in

Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms

[adace-ad id="91168"]
  • 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.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Davey ME, O’Toole GA. Microbial biofilms: From ecology to molecular genetics. Microbiol Mol. 2000;64:847–67.

    Article 
    CAS 

    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.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Karygianni L, Ren Z, Koo H, Thurnheer T. Biofilm matrixome: Extracellular components in structured microbial communities. Trends Microbiol. 2020;28:668–81.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Decho AW, Gutierrez T. Microbial extracellular polymeric substances (EPSs) in ocean systems. Front Microbiol. 2017;8:922.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    PubMed 

    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.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Myszka K, Czaczyk K. Characterization of adhesive exopolysaccharide (EPS) produced by Pseudomonas aeruginosa under starvation conditions. Curr Microbiol. 2009;58:541–6.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 

    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.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 

    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.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jakubovics NS, Goodman SD, Mashburn-Warren L, Stafford GP, Cieplik F. The dental plaque biofilm matrix. Periodontology 2000. 2021;86:32–56.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 2011;12:385.

    Article 

    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.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PloS One. 2010;5:e9490–e.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fulton KM, Smith JC, Twine SM. Clinical applications of bacterial glycoproteins. Expert Rev Proteom. 2016;13:345–53.

    Article 
    CAS 

    Google Scholar 

  • Upreti RK, Kumar M, Shankar V. Bacterial glycoproteins: Functions, biosynthesis and applications. Proteomics 2003;3:363–79.

    Article 
    CAS 
    PubMed 

    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.

    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Elias S, Banin E. Multi-species biofilms: Living with friendly neighbors. FEMS Microbiol Rev. 2012;36:990–1004.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 

    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.

    Article 
    PubMed 

    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.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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.

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Berlanga M, Guerrero R. Living together in biofilms: The microbial cell factory and its biotechnological implications. Micro Cell Fact. 2016;15:165.

    Article 

    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.

    Article 
    CAS 
    PubMed 

    Google Scholar 


  • Source: Ecology - nature.com

    Creating the steps to make organizational sustainability work

    No impact of nitrogen fertilization on carbon sequestration in a temperate Pinus densiflora forest