Actinobacteria with heavy metal tolerance from the Sinop coast: A molecular characterization approach

Aysel Veyisoğlu; Demet Tatar; Ali Tokatlı; Hünkar Avni Duyar

doi:10.12714/egejfas.42.4.03

TR EN

Sinop sahilinden elde edilen ağır metal toleransına sahip aktinobakteriler: Moleküler karakterizasyon yaklaşımı

Öz

Bu çalışmada, Sinop, Meydankapı sahilinden toplanan sediment örneklerinden ağır metal toleransına sahip olan deniz aktinobakterilerinin izolasyonu ve moleküler karakterizasyonu amaçlanmıştır. Sediment örnekleri üç farklı istasyondan alınmış ve beş seçici besiyerinde kültüre alınarak 54 aktinobakteri suşu izole edilmiştir. En yüksek izolasyon verimliliği R2A ve SM3 besiyerlerinde elde edilmiştir. İzolatların kurşun (Pb), bakır (Cu), çinko (Zn), cıva (Hg) ve kadmiyum (Cd) dahil olmak üzere ağır metallere toleransı test edilmiştir. Sonuçlar, tüm izolatların Hg ve Cd'ye duyarlı, ancak Pb'ye yüksek tolerans gösterdiğini ortaya koymuştur. Ağır metallere karşı en yüksek direnci gösteren on iki izolat, genomik DNA izolasyonu için seçilmiştir. 16S rRNA gen bölgesi, evrensel primerler kullanılarak çoğaltılmış ve dizilenmiştir. Dizi analizi, izolatların Streptomyces, Actinomadura, Nocardia ve Nonomuraea cinslerine ait olduğunu belirlemiştir. Yaklaşık 1500 baz çifti uzunluğundaki 16S rRNA gen dizileri, EzTaxon veri tabanıyla karşılaştırılarak en yakın türler belirlendi. Elde edilen diziler GenBank veri tabanına kaydedildi. Sonuçlar, Karadeniz'in kirliliği fazla olan sedimentlerinden izole edilen deniz aktinobakterilerinin, ağır metallere karşı direnç mekanizmaları nedeniyle biyoremediasyon ve çevresel biyoteknoloji uygulamaları için önemli bir potansiyele sahip olduğunu göstermektedir.

Anahtar Kelimeler

Actinobacteria with heavy metal tolerance from the Sinop coast: A molecular characterization approach

Abstract

This study aimed to isolate and molecularly characterize marine actinobacteria tolerant to heavy metals from sediment samples collected from the Meydankapı coast in Sinop, Türkiye. Sediment samples were obtained from three different stations and cultured on five selective media, leading to the isolation of 54 actinobacteria strains. The highest isolation efficiency was achieved on R2A and SM3 media. The tolerance of the isolates to heavy metals, including lead (Pb), copper (Cu), zinc (Zn), mercury (Hg), and cadmium (Cd), was tested. The results revealed that all isolates were sensitive to Hg and Cd but exhibited high tolerance to Pb. Twelve isolates, showing the highest resistance to heavy metals, were selected for genomic DNA isolation. The 16S rRNA gene region was amplified using universal primers and sequenced. Sequence analysis identified the isolates as belonging to the genera Streptomyces, Actinomadura, Nocardia and Nonomuraea. The approximately 1500-bp 16S rRNA gene sequences were compared with the EzTaxon database, and the closest species were determined. The obtained sequences were deposited in the GenBank database. The results indicate that marine actinobacteria isolated from polluted sediments of the Black Sea possess significant potential for bioremediation and environmental biotechnology applications due to their resistance mechanisms to heavy metals.

Keywords

Supporting Institution

This study was supported by Sinop University Scientific Research Projects Coordination Department

Project Number

SHMYO-1901-23-002

Ethical Statement

This article does not contain any studies with human participants and/or animals performed by any of the authors. Formal consent is not required in this study.

Thanks

We would like to thank Sinop University Scientific Research Projects Coordination Unit for the support provided in this study.

References

Álvarez, A., Catalano, S.A., & Amoroso, M.J. (2013). Heavy metal resistant strains are widespread along Streptomyces Phylogeny. Molecular Phylogenetics and Evolution, 66, 1083 1088. https://doi.org/10.1016/j.ympev.2012.11.025
Ashbolt, N. J., Amézquita, A., Backhaus, T., Borriello, P., Brandt, K. K., Collignon, P., Coors. A., Finley, R., Gaze, W. H., Heberer, T., Lawrence, J.R., Larsson, D.G.J., McEwen, S.A., Ryan, J.J., Schönfeld, J., Silley, P., Snape, J.R., den Eede, C.V., & Topp, E. (2013). Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environmental Health Perspectives, 121, 993-1001. https://doi.org/10.1289/ehp.1206316
Buchholz-Cleven, B.E.E., Rattunde, B., & Straub, K.L. (1997). Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Systematic and Applied Microbiology, 20, 301 309. https://doi.org/10.1016/S0723 2020(97)80077-X
Bull, A.T., & Stach, J.E. (2007). Marine actinobacteria: New opportunities for natural product search and discovery. Trends in Microbiology, 15(11), 491-499. https://doi.org/10.1016/j.tim.2007.10.004
Chun, J. (1995). Computer assisted classification and identification of actinomycetes. [Ph.D. Thesis. University of Newcastle].
Cimermanova, M., Pristas, P., & Piknova, M. (2021). Biodiversity of Actinomycetes from heavy metal contaminated technosols. Microorganisms, 9(8), 1635. https://doi.org/10.3390/microorganisms9081635
El Baz, S., Baz, M., Barakate, M., Hassani, L., El Gharmali, A., & Imziln, B. (2015). Resistance to and accumulation of heavy metals by Actinobacteria isolated from abandoned mining areas. The Scientiﬁc World Journal, 761834. https://doi.org/10.1155/2015/761834
El-Sayed, M.H., Abdellatif, M.M., Mostafa, H.M., Elsehemy, I.A., & Kobisi, A. E.N.A. (2024). Biodegradation and antimicrobial capability-induced heavy metal resistance of the marine-derived actinomycetes Nocardia harenae JJB5 and Amycolatopsis marina JJB11. World Journal of Microbiology and Biotechnology, 40(7), 202. https://doi.org/10.1007/s11274-024-04006-x

El-Sorogy, A.S., Nour, H., Essa, E., & Tawfik, M. (2013). Quaternary coral reefs of the Red Sea coast, Egypt: Diagenetic sequence, isotopes and trace metals contamination. Arabian Journal of Geosciences, 6, 4981-4991. https://doi.org/10.1007/s12517-012-0806-0
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
Felsenstein, J. (1985). Confidence limits on phylogeny: An appropriate use of the bootstrap. Evolution, 39, 783-791. https://doi.org/10.2307/2408678
Fernandes, L.L., & Nayak, G.N. (2012). Geochemical assessment in a creek environment in mumbai, west coast of India. Environmental Forensics, 13, 45-54. https://doi.org/10.1080/15275922.2011.643340
Jagannathan, S.V., Manemann, E.M., Rowe, S.E., Callender, M.C., & Soto, W. (2021). Marine actinomycetes, new sources of biotechnological products. Marine Drugs, 19(7), 365. https://doi.org/10.3390/md19070365
Kester, D.R., Duedall, I.W., Connors, D.N., & Pytkowicz, R.M. (1967). Preparation of artificial seawater. Limnology and Oceanography, 12, 176-179.
Kim, O.-S., Cho, Y.-J., Lee, K., Yoon, S.-H., Kim, M., Na, H., Park, S.-C., Jeon, J.S., Lee, J.-H., Yi, H., Won, S., & Chun, J. (2012). Introducing EzTaxon-e: A prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. International Journal of Systematic and Evolutionary Microbiology, 62, 716 721. https://doi.org/10.1099/ijs.0.038075-0
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111 120. https://doi.org/10.1007/BF01731581
Kluge, A.G., Farris, F.S. (1969). Quantitative phyletics and the evolution of anurans. Systematic Zoology, 18, 1-32.
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547-1549. https://doi.org/10.1093/molbev/msy096
Lane, D.J. (1991). 16S/23S rRNA sequencing. In: E. Stackebrandt, M. Goodfellow (Eds), Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, pp 115–175.
Li, H., Lin, Y., Guan, W., Chang, J., Xu, L., Guo, J., & Wei, G. (2010). Biosorption of Zn(II) by live and dead cells of Streptomyces ciscaucasicus strain CCNWHX 72-14. Journal of Hazardous Materials, 179, 151-159. https://doi.org/10.1016/j.jhazmat.2010.02.072
Li, K., Tang, X., Zhao, J., Guo, Y., Tang, Y., & Gao, J. (2019). Streptomyces cadmiisoli sp. nov., a novel actinomycete isolated from cadmium-contaminated soil. International Journal of Systematic and Evolutionary Microbiology, 69, 1024-1029. https://doi.org/10.1099/ijsem.0.003262
Lin, Y., Wang, X., Wang, B., Mohamad, O., & Wei, G. (2012). Bioaccumulation characterization of zinc and cadmium by Streptomyces zinciresistens, a novel actinomycete. Ecotoxicology and Environmental Safety, 77, 7-17. https://doi.org/10.1016/j.ecoenv.2011.09.016
Magarvey, N.A., Keller, J.M., Bernan, V., Dworkin, M., & Sherman, D.H. (2004). Isolation and characterization of novel marine-derived actinomycete taxa rich in bioactive metabolites. Applied and Environmental Microbiology, 70, 7520 7529. https://doi.org/10.1128/AEM.70.12.7520-7529.2004
Martin, Y.E., & Johnson, E.A. (2012). Biogeosciences survey: studying interactions of the biosphere with the lithosphere, hydrosphere and atmosphere. Progress in Physical Geography, 36, 833-852. https://doi.org/10.1177/0309133312457107
Masindi, V., & Muedi, K.L. (2018). Environmental contamination by heavy metals. In: H.E. Saleh, R.F. Aglan (Eds), Heavy metals (pp. 115-113). IntechOpen, Rijeka. https://doi.org/10.5772/intechopen.76082
Mincer, T.J., Jensen, P.R., Kauffman, C.A., & Fenical, W. (2002). Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Applied and Environmental Microbiology, 68(10), 5005-5011. https://doi.org/10.1128/AEM.68.10.5005-5011.2002
Mo, P., Yu, Y. Z., Zhao, J.-R., & Gao, J. (2017). Streptomyces xiangtanensis sp. nov., isolated from a manganese-contaminated soil. Antonie Leeuwenhoek, 110, 297-304. https://doi.org/10.1007/s10482-016-0797-z
Mondal, H., & Thomas, J. (2022). Isolation and characterization of a novel actinomycete isolated from marine sediments and its antibacterial activity against fish pathogens. Antibiotics, 11, 1546. https://doi.org/10.3390/antibiotics11111546
Pazirandeh, M., Wells, B.M., Ryan, R.L. (1998). Development of bacterium based heavy metal biosorbents: enhanced uptake of cadmium and mercury by Escherichia coli expressing a metal-binding motif. Applied and Environmental Microbiology, 64, 4068. https://doi.org/10.1128/AEM.64.10.4068-4072.1998
Polti, M.A., Amoroso, M.J., & Abate, C.M. (2007). Chromium (VI) resistance and removal by actinomycete strains isolated from sediments. Chemosphere, 67(4), 660 667. https://doi.org/10.1016/j.chemosphere.2006.11.008
Rahman, Z., & Singh, V.P. (2019). The relative impact of toxic heavy metals (THMs) (arsenic (As), cadmium (Cd), chromium (Cr)(VI), mercury (Hg), and lead (Pb)) on the total environment: An overview. Environmental Monitoring and Assessment, 191, 419. https://doi.org/10.1007/s10661-019-7528-7
Reasoner, D.J., & Geldreich, E.E. (1985). A new medium for the enumeration and subculture of bacteria from potable water. Applied and Environmental Microbiology, 49(1), 1-7. https://doi.org/10.1128/aem.49.1.1-7.1985
Sağlam, M.T. (1978). Toprak kimyası tatbikat notları. Atatürk Üniversitesi.
Saitou, N., & Nei, M. (1987). The neighbour-joining method: A new method for constructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sanjenbam, P., Saurav, K., & Kannabiran, K. (2012). Biosorption of mercury and lead by aqueous Streptomyces VITSVK9 sp. isolated from marine sediments from the Bay of Bengal, India. Frontiers of Chemical Science and Engineering, 6(2), 198-202. https://doi.org/10.1007/s11705-012-1285-2
Schmidt, A., Schmidt, A., Haferburg, G., & Kothe, E. (2007). Superoxide dismutases of heavy metal resistant Streptomycetes. The Journal of Basic Microbiology., 47, 56-62. https://doi.org/10.1002/jobm.200610213
Stackebrandt, E., & Ebers, J. (2006). Taxonomic parameters revisited: Tarnished gold standards. Microbiology Today, 33, 152–155.
Stackebrandt, E., & Goebel, B. (1994). Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology, 44(4), 846-849. https://doi.org/10.1099/00207713-44-4-846
Tan, G.Y.A., Ward, A.C., & Goodfellow, M. (2006). Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Systematic and Applied Microbiology, 29(7), 557-569. https://doi.org/10.1016/j.syapm.2006.01.007
Venkatramanan, S., Ramkumar, T., Anithamary, I., & Vasudevan, S. (2014). Heavy metal distribution in surface sediments of the tirumalairajan river estuary and the surrounding coastal area, east coast of india. The Arabian Journal of Geosciences, 7, 123-130. https://doi.org/10.1007/s12517-012-0734-z

Details

Primary Language

English

Subjects

Conservation and Biodiversity

Journal Section

Research Article

Authors

Aysel Veyisoğlu ^*
0000-0002-1406-5513
Türkiye

Demet Tatar
0000-0002-9317-3263
Türkiye

Ali Tokatlı
0000-0002-7559-8882
Türkiye

Hünkar Avni Duyar
0000-0002-2560-5407
Türkiye

Early Pub Date

December 1, 2025

Publication Date

December 10, 2025

Submission Date

May 17, 2025

Acceptance Date

September 16, 2025

Published in Issue

Year 2025 Volume: 42 Number: 4

DOI

https://doi.org/10.12714/egejfas.42.4.03

IZ

https://izlik.org/JA77CS45HR

Cite

RIS / Bibtex

APA

Veyisoğlu, A., Tatar, D., Tokatlı, A., & Duyar, H. A. (2025). Actinobacteria with heavy metal tolerance from the Sinop coast: A molecular characterization approach. Ege Journal of Fisheries and Aquatic Sciences, 42(4), 298-306. https://doi.org/10.12714/egejfas.42.4.03