在地球上，微生物幾乎無所不在，當然包括人類工業的機器組件中，例如：造紙機中。儘管機組設備裡常是營養 (碳、氮、磷源) 缺乏且溫度極端的環境，仍有許多各式各樣的微生物生存著，甚至隨著不同機器部位所產生的環境不同而出現不同的微生物族群組合，或者擁有異於一般微生物的生長能力、具備水解各種不同物質的分解能力。其中，有些造紙機中的微生物會產生生物膜 (biofilm) 黏液以吸附並大量叢生於金屬機械表面，卻因此造成成品污染破損、抄紙網或造紙機的損害，甚至引發工廠停擺，帶來經濟上巨大的損失；然而這些微生物常因為生物膜的保護且具高抗藥性，非常難以一般抗生素清除。因此對於工業造紙環境中的微生物之瞭解及研究，將有助於進一步開發以非抗生素殺菌的可能方法，也同時能研究極端環境對於微生物族群的組成與生長狀況、相互作用關係、生物膜的形成與發展以及特殊水解酵素的分泌等等之影響。
本論文其中一個主題便是針對於造紙機的缺磷環境中，兩株分類於不同目(order)的異營性細菌之間的競爭關係與其生物膜發展。我們從造紙機循環清洗儲水槽的生物膜中，分離出了13株具吸附能力的細菌株，並發現只有將其共同培養於缺磷的條件下時，沙雷氏桿菌分離株 (Serratia marcescens WW4)會跨物種地(intergeneric)抑制綠膿桿菌分離株(Pseudomonas aeruginosa WW5) 的生長。當沙雷氏桿菌分離株單獨培養於缺磷環境時，活菌數及生物膜產量於三天內便會下降，然而如果與綠膿桿菌分離株混合培養時，則明顯地提高沙雷氏桿菌分離株的存活率及生物膜產量；相反地，綠膿桿菌分離株於缺磷環境下單獨培養的三天中，活菌數及生物膜產量都可以維持良好，但若與沙雷氏桿菌分離株混合培養時，其存活率及生物膜產量則於一天內迅速下降。我們更進一步地找出這種與磷濃度相關的抑制作用之分子機制，發現可能與一個較物種專一性且具核酸內切酶 (endonuclease) 活性的細菌素 (bacteriocin) 有關。因此本論文發現於缺磷環境中，沙雷氏桿菌可能跨物種地以較專一性的細菌素抑制綠膿桿菌之生長，進而維持自身族群的生存及生物膜發展。另外，我們也解開了此沙雷氏桿菌分離株的完整染色體基因序列，總共含一個5,241,455 bp的環狀染色體及一個3,248 bp的質體。
另一個論文研究主題則是針對一株造紙機黑液中的耐熱分離菌(Paenibacillus campinasensis BL11) 所分泌的聚木醣酶 (xylanase) 之研究。我們將以分生技術複製得到的聚木醣酶基因XylX (1131bp) 表現於大腸桿菌蛋白質表現系統中，產生一個約41kDa大小的聚木醣內切酶表現蛋白，具有第11族配糖水解酶 (family 11 glycoside hydrolase) 的催化區及第6族纖維素結合區(family 6 cellulose-binding module)。此表現蛋白於60 °C、pH7的最適作用條件下，活性高達2392 IU/mg，酵素受質親和力有6.78 mg mL-1的 Km 值且最大反應速率(Vmax )可達4953 mol/min/mg，甚至於鹼性高溫環境中(pH 11, 60 °C) 依舊有極高的活性 (517 IU mg-1)，於pH5至pH9之間及45 °C 至65 °C之間都能保有60 %以上的活性；於最適條件下水解聚木醣12小時後，便可產生大量的主要產物xylotriose，且此酵素並不會非專一地分解avicel、carboxymethyl cellulose及 d-(+)-cellobiose。另外，汞與N-bromosuccinimide對於此聚木醣酶有明顯抑制活性現象，而tris-(2-carboxyethyl)-phosphine (TCEP) 及2-mercaptoethanol則可增加活性。因此，此分離菌株所產生的聚木醣酶具有較寬的pH與溫度耐受度，以及較專一的分解力，將極適合應用於生物質能轉換或食品、造紙加工方面。

Acar JF. (1986) Serratia marcescens infections. Infect. Control 7:273–278.
Al-Bakri AG, Gilbert P & Allison DG (2004) Immigration and emigration of Burkholderia cepacia and Pseudomonas aeruginosa between and within mixed biofilm communities. J Appl Microbiol 96: 455-463.
Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
Andersson S, Rajarao GK, Land CJ & Dalhammar G (2008) Biofilm formation and interactions of bacterial strains found in wastewater treatment systems. FEMS Microbiol Lett 283: 83-90.
Anhalt JP & Washington JA. (1985a) Antimicrobial susceptibility tests of aerobic and facultatively anaerobic bacteria. In: Washington, J.A. (Ed.), Laboratory Procedure in Clinical Microbiology, second ed. Springer, New York, pp. 281–314.
Anhalt JP & Washington JA. (1985b) Bactericidal tests. In: Washington, J.A. (Ed.), Laboratory Procedure in Clinical Microbiology, second ed. Springer-Verlag, New York, pp. 731–745.
Bai YG, Wang JS, Zhang ZF, Yang PL, Shi PJ & Luo HY. (2010) A new xylanase from thermoacidophilic Alicyclobacillus sp. A4 with broad-range pH activity and pH stability. J Ind Microbiol Biotechnol 37:187–194
Bajpai P. (1999) Application of enzymes in the pulp and paper industry. Biotechnol Prog 15:147–157
Banks MK & Bryers JD (1991) Bacterial species dominance within a binary culture biofilm. Appl Environ Microbiol 57: 1974-1979.
Bassler BL, Greenberg EP & Stevens, AM. (1997) Crossspecies induction of luminescence in the quorum-sensing bacterium Vibrio harveyi. J. Bacteriol. 179:4043–4045.
Bataillon M., Cardinali AN, Castillon N. & Duchiron F. (2000). Purification and characterization of a moderately thermostable xylanase from Bacillussp. strain SPS-0. Enzyme Microb Technol 26;187–192
Beg Q.K., Kapoor M., Mahajan L. & Hoondal G.S. (2001) Microbial xylanases and their industrial applications: a review. Appl Microbiol Biotechnol 56:326–338
Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J & Sayers EW (2012) GenBank. Nucleic Acids Res 40: D48-53
Biely P (1985) Microbial xylanolytic systems. Trends Biotechnol 3:286–290
Blanco A, Diaz P, Zueco J, Parascandola P & Pastor FIJ. (1999). A multidomain xylanase from a Bacillus sp. with a region homologous to thermostabilizing domains of thermophilic enzymes. Microbiology 145:2163–2170
Blanco A, Vidal T, Colom JF & Pastor FIJ. (1995) Purification and properties of xylanase A from alkali-tolerant Bacillus sp. strain BP-23. Appl Environ Microbiol 61:4468–4470
Blattner FR, Plunkett G, 3rd, Bloch CA, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462
Brown, M.R.W. & Gilbert, P. (1993) Sensitivity of biofilms to antimicrobial agents. Journal of Applied Bacteriology Symposium Supplement 74, 87S–97S.
Burgess JG, Jordan EM, Bregu M, Mearns-Spragg A & Boyd KG (1999) Microbial antagonism: a neglected avenue of natural products research. J. Biotechnol. 70: 27-32.
Burns JA, Butler JC, Moran J & Whitesides GM. (1991). Selective reduction of disulfides by tris (2-carboxyethyl) phosphine. J Org Chem 56:2648–2650
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K & Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
Cascales E, Buchanan SK, Duche D, et al. (2007) Colicin biology. Microbiol Mol Biol Rev 71: 158-229.
Castonguay MH, van der Schaaf S, Koester W, Krooneman J, van der Meer W, Harmsen H & Landini P (2006) Biofilm formation by Escherichia coli is stimulated by synergistic interactions and co-adhesion mechanisms with adherence-proficient bacteria. Res. Microbiol. 157: 471-478.
Castro DP, Seabra SH, Garcia ES, de Souza W & Azambuja P (2007) Trypanosoma cruzi: ultrastructural studies of adhesion, lysis and biofilm formation by Serratia marcescens. Exp Parasitol 117: 201-207.
Choudhury B., Chauhan S., Singh S.N. & Ghosh P. (2006) Production of Xylanase of Bacillus coagulans and its bleaching potential. World J Microbiol Biotechnol 22: 283–288
Christensen BB, Haagensen JAJ, Heydorn A & Molin S. (2002) Metabolic commensalism and competition in a two-species microbial consortium. Appl. Environ. Microbiol. 68:2495–2502.
Claus, G. & Mueller, R. (1996) Biofilms in a paper mill process water system. In Microbiably Influenced Corrosion of Materials ed. Heitz, E., Flemming, H.-C. and Sand, W. pp. 429–437. Heidelberg: Springer Verlag.
Conway BAD, Venu V & Speert DP. (2002) Biofilm formation and acyl homoserine lactone production in the Burkholderia cepacia complex. J. Bacteriol. 184:5678–5685.
Coulthurst SJ, Barnard AM & Salmond GP (2005) Regulation and biosynthesis of carbapenem antibiotics in bacteria. Nat Rev Microbiol 3: 295–306.
Cowan SE, Gilbert E, Liepmann D & Keasling JD (2000) Commensal interactions in a dual-species biofilm exposed to mixed organic compounds. Appl. Environ. Microbiol. 66: 4481-4485.
Davies DG, Parsek MR, Pearson JP, Iglewski BH, Costerton JW & Greenberg EP. (1998) The involvement of cell-cell signals in the development of a bacterial biofilm. Science 280:295–298.
De Lorenzo V, Herrero M, Jakubzik U & Timmis KN (1990) Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in Gram-negative eubacteria. J Bacteriol 172: 6568-7572.
Deshpande V, Hinge J & Rao M.D. (1990). Chemical modification of xylanases: evidence for essential tryptophan and cysteine residues at the active site. Biochim Biophys Acta 1041:172–177
Duport C, Baysse C & Michel-Briand Y. (1995) Molecular characterization of pyocin S3, a novel S-type pyocin from Pseudomonas aeruginosa. J. Biol. Chem. 270:8920–8927.
Eagon, RG. (1995) Paper, pulp and food grade paper. In Handbook of Biocide and Preservative Use ed. Rossmoore, H.W. pp. 83–132. London: Blackie Academic & Professional.
Elvers KT, Leeming K & Lappin-Scott HM. (2002) Binary and mixed population biofilms: time-lapse image analysis and disinfection with biocides. J Ind Microbiol Biotech 29:331–338..
Evans K, Passador L, Srikumar R, Tsang E, Nezezon J & Poole K (1998) Influence of theMexAB-OprM multidrug efflux system on quorum sensing in Pseudomonas aeruginosa. J Bacteriol 180: 5443–5447.
Farjalla VF, Esteves FA, Bozelli RL & Roland F (2002) Nutrient limitation of bacterial production in clear water Amazonian ecosystems. Hydrobiologia 489: 197-205.
Fuller AT & Horton JM. (1950) Marcescin, an antibiotic substance from Serratia marcescens. Micorbiol 4(3):417-433.
Fuqua WC, Winans SC & Greenberg EP. (1994) Quorum sensing in bacteria: the LuxR-LuxI family of cell densityresponsive transcriptional regulators. J. Bacteriol. 176:269–275
Gallardo O, Diaz P & Pastor FIJ. (2007). Cloning and production of Xylanase B from Paenibacillus barcinonensis in Bacillus subtilis hosts. Biocatal Biotransform 25(2–4):157–162
Gilbert P & McBain AJ (2001) Biofilms: their impact on health and their recalcitrance toward biocides. American J Inf Control 29:252–255.
Glazer, JA. (1991) Overview of deposit control. Tappi Journal 74:72–74.
Granéli W, Bertilsson S & Philibert A (2004) Phosphorus limitation of bacterial growth in high Arctic lakes and ponds. Aquat Sci 66: 430-439.
Grimont F & Grimont PAD (1991) The genus Serratia. Prokaryotes, Vol. 3 (Balows A, Tr¨uper HG, Dworkin M, Harder W & Schleifer KH, eds), pp. 2822–2848. Springer, New York.
Grimont P.A & Grimont F. (1978) The genus Serratia. Annu. Rev. Microbiol. 32:221–248.
Guasch JF, Enfedaque J, Ferror S, Gargallo D & Reque M. (1995) Bacteriaocin 28b, a chromosomally encoded bacteriocin produced by most Serratia marcescens biotypes. Res. Microbiol 146:477-48.
Guynn LJ, Dai W & Benedik MJ (1998) Nuclease overexpression mutants of Serratia marcescens. J Bacteriol 180: 2262-2264.
Haki G.D. & Rakshit S.K. (2003). Developments in industrially important thermostable enzymes: a review. Bioresour Technol 89(1):17–34
Hall-Stoodley L, Costerton JW & Stoodley P (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat. Rev. Microbiol. 2: 95-108.
Han SB, Kim HM, Kim YH, Lee CW, Jang ES, Son KH, Kim SU & Kim YK. (1998) T-cell specific immunosuppression by prodigiosin isolated from Serratia marcescens. Int. J. Immunopharmacol. 20:1–13.
Harris AK, Williamson NR, Slater H, Cox A, Abbasi S, Foulds I, Simonsen HT, Leeper FJ & Salmond, GP. (2004). The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and straindependent genome context variation. Microbiology 150:3547–3560.
Heir H, Sundheim G & Holck AL. (1995) Resistance to quaternary ammonium compounds in Staphylococcus spp. isolated from the food industry and nucleotide sequence of the resistance plasmid pST827. J Appl Bacteriol 79:149–156.
Hejazi & Falkiner (1997) Serratia marcescens. J. Med. Microbiol 46: 903-912.
Henke J.M & Bassler B.L. (2004) Bacterial social engagements. Trends Cell Biol. 14:648–656.
Herrero M, de Lorenzo V & Timmis KN. (1990) Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in Gram-negative bacteria. J Bacteriol. 172(11): 6557-67.
Hibbing ME, Fuqua C, Parsek MR & Peterson SB (2010) Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8: 15-25.
Huang CY, Hsieh SP, Kuo PA, Jane WN, Tu J, Wang YN & Ko CH (2009) Impact of disinfectant and nutrient concentration on growth and biofilm formation for a Pseudomonas strain and the mixed cultures from a fine papermachine system. Int Biodeter Biodegr 63: 998-1007.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW & Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119
Imada A., Kitano K., Kintaka K., Muroi M & Asai M. (1981) Sulfazecin and isosulfazecin, novel beta-lactam antibiotics of bacterial origin. Nature 289:590–591.
Jahn A, Griebe T, & Nielsen PH. (1999) Composition of Pseudomonas putida biofilms: accumulation of protein in the biofilm matrix. Biofouling 14:9–57.
Jahn GA, Kalia V, Hole D, Wilson CA & Deis RP (1999) Receptors and neurotransmitters involved in the dual modulation of prolactin release by the serotoninergic system in pregnant and lactating rats. J Reprod Fertil 116: 261-268.
Jansson M, Bergstrom AK, Lymer D, Vrede K & Karlsson J (2006) Bacterioplankton growth and nutrient use efficiencies under variable organic carbon and inorganic phosphorus ratios. Microb Ecol 52: 358-364.
Jefferson KK. (2004) What drives bacteria to produce a biofilm? FEMS Microbiol Lett 236(2): 163-73.
Jin S, Chen YC, Christie GE & Benedik MJ. (1996). Regulation of the Serratia marcescens extracellular nuclease: positive control by a homolog of P2 Ogr encoded by a cryptic prophage. J. Mol. Biol. 256:264–278.
Johnsrud, SC. (1997) Biotechnology for solving slime problems in the pulp and paper industry. In: Scheper, T., Berlin, H. (Eds.), Advances in Biochemical Engineering/Biotechnology, vol. 57. Springer, pp. 312–332.
Khandeparkar R. & Bhosle N.B. (2007) Application of thermoalkalophilic xylanase from Arthrobacter sp. MTCC 5214 in biobleaching of kraft pulp. Bioresour Technol 98:897–903
Khianngam S., Akaracharanya A. & Tanasupawat S. (2009) Paenibacillus thailandensis sp. nov. and Paenibacillus nanensis sp. nov., xylanase-producing bacteria isolated from soil. Int J Syst Evol Microbiol 59 (Pt 3):564–568
Klahre, J. & Flemming, H.-C. (2000) Monitoring of biofouling in papermill process waters. Water Research 34:3657–3665.
Ko CH, Chen WL, Tsai CH, Jane WN, Liu CC., Tu J. (2007) Paenibacillus campinasensis BL11: a wood material-utilizing bacterial strain isolated from black liquor. Bioresour Technol 98:2727–2733
Ko CH, Lin ZP, Tu J, Tsai CH, Liu CC, Chen HT. (2010) Xylanase production by Paenibacillus campinasensis BL11 and its pretreatment of hardwood kraft pulp bleaching. Int Biodeterior Biodegrad 64:13–19
Kohler T, van Delden C, Curty LK, Hamzehpour MM & Pechere JC (2001) Overexpression of the MexEF-OprN multidrug efflux system affects cell-to-cell signaling in Pseudomonas aeruginosa. J Bacteriol 183: 5213–5222.
Kolari M, Nuutinen J & Salkinoja-Salonen MS (2001) Mechanisms of biofilm formation in paper machine by Bacillus species: the role of Deinococcus geothermalis. J Ind Microbiol Biotechnol 27: 343-351.
Kolari M, Nuutinen J, Rainey FA & Salkinoja-Salonen MS (2003) Colored moderately thermophilic bacteria in paper-machine biofilms. J. Ind. Microbiol. Biotechnol. 30: 225-238.
Kolari M, Schmidt U, Kuismanen E & Salkinoja-Salonen MS (2002) Firm but slippery attachment of Deinococcus geothermalis. J. Bacteriol. 184: 2473-2480.
König J, Grasser R, Pikor H & Vogel K. (2002). Determination of xylanase, beta-glucanase, and cellulase activity. Anal Bioanal Chem 374(1):80–87
Kuhad RC & Singh A. (1993) Lignocellulosic biotechnology: current and future prospects. Crit Rev Biotechnol 13:151–172
Kulkarni N, Shendye A & Rao M. (1999) Molecular and biotechnological aspects of xylanases. FEMS Microbiol Rev, 23:411–456
Laemmli U.K. (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685
Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T & Ussery DW. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35(9):3100-8.
Lahtinen T, Kosonen M, Tiirola M, Vuento M & Oker-Blom C. (2006) Diversity of bacteria contaminating paper machines. J Ind Microbiol Biotechnol 33(9): 734-40.
Lai HC, Soo PC, Wei JR, Yi WC, Liaw SJ, Horng YT, Lin SM, Ho SW, Swift S & Williams P. (2005) The RssAB two-component signal transduction system in Serratia marcescens regulates swarming motility and cell envelope architecture in response to exogenous saturated fatty acids. J. Bacteriol. 187:3407–3414.
Laopaiboon L, Hall SJ & Smith RN. (2002) A study of the effect of isothiazolones on the performance and characteristics of a laboratory-scale rotating biological contactor. J Appl Microbiol 93:1051–1058
Laopaiboon L, Smith RN & Hall SJ. (2001) A study of the effect of isothiazolones on the performance and characteristics of a laboratory-scale rotating biological contactor. J Appl Microbiol 91:93–103.
Lee J. (1997) Biological conversion of lignocellulosic biomass to ethanol. J Biotechnol 56:1–24
Lee TH, Lim PO & Lee YE. (2007). Cloning, characterization, and expression of xylanase A gene from Paenibacillus sp. DG-22 in Escherichia coli. J Microbiol Biotechnol 17 (1):29–36
Lloube`s R, Granger-Schnarr M, Lazdunski C & Schnarr M. (1988) LexA repressor induces operator dependent DNA bending. J. Mol. Biol. 204:1049–1054.
Lorenzo Vd, Herrero M, JAKUBZIK U & TIMMIS KN (1990) Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J Bacteriol 172: 6568-7572.
Lowe TM & Eddy SR. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25(5):955-64.
Majeed H, Gillor O, Kerr B & Riley MA (2011) Competitive interactions in Escherichia coli populations: the role of bacteriocins. ISME J 5: 71-81.
Mamo G, Hatti-Kaul R & Mattiasson B. (2006). A thermostable alkaline active endo-β-1,4-xylanase from Bacillus halodurans S7: purification and characterization. Enzyme Microb Technol 39:1492–1498
Maniatis T, Fritsch E & Sambrook J (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
Martin VJ & Mohn WW (1999) An alternative inverse PCR (IPCR) method to amplify DNA sequences flanking Tn5 transposon insertions. J Microbiol Meth 35: 163-166.
Mattila-Sandholm T. & Wirtanen, G. (1992) Biofilm formation in the food industry: a review. Food Rev Int 8:537–603.
McEvoy JL, Murata H & Chatterjee AK. (1992) Genetic evidence for an activator required for induction of pectin lyase in Erwinia carotovora subsp. carotovora by DNA-damaging agents. J. Bacteriol. 174:5471–5474.
Michel-Briand Y & Baysse C (2002) The pyocins of Pseudomonas aeruginosa. Biochimie 84: 499-510.
Monds RD, Silby MW & Mahanty HK (2001) Expression of the Pho regulon negatively regulates biofilm formation by Pseudomonas aureofaciens PA147-2. Mol Microbiol 42: 415-426.
Moraes CS, Seabra SH, Castro DP, Brazil RP, de Souza W, Garcia ES & Azambuja P (2008) Leishmania (Leishmania) chagasi interactions with Serratia marcescens: ultrastructural studies, lysis and carbohydrate effects. Exp Parasitol 118: 561-568.
Morton LHG, Greenway DLA, Gavlarde CC & Surman SB. (1998). Consideration of some implications of the resistance of biofilms to biocides. Int Biodet Biodegrad 41:247–259.
Nakayama K, Takashima K, Ishihara H, Shinomiya T, Kageyama M, Kanaya S, Ohnishi M, Murata T, Mori H & Hayashi T. (2000) The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol. Microbiol 38: 213–231.
Nishimura Y, Kim C & Nagata T (2005) Vertical and seasonal variations of bacterioplankton subgroups with different nucleic acid contents: possible regulation by phosphorus. Appl Environ Microb 71: 5828-5836.
Ohkawa I, Maruo B & Kageyama M. (1975) Preferential inhibition of lipid synthesis by the bacteriocin pyocin S2. J. Biochem. (Tokyo) 78: 213–223.
Olsson L & Hahn-Hagerdal B. (1996) Fermentation of lignocellulosic hydrolysates for ethanol production. Enzyme Microb Technol 18:312–331
Pai CK, Wu ZY, Chen MJ, Zeng YF, Chen JW & Duan CH. (2010) Molecular cloning and characterization of a bifunctional xylanolytic enzyme from Neocallimastix patriciarum. Appl Microbiol Biotechnol 85:1451–1462
Parker M., Needham M &White R. (1982) Prostatic steroid binding protein: gene duplication and steroid binding. Nature 298:92–94.
Pason P, Kosugi A, Waeonukul R, Tachaapaikoon C, Ratanakhanokchai K & Arai T. (2010) Purification and characterization of a multienzyme complex produced by Paenibacillus curdlanolyticus B-6. Appl Microbiol Biotechnol 85(3): 573–580
Pason P, Kyu KL & Ratanakhanokchai K. (2006) Paenibacillus curdlanolyticus strain B-6 xylanolytic-cellulolytic enzyme system that degrades insoluble polysaccharides. Appl Environ Microbiol 72:2483–2490
Polizeli MLTM, Rizzatti ACS, Monti R, Terenzi HF, Jorge JA & Amorim DS. (2005) Xylanases from fungi: properties and industrial applications. Appl Microbiol Biotechnol 67(5):577–591
Poorna CA & Prema P. (2007) Production of cellulase-free endoxylanase from novel alkalophilic thermotolerent Bacillus pumilus by solid-state fermentation and its application in wastepaper recycling. Bioresour Technol 98: 485–490
Ratto M, Suihko ML & Siika-aho M (2005) Polysaccharide-producing bacteria isolated from paper machine slime deposits. J. Ind. Microbiol. Biotechnol. 32: 109-114.
Reese MG (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26: 51-56.
Rice SA, Koh KS, Queck SY, Labbate M, Lam KW & Kjelleberg S (2005) Biofilm formation and sloughing in Serratia marcescens are controlled by quorum sensing and nutrient cues. J Bacteriol 187: 3477-3485.
Riley MA & Wertz JE (2002) Bacteriocins: evolution, ecology, and application. Annu Rev Microbiol 56: 117-137.
Riley MA, Pinou T, Wertz JE, Tan Y & Valletta CM. (2001) Molecular characterization of the klebicin B plasmid of Klebsiella pneumoniae. Plasmid 45:209–221.
Rivas R, Garcia-Fraile P, Mateos PF, Martínez-Molina E & Velázquez E. (2006) Penibacillus cellulosilyticus sp nov., a cellulolytic and xylanolytic bacterium isolated from the bract phyllosphere of Phoenix dactylifera. Int J Syst Evol Microbiol 56:2777–2781
Rivas R, Mateos PF, Martínez-Molina E & Velázquez E. (2005) Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium. Int J Syst Evol Microbiol 55:405–408
Rivas R, Mateos PF, Martínez-Molina E & Velázquez E. (2005) Paenibacillus phyllosphaerae sp. nov., a xylanolytic bacterium isolated from the phyllosphere of Phoenix dactylifera. Int J Syst Evol Microbiol 55:476–743
Russell AD & Chopra I. (1996) Understanding Antibacterial Action and Resistance, second ed. Ellis Horwood, Chichester, England.
Sanchez MM, Fritze D, Blanco A, Sproer C, Tindall BJ & Schumann P. (2005) Paenibacillus barcinonensis sp nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta. Int J Syst Evol Microbiol 55:935–939
Sano Y, Matsui H, Kobayashi M & Kageyama M (1993) Molecular structures and functions of pyocins S1 and S2 in Pseudomonas aeruginosa. J Bacteriol 175: 2907-2916.
Sano Y, Matsui H, Kobayashi M & Kageyampa M. (1990) Pyocins S1 and S2, bacteriocins of Pseudomonas aeruginosa. Pseudomonas–Biotransformation, Pathogenesis and Evolving Biotechnology pp. 352–358. ASM, Washington, DC.
Sá-Pereira P, Mesquita A, Duarte JC, Barros MRA & Costa-Ferreira M. (2002) Rapid production of thermostable cellulase-free xylanase by a strain of Bacillus subtilisand its properties. Enzyme Microb Technol 30:924–933
Sá-Pereira P, Paveia H, Costa-Ferreira M & Aires-Barros M. (2003). A new look at xylanases: an overview of purification strategies. Mol Biotechnol 24(3):257–281
Schalk IJ, Hennard C, Dugave C, Poole K, Abdallah MA & Pattus F. (2001) Iron-free pyoverdin binds to its outer membrane receptor FpvA in Pseudomonas aeruginosa: a new mechanism for membrane iron transport. Mol. Microbiol. 39: 351–360.
Shank EA & Kolter R (2009) New developments in microbial interspecies signaling. Curr Opin Microbiol 12: 205-214.
Simoes LC, Simoes M & Vieira MJ (2008) Intergeneric coaggregation among drinking water bacteria: evidence of a role for Acinetobacter calcoaceticus as a bridging bacterium. Appl Environ Microb 74: 1259-1263.
Singh R, Paul D & Jain RK. (2006) Biofilms: implications in bioremediation. Trends in Microbiol 14(9):389-97.
Sjöström E. (1993) Wood chemistry: fundamentals and applications. pp 293, (2nd ed.) Academic Press, New York, NY, USA
Slater H., Crow M., Everson L & Salmond G.P. (2003) Phosphate availability regulates biosynthesis of two antibiotics, prodigiosin and carbapenem, in Serratia via both quorum-sensing-dependent and -independent pathways. Mol. Microbiol. 47:303–320.
Spormann AM (2008) Physiology of microbes in biofilms. Curr. Top. Microbiol. Immunol. 322: 17-36.
Srivastava R, Gopinathan KP & Ramakrishnan T. (1981) Deoxyribonucleic acid methylation in mycobacteria. J Bacteriol 148 (2):716–719
Stewart PS, Camper AK, Handran SD, Huang C & Warnecke M (1997) Spatial Distribution and Coexistence of Klebsiella pneumoniae and Pseudomonas aeruginosa in Biofilms. Microb Ecol 33: 2-10.
Subramaniyan S. & Prema P. (2002) Biotechnology of microbial xylanases: enzymology, molecular biology and application. Crit Rev Biotechnol 22:33–64
Sultan SZ, Silva AJ & Benitez JA (2010) The PhoB regulatory system modulates biofilm formation and stress response in El Tor biotype Vibrio cholerae. FEMS Microbiol Lett 302: 22-31.
Sykes RB, Cimarusti CM, Bonner DP, Bush K, Floyd DM, Georgopapadakou NH, Koster WM, Liu WC, Parker WL, Principe PA, Rathnum ML, Slusarchyk WA, Trejo WH & Wells JS. (1981) Monocyclic betalactam antibiotics produced by bacteria. Nature 291:489–491.
Techapun C, Poosaran N, Watanabe M & Sasaki K. (2003). Thermostable and alkaline-tolerant microbial cellulase-free xylanases produced from agricultural wastes and the properties required for use in pulp bleaching bioprocesses: a review. Process Biochem 38:1327–1340
Teleman A, Tenkanen M, Jacobs A & Dahlman O. (2002) Characterization of O-acetyl-(4-O-methylglucurono) xylan isolated from birch and beech. Carbohyd Res 337:373–377
Thomson NR, Crow MA, McGowan SJ, Cox A & Salmond GP (2000) Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing control. Mol Microbiol 36: 539–556.
Vadstein O, Olsen LM, Busch A, Andersen T & Reinertsen HR (2003) Is phosphorus limitation of planktonic heterotrophic bacteria and accumulation of degradable DOC a normal phenomenon in phosphorus-limited systems? A microcosm study. FEMS Microbiol Ecol 46: 307-316.
Vaisanen OM, Weber A, Bennasar A, Rainey FA, Busse HJ & Salkinoja-Salonen MS (1998) Microbial communities of printing paper machines. J Appl Microbiol 84: 1069-1084.
Van Houdt R, Givskov M & Michiels CW (2007) Quorum sensing in Serratia. FEMS Microbiol Rev 31: 407-424.
Von Frankenberg M, Golling M, Mehrabi A, et al. (1999) Destruction of Kupffer's cells increases total liver blood flow and decreases ischemia reperfusion injury in pigs. Transplant Proc 31: 3253-3254.
Weaver C, Redborg A.H & Konisky J. (1981) Plasmid-determined immunity of Escherichia coli K-12 to colicin Ia is mediated by a plasmidencoded membrane protein. J. Bacteriol. 148:817–828.
Wei JR & Lai HC (2006) N-acylhomoserine lactone-dependent cell-to-cell communication and social behavior in the genus Serratia. Int J Med Microbiol 296: 117-124.
Weisburg WG, Barns SM, Pelletier DA & Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697-703.
Whea RP, Zuckerman A & Rant LA. (1951) Infection due to chromobacteria: report of eleven cases. Arch. Intern. Med. 88:461–466.
Winson MK, Swift S, Hill PJ, et al. (1998) Engineering the luxCDABE genes from Photorhabdus luminescens to provide a bioluminescent reporter for constitutive and promoter probe plasmids and mini-Tn5 constructs. FEMS Microbiol Lett 163: 193-202.
Winzer K, Hardie KR & Williams P. (2003) LuxS and autoinducer-2: their contribution to quorum sensing and metabolism in bacteria. Adv. Appl. Microbiol. 53:91–396.
Withers H, Swift S & Williams P. (2001) Quorum sensing as an integral component of gene regulatory networks in Gram-negative bacteria. Curr. Opin. Microbiol. 4:186–193.
Wolf PA & Sterner P.W. (1972) 2,2-dibromo-3-nitrilopropionamide, a compound with slimicidal activity. Appl Microbiol 24:581–584.
Wolfaardt GM, Lawrence JR, Robarts RD, Caldwell SJ & Caldwell DE (1994) Multicellular organization in a degradative biofilm community. Appl Environ Microb 60: 434-446.
Wood PJ, Erfle JD & Teather RM. (1988). Use of complex formation between Congo red and polysaccharide in detection and assay of polysaccharide hydrolases. Methods Enzymol 160:59–74
Wu YT, Zhu H, Willcox M & Stapleton F (2010) Removal of Biofilm from Contact Lens Storage Cases. Invest Ophth Vis Sci 51: 6329-6333.
Xavier KB & Bassler BL. (2003) LuxS quorum sensing: more than just a numbers game. Curr Opin Microbiol 6:191–197.
Xu T, Rammner B, Margittai M, Artalejo AR, Neher E & Jahn R (1999) Inhibition of SNARE complex assembly differentially affects kinetic components of exocytosis. Cell 99: 713-722.
Yang CY, Niu Y, Su HJ, Wang Z, Tao F & Wang X. (2010) A novel microbial habitat of alkaline black liquor with very high pollution load: microbial diversity and the key members in application potentials. Bioresour Technol 101:1737–1744
Zerbino DR & Birney E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829