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Assessment of bacteria and archaea levels in Çakalburnu Lagoon (İzmir) sediments by real-time PCR

Year 2021, Volume 38, Issue 2, 147 - 154, 15.06.2021
https://doi.org/10.12714/egejfas.38.2.02

Abstract



Coastal lagoons are shallow water masses, discredited from the marines as a barrier that permits water to change through one or more inputs. These fragile ecosystems have a specific type of sediments with their own characteristics. Biogeochemical processes, mostly intervened by the benthic microbial loop, are significant for understanding the relationships among the lagoon and the contiguous coastal partition. This study was conducted in the Çakalburnu Lagoon (İzmir) area, which is located at the Bay of İzmir and the area covers 67 hectares. The aim of the present study is to constitute of determining the number of different microbial communities in the lagoon sediments. We collected from lagoon sediments samples at 7 stations and we applied a Real-time qPCR assay to determine levels of archaea (ARC), methanogenic archaea (MCRA), anaerobic methane oxidation archaea (ANME 1, ANME 2a, ANME 2c), bacteria (BAC) and sulfate-reducing bacteria (SRB2) in the study. The amount of maximum abundance of archaeal and bacterial 16S rRNA gene in sediments are 2,66x1010 gene copy numbers/g and 3,89x107 gene copy numbers/g, respectively. So, it was established that the archaeal abundance was intense in the lagoon sediments. The characterization of microbial diversity is significant for the comprehension of the biological fundamentals of the ecosystem. The data presented in our study contributes to the studies on preserving ecological and microbiological balance and determining biogeochemical cycles in sensitive ecosystems such as lagoons. The research will be conducted on studies to determine the abundance levels of seasonal and annual microbial groups in the future.



References

  • Al Amoudi, S. (2016). Bioprospecting Sediments from Red Sea Coastal Lagoons for Microorganisms and Their Antimicrobial Potential. King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia, PhD thesis. DOI: 10.3390/md14090165
  • Behera, P., Mohapatra, M., Kim J.Y. & Rastogi, G. (2020). Benthic archaeal community structure and carbon metabolic profiling of heterotrophic microbial communities in brackish sediments. Science of the Total Environment, 706, 135709. DOI:10.1016/j.scitotenv.2019.135709
  • Caumette, P. (1986). Phototrophic sulfur bacteria and sulfate-reducing bacteria causing red waters in a shallow brackish coastal lagoon (Prevost Lagoon, France). FEMS Microbiology Ecology, 38, 113-124. DOI: 10.1016/0378-1097(86)90148-5
  • Esbah, H. (2004). Agricultural land loss due to urbanization. Proceedings of Agro-Environs, (pp. 231-238), Udine, Italy.
  • Glud, R.N. (2008). Oxygen dynamics of marine sediments. Marine Biology Research, 4, 243–289. DOI: 10.1080/17451000801888726
  • Jørgensen, B.B. & Bak, F. (1991). Pathways and microbiology of thiosulfate transformations and sulfate reduction in a marine sediment (Kattegat, Denmark). Applied and Environmental Microbiology, 57, 847-856. DOI: 10.1128/AEM.57.3.847-856.1991
  • Kara, B. (2019). Agrarian and wetland areas under metropolitan threats: learning from the case of Inciralti, Izmir (Turkey). Applied Ecology and Environmental Research 17(6),15087-15102. DOI:10.15666/aeer/1706_1508715102
  • Li, W., Dou, Z., Cui, L., Zhao, X., Zhang, M., Zhang, Y., Gao, C., Yang, Z., Lei Y. & Pan X. (2020). Soil fauna diversity at different stages of reed restoration in a lakeshore wetland at Lake Taihu, China. Ecosystem Health and Sustainability, 6(1), 1722034. DOI:10.1080/20964129.2020.1722034
  • Lijklema, L. (1986). Phosphorus accumulation in sediments and internal loading. Aquatic Ecology, 20, 213-224. DOI:10.1007/BF02291164
  • Manini, E., Fiordelmondo, C., Gambi, C., Pusceddu, A. & Danovaro, R. (2003). Benthic microbial loop functioning in coastal lagoons: a comparative approach. Oceanologica Acta, 26, 27–38. DOI: 10.1016/S0399-1784(02)01227-6
  • Montoya, L., Lozada-Chavez, I., Amils, R., Rodriguez, N. & Marin, I. (2011). The sulfate-rich and extreme saline sediment of the ephemeral Tirez Lagoon: a biotope for acetoclastic sulfate-reducing bacteria and hydrogenotrophic methanogenic archaea. International Journal of Microbiology, 2011, 753758, 22. DOI:10.1155/2011/753758
  • Obi, C.C., Adebusoye, S.A., Ugoji, E.O., Ilori, M.O., Amund, O.O. & Hickey, W.J. (2016). Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes. Frontiers in Microbiology, 7, 1213. DOI: 10.3389/fmicb.2016.01213
  • Oueslati, W., Velde, S., Helali, M.A., Added, A., Aleya, L. & Meysman F.J.R. (2019). Carbon, iron and sulphur cycling in the sediments of a Mediterranean lagoon (Ghar El Melh, Tunisia). Estuarine, Coastal and Shelf Science, 221, 156–169. DOI: 10.1016/j.ecss.2019.03.008
  • Pomeroy, L.R., Smith, E.E. & Grant, C.M. (1965). The exchange of phosphate between estuarine water and sediments. Limnology and Oceanography, 10, 167-172. DOI: 10.4319/lo.1965.10.2.0167
  • Pusceddu, A., Serra, E., Sanna, O. & Fabiano, M. (1996). Seasonal fluctuations in the nutritional value of particulate organic matter in a lagoon. Chemistry and Ecology, 12, 199–212. DOI: 10.1080/02757549608039082
  • Ramsar Convention Bureau. (1992). Ramsar Convention, Slimbridge, England.
  • Reindl A.R. & Bolałek, J. (2017). Biological factor controlling methane production in surface sediment in the Polish part of the Vistula Lagoon. Oceanological and Hydrobiological Studies, 46(2), 223-230. DOI:10.1515/ohs-2017-0022
  • Ribeiro, C., Ribeiro, A.R. & Tiritan, M.E. (2016). Occurrence of persistent organic pollutants in sediments and biota from Portugal versus European incidence: a critical overview. Journal of Environmental Science and Health, Part B, 51, 143–153. DOI: 10.1080/03601234.2015.1108793
  • Steinberg, L.M. & Regan, J.M. (2009). McrA-targeted real-time quantitative PCR method to examine methanogen communities. Applied and Environmental Microbiology, 75 (13), 4435–4442. DOI: 10.1128/AEM.02858-08
  • Suzuki, M.T., Taylor, L.T. & DeLong, E.F. (2000). Quantitative analysis of small-subunit rRNA genes in mixed 50- microbial populations via nuclease assays. Applied and Environmental Microbiology, 66, 4605–4614. DOI: 10.1128/AEM.66.11.4605-4614.2000
  • Takii, S. & Fukui, M. (1991). Relative importance of methanogenesis, sulfate reduction and denitrification in sediments of the lower Tama river. Bulletin of the Japanese Society of Microbial Ecology, 6, 1-8. DOI: 10.1264/microbes1986.6.9
  • Timmers, P.H.A., Gieteling, J., Widjaja-Greefkes, H.C.A., Plugge, C.M., Stams, A.J.M., Lens, P.N.L. & Meulepas, R.J.W. (2015). Growth of anaerobic methane-oxidizing archaea and sulfate- reducing bacteria in a high-pressure membrane capsule bioreactor. Applied and Environmental Microbiology, 82(4), 1286-1296. DOI: 10.1128/AEM.03255-14
  • Timmers, H.A., Welte, C.U., Koehorst, J.J., Plugge, C.M., Jetten, M.S.M. & Stams A.J.M. (2017). Reverse Methanogenesis and Respiration in Methanotrophic Archaea Peer. Archaea, 2017, 1654237, 22. DOI:10.1155/2017/1654237
  • Torres-Alvarado, M.R. Calva-Benítez, L.G., Álvarez-Hernández, S. & Trejo-Aguilar, G. (2016). Anaerobic microbiota: spatial-temporal changes in the sediment of a tropical coastal lagoon with ephemeral inlet in the Gulf of Mexico. International Journal of Tropical Biology, 64(4), 1759-1770. DOI: 10.15517/rbt.v64i4.22449
  • Vigneron, A., Cruaud, P., Pignet, P., Caprais, J.C., Cambon-Bonavita, M.A., Godfroy, A. & Laurent, T. (2013). Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California). ISME Journal, 7, 1595–1608. DOI: 10.1038/ismej.2013.18
  • Yin, H. (2003). The Thoughts of Wetland Conservation in China. Wetland Science, 1, 68–72. Yu, Y., Lee, C., Kim, J. & Hwang, S. (2005). Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnololgy and Bioengineering, 89(6), 670-679. DOI:10.1002/bit.20347
  • Yucel-Gier, G., Kacar, A., Gonul, L.T., Pazi, I., Kucuksezgin, F., Erarslanoglu, N. & Toker, S.K. (2018). Evaluation of the relationship of picoplankton and viruses to environmental variables in a lagoon system (Çakalburnu Lagoon, Turkey). Chemistry and Ecology, 34 (3), 211–228. DOI:10.1080/02757540.2018.1427230
  • Zeitzschell, B. (1980). Sediment-water interaction in nutrient dynamics. In: Tenore, K.R., & Coull, B.C. (Edit.), Marine Benthic Dynamics. University of South Carolina, Columbia., pp 195-218

Çakalburnu Lagünü (İzmir) sedimentlerinde real-time PCR ile bakteri ve arke düzeylerinin değerlendirilmesi

Year 2021, Volume 38, Issue 2, 147 - 154, 15.06.2021
https://doi.org/10.12714/egejfas.38.2.02

Abstract



Kıyısal lagünler, bir veya daha fazla sayıda giriş ile su değişimine izin veren ve bir bariyer gibi denizden ayrılan sığ su kütleleridir. Bu kırılgan ekosistemler kendilerine özgü sediment yapılarına sahip olmaktadır. Büyük ölçüde bentik mikrobiyal döngü yoluyla yürütülen biyojeokimyasal süreçler; lagün ile bitişik kıyı bölgesi arasındaki ilişkiyi anlamak için oldukça önemlidir. Bu çalışma, İzmir Körfezi'nde bulunan ve 67 hektarlık bir alan kaplayan Çakalburnu Lagünü’nde gerçekleştirilmiştir. Çalışmanın amacını, lagün sedimentlerinde, farklı mikrobiyal toplulukların düzeylerinin belirlenmesi oluşturmaktadır. Araştırmada, lagünün 7 noktasından toplanan sediment örneklerinde, Genel Arke (ARC), Metanojenik Arke (MCRA), Anaerobik Metan Oksidasyonu yapan Arke (ANME 1, ANME 2a, ANME 2c), Genel Bakteri (BAC) ve Sülfat İndirgeyen Bakteri (SRB2) seviyelerinin tespitinde Real-Time qPCR analizleri gerçekleştirilmiştir. Çakalburnu Lagünü sedimentlerinde incelenen Genel Arke ve Genel Bakteri bollukların maksimum değerleri sırasıyla 2,66x1010 gen kopya sayısı/gr ve 3,89x107 gen kopya sayısı/gr olarak belirlenmiş olup, bu çalışmada lagün sedimentlerinde arkeal bolluğun yoğun olduğu görülmüştür. Mikrobiyal çeşitliliğin karakterizasyonu, ekosistemin biyolojik temellerinin anlaşılması açısından önemlidir. Çalışmamızda sunulan veriler, lagünler gibi hassas ekosistemlerde, ekolojik ve mikrobiyolojik dengenin korunması ile biyojeokimyasal döngülerin belirlenmesine yönelik çalışmalara katkı sağlamaktadır. Gelecekteki çalışmalarda, mikrobiyal grupların seviyelerinin mevsimlere ve yıllara göre değişimlerinin izlenmesi yönünde çalışmalar yürütülecektir. 


References

  • Al Amoudi, S. (2016). Bioprospecting Sediments from Red Sea Coastal Lagoons for Microorganisms and Their Antimicrobial Potential. King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia, PhD thesis. DOI: 10.3390/md14090165
  • Behera, P., Mohapatra, M., Kim J.Y. & Rastogi, G. (2020). Benthic archaeal community structure and carbon metabolic profiling of heterotrophic microbial communities in brackish sediments. Science of the Total Environment, 706, 135709. DOI:10.1016/j.scitotenv.2019.135709
  • Caumette, P. (1986). Phototrophic sulfur bacteria and sulfate-reducing bacteria causing red waters in a shallow brackish coastal lagoon (Prevost Lagoon, France). FEMS Microbiology Ecology, 38, 113-124. DOI: 10.1016/0378-1097(86)90148-5
  • Esbah, H. (2004). Agricultural land loss due to urbanization. Proceedings of Agro-Environs, (pp. 231-238), Udine, Italy.
  • Glud, R.N. (2008). Oxygen dynamics of marine sediments. Marine Biology Research, 4, 243–289. DOI: 10.1080/17451000801888726
  • Jørgensen, B.B. & Bak, F. (1991). Pathways and microbiology of thiosulfate transformations and sulfate reduction in a marine sediment (Kattegat, Denmark). Applied and Environmental Microbiology, 57, 847-856. DOI: 10.1128/AEM.57.3.847-856.1991
  • Kara, B. (2019). Agrarian and wetland areas under metropolitan threats: learning from the case of Inciralti, Izmir (Turkey). Applied Ecology and Environmental Research 17(6),15087-15102. DOI:10.15666/aeer/1706_1508715102
  • Li, W., Dou, Z., Cui, L., Zhao, X., Zhang, M., Zhang, Y., Gao, C., Yang, Z., Lei Y. & Pan X. (2020). Soil fauna diversity at different stages of reed restoration in a lakeshore wetland at Lake Taihu, China. Ecosystem Health and Sustainability, 6(1), 1722034. DOI:10.1080/20964129.2020.1722034
  • Lijklema, L. (1986). Phosphorus accumulation in sediments and internal loading. Aquatic Ecology, 20, 213-224. DOI:10.1007/BF02291164
  • Manini, E., Fiordelmondo, C., Gambi, C., Pusceddu, A. & Danovaro, R. (2003). Benthic microbial loop functioning in coastal lagoons: a comparative approach. Oceanologica Acta, 26, 27–38. DOI: 10.1016/S0399-1784(02)01227-6
  • Montoya, L., Lozada-Chavez, I., Amils, R., Rodriguez, N. & Marin, I. (2011). The sulfate-rich and extreme saline sediment of the ephemeral Tirez Lagoon: a biotope for acetoclastic sulfate-reducing bacteria and hydrogenotrophic methanogenic archaea. International Journal of Microbiology, 2011, 753758, 22. DOI:10.1155/2011/753758
  • Obi, C.C., Adebusoye, S.A., Ugoji, E.O., Ilori, M.O., Amund, O.O. & Hickey, W.J. (2016). Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes. Frontiers in Microbiology, 7, 1213. DOI: 10.3389/fmicb.2016.01213
  • Oueslati, W., Velde, S., Helali, M.A., Added, A., Aleya, L. & Meysman F.J.R. (2019). Carbon, iron and sulphur cycling in the sediments of a Mediterranean lagoon (Ghar El Melh, Tunisia). Estuarine, Coastal and Shelf Science, 221, 156–169. DOI: 10.1016/j.ecss.2019.03.008
  • Pomeroy, L.R., Smith, E.E. & Grant, C.M. (1965). The exchange of phosphate between estuarine water and sediments. Limnology and Oceanography, 10, 167-172. DOI: 10.4319/lo.1965.10.2.0167
  • Pusceddu, A., Serra, E., Sanna, O. & Fabiano, M. (1996). Seasonal fluctuations in the nutritional value of particulate organic matter in a lagoon. Chemistry and Ecology, 12, 199–212. DOI: 10.1080/02757549608039082
  • Ramsar Convention Bureau. (1992). Ramsar Convention, Slimbridge, England.
  • Reindl A.R. & Bolałek, J. (2017). Biological factor controlling methane production in surface sediment in the Polish part of the Vistula Lagoon. Oceanological and Hydrobiological Studies, 46(2), 223-230. DOI:10.1515/ohs-2017-0022
  • Ribeiro, C., Ribeiro, A.R. & Tiritan, M.E. (2016). Occurrence of persistent organic pollutants in sediments and biota from Portugal versus European incidence: a critical overview. Journal of Environmental Science and Health, Part B, 51, 143–153. DOI: 10.1080/03601234.2015.1108793
  • Steinberg, L.M. & Regan, J.M. (2009). McrA-targeted real-time quantitative PCR method to examine methanogen communities. Applied and Environmental Microbiology, 75 (13), 4435–4442. DOI: 10.1128/AEM.02858-08
  • Suzuki, M.T., Taylor, L.T. & DeLong, E.F. (2000). Quantitative analysis of small-subunit rRNA genes in mixed 50- microbial populations via nuclease assays. Applied and Environmental Microbiology, 66, 4605–4614. DOI: 10.1128/AEM.66.11.4605-4614.2000
  • Takii, S. & Fukui, M. (1991). Relative importance of methanogenesis, sulfate reduction and denitrification in sediments of the lower Tama river. Bulletin of the Japanese Society of Microbial Ecology, 6, 1-8. DOI: 10.1264/microbes1986.6.9
  • Timmers, P.H.A., Gieteling, J., Widjaja-Greefkes, H.C.A., Plugge, C.M., Stams, A.J.M., Lens, P.N.L. & Meulepas, R.J.W. (2015). Growth of anaerobic methane-oxidizing archaea and sulfate- reducing bacteria in a high-pressure membrane capsule bioreactor. Applied and Environmental Microbiology, 82(4), 1286-1296. DOI: 10.1128/AEM.03255-14
  • Timmers, H.A., Welte, C.U., Koehorst, J.J., Plugge, C.M., Jetten, M.S.M. & Stams A.J.M. (2017). Reverse Methanogenesis and Respiration in Methanotrophic Archaea Peer. Archaea, 2017, 1654237, 22. DOI:10.1155/2017/1654237
  • Torres-Alvarado, M.R. Calva-Benítez, L.G., Álvarez-Hernández, S. & Trejo-Aguilar, G. (2016). Anaerobic microbiota: spatial-temporal changes in the sediment of a tropical coastal lagoon with ephemeral inlet in the Gulf of Mexico. International Journal of Tropical Biology, 64(4), 1759-1770. DOI: 10.15517/rbt.v64i4.22449
  • Vigneron, A., Cruaud, P., Pignet, P., Caprais, J.C., Cambon-Bonavita, M.A., Godfroy, A. & Laurent, T. (2013). Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California). ISME Journal, 7, 1595–1608. DOI: 10.1038/ismej.2013.18
  • Yin, H. (2003). The Thoughts of Wetland Conservation in China. Wetland Science, 1, 68–72. Yu, Y., Lee, C., Kim, J. & Hwang, S. (2005). Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnololgy and Bioengineering, 89(6), 670-679. DOI:10.1002/bit.20347
  • Yucel-Gier, G., Kacar, A., Gonul, L.T., Pazi, I., Kucuksezgin, F., Erarslanoglu, N. & Toker, S.K. (2018). Evaluation of the relationship of picoplankton and viruses to environmental variables in a lagoon system (Çakalburnu Lagoon, Turkey). Chemistry and Ecology, 34 (3), 211–228. DOI:10.1080/02757540.2018.1427230
  • Zeitzschell, B. (1980). Sediment-water interaction in nutrient dynamics. In: Tenore, K.R., & Coull, B.C. (Edit.), Marine Benthic Dynamics. University of South Carolina, Columbia., pp 195-218

Details

Primary Language Turkish
Subjects Ecology
Journal Section Articles
Authors

Burcu OMUZBÜKEN
DOKUZ EYLÜL ÜNİVERSİTESİ
0000-0002-6681-7174
Türkiye


Aslı KAÇAR (Primary Author)
DOKUZ EYLÜL ÜNİVERSİTESİ
0000-0002-8705-3695
Türkiye

Publication Date June 15, 2021
Application Date September 21, 2020
Acceptance Date December 24, 2020
Published in Issue Year 2021, Volume 38, Issue 2

Cite

APA Omuzbüken, B. & Kaçar, A. (2021). Çakalburnu Lagünü (İzmir) sedimentlerinde real-time PCR ile bakteri ve arke düzeylerinin değerlendirilmesi . Ege Journal of Fisheries and Aquatic Sciences , 38 (2) , 147-154 . DOI: 10.12714/egejfas.38.2.02