Biodiversity of Bacteria Isolated from Different Soils

Abstract

The aim of this study was to determine the biodiversity of PHB producing bacteria isolated from soils where fruit and vegetable are cultivated (onion, grape, olive, mulberry and plum) in Aydın providence. Morphological, cultural, biochemical, and molecular methods were used for bacteria identification. These isolated bacteria were identified by 16S rRNA sequencing and using BLAST. The following bacteria Bacillus thuringiensis (6), Bacillus cereus (8), Bacillus anthrachis (1), Bacillus circulans (1), Bacillus weihenstephanensis (1), Pseudomonas putida (1), Azotobacter chroococcum (1), Brevibacterium frigoritolerans (1), Burkholderia sp. (1), Staphylococcus epidermidis (1), Streptomyces exfoliatus (1), Variovorax paradoxus (1) were found. The Maximum Likelihood method was used to produce a molecular phylogenetic analysis and a phylogenetic tree was constructed. These bacteria can produce polyhydroxybutyrate (PHB) which is an organic polymer with commercial potential as a biodegradable thermoplastic. PHB can be used instead of petrol derivated non-degradable plastics. For this reason, PHB producing microorganisms are substantial in industry.

Keywords

• PHB
• bacteria
• 16S rRNA
• biodiversity
• soil

Biodiversity of Bacteria Isolated from Different Soils

Abstract

The aim of this study was to determine the biodiversity of PHB producing bacteria isolated from soils where fruit and vegetable are cultivated (onion, grape, olive, mulberry and plum) in Aydın providence. Morphological, cultural, biochemical, and molecular methods were used for bacteria identification. These isolated bacteria were identified by 16S rRNA sequencing and using BLAST. The following bacteria Bacillus thuringiensis (6), Bacillus cereus (8), Bacillus anthrachis (1), Bacillus circulans (1), Bacillus weihenstephanensis (1), Pseudomonas putida (1), Azotobacter chroococcum (1), Brevibacterium frigoritolerans (1), Burkholderia sp. (1), Staphylococcus epidermidis (1), Streptomyces exfoliatus (1), Variovorax paradoxus (1) were found. The Maximum Likelihood method was used to produce a molecular phylogenetic analysis and a phylogenetic tree was constructed. These bacteria can produce polyhydroxybutyrate (PHB) which is an organic polymer with commercial potential as a biodegradable thermoplastic. PHB can be used instead of petrol derivated non-degradable plastics. For this reason, PHB producing microorganisms are substantial in industry.

Keywords

• PHB
• bacteria
• 16S rRNA
• biodiversity
• soil

References

1. [1]. Reddy, C.S., Ghai, R., Rashmi, K., Kalai, V.C., (2003). Polyhydroxyalkanoates: an overview. Bioresource Technol., 87 (2): 137-146.
2. [2]. Lee, S.Y., (1996). Bacterial polyhydroxyalkanoates. Biotechnol. Bioeng. 49: 1-14.
3. [3]. Verlinden, R.A.J., Hill, D.J., Kenward, M.A., Williams, C.D., Radecka, I., (2007). Bacterial synthesis of Biodegradable polyhydroxyalkanoates. J. Appl. Microbiol., 2:1437-1449.
4. [4]. Jacquel, N., Lo, C.W., Wu, H.S., Wei, Y.H., Wang, S.S., (2007). Solubility of polyhydroxyalkanoates by experiment and thermodynamic correlations. AlChE J., 53 (10): 2704-2714.
5. [5]. Anderson, A.J., Dawes, E.A., (1990). Occurrence metabolism, metabolic role and industrialuses of bacteria polyhydroxyalkanoates. Microbiol. Rev., 54: 450-472.
6. [6]. Luzier, W.D., (1992). Materials derived from biomass/biodegradable materials. Proc. Natl.Acad. Sci. USA., 89: 839-842.
7. [7]. Sujatha, K., Shenbagarathai, R., Mahalakshmi, A., (2005). Analysis of PCR products for PHB production in indigenous Pseudomonas sp. LDC-5. Indian J. Biotechnol., 4: 323-335.
8. [8]. López-Cortés, A., Lanz-Landázuri, A., García-Maldonado, J.Q., (2008). Screening and isolation of PHB- producing bacteria in a polluted marine microbial mat. Microb. Ecol. 56: 112-20.

9. [9]. Mauti, E.M., Mauti, G.O., Ouno, G.A., Mabeya, B.M., Kiprono, S.J., (2013). Molecular identification of soil bacteriaby 16s rDNA sequence. J. Natural Sci. Res.,3: 51-58.
10. [10]. Aagot, N., Nybroe, O., Nielsen, P., Johnsen, K., (2001). An altered Pseudomonas diversity is recovered from soil by using nutrient-poor Pseudomonas-selective soil extract media. Appl. Environ. Microbiol., 67 (11): 5233-5239.
11. [11]. Krieg, N.R., Holt, J.G., (1984). Bergey’s Manual of Systematic Bacteriology. Williams and Wilkins, Baltimore, MD.
12. [12]. Green, M.R., Sambrook, J. (2012). Molecular Cloning: A Laboratory Manual, 4th edn., Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
13. [13]. Tamura, K., Nei, M., (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol., 10: 512-526.
14. [14]. Kumar, S., Stecher, G., Tamura, K., (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger data sets. Mol. Biol. Evol., 33 (7): 1870-1874.
15. [15]. Nubia, M., Ivonne, G., Dionisio, M., Victoria, G., Dolly, R., Diego, S., Juan, G., Fabio, A., Armando, E., Dolly, M., (2007). Bioprospecting and characterization of poly-β- hydroxyalkanoate (PHAs) producing bacteria isolated from Colombian sugarcane producing areas. Afr. J. Biotech., 6 (13): 1536-1543.
16. [16]. Singh, P., Parmar, N. (2011). Isolation and characterization of two novel polyhydroxybutyrate (PHB) - producing bacteria. Afr. J. Biotech., 10 (24): 4907-4919.
17. [17]. Aarthi, N., Ramana, K.V., (2011). Identification and characterization of polyhydroxybutyrate producing Bacillus cereus and Bacillus mycoides strains. Int. J. Environ. Sci., 1 (5): 744-756.
18. [18]. Goh, Y.S., Tan, I.K.P., (2012). Polyhydroxyalkanoate production by antarctic soil bacteria isolated from Casey Station and Signy Island. Microbiol. Res., 167 (4): 211-219.
19. [19]. Reji, S.R., Potty, P.V., Nair, M.G., (2012). Molecular identification of a novel PHB producing bacterium through 16S rRNA sequencing. Int. J.Biotechnol.Biochem., 8 (2): 223-233.
20. [20]. Dul’tseva, N.M., Chemitsina, S.M., Zemskaya, T.I., (2012). Isolation of bacteria of the genus Variovorax from the Thioploca mats of Lake Baikal.Microbiol., 81 (1): 67-78.
21. [21]. Tonouchi, A., Kitamura, K., Fujita, T., (2013). Brevibacterium yomogidensesp. nov., isolated from a soil conditioner made from poultry manure.Int. J. Syst. Evol. Microbiol., 63 (2): 516-520.
22. [22]. Panigrahi, S., Badveli, U., (2013).Screening, isolation and quantification of PHB-producing soil bacteria. Int. J. Eng. Sci. Invent., 2 (9): 1-6.
23. [23]. Ciesielski, S., Pokoj, T., Mozejko, J., Klimiuk, E., (2013). Molecular identification of polyhydroxyalkanoates-producing bacteria isolated from enriched microbial community. Pol. J. Microbiol. 62 (1): 45-50.
24. [24]. Mazinani, Z., Asgharzadeh, A., (2014). Genetic diversity of Azotobacter strains isolated from soils by amplified ribosomal DNA restriction analysis.,Cytol. Genet., 48 (5): 293-301.
25. [25]. Chandani, N., Mazumder, P.B., Bhattacharjee, A., (2014). Production of polyhydroxybutyrate (biopolymer) by Bacillus tequilensis NCS-3 isolated from municipal waste areas of Silchar, Assam. Int. J. Sci. Res., 3 (12): 198-203.
26. [26]. Prakash, A., Thavaselvam, D., Kumar, A., Kumar, A., Arora, S.,Tiwari, S., Barua, A., Sathyaseelan, K., (2014). Isolation, identification and characterization of Burkholderia pseudomallei from soil of coastal region of India. SpringerPlus, 3: 438-448.
27. [27]. Agrawal, T., Kotasthane, A.S., Kushwah, R., (2015). Genotypic and phenotypic diversity of polyhydroxybutyrate (PHB) producing Pseudomonas putida isolates of Chhattisgarh region and assessment of its phosphate solubilizing ability. 3 Biotech, 5: 45–60.
28. [28]. Osman, Y.A., Elrazak, A.A., Khater, W., Nashy, E.S., Mohamedin, A., (2015). Molecular characterization of a poly-β-hydroxybutyrate producing Microbacteriumisolate. Int. J. Appl. Sci. Biotech., 3(2):143-150.
29. [29]. Biradar, G.G., Shivasharana, C.T., Kaliwal, B.B., (2015). Isolation and characterization of polyhydroxybutyrate (PHB) producing Bacillus species from agricultural soil. Europ. J. Exp. Biol., 5(3):58-65.
30. [30]. Hall, C.M., Busch, J.D., Shippy, K., Allender, C.J., Kaestli, M., Mayo, M., Sahl, J.W., Schupp, J.M, Colman, R.E., Keim, P., Currie, B.J., Wagner, D.M., (2015). Diverse Burkholderiaspecies isolated from soils in the Southern United States with no evidence of B. pseudomallei.PLoS One, 10 (11): 1-15.
31. [31]. Kıran, N., Chhabra, N., Sidhu, P.K., Lathwaland, P., Rana, J.S., (2015). Molecular identification and characterization of Poly-β-hydroxybutyrate (PHB) producing bacteria isolated from contaminated soils. Asian J. Microbiol. Biotech. Env. Sci., 17 (4): 281-290.
32. [32]. Hoseinabadi, A., Rasooli, I., Taran, M. (2015). Isolation and identification of poly β-Hydroxybutyrate over-producing bacteria and optimization of production medium. Jundishapur J. Microbiol., 8 (7):1-10.
33. [33]. Hassan, M.A., Bakhiet, E.K., Ali, S.G., Hussien, H.R., (2016). Production and characterization of polyhydroxybutyrate (PHB) produced by Bacillus sp. isolated from Egypt. J. App. Pharm. Sci., 6 (4): 46-51.