2012

Identification of alkaliphilic Bacillus species isolated from lake Van and its surrounings by computerized analysis of extracellular protein profiles

Bu çalışmada, 5 referans Bacillus türü ve Van Gölü suyu ve çevresindeki topraklardan izole edilen toplam 17 yerel alkalofilik Bacillus izolatı fenotipik özellikleri ve sodyum dodesil sülfat poliakrilamidjel elektroforez kullanılarak elde edilen ekstraselülar protein profillerine göre identifiye edilmiştir. Fenotipik özelliklerine göre, yerel izolatların tümünün Gram pozitif, aerobik, endospor oluşturan, hareketli ve fakültatif alkalofilik Bacillus cinsine ait türler olduğu belirlenmiştir. Ayrıca, yerel alkalofilik izolatların fenotipik olarak diğer referans Bacillus türlerinden farklı olduğu bulunmuştur. Ekstraselülar protein profil sonuçları esas alınarak yapılan nümerik analiz; yerel izoiatlar ve B. megaterium'u içeren benzerlik seviyesi % 69 ve % 100 arasında değişen dört grup ve benzerlik seviyesi % 70'in üzerinde diğer referans Bacillus türlerini içeren bir grup olmak üzere beş ayrı grup ortaya koymuştur. Bu araştırma, SDS-PAGE yöntemiyle elde edilen ekstraselülar protein profillerinin yerel alkalofilik Bacillus izolatları ve diğer Bacillus türlerinin taksonomik ilişkilerinin incelenmesinde etkili bir yaklaşım sağladığını göstermiştir.

Van Gölü ve çevresinden izole edilen alkolofilik Bacillus türlerinin ekstraselülar protein profillerinin bilgisayar analiziyle identifikasyonu

Five reference Bacillus species and 17 native alkaliphilic Bacillus strains, isolated from the water of Lake Van and the soil surrounding it, were identified using phenotypic characteristics and extracellular protein profiles by the method of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). According to the phenotypic characteristics, all the native isolates were Gram-positive, aerobic, endospore-forming, motile, facultatively alkaliphilic Bacillus spp. It was also found that the native alkaliphilic Bacillus isolates were distinguished phenotypically from other Bacillus species. A numerical analysis based on the resulting extracellular protein profiles revealed 5 distinct clusters: native isolates and B. megaterium formed 4 clusters that varied between 69% and 100% similarity, and the other reference Bacillus species formed a cluster with a similarity of above 70%. The research showed that extracellular protein profiles obtained by SDS-PAGE provide an effective approach to the investigation of taxonomic relationships within native alkaliphilic Bacillus isolates and other Bacillus species.

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1. Kempe S, Kazmlerczak J, Landmann G et al. Largest known Microbialites discovered in Lake Van, Turkey. Macmillan Magazines 349: 605-608, 1991.
2. Granth WD, Jones BE, Mwatha WE. Alkaliphiles: ecology, diversity and applications. FEMS Microbiol Rev 75: 255-270, 1999.
3. Krulwich TA, Guffanti AA. Alkalophilic Bacteria. Ann Rev Microbiol 43: 435-463, 1989.
4. Saeki K, Hitomi J, Okuda M et al. A novel species of alkaliphilic Bacillus that produces an oxydatively stable alkaline serine protease. Extremophiles 6: 65-72, 2002.
5. Spanka R, Fritre D. Bacillus cohnii sp. nov., a new, obligately alkaliphilic, oval-spore-forming Bacillus species with ornithine and aspartic acid instead of diaminopimalic acid in the cell wall. Int Journal Syst Bacteriol 43: 150-156, 1993.
6. Agnew MD, Kowal SF, Jarell KF. Isolation and characterization of novel alkaliphiles from bauxite-processing waste and description of Bacillus vedderi sp. nov., a new obligate alkaliphile. Syst Appl Microbiol 18: 221-230, 1995.
7. Nielsen P, Fritre D, Priets FG. Phenetic diversity of alkaliphilic Bacillus strains. Proposal for nine new species. Microbiology 141: 1745-61,1995.
8. . Fritre D. Bacillus haloalkaliphilus sp. nov. International Journal Systematic Bacteriology 46: 98-101, 1996.
9. Yumoto I, Yamazaki K, Hishinuma M et al. Identification of facultatively alkaliphilic Bacillus sp. strain YN-2000 and its fatty acid composition and cell-surface aspects depending on culture pH. Extremophiles 4: 285-290, 2000.
10. Ash E, Farrow JAE, Wallbanks S et al. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small- subunit-ribosomal RNA sequences. Letters in Applied Microbiolgy 13:2002-06, 1991.
11. Muntayan MS, Tourava TP, Lysenko et al. Molecular identification of alkaliphilic and halotolerant strain Bacillus sp. FTU as Bacillus pseudofirmus. Extremophiles 6: 195-199, 2002.
12. Goodfellow M, O'Donnell A. Handbook of New Bacterial Systematics. Academic Press Limited, London; 1993.
13. Vauterin L, Vantomme R, Pot B et al. Taxonomic analysis of Xhantomonas campestris pv. begonidae and X. campestris pv. pelargonii by means of phythopathological, phenotypic, protein electrophoretic and DNA hybridization methods. Systematic and Applied Bacteriol 13: 166-167, 1990.
14. Nıemi RM, Niemela Sİ, Bamford DH et al. Presumptive fecal Streptococci in environmental samples characterized by one- dimensional sodium dodecyl sulfate-polyacrilamide gel electrophoresis. App Env Microbiol 59: 2190-96, 1993.
15. Berber I, Cokmus C, Atalan E. Characterization of Staphylococcus species by SDS-PAGE of Whole-Cell and Extracellular Proteins. Microbiology 72: 42-47, 2003.
16. Kersters K. Numerical methods in the classification of bacteria by protein electrophoresis. In: Goodfellow M, Jones D, Priest FG et al. Computer Assisted Bacterial Systematic. Academic Press; 1985: pp. 337-368.
17. Costas M, Holmes B, Frith KA et al. Identification and typing of Proteus penneri and Proteus vulgaris biogroups 2 and 3, from clinical sources, by computerized analysis of electrophoretic protein patterns. J Applied Bacteriology 75: 489-498, 1993.
18. Horikoshi K, Akiba T. Alkalophilic Microorganisms. Japan Scientific Societies Press, Tokyo, Japan, 1982.
19. Gordon RE. One hundered and seven years of the genus Bacillus. In: Berkeley RC, Goodfellow M. ed. The aerobic endosporeforming bacteria. Academic Press, London; 1981:pp.322-344.
20. Fritze D, Flossdorf J, Clause D. Taxonomy of alkaliphilic strains. International Journal Systematic Bacteriology 40: 92-97, 1990.
21. Slepecky RA, Hemphill HE. The Genus Bacillus Nonmedical. In: Balows A, Trüper HG, Drowkin, et al. ed. The Prokaryotes. Springer-Verlag, London; 1992: pp.1662-1695.
22. Wessel D, Flugge Ul. A method for the quantitative recovery of protein in dilute solution presence of detergents and lipids. Anal Biochem 138: 141-143, 1984.
23. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (London) 227: 680-85, 1970.
24. Claus D, Berkeley CW. The Genus Bacillus. In: Sneath PHA ed. Bergey's Manual of Systematic Bacteriology. Williams and Wilkins, Baltimore; 1986: pp.1105-1139.
25. Takami H, Han C, Takaki et al. Identification and distribution of new insertion sequences in the genome of alkaliphilic Bacillus halodurans C-125. Journal of Bacteriology 183: 4345-56, 2001.
26. Woese CR. Bacterial Evolution. Microbiological Reviews 51: 221-271, 1987.
27. Maggs AF, Pennington TH. Temporal study of Staphylococcal species on skin of human subjected in isolation and clonal analysis of Staphylococcus capitis by sodium dodecyl sulphate polyacrylamide gel electrophoresis. J Clin Microbiol 27: 2627-32,1988.
28. Cokmus C, Yousten AA. Characterization of Bacillus sphaericus strains by SDS-PAGE. J lnvertebr Pathol 64: 267-268, 1987. 29. Berber 1, Cokmus C. Characterization of Bacillus sphaericus strains by Native-PAGE. Bull Pure Appl Sci 20: 17-21, 2001.
30. Berber 1. Characterization of Bacillus species by numerical analysis of their SDS-PAGE protein profiles. J Cell Mol Biol 3: 33-37, 2004.