Miseq sequence identification of bacteria isolated from Çıldır Lake

Abstract

In this study, it was aimed to identify and phylogenetic evaluation of bacteria isolated from Çıldır lake sediment. Four sediment sampling was done from two different regions. For bacterial isolations, samples were incubated in Bennet's agar at 28 oC for 7 days. The isolated bacteria morphological and microscopic (Scaninning Electron Microscope-SEM) images were taken. After the PCR process performed with universal primers, the isolated bacteria were identified by sequencing the PCR amplicons using the MiSeq sequence method. In the results of working; 2 Nocardia sp and 1 Amycolatopsis sp species were isolated. When looking at the spore chain morphology in the SEM image, it was observed that a knobby structure was formed, the sequence alignment of 16S rRNA longer than 1000 bp and the sequences obtained from GenBank in the phylogenetic tree were closely similar (99 % <). It has been observed that the bacterial fauna of Çıldır Lake has a low bacterial density that does not pose a risk. The high accuracy of the sequence analysis process for the identification of bacteria has been confirmed. We believe that entering the sequence data of the isolated bacterial species as GenBank data set will be important in terms of providing data for other studies with nucleotide sequences.

Keywords

• 16S rRNA
• Bacteria
• Çıldır lake
• MiSeq sequencing
• SEM

References

1. Benhadj, M., Gacemi-Kirane, D., Menasria, T., Guebla, K., Ahmane, Z. 2019. Screening of rare actinomycetes isolated from natural wetland ecosystem (Fetzara Lake, northeastern Algeria) for hydrolytic enzymes and antimicrobial activities. Journal of King Saud University – Science. 31:(4), 706-712.
2. Bilgi, B.H.G. 2006. Determination of Some Metabolic Properties of Bacillus Bacteria Isolated from Fishes, Investigation of Plasmid DNA and Protein Profiles. Orlab On-line Journal of Microbiology, 4(3): 1-30.
3. Chen, S.C. and Wang, P.C. 1993. In vitro activitiy of antimicrobial agents against Nocardia asteroites. J. Fish Diseases, 16: 269-272.
4. Conville, P.S., Zelazny, A.M., Witebsky, F.G. (2006). Analysis of secA1 Gene Sequences for Identification of Nocardia Species. JOURNAL OF CLINICAL MICROBIOLOGY, Vol. 44, No. 8, 2760–2766.
5. Dasari, V.R.R.K., Donthireddy, S.R.R. 2011. Amycolatopsis alba var nov DVR D4, a bioactive actinomycete isolated from Indian marine environment. J Biochem Tech. 3:(2), 251-256.
6. Fguira, L.F., Fotso, S., Ameur-Mehdi, R.B., Mellouli, L., Laatsch, H. 2005. Purification and Structure Elucidation of Antifungal and Antibacterial Activities of Newly Isolated Streptomyces sp. Strain US80. Research in Microbiology, 156: (3), 341-345.
7. Goodfellow, M., Kämpfer, P., Busse, H.J., Trujillo, M., Suzuki, K.I., Ludwig, W., Whitman, W. 2012. Bergey’s manual of systematic bacteriology.
8. Niu, M.M., Ming, H., Cheng, L.J., Zhao, Z.L., Ji, W.L., Li, M., Yi, B.F., Xia, T.T., Nie, G.X. 2020. Amycolatopsis nivea sp. nov., isolated from a Yellow River sample. Int J Syst Evol Microbiol. 70:(5), 3084-3090.

9. Önalan, Ş. 2019. Expression Differences of Stress and Immunity Genes in Rainbow Trout (Oncorhynchus mykiss, Walbaum 1792) with Different Bacterial Fish Diseases. The Israeli Journal of Aquaculture - Bamidgeh, 71:(1), 1-10.
10. Önalan, Ş. and Çevik, M. 2020. Investigation of the effects of some phytochemicals on Yersinia ruckeri and antimicrobial resistance. Brazilian Journal of Biology, 80:(4), 934-942.
11. Prakash, O., Verma, M., Sharma, P., Kumar, M., Kumari, K., Singh A., Kumari, H., Jit, S., Gupta, S.K. 2007. Polyphasic Approach of Bacterial Classification – An Overview of Recent Advances. Indian Journal of Microbiology, 47:(2), 98-108.
12. Seçkin, H. and Önalan, Ş. 2020. Phylogenetic Diversity of Nocardia sp. Obtained from Different Water Environments Research Journal of Biology Sciences. 13(2): 37-44.
13. Sikkema‐Raddatz, B., Johansson, L.F., de-Boer, E.N., Almomani, R., Boven, L.G. 2013. Targeted next‐generation sequencing can replace Sanger sequencing in clinical diagnostics. Human mutation 34:(7), 1035-1042.
14. Voytsekhovskaya, I.V., Axenov-Gribanov, D.V., Murzina, S.A., Pekkoeva, S.N., Protasov, E.S., Gamaiunov, S.V., Timofeyev, M.A. 2018. Estimation of antimicrobial activities and fatty acid composition of Actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia. Peerj-Life&Environment, 25(6): 5832. doi: 10.7717/peerj 5832.
15. Wei, M., Wang, P., Yang, C., Gu, L. 2019. Molecular identification and phylogenetic relationships of clinical Nocardia isolates. Antonie van Leeuwenhoek. 112:(1), 1755–1766.