[1] Ghannoum M and O’Toole GA. Microbial Biofilms, Washington, DC: ASM Press (2004).
[2] Stewart PS and Franklin MJ. Physiological Heterogeneity in Biofilms. Nat. Rev. Microbiol. 2008; 6: 199-210.
[3] López D, Kolter R. Functional microdomains in bacterial membranes. Genes Dev. 2010; 24: 1893–1902.
[4] Branda SS, Vik Å, Friedman Land Kolter R. Biofilms: the matrix revisited. Trends Microbiol. 2005; 13(1): 0-26.
[5] Flemming H-C, Wingender J. The biofilm matrix. Nat. Rev. Microbiol. 2010; 8: 623–633.
[6] Whitchurch CB, Tolker-Nielsen T, Ragas PC, Mattick JS. Extracellular DNA required for bacterial biofilm formation. Science. 2002; 295: 1487.
[7] Dominiak DM, Nielsen JL, and Nielsen PH. Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms. Environ. Microbiol. 2011: 13: 710–721.
[8] Finkel SE, and Kolter R. DNA as a nutrient: novel role for bacterial competence gene homologs. J Bacteriol. 2001; 183: 6288–6293.
[9] Molin S, Tolker-Nielsen T. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilization of the biofilm structure. Curr. Opin. Biotechnol. 2003; 14: 255–261.
[10] Qin Z, Ou Y, Yang L, et al. Role of autolysin-mediated DNA release in biofilm formation of Staphylococcus epidermidis. Microbiology. 2007; 153: 2083–2092.
[11] Hall-stoodley L, Nistico L, Sambanthamoorthy K, et al. Characterization of biofilm matrix, degradation by DNase treatment and evidence of capsule downregulation in Streptococcus pneumoniae clinical isolates. BMC Microbiol. 2008; 8: 173.
[12] Seper A, Fengler VHI, Roier S, et al. Extracellular nucleases and extracellular DNA play important roles in Vibrio cholerae biofilm formation. Mol. Microbiol. 2011; 82: 1015–1037.
[13] Ma L, Conover M, Lu H, Parsek MR, Bayles K and Wozniak DJ. Assembly and development of the Pseudomonas aeruginosa biofilm matrix. PLoS Pathog. 2009; 5: e1000354.
[14] Sutherland IW. in Comprehensive Glycoscience Vol. 2 (ed. Kamerling, J. P.) 521–558 (Elsevier, Doordrecht, 2007).
[15] Xiao J, Klein MI, Falsetta ML, et al. The exopolysaccharide matrix modulates the interaction between 3D architecture and virulence of a mixed-species oral biofilm. PLoS Pathog. 2012; 8: e1002623.
[16] Liao S, Klein MI, Heim KP, et al. Wen. Streptococcus mutans extracellular DNA is upregulated during growth in biofilms, actively released via membrane vesicles, and influenced by components of the protein secretion machinery. J Bacteriol. 2014; 196: 2355-2366.
[17] Wang S, Liu X, Zhang L, et al. The exopolysaccharide Psl–eDNA interaction enables the formation of a biofilm skeleton in Pseudomonas aeruginosa. Environ. Microbiol. Rep. 2015; 7(2): 330-340.
[18] Bais HP, Fall R, Vivanco JM. Biocontrol of Bacillus subtilis against infection of Arabidopsis Roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant Physio. 2004; 134(1): 307-319.
[19] Stein T, Dusterhus S, Stroh A, Entian KD. Subtilosin production by two Bacillus subtilis subspecies and variance of the sbo‐alb cluster. Appl Environ Microbiol. 2004; 70: 2349–2353.
[20] Butcher RA, Schroeder FC, Fischbach MA, et al. The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis. Proc. Natl. Acad. Sci. U. S. A. 2007: 104: 1506–1509.
[21] Nagorska K, Bikowski M, Obuchowskji M. Multicellular behaviour and production of a wide variety of toxic substances support usage of Bacillus subtilis as a powerful biocontrol agent. Acta Biochim Pol. 2007; 54: 495–508.
[22] Ongena M, Jourdan E, Adam A, et al. Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants. Environ. Microbiol. 2007; 9: 1084–1090.
[23] Ongena M, Jacques P. Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol. 2008; 16: 115–125.
[24] Chen Y, Cao S, Chai Y, et al. A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants. Mol Microbiol. 2012; 85: 418–430.
[25] Chen Y, Yan F, Chai Y, et al. Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation. Environ Microbiol. 2013; 15: 848–864.
[26] Beauregard PB, Chai Y, Vlamakis H, Losick R, Kolter R. Bacillus subtilis biofilm induction by plant polysaccharides. Proc Natl Acad Sci U S A. 2013; 110: E1621–1630.
[27] Branda SS, Chu F, Kearns DB, Losick R, Kolter R. A major protein component of the Bacillus subtilis biofilm matrix. Mol Microbiol. 2006; 59: 1229–1238.
[28] Sinha RP, Iyer VN. Competence for genetic transformation and the release of DNA from Bacillus subtilis[J]. Biochimica et Biophysica Acta (BBA)-Nucleic Acids and Protein Synthesis. 1971; 232(1): 61-71.
[29] López D, Vlamakis H, Losick R, and Kolter R. Cannibalism enhances biofilm development in Bacillus subtilis. Mol. Microbiol. 2009; 74: 609–618.
[30] Crabb WD, Streips UN, and Doyle RJ. Selective enrichment for genetic markers in DNA released by competent cultures of Bacillus subtilis. Mol. Gen. Genet. 1977; 155: 179–183.
[31] Ibáñez de Aldecoa AL, Zafra O and González-Pastor JE. Mechanisms and regulation of extracellular DNA release and its biological roles in microbial communities. Front Microbiol. 2017; 8: 1390.
[32] Zafra O, Lamprecht-Grandío M, González de Figueras C and González-Pastor JE. Extracellular DNA release by undomesticated Bacillus subtilis is regulated by early competence. PLOS ONE. 2012; 7.
[33] Harmsen M, Lappann M, Knøchel S, Molin S. Role of extracellular DNA during biofilm formation by Listeria monocytogenes. Appl Environ Microbiol. 2010; 76: 2271–2279.
[34] Hobley L, Harkins C, Macphee CE, Stanleywall NR. Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. FEMS Microbiol. Rev. 2015; 39: 649-69.
[35] Branda SS, González-Pastor JE, Ben-Yehuda S, Losick R, Kolter R. Fruiting body formation in Bacillus subtilis. Proc Natl Acad Sci U S A. 2001: 98: 11621-11626.
[36] Kearns DB, Chu F, Branda SS, Kolter R, Losick R. A master regulator for biofilm formation by Bacillus subtilis. Mol Microbiol. 2005; 55: 739–749.
[37] Gerwig J, Kiley TB, Gunka K, Stanley-Wall N, Stulke J. The protein tyrosine kinases EpsB and PtkA differentially affect biofilm formation in Bacillus subti- lis. Microbiology. 2014; 160: 682–691.
[38] Guttenplan SB, Blair KM, Kearns DB. The EpsE flagellar clutch is bifunctional and synergizes with EPS biosynthesis to promote Bacillus subtilis biofilm formation[J]. PLoS Genet. 2010; 6: e1001243.
[39] Terra R, Stanley-Wall NR, Cao G, Lazazzera BA. Identification of Bacillus subtilis sipW as a bifunctional signal peptidase that controls surface-adhered biofilm formation. J. Bacteriol. 2012; 194: 2781–2790.
[40] Yang L, Hu Y, Liu Y, Zhang J, Ulstrup J, Molin S. Distinct roles of extracellular polymeric substances in Pseudomonas aeruginosa biofilm development. Environ Microbiol. 2011 13: 1705-1717.
[41] Castillo Pedraza MC, Novais TF, Faustoferri RC, et al. Klein. Extracellular DNA and lipoteichoic acids interact with exopolysaccharides in the extracellular matrix of Streptococcus mutans biofilms. Biofouling. 2017; 33: 722–740.
[42] Gries A, Prassl R, Fukuoka S, et al. Biophysical analysis of the interaction of the serum protein human beta2GPI with bacterial lipopolysaccharide. FEBS Open Bio. 2014; 4: 432–440.
[43] Tawfik DS. Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency? Curr. Opin. Chem. Biol. 2014; 21: 73−80
[44] Grundmann GL. Spatial scales of soil bacterial diversity – the size of a clone. FEMS Microbiol Ecol. 2004; 48: 119–127.
[45] Nunan N, Wu KJ, Young IM, Crawford JW and Ritz K. Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiol Ecol. 2003; 44: 203–215.
[46] Burmølle M, Thomsen TR, Fazli M, et al. Biofilms in chronic infections - a matter of opportunity monospecies biofilms in multispecies infections. FEMS Immunol Med Microbiol. 2010; 59: 324-336.
[47] Ma W, Peng D, Walker SL, et al. Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides. npj Biofilms and Microbiomes.2017; 3: 4.
[48] Dubnau D. Genetic exchange and homologous recombination[M] Bacillus subtilis and other gram-positive bacteria. American Society of Microbiology. 1993; 555-584.
[49] Cue D, Lam H, Dillingham RL, et al. Genetic manipulation of Bacillus methanolicus, a gram-positive, thermotolerant methylotroph[J]. Appl. Environ. Microbiol. 1997; 63: 1406-1420.
[50] Wecke T, Bauer T, Harth H, et al. The rhamnolipid stress response of Bacillus subtilis[J]. FEMS microbiology letters.2011 323: 113-123.
[51] Brimacombe CA, Stevens A, Jun D, Mercer R, Lang AS and Beatty JT. Quorum-sensing regulation of a capsular polysaccharide receptor for the Rhodobacter capsulatus gene transfer agent (RcGTA). Mol Microbiol. 2013; 87 802-817.
[52] Coffey BM and Anderson GG. Biofilm formation in the 96-well microtiter plate. In Pseudomonas Methods and Protocols (pp. 631-641). Humana Press, New York, NY; 2014.
[53] Gloag ES, Turnbull L, Huang A, et al. Self-organization of bacterial biofilms is facilitated by extracellular DNA. Proceedings of the National Academy of Sciences. 2013; 110(28): 11541-11546.
[54] Okshevsky M and Meyer RL. Evaluation of fluorescent stains for visualizing extracellular DNA in biofilms. J Microbiol Meth. 2014; 105: 102-104.
[55] Yu GH, Tang Z, Xu YC and Shen QR. Multiple fluorescence labeling and two dimensional FTIR–13C NMR heterospectral correlation spectroscopy to characterize extracellular polymeric substances in biofilms produced during composting. Environmental Science & Technology. 2011 45: 9224-9231.
[56] Xiao J, Koo H. Structural organization and dynamics of exopolysaccharide matrix and microcolonies formation by Streptococcus mutans in biofilms[J]. J. Appl. Microbiol. 2010; 108: 2103-2113.
[57] Rasband WS. ImageJ. US National Institutes of Health, Bethesda, MD, U.S.A (1997–2006).
[58] Ni B, Huang Z, Fan Z, Jiang CY, and Liu SJ. Comamonas testosteroni uses a chemoreceptor for tricarboxylic acid cycle intermediates to trigger chemotactic responses towards aromatic compounds. Mol Microbiol. 2013;90: 813–823.