Prokaryotik çeşitliliğin potansiyel biyoremediasyon enzimlerinin aşırı habitatlarda mevsimsel değişimi

Öz

Biyoremediasyon uygulamalarında genellikle ekstremofil olmayan mikroorganizmalar kullanılmaktadır. Ancak bu uygulamalarda, ekstremofil olmayan mikroorganizmaların yüksek tuz konsantrasyonlarında organik kirleticileri giderimi, olumsuz tuz etkisinin üstesinden gelmek için bir ön arıtma işlemi gerektirmektedir. Halofil mikroorganizmalar, hipersalin ortamlara uyum sağlamalarını sağlayan önemli enzimatik yapılara sahiptir. Halofiller, hidrokarbonları tek karbon ve enerji kaynağı olarak etkili bir şekilde kullanabilmeleri nedeniyle yüksek tuz konsantrasyonlarında organik kirletici gideriminin tedavisi için uygun biyoremediasyon ajanları olarak öne çıkmaktadır. Bu çalışmada, 16S rDNA amplikon dizileme verilerini kullanarak Tuz Gölü'ndeki prokaryotik çeşitliliğin biyoremediasyon enzimlerini tahmin etmek için PICRUSt2 aracı uygulandı. Fonksiyonel analiz sonucunda, Tuz Gölü metagenom verilerinde biyoremediasyon süreciyle ilgili çeşitli enzimler tespit edildi. Arsenit taşıyıcı ATPaz (EC:3.6.3.16), arsenat redüktaz EC:1.20.4.1), (S)-2-haloasit dehalojenaz (EC:3.8.1.2), nitrat redüktaz (EC:1.7.99.4) ve katekol 2,3-dioksijenaz (EC:1.13.11.2) enzimleri yüksek bollukta gözlendi. Ayrıca, (S)-2-haloasit dehalojenaz, selenit su dikinazı, cıva (II) redüktazı, arsenit taşıyıcı ATPaz ve 4-hidroksifenilpiruvat dioksijenaz enzimleriyle ilişkili diziler önemli mevsimsel farklılık gösterdi.

Anahtar Kelimeler

• PICRUSt2
• ekstremofilik
• fonksiyonel genler
• biyoremediasyon enzimleri
• mevsimsel değişim

Seasonal variation of potential bioremediation enzymes of prokaryotic diversity in extreme habitat

Öz

In bioremediation applications, non-extremophilic microorganisms are generally used. However, in these applications, the removal of organic pollutants by non-extremophilic microorganisms at high salt concentrations requires a pretreatment process to overcome the negative salt effect. Halophilic microorganisms have important enzymatic structures that allow them to adapt to hypersaline environments. Halophiles stand out as suitable bioremediation agents for the treatment of organic pollutant removal at high salt concentrations because they can effectively use hydrocarbons as sole carbon and energy sources. In this study PICRUSt2 tool was applied to predict bioremediation enzymes of prokaryotic diversity in Tuz Lake using 16S rDNA amplicon sequencing data. As a result of functional analysis, various enzymes related to bioremediation process were detected in Tuz Lake metagenome data. Arsenite transporter ATPase (EC:3.6.3.16), arsenate reductase EC:1.20.4.1), (S)-2-haloacid dehalogenase (EC:3.8.1.2), nitrate reductase (EC:1.7.99.4), and catechol 2,3-dioxygenase (EC:1.13.11.2) enzymes were observed in high abundance. Moreover, the sequences associated with (S)-2-haloacid dehalogenase, selenite water dikinase, mercury (II) reductase, arsenite transporter ATPase and 4-hydroxyphenylpyruvate dioxygenase enzymes were showed significant seasonal difference.

Anahtar Kelimeler

• PICRUSt2
• extremophilic
• functional genes
• bioremediation enzymes
• seasonal variation

Kaynakça

1. [1] Ali, H.A., Farhan, M.B., Bioremediation techniques for water and soil pollution: Review, Natural and Engineering Sciences, 10(1), 89–109, 2025.
2. [2] Birhanlı, E., Yeşilada, Ö., Çabuk, A., Boran, F., Tatlıcı, E., Comparatively Investigation of Textile Dye Decolorization by a White Rot Fungus and Various Bacterial Strains, Adıyaman University Journal of Science, 2021.
3. [3] Alori, E.T., Gabasawa, A.I., Elenwo, C.E., Agbeyegbe, O.O., Bioremediation techniques as affected by limiting factors in soil environment, Frontiers in Soil Science, 2, 2022.
4. [4] Narayanan, M., Ali, S.S., El-Sheekh, M., A comprehensive review on the potential of microbial enzymes in multipollutant bioremediation: Mechanisms, challenges, and future prospects, Journal of Environmental Management, 334, 117532, 2023.
5. [5] Orellana, R. et al., Living at the frontiers of life: extremophiles in chile and their potential for bioremediation, Frontiers in Microbiology, 9, 2018.
6. [6] Margesin, R., Feller, G., Biotechnological applications of psychrophiles, Environmental Technology, 31(8–9), 835–844, 2010.
7. [7] Edbeib, M.F., Wahab, R.A., Huyop, F., Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments, World Journal of Microbiology and Biotechnology, 32(8), 135, 2016.
8. [8] Le Borgne, S., Paniagua, D., Vazquez-Duhalt, R., Biodegradation of organic pollutants by halophilic bacteria and archaea, Microbial Physiology, 15(2–3), 74–92, 2008.

9. [9] Simachew, A., Lanzén, A., Gessesse, A., Øvreås, L., Prokaryotic community diversity along an increasing salt gradient in a soda ash concentration pond, Microbial Ecology, 71(2), 326–338, 2016.
10. [10] Oren, A., Adaptation of halophilic archaea to life at high salt concentrations, in Salinity: Environment – Plants – Molecules, Springer Netherlands, 81–96, 2002.
11. [11] Paul, S., Bag, S. K., Das, S., Harvill, E. T., Dutta, C., Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes, Genome Biology, 9(4), R70, 2008.
12. [12] Rhodes, M. E., Fitz-Gibbon, S. T., Oren, A., House, C. H., Amino acid signatures of salinity on an environmental scale with a focus on the Dead Sea, Environmental Microbiology, 12(9), 2613–2623, 2010.
13. [13] Şahin Doğan, S., Kocabaş, A., Seasonal dynamics of eukaryotic microbial diversity in hypersaline Tuz Lake characterized by 18S rDNA sequencing, Journal of Eukaryotic Microbiology, 70(6), 2023.
14. [14] Doğan, S.Ş., Kocabaş, A., Metagenomic assessment of prokaryotic diversity within hypersaline tuz lake, Turkey, Microbiology, 90(5), 647–655, 2021.
15. [15] Caporaso, J. G. et al., Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proceedings of the National Academy of Sciences of the United States of America, 108(Suppl. 1), 4516–4522, 2011.
16. [16] Douglas, G.M. et al., PICRUSt2 for prediction of metagenome functions, Nature Biotechnology, 38(6), 685–688, 2020.
17. [17] Parks, D.H., Tyson, G.W., Hugenholtz, P., Beiko, R.G., STAMP: statistical analysis of taxonomic and functional profiles, Bioinformatics, 30(21), 3123–3124, 2014.
18. [18] Oyewusi, H. A., Muhammad, M., Wahab, R. A., Huyop, F., A review on enzymatic response to salt stress and genomic/metagenomic analysis of adaptation protein in hypersaline environment, Journal of Tropical Life Science, 11(3), 339–360, 2021.
19. [19] Saravanan, A., Kumar, P.S., Vo, D.-V.N., Jeevanantham, S., Karishma, S., Yaashikaa, P. R., A review on catalytic-enzyme degradation of toxic environmental pollutants: Microbial enzymes, Journal of Hazardous Materials, 419, 126451, 2021.
20. [20] Mori, M., Ponce-de-León, M., Peretó, J., Montero, F., Metabolic complementation in bacterial communities: necessary conditions and optimality, Frontiers in Microbiology, 7, 2016.
21. [21] Sahin Dogan, S., Kocabas, A., Profiling the genes associated with osmoadaptation and their variation by seasonally in Tuz Lake, Communications Faculty of Science University of Ankara Series C Biology, Geological Engineering and Geophysical Engineering, 32(2), 174–191, 2023.
22. [22] Banda, J.F. et al., Both pH and salinity shape the microbial communities of the lakes in Badain Jaran Desert, NW China, Science of the Total Environment, 791, 148108, 2021.
23. [23] Yavari-Bafghi, M., Amoozegar, M. A., Pharmaceutical applications of halophilic enzymes, Heliyon, 11(4), e42754, 2025.
24. [24] Oyewusi, H.A., Wahab, R.A., Kaya, Y., Edbeib, M.F., Huyop, F., Alternative bioremediation agents against haloacids, haloacetates and chlorpyrifos using novel halogen-degrading bacterial isolates from the hypersaline lake Tuz, Catalysts, 10(6), 651, 2020.
25. [25] Hullar, M.A.J., Kaplan, L.A., Stahl, D.A., Recurring seasonal dynamics of microbial communities in stream habitats, Applied and Environmental Microbiology, 72(1), 713–722, 2006.
26. [26] Lara, J., Escudero González, L., Ferrero, M., Chong Díaz, G., Pedrós-Alió, C., Demergasso, C., Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile, Extremophiles, 16(3), 523–538, 2012.
27. [27] Wang, C., Huang, Y., Zhang, Z., Wang, H., Salinity effect on the metabolic pathway and microbial function in phenanthrene degradation by a halophilic consortium, AMB Express, 8(1), 67, 2018.
28. [28] Madern, D., Ebel, C., Zaccai, G., Halophilic adaptation of enzymes, Extremophiles, 4(2), 91–98, 2000.