Research Article
PDF EndNote BibTex Cite

Isolation and Identification of Bacteria from Fruit Garden Soils in Aydın Province

Year 2017, Volume 4, Issue 2, 66 - 73, 01.07.2017
https://doi.org/10.21448/ijsm.288220

Abstract

In this study, different fruit garden soil samples were collected in Aydın province and bacterial diversity was examined. These isolated bacteria were identified by 16S rRNA sequencing and using BLAST. The Maximum Parsimony method was used to produce a Molecular Phylogenetic analysis and a phylogenetic tree was constructed. As a result of this study the following bacteria Bacillus thuringiensis (5), Bacillus mycoides (1), Brevibacterium frigoritolerans (1), Bacillus circulans (1), Bacillus cereus (5), Bacillus weihenstephanensis (1), Pseudomonas putida (1), Stenotrophomonas maltophilia (1), Azotobacter chroococcum (1), Paenibacillus xylanilyticus (1), Variovorax paradoxus (1), Aerococcus viridans (1) were found. These bacteria are significant because they regulate soil ecosystem. In addition bacteria isolated from soil are used in industrial applications such as agriculture, textile, plastic industry, chemical industry.

References

  • Dominati, E., Patterson, M., MacKay, A. (2010). A framework for classifying and quantifying natural capital and ecosystem services of soils. Ecol. Economics, 69:1858-1868.
  • Fierer, N., Bradford, M.A., Jackson, R.B. (2007). Towards an ecological classifi cation of soil bacteria. Ecology, 88:1354–1364.
  • Aislabie, J., Deslippe, J.R. (2013). Soil microbes and their contribution to soil services. In Dymond JR ed. Ecosystem services in New Zealand – conditions and trends. Manaaki Whenua Press, Lincoln, New Zealand.
  • Hayat, R., Ali, S., Amara, U., Khalid, R., Ahmed, I. (2010). Soil beneficial bacteria and their role in plant growth promotion: A Review. Annals Microbiol., 60(4): 579–598.
  • 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.
  • Nehra, K., Jaglan, A., Shaheen, A., Yadav, J., Lathwal, P. (2015). Production of Poly-β-Hydroxybutyrate (PHB) by bacteria isolated from rhizospheric soils. Int. J. Microbial Resource Techn., 2(3):38-48.
  • Alves, P.D.D., Siqueira, F.F., Facchin, S., Horta, C.C.R., Victória, J.M.N., Kalapothakis, E. (2014). Survey of microbial enzymes in soil, water, and plant microenvironments. The Open Microbiol. J., 8:25-31.
  • Abdulkadir, M., Waliyu, S. (2012). Screening and isolation of the soil bacteria for ability to produce antibiotics. European J. Appl. Sci., 4 (5):211-215.
  • Mauti, E.M., Mauti, G.O., Ouno, G.A., Mabeya, B.M., Kiprono, S. (2013). Molecular identification of soil bacteria by 16srDNA sequence. J. Natural Sci. Res., 3(14):51-58.
  • Janssen, P.H. (2006). Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol., 72:1719–1728.
  • Nemergut, D.R., Costello, E.K., Hamady, M., Lozupone, C., Jiang, L., Schmidt, S., Fierer, N., Townsend, A.R., Cleveland, C.C., Stanish, L., Knight, R. (2011). Global pattern in the biogeography of bacterial taxa. Environ. Microbiol., 13:135–144.
  • Nacke, H, Thurmer, A, Wollherr, A, Will, C, Hodac, L, Herold, N, Schöning, I., Schrumpf, M., Daniel, R. (2011). Pyrosequencing-based assessment of bacterial community structure along different management types in german Forest and grassland soils. Plos One, 6(2):1-12.
  • 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.
  • Krieg, N. R., Holt, J. G., (1984). Bergey’s Manual of Systematic Bacteriology. Williams and Wilkins, Baltimore, MD.
  • Green, M.R., Sambrook, J. (2012). Molecular Cloning: A Laboratory Manual, 4thedn., Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
  • 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.
  • 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.
  • Issar, S., Sharma, S., Choudhary, D.K., Gautam, H.K., Gaur, R.K. (2012). Molecular Characterization of Pseudomonas spp. ısolated from root nodules of various leguminous plants of Shekhawati Region, Rajasthan, India. American J. Plant Sci., 3, 60-63.
  • Lakshmi, V., Kumari, S., Singh, A., Prabha, C. (2015). Isolation and characterization of deleterious Pseudomonas aeruginosa KC1 from rhizospheric soils and its interaction with weed seedlings. J. King Saud University Sci., 27:113–119.
  • Kasa, P., Modugapalem, H., Battini, K. (2015). Isolation, screening, and molecular characterization of plant growth promoting rhizobacteria isolates of Azotobacter and Trichoderma and their beneficial activities. J. Nat. Sci. Biol. Med., 6(2):360–363.
  • Pathania, N., Gosal, S.K., Saroa, G.S., Vikal, Y. (2014). Molecular characterization of diazotrophic bacteria isolated from rhizosphere of wheat cropping system from central plain region of Punjab. Afr. J. Microbiol. Res., 8(9):862-871.
  • Dadook, M., Mehrabian, S., Salehi, M., Irian, S. (2014). Morphological, biochemical and molecular characterization of twelve nitrogen-fixing bacteria and their response to various zinc concentration. Jundishapur J. Microbiol., 7(4):1-5.
  • Bhuvaneswari, G. (2013). Molecular characterization of camphor utilizing bacterial isolates from refinery sludge and detection of target loci-Cytochrome P-450 cam mono oxygenase (cam C gene) by PCR and gene probe. Springerplus, 2(1):1-9.
  • Kumar, S.N., Jacob, J., Reshma, U.R., Rajesh, R.O., Kumar, B.S.D. (2015). Molecular characterization of forest soil based Paenibacillus elgii and optimization of various culture conditions for its improved antimicrobial activity. Frontiers Microbiol., 6:1-11.
  • Someya, N., Kobayashi, Y.O., Tsuda,S., Ikeda, S. (2013). Molecular characterization of the bacterial community in a potato phytospher. Microbes Environ., 28(3):295–305.
  • Olukunle, O.F. (2013). Characterization of indigenous microorganisms associated with crude oil-polluted soils and water using traditional techniques. Microbiol. J., 3:1-11.

Isolation and Identification of Bacteria from Fruit Garden Soils in Aydın Province

Year 2017, Volume 4, Issue 2, 66 - 73, 01.07.2017
https://doi.org/10.21448/ijsm.288220

Abstract

In this study, different fruit garden soil samples were collected in Aydın province and bacterial diversity was examined. These isolated bacteria were identified by 16S rRNA sequencing and using BLAST. The Maximum Parsimony method was used to produce a Molecular Phylogenetic analysis and a phylogenetic tree was constructed. As a result of this study the following bacteria Bacillus thuringiensis (5), Bacillus mycoides (1), Brevibacterium frigoritolerans (1), Bacillus circulans (1), Bacillus cereus (5), Bacillus weihenstephanensis (1), Pseudomonas putida (1),  Stenotrophomonas maltophilia (1), Azotobacter chroococcum (1), Paenibacillus xylanilyticus (1), Variovorax paradoxus (1), Aerococcus viridans (1) were found. These bacteria are significant because they regulate soil ecosystem. In addition bacteria isolated from soil are used in industrial applications such as agriculture, textile, plastic industry, chemical industry.

References

  • Dominati, E., Patterson, M., MacKay, A. (2010). A framework for classifying and quantifying natural capital and ecosystem services of soils. Ecol. Economics, 69:1858-1868.
  • Fierer, N., Bradford, M.A., Jackson, R.B. (2007). Towards an ecological classifi cation of soil bacteria. Ecology, 88:1354–1364.
  • Aislabie, J., Deslippe, J.R. (2013). Soil microbes and their contribution to soil services. In Dymond JR ed. Ecosystem services in New Zealand – conditions and trends. Manaaki Whenua Press, Lincoln, New Zealand.
  • Hayat, R., Ali, S., Amara, U., Khalid, R., Ahmed, I. (2010). Soil beneficial bacteria and their role in plant growth promotion: A Review. Annals Microbiol., 60(4): 579–598.
  • 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.
  • Nehra, K., Jaglan, A., Shaheen, A., Yadav, J., Lathwal, P. (2015). Production of Poly-β-Hydroxybutyrate (PHB) by bacteria isolated from rhizospheric soils. Int. J. Microbial Resource Techn., 2(3):38-48.
  • Alves, P.D.D., Siqueira, F.F., Facchin, S., Horta, C.C.R., Victória, J.M.N., Kalapothakis, E. (2014). Survey of microbial enzymes in soil, water, and plant microenvironments. The Open Microbiol. J., 8:25-31.
  • Abdulkadir, M., Waliyu, S. (2012). Screening and isolation of the soil bacteria for ability to produce antibiotics. European J. Appl. Sci., 4 (5):211-215.
  • Mauti, E.M., Mauti, G.O., Ouno, G.A., Mabeya, B.M., Kiprono, S. (2013). Molecular identification of soil bacteria by 16srDNA sequence. J. Natural Sci. Res., 3(14):51-58.
  • Janssen, P.H. (2006). Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol., 72:1719–1728.
  • Nemergut, D.R., Costello, E.K., Hamady, M., Lozupone, C., Jiang, L., Schmidt, S., Fierer, N., Townsend, A.R., Cleveland, C.C., Stanish, L., Knight, R. (2011). Global pattern in the biogeography of bacterial taxa. Environ. Microbiol., 13:135–144.
  • Nacke, H, Thurmer, A, Wollherr, A, Will, C, Hodac, L, Herold, N, Schöning, I., Schrumpf, M., Daniel, R. (2011). Pyrosequencing-based assessment of bacterial community structure along different management types in german Forest and grassland soils. Plos One, 6(2):1-12.
  • 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.
  • Krieg, N. R., Holt, J. G., (1984). Bergey’s Manual of Systematic Bacteriology. Williams and Wilkins, Baltimore, MD.
  • Green, M.R., Sambrook, J. (2012). Molecular Cloning: A Laboratory Manual, 4thedn., Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
  • 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.
  • 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.
  • Issar, S., Sharma, S., Choudhary, D.K., Gautam, H.K., Gaur, R.K. (2012). Molecular Characterization of Pseudomonas spp. ısolated from root nodules of various leguminous plants of Shekhawati Region, Rajasthan, India. American J. Plant Sci., 3, 60-63.
  • Lakshmi, V., Kumari, S., Singh, A., Prabha, C. (2015). Isolation and characterization of deleterious Pseudomonas aeruginosa KC1 from rhizospheric soils and its interaction with weed seedlings. J. King Saud University Sci., 27:113–119.
  • Kasa, P., Modugapalem, H., Battini, K. (2015). Isolation, screening, and molecular characterization of plant growth promoting rhizobacteria isolates of Azotobacter and Trichoderma and their beneficial activities. J. Nat. Sci. Biol. Med., 6(2):360–363.
  • Pathania, N., Gosal, S.K., Saroa, G.S., Vikal, Y. (2014). Molecular characterization of diazotrophic bacteria isolated from rhizosphere of wheat cropping system from central plain region of Punjab. Afr. J. Microbiol. Res., 8(9):862-871.
  • Dadook, M., Mehrabian, S., Salehi, M., Irian, S. (2014). Morphological, biochemical and molecular characterization of twelve nitrogen-fixing bacteria and their response to various zinc concentration. Jundishapur J. Microbiol., 7(4):1-5.
  • Bhuvaneswari, G. (2013). Molecular characterization of camphor utilizing bacterial isolates from refinery sludge and detection of target loci-Cytochrome P-450 cam mono oxygenase (cam C gene) by PCR and gene probe. Springerplus, 2(1):1-9.
  • Kumar, S.N., Jacob, J., Reshma, U.R., Rajesh, R.O., Kumar, B.S.D. (2015). Molecular characterization of forest soil based Paenibacillus elgii and optimization of various culture conditions for its improved antimicrobial activity. Frontiers Microbiol., 6:1-11.
  • Someya, N., Kobayashi, Y.O., Tsuda,S., Ikeda, S. (2013). Molecular characterization of the bacterial community in a potato phytospher. Microbes Environ., 28(3):295–305.
  • Olukunle, O.F. (2013). Characterization of indigenous microorganisms associated with crude oil-polluted soils and water using traditional techniques. Microbiol. J., 3:1-11.

Details

Primary Language English
Subjects Biology
Published Date July
Journal Section Articles
Authors

Mehmet Ali YÖRÜKÇE This is me
ADNAN MENDERES UNIV


Betül Aktaş This is me
ADNAN MENDERES UNIV


Yusuf Geroğlu This is me


Esin Poyrazoğlu This is me
ADNAN MENDERES UNIV


H. Halil Bıyık>
ADNAN MENDERES UNIV

Publication Date July 1, 2017
Published in Issue Year 2017, Volume 4, Issue 2

Cite

APA Yörükçe, M. A. , Aktaş, B. , Geroğlu, Y. , Poyrazoğlu, E. & Bıyık, H. H. (2017). Isolation and Identification of Bacteria from Fruit Garden Soils in Aydın Province . International Journal of Secondary Metabolite , 4 (2) , 66-73 . DOI: 10.21448/ijsm.288220

International Journal of Secondary Metabolite (IJSM)

ISSN-e: 2148-6905