Eber Gölü Prokaryotik Çeşitliliğinin Metagenomik Çalışmasıyla Karakterizasyonu

Abstract

Eber Gölü, Türkiye'de göçmen kuşların geçiş rotası üzerinde yer almakta ve sazlık alanları sayesinde birçok kuş türüne doğal üreme ve yaşam alanı sağlamaktadır. Ülkemizde bu kadar önemli bir göl olmasına rağmen prokaryotik çeşitlilik konusunda yeterli çalışma olmadığı görülmüştür. Metagenomik analiz DNA izolasyonu ile elde edilen mikroorganizmaların türlerini, genetik yapılarını, fonksiyonel rollerini ve insan ile ekolojik sağlık üzerindeki etkilerini belirlemeyi mümkün kılmaktadır. Yeni nesil dizileme (YND), birçok DNA veya RNA örneğinin eşzamanlı olarak yüksek hızda ve yüksek hassasiyetle dizilenmesini mümkün kılan, modern bir DNA/RNA dizileme teknolojisidir. Bu çalışmamızda Eber Gölü'ne ait 16S ribozomal DNA (rDNA) (V3-V4 bölgeleri) dizilerinin metagenomik analizi için yüksek verimli YND yöntemleri kullanılmıştır. Prokaryotik çeşitliliği incelemek amacıyla MOTHUR yazılımı kullanılarak Illumina NovaSeq teknolojisi ile elde edilen dizi verileri analiz edilmiştir. Analizler sonucu Proteobacteria, Verrucomicrobia, Bacteroidetes ve Actinobacteria Şubelerinin baskın olduğu ortaya çıkarılarak Eber Gölü'ndeki prokaryotik çeşitlilik detaylı bir şekilde karakterize edilmiştir.

Keywords

• Prokaryotik çeşitlilik
• metagenomik
• ekoloji
• 16s rRNA
• İllumina dizileme

Supporting Institution

İstanbul Üniversitesi Bilimsel Araştırma Projeleri Birimi

Project Number

FDK-2019-34349

Thanks

Bu çalışmanın laboratuvar çalışmaları İstanbul Üniversitesi Fen Fakültesi moleküler biyoloji ve genetik laboratuvarlarında gerçekleştirilmiştir. İstanbul Üniversitesi Bilimsel Araştırma Projeleri Koordinasyon Birimi tarafından finanse edilen bu çalışma, proje numarası: FDK-2019-34349, Türkiye

Characterization of Prokaryotic Diversity in Eber Lake through Metagenomic Analysis

Abstract

Eber Lake is located on the migration route of birds in Turkey and provides natural breeding and habitat for many bird species thanks to its reed areas. Despite being such an important lake in our country, there has been insufficient research on prokaryotic diversity. Metagenomic analysis enables the determination of the species, genetic structures, functional roles, and their effects on human and ecological health of microorganisms obtained through DNA isolation. Next-generation sequencing (NGS) is a modern DNA/RNA sequencing technology that allows for the simultaneous high-speed and high-precision sequencing of many DNA or RNA samples. In this study, we used high-throughput NGS methods for metagenomic analysis of 16S ribosomal DNA (rDNA) (V3-V4 regions) sequences from Eber Lake. The obtained sequence data using Illumina NovaSeq technology was analyzed with MOTHUR software to investigate prokaryotic diversity. The analysis revealed that the Proteobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria phyla were dominant, and the prokaryotic diversity in Eber Lake was characterized in detail.

Keywords

• metagenomics
• ecology
• prokaryotic diversity
• illimina Sequencing
• 16s rRNA

Project Number

FDK-2019-34349

References

1. Anonim. (2023). Türkiye Kültür Portalı URL: https://www.kulturportali.gov.tr/turkiye/afyonkarahisar/TurizmAktiviteleri/eber-golu (accessed date: March 07, 2023).
2. Balkwill, D. L., Reeves, R. H., Drake, G. R., Reeves, J. Y., Crocker, F. H., King, M. B., & Boone, D. R. (1997). Phylogenetic characterization of bacteria in the subsurface microbial culture collection. FEMS microbiology reviews, 20(3-4), 201–216. https://doi.org/10.1111/j.1574-6976.1997.tb00309.x
3. Bhaduri, Anik & Ringler, Claudia & Dombrowski, Ines & Mohtar, Rabi & Scheumann, Waltina. (2015). Sustainability in the water–energy–food nexus. Water International. 40. 723-732. 10.1080/02508060.2015.1096110.
4. Carpenter, Stephen & Cole, Jonathan & Pace, M & Batt, R & Brock, WA & Cline, Timothy & Coloso, James & Hodgson, James & Kitchell, J & Seekell, DA & Patrick, Laura & Weidel, Brian. (2011). Early Warnings of Regime Shifts: A Whole-Ecosystem Experiment. Science (New York, N.Y.). 332. 1079-82. 10.1126/science.1203672.
5. Cipriano, R.C. ve R.A. Holt. 2005. Flavobacterium psychrophilum, cause of Bacterial Cold-Water Disease and Rainbow Trout Fry Syndrome. Fish Disease Leaflet No. 86. United States Dept. of the Interior. U.S. Geological Service, National Fish Health Research Laboratory, Kearneysville, WV.
6. Culligan, E.P., Sleator, R.D., Marchesi, J.R., Hill, C., 2014. Metagenomics and novel gene discovery. Promise and potential for novel therapeutics. Virulence 5, 399–412.
7. Cseke, L.J., Kaufman, P.B., Podila, G.K., & Tsai, C.-J. (2003). Handbook of Molecular and Cellular Methods in Biology and Medicine (2nd ed.). Boca Raton: CRC Press. doi:https://doi.org/10.1201/9781420041712
8. Eiler, A., Zaremba-Niedzwiedzka, K., Martínez-García, M., McMahon, K. D., Stepanauskas, R., Andersson, S. G., & Bertilsson, S. (2014). Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics. Environmental microbiology, 16(9), 2682–2698. https://doi.org/10.1111/1462-2920.12301.

9. Garcia Moreno, Jaime & Harrison, Ian & Dudgeon, David & Clausnitzer, V. & Darwall, William & Farrell, Tracy & Savy, C. & Tockner, Klement & Tubbs, N.. (2014). Sustaining Freshwater Biodiversity in the Anthropocene. 10.1007/978-3-319-07548-8_17.Gulçin, İ., Taslimi, P., Aygün, A., Sadeghian, N., Bastem, E., Kufrevioglu, O. I., ... & Şen, F. (2018). Antidiabetic and antiparasitic potentials: Inhibition effects of some natural antioxidant compounds on α-glycosidase, α-amylase and human glutathione S-transferase enzymes. International journal of biological macromolecules, 119, 741-746.
10. Goller.gen.tr. (03.04.2021). Eber Gölü. Goller.gen.tr. https://www.goller.gen.tr/eber-golu.html (Erişim adresi: 14 03, 2023).
11. Gilbert et al. (2011). The earth microbiome project: The meeting report for the 1st international earth microbiome project confer‐ence, Shenzhen, China, June 13th–15th 2011. Standards in Genomic Sciences, 5(2), 243–247. doi:https://doi.org/10.4056/sigs.2134923
12. He, R., Cui, Y., Li, Y., & Ge, X. (2022). Tetrahydroisoquinoline N-methyltransferase from Methylotenera Is an Essential Enzyme for the Biodegradation of Berberine in Soil Water. Molecules, 27(17), 5442. https://doi.org/10.3390/molecules27175442
13. Hahn, M. W., Schmidt, J., Taipale, S. J., Doolittle, W. F., & Koll, U. (2014). Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome. International journal of systematic and evolutionary microbiology, 64(Pt 9), 3254–3263. https://doi.org/10.1099/ijs.0.065292-0
14. Kuri, M. L., Kumari, V., & Roy, S. (2019). Phenylobacterium Korensee Best Indigenous Petroleum Hydrocarbon Degrading Bacteria Isolated from Contaminated Soil of Bahror, Alwar Region, India. International Journal of Contemporary Research and Review, 10(08), 20203–20211. https://doi.org/10.15520/ijcrr.v10i08.729
15. Klindworth, et al. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and nextgeneration sequencing-based diversity studies. Nucleic acids Research, 41(1)
16. Iliev, I, Yahubyan, G, Marhova, M, et al. Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs. J Basic Microbiol. 2017; 57: 669– 679. https://doi.org/10.1002/jobm.201700137
17. Jongman, M., Carmichael, P.C., Bill, M., 2020, Technological advances in phytopathogen detection and metagenome profiling techniques, Current Microbiology, 77, 675-681.
18. Jovel, J., Patterson, J., Wang, W., Hotte, N., O'Keefe, S., Mitchel, T., Perry, T., Kao, D., Mason, A. L., Madsen, K. L., & Wong, G. K. (2016). Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics. Frontiers in microbiology, 7, 459. https://doi.org/10.3389/fmicb.2016.00459
19. Nair, H. P., & Bhat, S. G. (2019). Metagenomic data on bacterial diversity profiling of Arabian sea sediment by amplicon sequencing. Data in brief, 28, 104791. https://doi.org/10.1016/j.dib.2019.104791
20. Ondov BD, Bergman NH, Phillippy AM. (2011). Interactive metagenomic. BMC Bioinf, 12:385. doi:https://doi.org/10.1186/1471-2105-12-385
21. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing. Nucleic Acids Res., 41, D590–D596. doi:https://doi.org/10.1093/nar/gks1219
22. Polat, H. ve Ekici, L., 2019. Akkermansia muciniphila: Obezite ve Diyabetten Korunmada Yeni Bir Alternatif Olabilir mi?. Avrupa Bilim ve Teknoloji Dergisi, 16, 533-543.
23. Rognes, T., Flouri, T., Nichols, B., Quince, C., ve Mahé, F. (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ, 1–22. doi:https://doi.org/10.7717/peerj.2584
24. Sembries, S., & Crawford, R. L. (1997). Production of Clostridium bifermentans Spores as Inoculum for Bioremediation of Nitroaromatic Contaminants. Applied and environmental microbiology, 63(5), 2100–2104. https://doi.org/10.1128/aem.63.5.2100-2104.1997
25. Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister,. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol, 75, 7537–7541. doi:https://doi.org/10.1128/AEM.01541-1549
26. Vörösmarty, C. & McIntyre, P. & Gessner, Mark & Dudgeon, David & Proussevitch, Alexander & Green, Pamela & Glidden, Stanley & Bunn, Stuart & Sullivan, Caroline & Reidy Liermann, Catherine & Davies, Peter. (2010). Global threats to human water security and river biodiversity. Nature. 467. 555-561. 10.1038/nature09440.
27. Wake up to the looming water crisis, report warns. (2021, October 11). Retrieved from https://public.wmo.int/en/media/press-release/wake-looming-water-crisis-report-warns
28. Wang, Q., Garrity, G. M., Tiedje, J. M., ve Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 73, 5261–5267. doi:https://doi.org/10.1128/AEM.00062-67
29. Water: Facts and trends. (n.d.). Retrieved from https://www.wbcsd.org/Programs/Food-and-Nature/Water/Resources/Water-Facts-and-trends
30. Westcott, S. L., ve Schloss, P. D. (2017). OptiClust, an improved method for assigning amplicon-based sequence data to Operational Taxonomic Units. mSphere, 2:e00073-17. doi:https://doi.org/10.1128/mSphereDirect.00073-17
31. Tranvik, Lars & Downing, John & Cotner, James & Loiselle, Steven & Striegl, Robert & Ballatore, Thomas & Dillon, Peter & Finlay, Kerri & Fortino, Kenneth & Knoll, Lesley & Kortelainen, Pirkko & Kutser, Tiit & Larsen, Soren & Laurion, Isabelle & Leech, Dina & Mccallister, S. & Mcknight, Diane & Melack, John & Overholt, Erin & Weyhenmeyer, Gesa. (2009). Lakes and reservoirs as regulators of carbon cycling and climate. Limnology and Oceanography. 54. 2298-2314. 10.4319/lo.2009.54.6_part_2.2298.