Al-Ajlani M.M., Sheikh M.A., Ahmad Z., Hasnain S. 2007. Production of surfactin from Bacillus subtilis MZ-7 grown on pharmamedia commercial medium. Microbial Cell Factories, 6: 17, doi:10.1186/1475-2859-6-17: 17 str.
Ansaldi M., Marolt D., Stebe T., Mandić-Mulec I., Dubnau D. 2002. Specific activation of the Bacillus quorum-sensing systems by isoprenylated pheromone variants. Molecular Microbiology, 44, 6: 1561-1573
Bacon Schneider K., Palmer T.M., Grossman A.D. 2002. Characterization of comQ and comX, two genes required for production of ComX pheromone in Bacillus subtilis.
Journal of Bacteriology, 184, 2: 410-419
Benigar E. 2011. Vpliv ekotipov in ferotipov na sobivanje izolatov Bacillus subtilis.
Diplomsko delo. Ljubljana, Biotehniška fakulteta, Oddelek za živilstvo: 45 str.
Bent S.J., Gucker S.L., Oda Y., Forney L.J. 2003. Spatial distribution of Rhodopseudomonas palustris ecotypes on a local scale. Applied and Environmental Microbiology, 69, 9: 5192-5197
Brusetti L., Malkhazova I., Gtari M., Tamagnini I., Borin S., Merabishvili M., Chanishvili N., Mora D., Cappitelli F., Daffonchio D. 2008. Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography. BMC Microbiology, 8: 220, doi:10.1186/1471-2180-8-220: 13 str.
Budding A.E., Ingham C.J., Bitter W., Vandenbroucke-Grauls C.M., Schneeberger P.M.
2009. The Dienes phenomenon: competition and territoriality in swarming Proteus mirabilis. Journal of Bacteriology, 191, 12: 3892-3900
Carson C.A., Shear B.L., Ellersieck M.R., Schnell J.D. 2003. Comparison of ribotyping and repetative extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals. Applied and Environmental Microbiology, 69, 3: 1836-1839
Cherif A., Borin S., Rizzi A., Ouzari H., Boudabous A., Daffonchio D. 2002.
Characterization of a repetitive element polymorphism-polymerase chain reaction chromosomal marker that discriminates Bacillus anthracis from related species.
Journal of Applied Microbiology, 93, 3: 456-462
Chun J., Kyung S.B. 2000. Phylogenetic analysis of Bacillus subtilis and related taxa based on partial gyrA gene sequences. Antonie van Leeuwenhoek, 78, 2: 123-127
Cohan F.M., Roberts M.S., King E.C. 1991. The potential for genetic exchange by transformation within a natural population of Bacillus subtilis. Evolution, 45, 6: 1383–
1421
Cohan M.F., Koeppel A.F., Krizanc D. 2006. Sequence-based discovery of ecological diversity within Legionella. V: Legionella state of the art 30 years after its recognition.
Cianciotto N.P., Abu Kwaik Y., Edelstein P.H., Fields B.S., Geary D.F., Harrison T.G., Joseph C.A., Ratcliff R., Stout J., Swanson M.S. (eds.). Washington, ASM Press: 367-376.
Cohan M.F., Perry E.B. 2007. A systematics for discovering the fundamental units of bacterial diversity. Current Biology, 17, 10: 373-386
Connelly M.B., Young G.M., Sloma A. 2004. Extracellular proteolytic activity plays a central role in swarming motility in Bacillus subtilis. Journal of Bacteriology, 186, 13:
4159-4167
Connor N., Sikorski J., Rooney A.P., Kopac S., Koeppel A.F., Burger A., Cole S.G., Perry E.B., Krizanc D., Feld N C., Slaton M., Cohan F.M. 2010. Ecology of speciation in the genus Bacillus. Applied and Environmental Microbiology, 76, 5: 1349-1358
Cosmina P., Rodriguez F., de Ferra F.,Grandi G., Perego M., Venema G., van Sinderen D.
1993. Sequence and analysis of the genetic locus responsible for surfactin synthesis in Bacillus subtilis. Molecular Microbiology, 8, 5: 821-831
Cvitkovitch D.G., Li Y., Ellen R.P. 2003 Quorum sensing and biofilm formation in streptococcal infections. Journal of Clinical Investigation, 112, 11: 1626-1632
Dahloff I., Baillie H., Kjelleberg S. 2000. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Applied and Environmental Microbiology, 66, 8: 3376-3380
Deleu M., Paquot M., Nylander T. 2008. Effect of fengycin, a lipopeptide produced by Bacillus subtilis, on model biomembranes. Biophysical Journal, 94, 7: 2667-2679
Dienes L. 1946. Reproductive processes in Proteus cultures. Proceedings of the Society for Experimental Biology and Medicine, 63: 265-270 operon that regulates the establishment of genetic competence in Bacillus subtilis.
Proceedings of the National Academy of Sciences of the United States of America, 91, 20: 9397-9401
Dubnau D. 1991. Genetic competence in Bacillus subtilis. Microbiology and Molecular Biology Reviews, 55, 3: 395-424
Earl A.M., Losick R., Kolter R. 2008. Ecology and genomics of Bacillus subtilis. Trends in Microbiology, 16, 6: 269-275
Fajardo-Cavazos P., Nicholson W. 2006. Bacillus endospores isolated from granite; close molecular ralationship to globally distributed Bacillus spp. from endolithic and extreme environments. Applied and Environmental Microbiology, 72, 4: 2856-2863
Ferris M.J., Kuhl M., Wieland A., Ward D.M. 2003. Cyanobacterial ecotypes in different optical microenvironments of a 68 degrees C hot spring mat community revealed by
16S-23S rRNA internal transcribed spacer region variation. Applied and Environmental Microbiology, 69: 2893-2898
Freitas D.B., Reis M.P., Lima-Bittencourt C.I., Costa P.S., Assis P.S., Chartone-Souza E., Nascimento A. MA. 2008. Genotypic and phenotypic diversity of Bacillus spp. Isolated from steel plant waste. BMC Research Notes, 1: 92, doi: 10.1186/1756-0500-1-92: 11 str.
Fuqua W.C., Winans S.C., Greenberg E.P. 1996. Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators.
Annual Review in Microbiology, 50: 727-751
Gevers D., Cohan D.M., Lawrence J.G., Spratt B.G., Coenye T., Feil E.J., Stackenbrandt E., Van de Peer Y., Vandamme P., Thompson F.L., Swings J. 2005. Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology, 3, 9: 733-739
Gibbs K.A., Urbanowski M.L., Greenberg E.P. 2008. Genetic determinants of self identity and social recognition in bacteria. Science, 321, 5886: 256-259
Gibbs K.A., Wenren L.M., Greenberg E.P. 2011. Identity gene expression in Proteus mirabilis. Journal of Bacteriology, 193, 13: 3286-3292
Gonzalez-Pastor J.E., Hobbs E.C., Losick R. 2003. Cannibalism by sporulating bacteria.
Science, 301: 510-513
Hamoen L.W., Venema G., Kuipers O. P. 2003. Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology, 194: 9-17
Johnson J. 1973. Use of nucleic-acid homologies in the taxonomy of anaerobic bacteria.
International Journal of Systematic Bacteriology, 23, 4: 308- 315
Julkowska D., Obuchowski M., Holland I.B., Séror S.J. 2004. Branched swarming patterns on a synthetic medium formed by wild-type Bacillus subtilis strain 3610: detection of different cellular morphologies and constellations of cells as the complex architecture develops. Microbiology, 150, 6: 1839-1894
Julkowska D., Obuchowski M., Holland I.B., Séror S.J. 2005. Comparative analysis of the development of swarming communities of Bacillus subtilis 168 and a natural wild type:
critical effects of surfactin and the composition of the medium. Journal of Bacteriology, 187, 1: 65-76
Kearns D.B., Losick R. 2003. Swarming motility in undomesticated Bacillus subtilis.
Molecular Microbiology, 49, 3: 581-590
Kearns D.B., Losick R. 2005. Cell population heterogeneity during growth of Bacillus subtilis. Genes Development, 24, 19 : 3083-3094
Kearns D.B. 2010. A field guide to bacterial swarming motility. Nature Reviews Microbiology, 8, 9: 634-644
Kim W., Hong Y., Yoo J., Lee W., Choi C., Chung S. 2001. Genetic relationship of Bacillus anthracis and closely related species based on variable-number repeat analysis and BOX-PCR genomic fingerprinring. FEMS Microbiology Letters, 207, 1: 21-27 Koeppel A.F., Perry E.B., Sikorski J., Krizanc D., Warner A., Ward D.M., Rooney A.P.,
Brambilla E., Connor N., Ratcliff R.M., Nevo E., Cohan F.M. 2008. Identifying the fundamental units of bacterial diversity: a paradigm to incorporate ecology into bacterial systematics. Proceedings of the National Academy of Sciences of the United States of America, 105, 7: 2504-2509
Lazzazera B.A. 2000. Quorum sensing and starvation: signals for entry into stationary phase. Current Opinion in Microbiology, 3, 2: 177-182
Lemon K.P., Earl A.M., Vlamakis H.C., Aguilar C., Kolter R. 2008. Biofilm development with an emphasis on Bacillus subtilis. Current Toppics in Microbiology and Immunology, 332: 1-16
Lopez D., Vlamakis H.C, Kolter R. 2009. Generation of mulitple cell types in Bacillus subtilis. FEMS Microbiology Reviews, 33, 1: 152-163
Magnuson R., Solomon J., Grossman A.D. 1994. Biochemical and genetical characterization of a competence pheromone from Bacillus subtilis. Cell, 77, 2: 207-216
Maamar H., Dubnau D. 2005. Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Molecular Microbiology, 56, 3: 615-624 Martin B., Humbert O., Camara M., Guenzi E., Walker J., Mitchell T., Andrew P.,
Prudhomme M., Alloing G., Haekenbeck R. Morrison D.A., Boulnois G.J., Claverys J.
1992. A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Research, 20, 13: 3479-3483
Miller M.B., Bassler B.L. 2001. Quorum sensing in bacteria.. Annual Review of Microbiology, 55, 1: 165-199
Mirouze N., Desai Y., Dubnau D. 2012. Spo0A∼P imposes a temporal gate for the bimodal expression of competence in Bacillus subtilis. PLoS Genetics, 8, 3: e1002586, doi: 10.1371/journal.pgen.1002586: 18 str.
Morán A.C., Martínez M.A., Siñeriz F. 2002. Quantification of surfactin in culture supernatants by hemolytic activity. Biotechnology Letters, 24, 3: 177-180
Munson E., Pfaller M.A., Doern G.V. 2002 Modification of Dienes inhibition test for epidemiological characterization of Pseudomonas aeruginosa isolates. Journal of Clinical Microbiology, 40, 11: 4285-4288
Nakamura L.K., Roberts M.S., Cohan F.M. 1999. Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. International Journal of Systematic Bacteriology, 49: 1211-1215
Nakano M.M., Corbell N., Besson J., Zuber P. 1992. Isolation and characterization of sfp:
a gene that functions in the production of the lipopeptide biosurfactant, surfactin, in Bacillus subtilis. Molecular and General Genetics, 232, 2: 313-321
Nakano M.M., Magnuson R., Myers A., Curry J., Grossman A., Zuber P. 1991. srfA is an operon required for surfactin production, competence development, and efficient sporulation in Bacillus subtilis. Journal of Bacteriology, 173, 5: 1770-1778
Ongena M., Jacques P. 2007. Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends in Microbiology, 16, 3: 115-125
Oslizlo A., Štefanič P., Dogša I., Mandić-Mulec I. 2014. Private link between signal and response in Bacillus subtilis quorum sensing. Proceedings of the National Academy of Sciences of the United States of America, 111, 4: 1586-1591
Pfaller M.A., Mujeeb I., Hollis R.J., Jones R.N., Doern G.V. 2000. Evaluation of the discriminatory powers of the Dienes test and ribotyping as typing methods for Proteus mirabilis. Journal of Clinical Microbiology, 38, 3: 1077-1080
Piazza F., Tortosa P., Dubnau D. 1999. Mutational analysis and membrane topology of ComP, a quorum-sensing histidine kinase of Bacillus subtilis controlling competence development. Journal of Bacteriology, 181, 15: 4540-4548
Piggot P.J., Hillbert D.W. 2004. Sporulation of Bacillus subtilis. Current Opinion in Microbiology, 7, 6: 579-586
Roberts M.S., Cohan F.M. 1995. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution, 49, 6: 1081-1094
Senior B.W. 1977. The Dienes phenomenon: Identification of the determinants of compatibility. Journal of General Microbiology, 102, 2: 235-244
Seydlová G., Svobodová J. 2008. Review of surfactin chemical properties and the potential biomedical applications. Central European Journal of Medicine, 3, 2: 123-133
Solomon J.M., Grossman A. D. 1996. Who´s competent and when: regulation of natural genetic competence in bacteria. Trends in Genetics, 12, 4: 150-155
Solomon J.M., Lazzazera B.A., Grossman A.D. 1996. Purification and characterization of an extracellular peptide factor that affects two different developmental pathways in Bacillus subtilis. Genes Development, 10, 16: 2014–2024
Sonensheim A.L., Hoch J.A., Losick R. 2002. Bacillus subtilis and its closest relatives:
from genes to cells. Washington, ASM Press: 629 str.
Stackenbrandt E., Ebers J. 2006. Taxonomic parameters revisited: tarnished gold standards. Microbiology Today, 33, 4: 152-155
Stein T. 2005. Bacillus subtilis antibiotics: structures, syntheses and specific functions.
Molecular Microbiology, 56, 4: 845-857
Štefanič P. 2009. Polimorfizem in specifičnost sistema za zaznavanje kvoruma bakterije Bacillus subtilis v talnem mikrohabitatu. Doktorska disertacija. Ljubljana, Univerza v Ljubljani, Biotehniška fakulteta: 190 str.
Štefanič P., Decorosi F., Viti C., Petito J., Cohan F.M., Mandić-Mulec I. 2012. The quorum sensing diversity within and between ecotypes of Bacillus subtilis.
Environmental Microbiology, 14; 6: 1378-1389
Štefanič P., Mandić-Mulec I. 2009. Social interactions and distribution of Bacillus subtilis pherotypes at microscale. Journal of Bacteriology, 191, 6: 1756-1764
Tacão M., Alves A., Saavedra M.J., Correia A. 2005. BOX-PCR is an adequate tool for typing Aeromonas spp. Antonie van Leeuwenhoek, 88, 2: 173-179
Tam N.M.K., Uyen N.K., Hong H.A., Duc L.H., Hoa T.T., Serra C.R., Henriques A.O., Cutting S.M. 2006. The intestinal life cycle of Bacillus subtilis and close relatives.
Journal of Bacteriology, 188, 7: 2692-2700
Tortosa P., Logsdon L., Kraigher B., Itoh Y., Mandić-Mulec I., Dubnau D. 2001.
Specificity and genetic polymorphism of the Bacillus competence quorum-sensing system. Journal of Bacteriology, 183, 2: 451-460
Tran L.S.P., Nagai T., Itoh Y. 2000. Divergent structure of the ComQXPA quorum sensing components: molecular basis of strain-specific communication mechanism in Bacillus subtilis. Molecular Microbiology, 37, 5: 1159-1171
Versalovic J., De Bruijn F.J., Lupski R.J. 1998. Repetitive sequence-based PCR (rep-PCR) DNA fingerprinting of bacterial genomes. V: Bacterial genomes. de Brujin F.J., Lupski J.R., Weinstock G. M. (eds.). New York, Kluwer Academic Publishers: 437-452
Versalovic J., Schneider M., de Bruijn F.J., Lupski R.J. 1994. Genomic fingerprinting of bacteria using repetitive sequence based polymerase chain reaction. Methods in Molecular and Cellular Biology, 5: 25-40
Vlamakis H., Aguilar C., Losick R., Kolter R. 2008. Control of cell fate by the formation of an architecturally complex bacterial community. Genes Development, 22, 7: 945-953
Wenren L.M., Sullivan N.L., Cardarelli L., Septer A.N., Gibbs K.A. 2013. Two independent pathways for self-recognition in Proteus mirabilis are linked by type VI-dependent export. mBio, 4, 4: e00374-13, doi: 10.1128/mBio.00374-13: 10 str.
ZAHVALA
Mentorici prof. dr. Ines Mandić-Mulec in somentorici prof. dr. Nives Ogrinc za mentorstvo in somentorstvo magistrskega dela ter prijaznost in spodbudo tekom celotnega procesa izdelave naloge.
Doc. dr. Blagajani Herzog-Velikonja za kritičen pregled dela in predsedniku komisije doc.
dr. Mateju Butali za hiter odziv.
Lini Burkan Makivić za hiter odziv in strokovni pregled oblikovne ustreznosti magistrskega dela.
Barbari Kraigher za usmerjanje pri laboratorijskem delu, nasvete, spodbudo, motivacijo, družbo pri kosilih…in prijateljstvo.
Polonci Štefanič in vsem ostalim zaposlenim ter diplomantom na Katedri za mikrobiologijo: za pomoč, koristne nasvete in krajšanje časa med avtoklaviranji, PCR-ji, inkubacijami, meritvami…Hvala vsem, ker ste mi lepšali dneve na Katedri.
Mamici, očiju, sestri Anji in mami Faniki: ker ste me vseskozi podpirali, verjeli vame, se smejali z mano ob lepih in me bodrili v »kriznih« trenutkih.
Aleksandru za potrpežljivost in pomoč pri urejanju kazala.
Prijateljicam Tjaši, Kamili in Ani, ker ste...Prijateljice.
Ostalim prijateljem in sošolcem, ker ste poskrbeli, da mi bodo študijska leta ostala v prečudovitem spominu.
PRILOGE
Priloga A: Rastna krivulja sevov PS-218, PS-52 in PS-216. Na podlagi rastnih krivulj smo določili točki T2 in T4 (2 oziroma 4 ure po vstopu izolatov v stacionarno fazo rasti). Vsi trije sevi so v stacionarno fazo rasti vstopili po 10 urah (točke, označene s črno puščico).
Sevi spadajo v različne ferotipe in ekotipe.
Priloga B: Normalizacija optične gostote. Na grafih so prikazane enačbe pripadajočih krivulj in vrednosti R2. Za izračun dejanske vrednosti OD650 (y) smo izmerjeno vrednost OD650 prekonočne kulture posameznega seva kot neznanko x vstavili v dobljene enačbe.
Tako smo dobili 11 vrednosti y za posamezen sev, ki smo jih povprečili in končno (povprečeno) vrednost uporabili pri izračunu relativne hemolitične aktivnosti izrabljenih gojišč B. Na horizontalni osi so prikazane vrednosti izmerjene vrednosti, na vertikalni pa preračunane (dejanske) vrednosti.
:
Priloga C: Matrika s prikazanimi odstotki identičnosti v razporeditvi ponavljajočih zaporedij med elementi BOX. Poleg nabrežnih (PS) in puščavskega (RO-FF-1) izolata iz podvrste B. subtilis subsp. subtilis smo v analizo vključili še puščavski izolat DV3-E-3 iz podvrste B.
subtilis subsp. inaquosorum ter nabrežni izolat PS-122 iz vrste B. amyloliquefacuens.
Priloga D: Primerjava relativne hemolitične aktivnosti izrabljenih gojišč B, odvzetih 2 (T2) oziroma 4 (T4) ure po prehodu v stacionarno fazo rasti. Z izjemo sevov 15 in PS-52 (označeno z zvezdico nad stolpcem) med izbranima časovnima točkama ni 217 0,1025 0,1366 0,0002 0,0012 0,0013 0,0271 0,0003 0,1366
24 0,0176 0,0111 0,0066 0,4446 0,0666 0,9626 0,0082 0,0016 0,0085 15 0,0040 0,7893 0,1940 0,0007 0,0274 0,0169 0,2500 0,0000 0,0002 0,0045 68 0,0598 0,0009 0,0002 0,0014 0,0018 0,0583 0,0003 0,0138 0,2181 0,0177 0,0002 51 0,0229 0,0360 0,0378 0,6606 0,1745 0,9684 0,0401 0,0111 0,0323 0,9977 0,0232 0,0682 216 0,2107 0,0082 0,0083 0,0357 0,0184 0,0785 0,0086 0,7782 0,7386 0,0591 0,0064 0,3901 0,0813 ROFF10,0010 0,0012 0,0001 0,0000 0,0002 0,0007 0,0002 0,0000 0,0000 0,0001 0,0003 0,0000 0,0010 0,0010
∆216 0,0008 0,0008 0,0001 0,0000 0,0002 0,0006 0,0002 0,0000 0,0000 0,0001 0,0003 0,0000 0,0008 0,0008 0,0940
Priloga E: T-statistika, s katero smo preverjali signifikantnost razlik v hemolitični aktivnosti med posameznimi izolati. Vrednosti, nižje od 0,05 pomenijo, da so razlike v relativni hemolitični aktivnosti med izbranima izolatoma signifikantne, vrednosti nad 0,05 pa pomenijo, da med izolatoma ni signifikantnih razlik v relativni hemolitični aktivnosti (obarvani kvadratki).