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Çanakkale Boğazı Yüzey Sularındaki Müsilaj İçin Shotgun Metagenomik Analizi: Metabolik Çeşitlilik, Mikrobiyal Topluluk Yapısı ve Antibiyotik Direnç Genleri

Yıl 2021, Cilt: 6 Sayı: 4, 717 - 726, 31.12.2021
https://doi.org/10.35229/jaes.989058

Öz

Bu çalışma da Çanakkale Boğazı yüzey sularındaki müsilajın metabolik çeşitliliğini, mikrobiyal topluluk yapısını ve çeşitli antimikrobiyal direnç genlerini incelemek için shotgun metagenom dizilimi kullandık. Nisan 2021'de Çanakkale Boğazı'nın üç farklı istasyonundan müsilaj örnekleri toplandı. Filum düzeyinde baskın mikrobiyal topluluklar Bacteroidetes (%20.06), Proteobacteria (%13.68), Verrucomicrobia (%6.25), Planctomycetes (%3.02) ve Cyanobacteria (%2.5) olarak belirlendi. KEGG (Kyoto Genler ve Genomlar Ansiklopedisi) kullanılarak yapılan metabolik yol analizi, müsilaj örneklerinin genlerinin çoğunun sınıflandırılmamış (%73.86), ardından sırasıyla metabolizma (%14.45), genetik prosesler (%4.16), çevresel prosesler ( %2.57, hücresel prosesler (%1.88), insan hastalıkları (%1.61) ve organizma sistemleri (%1.47) ile ilişkili olduğunu göstermiştir. dfrA3 geni baskın olup (%20,36), ardından sırasıyla CRP (%18,17), PmrE (%14,92), rpoB2 (%11,17), SoxR (%7,49), AbeS (%6,83), baeR (%5,22), PmrF (%3,70), dfrA22 (%2,20), dfrA26 (%1,76), dfrA20 (%1,63), golS (%1,26), CAT (%1,03), mtrA (%1,01), TMB-1 (%0,64), novA (%0,64), dfrK (%0,59), vanXB (%0,48), dfrG (%0,39), FosC2 (%0,31) ve MexA (%0,20) genleri yer almıştır. Antibiyotik direnç geni (ARG) tipleri, temel olarak çoklu ilaç direnci (%40,19), trimetoprim (%26,93), polimiksin (%18,62), rifamisin (%11,17), kloramfenikol (%1,03), aminokumarin (%0,64), beta-laktamaz (%0,64), fosfomisin (%0,31) ve vankomisin (%0,48) direnç genlerini içeriyordu. Müsilaj yapısında yüksek çoklu antibiyotik direnci ve trimetoprim, polimiksin, rifamisin ve kloramfenikol gibi önemli antibiyotik dirençlerinin bulunması halk sağlığı açısından riskli bir durum olarak değerlendirilebilir. Bu bulgular ışığında gelecekte farklı zamanlarda ve derinliklerden alınacak örneklerle daha detaylı çalışmalara ihtiyaç olduğu gözlemlenmiştir.

Kaynakça

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  • 8. Bobrova, O. Y., Kristoffersen, J. B., Oulas, A., & Ivanytsia, V. O. (2016). Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine. Acta Biochimica Polonica 63(2), 315-319. DOI: 10.18388/abp.2015_1145
  • 9. Calero-Cáceres, W., & Balcázar, J. L. (2019). Antibiotic resistance genes in bacteriophages from diverse marine habitats. Science of the Total Environment, 654, 452-455. DOI: 10.1016/j.scitotenv.2018.11.166
  • 10. Chiang, E., Schmidt, M. L., Berry, M. A., Biddanda, B. A., Burtner, A., Johengen, T. H., ... & Denef, V. J. (2018). Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS One, 13(3), e0195112. DOI:10.1371/journal.pone.0195112
  • 11. Cortés-Lorenzo, C., Sipkema, D., Rodríguez-Díaz, M., Fuentes, S., Juárez-Jiménez, B., Rodelas, B., ... & González-López, J. (2014). Microbial community dynamics in a submerged fixed bed bioreactor during biological treatment of saline urban wastewater. Ecological Engineering, 71, 126-132. DOI:10.1016/j.ecoleng.2014.07.025
  • 12. Dalcin Martins, P., de Jong, A., Lenstra, W. K., van Helmond, N. A., Slomp, C. P., Jetten, M. S., ... & Rasigraf, O. (2021). Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen‐limited methane‐and iron‐fed bioreactor inoculated with Bothnian Sea sediments. MicrobiologyOpen, 10(1), e1175. DOI:10.1101/2020.09.22.307553
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Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes

Yıl 2021, Cilt: 6 Sayı: 4, 717 - 726, 31.12.2021
https://doi.org/10.35229/jaes.989058

Öz

In this study, we used shotgun metagenome sequencing to examine the metabolic diversity, microbial community structure and diverse antimicrobial resistance genes of mucilage in the surface waters of the Çanakkale Strait (Dardanelles). Mucilage samples were collected in April 2021 from the three different stations of the Dardanelles. The dominant microbial communities at the phylum level were Bacteroidetes (20.06%), Proteobacteria (13.68%), Verrucomicrobia (6.25%), Planctomycetes (3.02%) and Cyanobacteria (2.5%). Metabolic pathway analysis using KEGG (Kyoto Encyclopedia of Genes and Genomes) revealed that most of the genes of mucilage samples were involved in unclassified (73.86%) followed by metabolism (14.45%), genetic information processing (4.16%), environmental information processing (2.57%), cellular processing (1.88%), human diseases (1.61%), and organismal systems (1.47%). The dfrA3 gene was the most prevalent (20.36%) followed by CRP (18.17%), PmrE (14.92%), rpoB2 (11.17%), SoxR (7.49%), AbeS (6.83%), baeR (5.22%), PmrF (3.70%), dfrA22 (2.20%), dfrA26 (1.76%), dfrA20 (1.63%), golS (1.26%), CAT (1.03%), mtrA (1.01%), TMB-1 (0.64%), novA (0.64%), dfrK (0.59%), vanXB (0.48%), dfrG (0.39%), FosC2 (0.31%), and MexA (0.20%) genes. Antibiotic resistance gene (ARG) types mainly included the resistance genes of multidrug (40.19%), trimethoprim (26.93%), polymyxin (18.62%), rifamycin (11.17%), chloramphenicol (1.03%), aminocoumarin (0.64%), beta-lactamase (0.64%), fosfomycin (0.31%), and vancomycin (0.48%). Antibiotic-resistant bacteria in mucilage can adhere to human skin during swimming, fishing, water sports etc., enter the body through the nose and mouth, and transfer genetic information to the bacteria in contact areas in the human body. Therefore, this situation is risky in public health, and necessary precautions should be taken. In the light of these findings, it has been observed that there is a need for more detailed studies in the future.

Kaynakça

  • 1. Aktan, Y., Dede, A., & Çiftci, P.S. (2008). Mucilage event associated with diatoms and dinoflagellates in Sea of Marmara, Turkey, Harmful Algae News, 36: 1-3.
  • 2. Arnds, J., Knittel, K., Buck, U., Winkel, M., & Amann, R. (2010). Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake. Systematic and Applied Microbiology, 33(3), 139-148. DOI: 10.1016/j.syapm.2009.12.005
  • 3. Balkis, N., Atabay, H., Türetgen, I., Albayrak, S., Balkis, H., & Tüfekçi, V. (2011). Role of single-celled organisms in mucilage formation on the shores of Büyükada Island (the Marmara Sea). Journal of the Marine Biological Association of the United Kingdom, 91(4), 771-781. DOI:10.1017/S0025315410000081
  • 4. Balkıs-Ozdelice, N., Durmuş, T., & Balcı, M. (2021). “A Preliminary Study on the Intense Pelagic and Benthic Mucilage Phenomenon Observed in the Sea of Marmara”, International Journal of Environment and Geoinformatics, 8(4), 414-422. DOI:10.30897/ijegeo.954787
  • 5. Bano, N., & Hollibaugh, J. T. (2002). Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Applied and Environmental Microbiology, 68(2), 505-518. DOI: 10.1128/AEM.70.2.781-789.2004
  • 6. Bengtsson, M. M., & Øvreås, L. (2010). Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea. BMC Microbiology, 10(1), 1-12. DOI: 10.1186/1471-2180-10-261
  • 7. Bergmann, G. T., Bates, S. T., Eilers, K. G., Lauber, C. L., Caporaso, J. G., Walters, W. A., ... & Fierer, N. (2011). The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biology and Biochemistry, 43(7), 1450-1455. DOI: 10.1016/j.soilbio.2011.03.012
  • 8. Bobrova, O. Y., Kristoffersen, J. B., Oulas, A., & Ivanytsia, V. O. (2016). Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine. Acta Biochimica Polonica 63(2), 315-319. DOI: 10.18388/abp.2015_1145
  • 9. Calero-Cáceres, W., & Balcázar, J. L. (2019). Antibiotic resistance genes in bacteriophages from diverse marine habitats. Science of the Total Environment, 654, 452-455. DOI: 10.1016/j.scitotenv.2018.11.166
  • 10. Chiang, E., Schmidt, M. L., Berry, M. A., Biddanda, B. A., Burtner, A., Johengen, T. H., ... & Denef, V. J. (2018). Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS One, 13(3), e0195112. DOI:10.1371/journal.pone.0195112
  • 11. Cortés-Lorenzo, C., Sipkema, D., Rodríguez-Díaz, M., Fuentes, S., Juárez-Jiménez, B., Rodelas, B., ... & González-López, J. (2014). Microbial community dynamics in a submerged fixed bed bioreactor during biological treatment of saline urban wastewater. Ecological Engineering, 71, 126-132. DOI:10.1016/j.ecoleng.2014.07.025
  • 12. Dalcin Martins, P., de Jong, A., Lenstra, W. K., van Helmond, N. A., Slomp, C. P., Jetten, M. S., ... & Rasigraf, O. (2021). Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen‐limited methane‐and iron‐fed bioreactor inoculated with Bothnian Sea sediments. MicrobiologyOpen, 10(1), e1175. DOI:10.1101/2020.09.22.307553
  • 13. Danovaro, R., Fonda Umani, S., & Pusceddu, A. (2009). “Climate change and the potential spreading of marine mucilage and microbial pathogens in the Mediterranean Sea”, PLoS One, 4(9), 7006. DOI:10.1371/journal.pone.0007006
  • 14. DeLong, E. F., Franks, D. G., & Alldredge, A. L. (1993). Phylogenetic diversity of aggregate‐attached vs. free‐living marine bacterial assemblages. Limnology and Oceanography, 38(5), 924-934. DOI: 10.4319/lo.1993.38.5.0924
  • 15. FAO 2002. FAO urges countries to discontinue the use of chloramphenicol in animal production. 24/01/2002
  • 16. Fernández-Gómez, B. (2012). Ecology of marine Bacteroidetes: a genomics approach. Ph.D. thesis. Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.
  • 17. Floss, H. G., & Yu, T. W. (2005). Rifamycin mode of action, resistance, and biosynthesis. Chemical Reviews, 105(2), 621-632. DOI: 10.1021/cr030112j
  • 18. Freitas, S., Hatosy, S., Fuhrman, J. A., Huse, S. M., Welch, D. B. M., Sogin, M. L., & Martiny, A. C. (2012). Global distribution and diversity of marine Verrucomicrobia. The ISME Journal, 6(8), 1499-1505. DOI:10.1038/ismej.2012.3
  • 19. Fuchsman, C. A., Staley, J. T., Oakley, B. B., Kirkpatrick, J. B., & Murray, J. W. (2012). Free-living and aggregate-associated Planctomycetes in the Black Sea. FEMS Microbiology Ecology, 80(2), 402-416. DOI:10.1111/j.1574-6941.2012.01306.x
  • 20. Giani M., Berto D., Zangrando V., Castelli S., Sist P., & Urbani R. (2005). Chemical characterization of different typologies of mucilaginous aggregates in the Northern Adriatic Sea. Science of the Total Environment, 353, 232– 246. DOI:10.1016/j.scitotenv.2005.09.027
  • 21. Gilbert, J. A., Field, D., Huang, Y., Edwards, R., Li, W., Gilna, P., & Joint, I. (2008). Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PloS One, 3(8), e3042. DOI:10.1371/journal.pone.0003042
  • 22. Grenni, P., Ancona, V., & Caracciolo, A. B. (2018). Ecological effects of antibiotics on natural ecosystems: A review. Microchemical Journal, 136, 25-39. DOI:10.1016/j.microc.2017.02.006
  • 23. Huovinen, P., Sundström, L., Swedberg, G., & Sköld, O. (1995). Trimethoprim and sulfonamide resistance. Antimicrobial Agents and Chemotherapy, 39(2), 279-289. DOI: 10.1128/aac.39.2.279
  • 24. Isli F, Aksoy M, Aydıngoz Emre S, Kadı E. Rational Use of Antibiotics By Family Physicians in Turkey During Primary Healthcare Service: A CrossSectional Analysis Through The Prescription Information System. TJFMPC, 14(1), 87-95. DOI:10.21763/tjfmpc.618125
  • 25. Kılıç, E., & Yenizlmez, F. (2019). Türkiye ve AB Ülkelerinde Antibiyotik Kullanımı, Antibiyotik Direnci ve Dış Ticaret Dengesi Üzerine Bir Değerlendirme. ESTÜDAM Halk Sağlığı Dergisi, 4(1):45-54 DOI:10.35232/estudamhsd.503456
  • 26. Lampitt, R. S., Wishner, K. F., Turley, C. M., & Angel, M. V. (1993). Marine snow studies in the Northeast Atlantic Ocean: distribution, composition and role as a food source for migrating plankton. Marine Biology, 116(4), 689-702. DOI:10.1007/BF00355486
  • 27. Lundgreen, R. B., Jaspers, C., Traving, S. J., Ayala, D. J., Lombard, F., Grossart, H. P., & Riemann, L. (2019). Eukaryotic and cyanobacterial communities associated with marine snow particles in the oligotrophic Sargasso Sea. Scientific Reports, 9(1), 1-12. DOI: 10.1038/s41598-019-45146-7
  • 28. Meenakshisundaram, M., Sugantham, F., Muthukumar, C., & Chandrasekar, M. S. (2021). Metagenomic characterization of biofloc in the grow‐out culture of Genetically Improved Farmed Tilapia (GIFT). Aquaculture Research. DOI:10.1111/are.15263
  • 29. Ondov, B. D., Bergman, N. H., & Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12(1), 1-10. DOI:10.1186/1471-2105-12-385
  • 30. Oong, G. C., & Tadi, P. (2021). Chloramphenicol. StatPearls (Last Update: July 9, 2021). https://www.ncbi.nlm.nih.gov/books/NBK555966/
  • 31. Öztürk, İ., Yanalak, M., Arslan, E., Koyuncu, İ., Dülekgürgen, E., Erşahin, M.E., & Türken, T. 2021. “Marmara Denizi’nde Deniz Salyası Sorunu İle İlgili Görüş Ve Öneriler”, İTÜ Raporu, İstanbul. DOI:10.1186/1471-2105-12-385
  • 32. Paul, S., Cortez, Y., Vera, N., Villena, G. K., & Gutiérrez-Correa, M. (2016). Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru. Genomics data, 9, 63-66. DOI:10.3232/SJSS.2019.V9.N1.01
  • 33. Pinnell, L. J., & Turner, J. W. (2019). Shotgun metagenomics reveals the benthic microbial community response to plastic and bioplastic in a coastal marine environment. Frontiers in Microbiology, 10, 1252. DOI:10.3389/fmicb.2019.01252
  • 34. Polymenakou, P. N., Nomikou, P., Mandalakis, M., Kilias, S., Kotoulas, G., Kyrpides, N. C., & Magoulas, A. (2020). Microbial Benthic Communities in the Aegean Sea. In: The Handbook of Environmental Chemistry. Springer, Berlin, Heidelberg. 1-31 p, Springer: Berlin, Heidelberg. DOI:10.1007/698_2020_685
  • 35. Qian, P. Y., Wang, Y., Lee, O. O., Lau, S. C., Yang, J., Lafi, F. F., & Wong, T. Y. (2011). Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. The ISME Journal, 5(3), 507-518. DOI: 10.1038/ismej.2010.112
  • 36. Quillaguamán, J., Guzmán, D., Campero, M., Hoepfner, C., Relos, L., Mendieta, D., ... & Fernández, C. E. (2021). The microbiome of a polluted urban lake harbors pathogens with diverse antimicrobial resistance and virulence genes. Environmental Pollution, 273, 116488. DOI: 10.1016/j.envpol.2021.116488
  • 37. Turgut, H., (2017). Polimiksinler (Kolistin ve Polimiksin B). Turkiye Klinikleri J Inf Dis-Special Topics. 10(1):106-109. DOI:10.32322/jhsm.456990
  • 38. Tüfekçi, V., Balkis, N., Beken, C. P., Ediger, D., & Mantikci, M. (2010). Phytoplankton composition and environmental conditions of the mucilage event in the Sea of Marmara. Turkish Journal of Biology, 34(2), 199-210.
  • 39. Fonda-Umani, S., Ghirardelli, E., & Specchi, M. (1989). Gli episodi di" mare sporco" nell'Adriatico dal 1729 ai giorni nostri. Regione Autonoma Friuli-Venezia Giulia. Direzione Regionale Ambiente, Trieste, p 178. DOI:10.1371/journal.pone.0007006
  • 40. Urakawa, H., Kita-Tsukamoto, K., & Ohwada, K. (1999). Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis The DDBJ accession numbers for the sequences reported in this paper are AB022607–AB022642. Microbiology, 145(11), 3305-3315. DOI:10.1099/00221287-145-11-3305
  • 41. Vojvoda, J., Lamy, D., Sintes, E., Garcia, J. A., Turk, V., & Herndl, G. J. (2014). Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea. Aquatic Microbial Ecology, 73(3), 211-224. DOI:10.3389/fmicb.2020.584222
  • 42. Wang, Y., Liao, S., Gai, Y., Liu, G., Jin, T., Liu, H., ... & Wang, D. Z. (2021). Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean. Frontiers in Microbiology, 12, 229. DOI:10.3389/fmicb.2021.518865
  • 43. WHO (2018). WHO, World Health Organization. Central Asian and Eastern European Surveillance of Antimicrobial Resistance: Annual Report 2018.
  • 44. Woebken, D., Teeling, H., Wecker, P., Dumitriu, A., Kostadinov, I., DeLong, E. F., ... & Glöckner, F. O. (2007). Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. The ISME journal, 1(5), 419-435.
  • 45. Yoon, J., Yasumoto-Hirose, M., Matsuo, Y., Nozawa, M., Matsuda, S., Kasai, H., & Yokota, A. (2007). Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum ‘Verrucomicrobia’, isolated from seawater by in situ cultivation. International Journal of Systematic and Evolutionary Microbiology, 57(7), 1377-1385. DOI: 10.1099/ijs.0.64970-0
  • 46. Zhang, L., Shen, Z., Fang, W., & Gao, G. (2019). Composition of bacterial communities in municipal wastewater treatment plant. Science of the Total Environment, 689, 1181-1191. DOI: 10.1016/j.scitotenv.2019.06.432
Toplam 46 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm Makaleler
Yazarlar

Sevdan Yılmaz 0000-0002-4809-5809

Dilek Kahraman Yılmaz 0000-0002-9626-5446

Ekrem Şanver Çelik 0000-0003-4514-457X

Mehmet Ali Küçüker 0000-0001-9648-8925

Erken Görünüm Tarihi 30 Aralık 2021
Yayımlanma Tarihi 31 Aralık 2021
Gönderilme Tarihi 31 Ağustos 2021
Kabul Tarihi 27 Aralık 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 6 Sayı: 4

Kaynak Göster

APA Yılmaz, S., Kahraman Yılmaz, D., Çelik, E. Ş., Küçüker, M. A. (2021). Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes. Journal of Anatolian Environmental and Animal Sciences, 6(4), 717-726. https://doi.org/10.35229/jaes.989058


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