chem Eng J. 2019;374:112–22.
Google Scholar
Lotti T, Carretti E, Berti D, Montis C, Del Buffa S, Lubello C, et al. Hydrogels formed by anammox extracellular polymeric substances: Structural and mechanical insights. Sci Rep. 2019;9:11633.
Google Scholar
Jakubovics NS, Goodman SD, Mashburn-Warren L, Stafford GP, Cieplik F. The dental plaque biofilm matrix. Periodontology 2000. 2021;86:32–56.
Google Scholar
Ðapa T, Leuzzi R, Ng YK, Baban ST, Adamo R, Kuehne SA, et al. Multiple factors modulate biofilm formation by the anaerobic pathogen Clostridium difficile. J Bacteriol. 2013;195:545–55.
Google Scholar
Honma K, Inagaki S, Okuda K, Kuramitsu HK, Sharma A. Role of a Tannerella forsythia exopolysaccharide synthesis operon in biofilm development. Micro Pathog. 2007;42:156–66.
Google Scholar
Li X-R, Du B, Fu H-X, Wang R-F, Shi J-H, Wang Y, et al. The bacterial diversity in an anaerobic ammonium-oxidizing (anammox) reactor community. Syst Appl Microbiol. 2009;32:278–89.
Google Scholar
Cho S, Takahashi Y, Fujii N, Yamada Y, Satoh H, Okabe S. Nitrogen removal performance and microbial community analysis of an anaerobic up-flow granular bed anammox reactor. Chemosphere 2010;78:1129–35.
Google Scholar
Morgenroth E, Sherden T, Van Loosdrecht MCM, Heijnen JJ, Wilderer PA. Aerobic granular sludge in a sequencing batch reactor. Water Res. 1997;31:3191–4.
Google Scholar
Wong LL, Natarajan G, Boleij M, Thi SS, Winnerdy FR, Mugunthan S, et al. Extracellular protein isolation from the matrix of anammox biofilm using ionic liquid extraction. Appl Microbiol Biotechnol. 2020;104:3643–54.
Google Scholar
Law Y, Kirkegaard RH, Cokro AA, Liu X, Arumugam K, Xie C, et al. Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions. Sci Rep. 2016;6:25719.
Google Scholar
Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 2011;12:385.
Google Scholar
Liu X, Arumugam K, Natarajan G, Seviour TW, Drautz-Moses DI, Wuertz S, et al. Draft genome sequence of a Candidatus brocadia bacterium enriched from activated sludge collected in a tropical climate. Genome Announc. 2018;6:e00406–18.
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PloS One. 2010;5:e9490–e.
Google Scholar
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol. 2018;36:566–9.
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Google Scholar
Buchfink B, Reuter K, Drost H-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021;18:366–8.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Google Scholar
Daims H, Nielsen JL, Nielsen PH, Schleifer K-H, Wagner M. In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl Environ Microbiol. 2001;67:5273–84.
Google Scholar
Seviour T, Wong LL, Lu Y, Mugunthan S, Yang Q, Shankari UDOCS, et al. Phase transitions by an abundant protein in the anammox extracellular matrix mediate cell-to-cell aggregation and biofilm formation. mBio 2020;11:e02052–20.
Google Scholar
Protter DSW, Rao BS, Van Treeck B, Lin Y, Mizoue L, Rosen MK, et al. Intrinsically disordered regions can contribute promiscuous interactions to RNP granule assembly. Cell Rep. 2018;22:1401–12.
Google Scholar
Fulton KM, Smith JC, Twine SM. Clinical applications of bacterial glycoproteins. Expert Rev Proteom. 2016;13:345–53.
Google Scholar
Upreti RK, Kumar M, Shankar V. Bacterial glycoproteins: Functions, biosynthesis and applications. Proteomics 2003;3:363–79.
Google Scholar
van Teeseling MCF, Maresch D, Rath CB, Figl R, Altmann F, Jetten MSM, et al. The S-layer protein of the anammox bacterium Kuenenia stuttgartiensiss is heavily O-glycosylated. Front Microbiol. 2016;7:1721.
Google Scholar
McGonigle JM, Lang SQ, Brazelton WJ, Parales RE. Genomic evidence for formate metabolism by Chloroflexi as the key to unlocking deep carbon in lost city microbial ecosystems. Appl Environ Microbiol. 2020;86:e02583–19.
Google Scholar
Vuillemin A, Kerrigan Z, D’Hondt S, Orsi WD. Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay. FEMS Microbiol Ecol. 2020;96:fiaa223.
Google Scholar
Kartal B, de Almeida NM, Maalcke WJ, Op den Camp HJ, Jetten MS, Keltjens JT. How to make a living from anaerobic ammonium oxidation. FEMS Microbiol Rev. 2013;37:428–61.
Google Scholar
Loera-Muro A, Guerrero-Barrera A, Tremblay DNY, Hathroubi S, Angulo C. Bacterial biofilm-derived antigens: A new strategy for vaccine development against infectious diseases. Expert Rev Vaccines. 2021;20:385–96.
Google Scholar
Hobley L, Harkins C, MacPhee CE, Stanley-Wall NR. Giving structure to the biofilm matrix: An overview of individual strategies and emerging common themes. FEMS Microbiol Rev. 2015;39:649–69.
Google Scholar
Elias S, Banin E. Multi-species biofilms: Living with friendly neighbors. FEMS Microbiol Rev. 2012;36:990–1004.
Google Scholar
Teeseling MCFV, Almeida NMD, Klingl A, Speth DR, Camp HJMOD, Rachel R, et al. A new addition to the cell plan of anammox bacteria: Candidatus Kuenenia stuttgartiensis has a protein surface layer as the outermost layer of the cell. J Bacteriol. 2014;196:80–9.
Google Scholar
Paula AJ, Hwang G, Koo H. Dynamics of bacterial population growth in biofilms resemble spatial and structural aspects of urbanization. Nat Commun. 2020;11:1354.
Google Scholar
Kragelund C, Caterina L, Borger A, Thelen K, Eikelboom D, Tandoi V, et al. Identity, abundance and ecophysiology of filamentous Chloroflexi species present in activated sludge treatment plants. FEMS Microbiol Ecol. 2007;59:671–82.
Google Scholar
Nierychlo M, Miłobędzka A, Petriglieri F, McIlroy B, Nielsen PH, McIlroy SJ. The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants. FEMS Microbiol Ecol. 2018;95.
Kragelund C, Thomsen TR, Mielczarek AT, Nielsen PH. Eikelboom’s morphotype 0803 in activated sludge belongs to the genus Caldilinea in the phylum Chloroflexi. FEMS Microbiol Ecol. 2011;76:451–62.
Google Scholar
Zhang J, Miao Y, Zhang Q, Sun Y, Wu L, Peng Y. Mechanism of stable sewage nitrogen removal in a partial nitrification-anammox biofilm system at low temperatures: Microbial community and EPS analysis. Bioresour Technol. 2020;297:122459.
Google Scholar
Björnsson L, Hugenholtz P, Tyson GW, Blackall LL. Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology 2002;148:2309–18.
Google Scholar
Boleij M, Pabst M, Neu TR, van Loosdrecht MCM, Lin Y. Identification of glycoproteins isolated from extracellular polymeric substances of full-scale anammox granular sludge. Environ Sci Technol. 2018;52:13127–35.
Google Scholar
Pabst M, Grouzdev DS, Lawson CE, Kleikamp HBC, de Ram C, Louwen R, et al. A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium. ISME J. 2022;16:346–57.
Google Scholar
Berlanga M, Guerrero R. Living together in biofilms: The microbial cell factory and its biotechnological implications. Micro Cell Fact. 2016;15:165.
Google Scholar
Liu T, Tian R, Li Q, Wu N, Quan X. Strengthened attachment of anammox bacteria on iron-based modified carrier and its effects on anammox performance in integrated floating-film activated sludge (IFFAS) process. Sci Total Environ. 2021;787:147679.
Google Scholar
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