Afonso AC, Gomes IB, Saavedra MJ, Giaouris E, Simões LC, Simões M (2021) Bacterial coaggregation in aquatic systems. Water Res 196:117037. https://doi.org/10.1016/j.watres.2021.117037

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 (camb) 5:2072–2089. https://doi.org/10.1039/C9EW00450E

Article  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. https://doi.org/10.1038/srep28327

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bao J, de Dios ME, Scheller S (2022) Efficient CRISPR/Cas12a-based genome-editing toolbox for metabolic engineering in Methanococcus maripaludis. ACS Synth Biol 11:2496–2503. https://doi.org/10.1021/acssynbio.2c00137

Article  CAS  PubMed  PubMed Central  Google Scholar 

Belas R (2014) Biofilms, flagella, and mechanosensing of surfaces by bacteria. Trends Microbiol 22:517–527. https://doi.org/10.1016/j.tim.2014.05.002

Article  CAS  PubMed  Google Scholar 

Benito Merino D, Zehnle H, Teske A, Wegener G (2022) Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane. Front Microbiol 13. https://doi.org/10.3389/fmicb.2022.988871

Besteman MS, Doloman A, Sousa DZ (2024) Transcriptomic evidence for an energetically advantageous relationship between Syntrophomonas wolfei and Methanothrix soehngenii. Environ Microbiol Rep 16. https://doi.org/10.1111/1758-2229.13276

Bhattarai S, Cassarini C, Lens PNL (2019) Physiology and distribution of archaeal methanotrophs that couple anaerobic oxidation of methane with sulfate reduction. Microbiol Mol Biol 83. https://doi.org/10.1128/MMBR.00074-18

Boleij M, Pabst M, Neu TR, Van Loosdrecht MCM, Lin Y (2018) Identification of glycoproteins isolated from extracellular polymeric substances of full-scale anammox granular sludge. Environ Sci Technol 52:13127–13135. https://doi.org/10.1021/acs.est.8b03180

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bordeleau E, Purcell EB, Lafontaine DA, Fortier L-C, Tamayo R, Burrus V (2015) Cyclic di-GMP riboswitch-regulated type IV pili contribute to aggregation of Clostridium difficile. J Bacteriol 197:819–832. https://doi.org/10.1128/JB.02340-14

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bridges AA, Prentice JA, Wingreen NS, Bassler BL (2022) Signal transduction network principles underlying bacterial collective behaviors. Annu Rev Microbiol 76:235–257. https://doi.org/10.1146/annurev-micro-042922-122020

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cai Y-M (2020) Non-surface attached bacterial aggregates: a ubiquitous third lifestyle. Front Microbiol 11. https://doi.org/10.3389/fmicb.2020.557035

Chajwa R, Flaum E, Bidle DK, Van Mooy B, Prakash M (2023) Hidden comet-tails of marine snow impede ocean-based carbon sequestration. Atmos Ocean Phys, arXiv

Chia HE, Zuo T, Koropatkin NM, Marsh ENG, Biteen JS (2020) Imaging living obligate anaerobic bacteria with bilin-binding fluorescent proteins. Curr Res Microb Sci 1:1–6. https://doi.org/10.1016/j.crmicr.2020.04.001

Article  PubMed  PubMed Central  Google Scholar 

Choo SW, Mohammed WK, Mutha NVR, Rostami N, Ahmed H, Krasnogor N, Tan GYA, Jakubovics NS (2021) Transcriptomic responses to coaggregation between Streptococcus gordonii and Streptococcus oralis. Appl Environ Microbiol 87. https://doi.org/10.1128/AEM.01558-21

Christensen LFB, Hansen LM, Finster K, Christiansen G, Nielsen PH, Otzen DE, Dueholm MS (2018) The sheaths of Methanospirillum are made of a new type of amyloid protein. Front Microbiol 9. https://doi.org/10.3389/fmicb.2018.02729

Condinho M, Carvalho B, Cruz A, Pinto SN, Arraiano CM, Pobre V (2023) The role of RNA regulators, quorum sensing and c-di-GMP in bacterial biofilm formation. FEBS Open Bio 13:975–991. https://doi.org/10.1002/2211-5463.13389

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. https://doi.org/10.1016/j.scitotenv.2022.154253

Article  CAS  PubMed  Google Scholar 

Daffonchio D, Thaveesri J, Verstraete W (1995) Contact angle measurement and cell hydrophobicity of granular sludge from upflow anaerobic sludge bed reactors. Appl Environ Microbiol 61:3676–3680. https://doi.org/10.1128/aem.61.10.3676-3680.1995

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dal Co A, van Vliet S, Kiviet DJ, Schlegel S, Ackermann M (2020) Short-range interactions govern the dynamics and functions of microbial communities. Nat Ecol Evol 4:366–375. https://doi.org/10.1038/s41559-019-1080-2

Article  Google Scholar 

Doloman A, Varghese H, Miller CD, Flann NS (2017) Modeling de novo granulation of anaerobic sludge. BMC Syst Biol 11:69. https://doi.org/10.1186/s12918-017-0443-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doloman A, Mahajan A, Pererva Y, Flann NS, Miller CD (2020) A model for bioaugmented anaerobic granulation. Front Microbiol 11. https://doi.org/10.3389/fmicb.2020.566826

Doloman A, Boeren S, Miller CD, Sousa DZ (2022) Stimulating effect of Trichococcus flocculiformis on a coculture of Syntrophomonas wolfei and Methanospirillum hungatei. Appl Environ Microbiol 88. https://doi.org/10.1128/aem.00391-22

Doloman A, Besteman MS, Sanders MG, Sousa DZ (2024a) Methanogenic partner influences cell aggregation and signalling of Syntrophobacterium fumaroxidans. Appl Microbiol Biotechnol 108:127. https://doi.org/10.1007/s00253-023-12955-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doloman A, de Bruin S, van Loosdrecht MCM, Sousa DZ, Lin Y (2024b) Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges. Water Res 252:121240. https://doi.org/10.1016/j.watres.2024.121240

Article  CAS  PubMed  Google Scholar 

Dueholm MS, Larsen P, Finster K, Stenvang MR, Christiansen G, Vad BS, Bøggild A, Otzen DE, Nielsen PH (2015) The tubular sheaths encasing Methanosaeta thermophila filaments are functional amyloids. JBC 290:20590–20600. https://doi.org/10.1074/jbc.M115.654780

Article  CAS  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. https://doi.org/10.1016/j.watres.2022.119485

Article  CAS  PubMed  Google Scholar 

Elias S, Banin E (2012) Multi-species biofilms: living with friendly neighbors. FEMS Microbiol Rev 36:990–1004. https://doi.org/10.1111/j.1574-6976.2012.00325.x

Article  CAS  PubMed  Google Scholar 

Feng W, Zhang Q, Li J, Duan C, Peng Y (2024) Novel anammox granules formation from conventional activated sludge for municipal wastewater treatment through flocs management. Bioresour Technol 396:130384. https://doi.org/10.1016/j.biortech.2024.130384

Article  CAS  PubMed  Google Scholar 

Fink C, Martinez-Cano G, Shuster J, Panzera A, Rennhack KE, Rohbohm N, Angenent LT, Molitor B (2023) The targeted deletion of genes responsible for expression of the Mth60 fimbriae leads to loss of cell-cell connections in Methanothermobacter thermautotrophicus ΔH. Appl Environ Microbiol 89. https://doi.org/10.1128/aem.00575-23

Flaiz M, Baur T, Gaibler J, Kröly C, Dürre P (2022) Establishment of green- and red-fluorescent reporter proteins based on the fluorescence-activating and absorption-shifting tag for use in acetogenic and solventogenic anaerobes. ACS Synth Biol 11:953–967. https://doi.org/10.1021/acssynbio.1c00554

Article  CAS  PubMed  Google Scholar 

Flemming H-C, Wuertz S (2019) Bacteria and archaea on Earth and their abundance in biofilms. Nat Rev Microbiol 17:247–260. https://doi.org/10.1038/s41579-019-0158-9

Article  CAS  PubMed  Google Scholar 

Flemming H-C, van Hullebusch ED, Neu TR, Nielsen PH, Seviour T, Stoodley P, Wingender J, Wuertz S (2023) The biofilm matrix: multitasking in a shared space. Nat Rev Microbiol 21:70–86. https://doi.org/10.1038/s41579-022-00791-0

Article  CAS  PubMed  Google Scholar 

Fritts RK, McCully AL, McKinlay JB (2021) Extracellular metabolism sets the table for microbial cross-feeding. Microbiol Mol Biol 85. https://doi.org/10.1128/MMBR.00135-20

Fulaz S, Vitale S, Quinn L, Casey E (2019) Nanoparticle–biofilm interactions: the role of the EPS matrix. Trends Microbiol 27:915–926. https://doi.org/10.1016/j.tim.2019.07.004

Article  CAS  PubMed  Google Scholar 

Gagliano MC, Neu TR, Kuhlicke U, Sudmalis D, Temmink H, Plugge CM (2018) EPS glycoconjugate profiles shift