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Van Gölü Kıyı Kumlarından İzole Edilen Spathidiid Siliyatlar (Ciliophora, Spathidiida) Üzerinde Morfolojik ve Moleküler Filogenetik Araştırmalar

Year 2023, Volume: 28 Issue: 2, 345 - 358, 31.08.2023

N. Fırat Dicle İsmail Yıldız

https://doi.org/10.53433/yyufbed.1239915

Abstract

Bu çalışmada Van Gölü kıyı kumlarından izole edilen bir Spathidium türünün morfolojik ve 18S rDNA gen dizisine dayalı filogenetik özellikleri araştırıldı. Kültürlerde farklı morfoloji sergileyen üç siliyat popülasyonu gözlendi. Bu popülasyonların 18S rDNA gen bölgesine ait nükleotid dizilerinin benzer olduğu görüldü ve bunların aynı türün farklı gelişim evreleri olduğuna karar verildi. 18S rDNA gen bölgesine ait nükleotid dizilerine dayalı filogenetik analizlerde bu çalışmada izole edilen Spathidium sp.’nin hemcinslerinden ziyade Lagynophrya acuminata, Enchelys gasterosterus ve Balantidion pellucidum ile birlikte kümelendikleri görüldü. Spathidiid siliyatların morfolojik sınıflandırma sistemi ile moleküler filogenisi arasında çelişkiler mevcut olup, Spathidium cinsinin parafiletik bir takson olduğu görülmektedir. Bununla birlikte tür zengini Spathidium cinsinin pek çok türü ile ilgili gen dizisinin bilinmemesi bu taksonun moleküler filogenetik durumunun açıklığa kavuşturulmasını sınırlamakta olup, farklı habitatlardan izole edilecek ayrıntılı morfolojik veriler ile birlikte farklı gen bölgelerinin de kullanılacağı filogenetik analizlere ihtiyaç duyulmaktadır.

Keywords

18S rDNA gen dizisi Filogeni Morfoloji Spathidium sp. Van Gölü

Supporting Institution

Van Yüzüncü Yıl Üniversitesi, Bilimsel Araştırma Projeleri Koordinasyon Birimi

Project Number

FYL-2019-7960

Thanks

Bu çalışmaya FYL-2019-7960 numaralı tez projesi kapsamında maddi destek veren Van Yüzüncü Yıl Üniversitesi, Bilimsel Araştırma Projeleri Koordinasyon Birimi’ne teşekkür ederiz.

References

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  • Ayres, D. L., Darling, A., Zwickl, D. J., Beerli, P., Holder, M. T., Lewis, P. O., … , & Suchard, M. A. (2012). BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology, 61, 170–173. doi:10.1093/sysbio/syr100
  • Corliss, J. O. (2001). Protozoan Taxonomy and Systematics. In G. Pettis (Ed.), Encyclopedia of Life Sciences (pp. 1-7). John Wiley & Sons. doi:10.1038/npg.els.0001925
  • Curds, C. R. (1983). British and Other Freshwater Ciliated Protozoa. U.S.A: Cambridge University Press.
  • Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772. doi:10.1038/nmeth.2109
  • Foissner, W. (1991). Basic light and scanning electron microscopic methods for taxonomic studies of ciliated protozoa. European Journal of Protistology, 27(4), 313 - 330. doi:10.1016/S0932-4739(11)80248-8
  • Foissner, W. (2014). An update of 'basic light and scanning electron microscopic methods for taxonomic studies of ciliated protozoa'. International Journal of Systematic and Evolutionary Microbiology, 64, 271 - 292. doi:10.1099/ijs.0.057893-0
  • Foissner, W., Berger, H. & Schaumburg, J. (1999). Identification and Ecology of Limnetic Plankton Ciliates. München, Germany: Informationsberichte des Bayerischen Landesamtes für Wasserwirtschaft.
  • Foissner, W., & Lei, Y. L. (2004). Morphology and ontogenesis of some soil spathidiids (Ciliophora, Haptoria). Linzer biologische Beitrage, 36, 159–199.
  • Foissner, W., & Xu, K. (2007). Monograph of the Spathidiida (Ciliophora, Haptoria) Vol. I: Protospathidiidae, Arcuospathidiidae, Apertospathulidae. Monographiae Biologicae, 81, 1–485.
  • Foissner, W., Wolf, K. W., Kumar, S., Xu, K. D., & Quintela-Alonso, P. (2014). Five new spathidiids (Ciliophora: Haptoria) from Caribbean Tank Bromeliads. Acta Protozoologica, 53(2), 159 - 194. doi:10.4467/16890027AP.14.015.1596
  • Gong, J., Kim, S. J., Kim, S. Y., Min, G. S., Roberts, D. M., Warren, A., & Choi, J. K. (2007). Taxonomic redescriptions of two ciliates, Protogastrostyla pulchra n. g., n. comb. and Hemigastrostyla enigmatica (Ciliophora: Spirotrichea, Stichotrichia), with phylogenetic analyses based on 18S and 28S rRNA gene sequences. Journal of Eukaryotic Microbiology, 54(6), 468 - 478. doi:10.1111/j.1550-7408.2007.00288.x
  • Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018). UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35(2), 518 - 522. doi:10.1093/molbev/msx281
  • Jang, S. W., Vd’acný, P., Shazib, S. U. A., & Shin, M. K. (2015). Morphology, ciliary pattern and molecular phylogeny of Trachelophyllum brachypharynx Levander, 1894 (Litostomatea, Haptoria, Spathidiida). Acta Protozoologica, 54(2), 123 - 135. doi:10.4467/16890027AP.15.010.2735
  • Jang, S. W., Vd’acný, P., Shazib, S. U. A., & Shin, M. K. (2017). Linking morphology and molecules: integrative taxonomy of spathidiids (Protista: Ciliophora: Litostomatea) from Korea. Journal of Natural History, 51(17-18), 939 - 974. doi:10.1080/00222933.2017.1319520
  • Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870 - 1874. doi:10.1093/molbev/msw054
  • Lynn, D. H. & Small, E. B. (2000). Phylum Ciliophora Doflein, 1901. In J. J. Lee, G. F. Leedale, P. Bradbury (Eds.), The Illustrated Guide to the Protozoa (pp. 371-656). Lawrence, Kansas, USA: Society of Protozoolgists.
  • Nguyen, L. T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1), 268 - 274. doi:10.1093/molbev/msu300
  • Özdamar, K. (1999a). Paket Programlar ile İstatistiksel Veri Analizi 1. Eskişehir: Kaan Kitabevi.
  • Özdamar, K. (1999b). Paket Programlar ile İstatistiksel Veri Analizi 2. Eskişehir: Kaan Kitabevi.
  • Posada, D. (2008). jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution, 25(7), 1253 - 1256. doi:10.1093/molbev/msn083
  • Rajter, L., & Vd’acný, P. (2016). Rapid radiation, gradual extinction and parallel evolution challenge generic classification of spathidiid ciliates (Protista,Ciliophora). Zoologica Scripta, 45(2), 200 - 223. doi:10.1111/zsc.12143
  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Hohna, S., … , & Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3), 539 - 542. doi:10.1093/sysbio/sys029
  • Shazib, S. U. A., Vd'acny, P., Kim, J. H., Jang, S. W., & Shin, M. K. (2016). Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region. Molecular Phylogenetics and Evolution, 102, 128 - 144. doi:10.1016/j.ympev.2016.05.041
  • Talavera, G., & Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56(4), 564 - 577. doi:10.1080/10635150701472164
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725 - 2729. doi:10.1093/molbev/mst197
  • Vd’acný, P., Bourland, W. A., Orsi, W., Epstein, S. S., & Foissner, W. (2011). Phylogeny and classification of the Litostomatea (Protista, Ciliophora), with emphasis on free-living taxa and the 18SrRNA gene. Molecular Phylogenetics and Evolution, 59(2), 510 - 522. doi:10.1016/j.ympev.2011.02.016
  • Vd’acný, P., & Foissner, W. (2012). Monograph of the Dileptids (Protista, Ciliophora, Rhynchostomatia). Denisia, 31, 1–529.
  • Vd’acný, P., & Foissner, W. (2013). Synergistic effects of combining morphological and molecular data in resolving the phylogenetic position of Semispathidium (Ciliophora, Haptoria) with description of Semispathidium breviarmatum sp n. from tropical Africa. Zoologica Scripta, 42(5), 529 - 549. doi:10.1111/zsc.12023
  • Vd’acný, P., Breiner, H. W., Yashchenko, V., Dunthorn, M., Stoeck, T., & Foissner, W. (2014). The chaos prevails: molecular phylogeny of the Haptoria (Ciliophora, Litostomatea). Protist, 165(1), 93 - 111. doi:10.1016/j.protis.2013.11.001
  • Xu, K., & Foissner, W. (2005). Morphology, ontogenesis and encystment of a soil ciliate (Ciliophora, Haptorida), Arcuospathidium cultriforme (Penard, 1922), with models for the formation of the oral bulge, the ciliary patterns, and the evolution of the spathidiids. Protistology, 4, 5 - 55.
  • Yıldız, İ. (2018). Morphology and phylogeny of Apertospathula oktemae n. sp. (Ciliophora, Haptoria, Spathidiida) from Lake Van, Turkey. European Journal of Protistology, 66, 1 - 8. doi:10.1016/j.ejop.2018.06.001
  • Yıldız, İ. (2021). Morphology and phylogeny of a new soil ciliate, Colpodidium zelihayildizae n. sp. (Ciliophora, Nassophorea, Colpodidiidae), from Van, Turkey. Turkish Journal of Zoology, 45, 304 - 313. doi:10.3906/zoo-2101-20

Morphological and Molecular Investigations on Spathidiid Ciliates (Ciliophora, Spathidiida) Isolated from Coastal Sands of Lake Van

Year 2023, Volume: 28 Issue: 2, 345 - 358, 31.08.2023

N. Fırat Dicle İsmail Yıldız

https://doi.org/10.53433/yyufbed.1239915

Abstract

In this study, we investigated the morphological characteristics and phylogenetic position based on the 18S rDNA gene sequence of the Spathidium species isolated from the coastal sands of Lake Van. Three populations of ciliates were observed, showing different morphology in cultures. Our results indicate that the nucleotide sequences of the 18S rDNA gene region of these populations were similar and they were different developmental stages of the same species. Phylogenetic analyses based on the nucleotide sequences of the 18S rDNA gene region showed that Spathidium sp. isolated in this study clustered together with Lagnophrya acuminata, Enchelys gasterosterus, and Balantidion pellucidum rather than their congeners. There are contradictions between the morphological classification system and molecular phylogeny of Spathidiid ciliates, and it is seen that the genus Spathidium is a paraphyletic taxon. However, the lack of nucleotide sequence data for many species of the species-rich genus Spathidium limits the elucidation of the molecular phylogenetic status of this taxon. Phylogenetic analyzes using different gene regions with the support of detailed morphological data to be isolated from different habitats will clarify this problem.

Keywords

18S rDNA gene sequence Lake Van Morphology Phylogeny Spathidium sp.

Project Number

FYL-2019-7960

References

  • Adl, S. M., Simpson, A. G. B., Farmer, M. A., Andersen, R. A., Anderson, O. R., Barta, J. R., … , & Taylor, M. F. J. R. (2005). The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology, 52(5), 399 - 451. doi:10.1111/j.1550-7408.2005.00053.x
  • Ayres, D. L., Darling, A., Zwickl, D. J., Beerli, P., Holder, M. T., Lewis, P. O., … , & Suchard, M. A. (2012). BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology, 61, 170–173. doi:10.1093/sysbio/syr100
  • Corliss, J. O. (2001). Protozoan Taxonomy and Systematics. In G. Pettis (Ed.), Encyclopedia of Life Sciences (pp. 1-7). John Wiley & Sons. doi:10.1038/npg.els.0001925
  • Curds, C. R. (1983). British and Other Freshwater Ciliated Protozoa. U.S.A: Cambridge University Press.
  • Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772. doi:10.1038/nmeth.2109
  • Foissner, W. (1991). Basic light and scanning electron microscopic methods for taxonomic studies of ciliated protozoa. European Journal of Protistology, 27(4), 313 - 330. doi:10.1016/S0932-4739(11)80248-8
  • Foissner, W. (2014). An update of 'basic light and scanning electron microscopic methods for taxonomic studies of ciliated protozoa'. International Journal of Systematic and Evolutionary Microbiology, 64, 271 - 292. doi:10.1099/ijs.0.057893-0
  • Foissner, W., Berger, H. & Schaumburg, J. (1999). Identification and Ecology of Limnetic Plankton Ciliates. München, Germany: Informationsberichte des Bayerischen Landesamtes für Wasserwirtschaft.
  • Foissner, W., & Lei, Y. L. (2004). Morphology and ontogenesis of some soil spathidiids (Ciliophora, Haptoria). Linzer biologische Beitrage, 36, 159–199.
  • Foissner, W., & Xu, K. (2007). Monograph of the Spathidiida (Ciliophora, Haptoria) Vol. I: Protospathidiidae, Arcuospathidiidae, Apertospathulidae. Monographiae Biologicae, 81, 1–485.
  • Foissner, W., Wolf, K. W., Kumar, S., Xu, K. D., & Quintela-Alonso, P. (2014). Five new spathidiids (Ciliophora: Haptoria) from Caribbean Tank Bromeliads. Acta Protozoologica, 53(2), 159 - 194. doi:10.4467/16890027AP.14.015.1596
  • Gong, J., Kim, S. J., Kim, S. Y., Min, G. S., Roberts, D. M., Warren, A., & Choi, J. K. (2007). Taxonomic redescriptions of two ciliates, Protogastrostyla pulchra n. g., n. comb. and Hemigastrostyla enigmatica (Ciliophora: Spirotrichea, Stichotrichia), with phylogenetic analyses based on 18S and 28S rRNA gene sequences. Journal of Eukaryotic Microbiology, 54(6), 468 - 478. doi:10.1111/j.1550-7408.2007.00288.x
  • Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018). UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35(2), 518 - 522. doi:10.1093/molbev/msx281
  • Jang, S. W., Vd’acný, P., Shazib, S. U. A., & Shin, M. K. (2015). Morphology, ciliary pattern and molecular phylogeny of Trachelophyllum brachypharynx Levander, 1894 (Litostomatea, Haptoria, Spathidiida). Acta Protozoologica, 54(2), 123 - 135. doi:10.4467/16890027AP.15.010.2735
  • Jang, S. W., Vd’acný, P., Shazib, S. U. A., & Shin, M. K. (2017). Linking morphology and molecules: integrative taxonomy of spathidiids (Protista: Ciliophora: Litostomatea) from Korea. Journal of Natural History, 51(17-18), 939 - 974. doi:10.1080/00222933.2017.1319520
  • Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870 - 1874. doi:10.1093/molbev/msw054
  • Lynn, D. H. & Small, E. B. (2000). Phylum Ciliophora Doflein, 1901. In J. J. Lee, G. F. Leedale, P. Bradbury (Eds.), The Illustrated Guide to the Protozoa (pp. 371-656). Lawrence, Kansas, USA: Society of Protozoolgists.
  • Nguyen, L. T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1), 268 - 274. doi:10.1093/molbev/msu300
  • Özdamar, K. (1999a). Paket Programlar ile İstatistiksel Veri Analizi 1. Eskişehir: Kaan Kitabevi.
  • Özdamar, K. (1999b). Paket Programlar ile İstatistiksel Veri Analizi 2. Eskişehir: Kaan Kitabevi.
  • Posada, D. (2008). jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution, 25(7), 1253 - 1256. doi:10.1093/molbev/msn083
  • Rajter, L., & Vd’acný, P. (2016). Rapid radiation, gradual extinction and parallel evolution challenge generic classification of spathidiid ciliates (Protista,Ciliophora). Zoologica Scripta, 45(2), 200 - 223. doi:10.1111/zsc.12143
  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Hohna, S., … , & Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3), 539 - 542. doi:10.1093/sysbio/sys029
  • Shazib, S. U. A., Vd'acny, P., Kim, J. H., Jang, S. W., & Shin, M. K. (2016). Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region. Molecular Phylogenetics and Evolution, 102, 128 - 144. doi:10.1016/j.ympev.2016.05.041
  • Talavera, G., & Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56(4), 564 - 577. doi:10.1080/10635150701472164
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725 - 2729. doi:10.1093/molbev/mst197
  • Vd’acný, P., Bourland, W. A., Orsi, W., Epstein, S. S., & Foissner, W. (2011). Phylogeny and classification of the Litostomatea (Protista, Ciliophora), with emphasis on free-living taxa and the 18SrRNA gene. Molecular Phylogenetics and Evolution, 59(2), 510 - 522. doi:10.1016/j.ympev.2011.02.016
  • Vd’acný, P., & Foissner, W. (2012). Monograph of the Dileptids (Protista, Ciliophora, Rhynchostomatia). Denisia, 31, 1–529.
  • Vd’acný, P., & Foissner, W. (2013). Synergistic effects of combining morphological and molecular data in resolving the phylogenetic position of Semispathidium (Ciliophora, Haptoria) with description of Semispathidium breviarmatum sp n. from tropical Africa. Zoologica Scripta, 42(5), 529 - 549. doi:10.1111/zsc.12023
  • Vd’acný, P., Breiner, H. W., Yashchenko, V., Dunthorn, M., Stoeck, T., & Foissner, W. (2014). The chaos prevails: molecular phylogeny of the Haptoria (Ciliophora, Litostomatea). Protist, 165(1), 93 - 111. doi:10.1016/j.protis.2013.11.001
  • Xu, K., & Foissner, W. (2005). Morphology, ontogenesis and encystment of a soil ciliate (Ciliophora, Haptorida), Arcuospathidium cultriforme (Penard, 1922), with models for the formation of the oral bulge, the ciliary patterns, and the evolution of the spathidiids. Protistology, 4, 5 - 55.
  • Yıldız, İ. (2018). Morphology and phylogeny of Apertospathula oktemae n. sp. (Ciliophora, Haptoria, Spathidiida) from Lake Van, Turkey. European Journal of Protistology, 66, 1 - 8. doi:10.1016/j.ejop.2018.06.001
  • Yıldız, İ. (2021). Morphology and phylogeny of a new soil ciliate, Colpodidium zelihayildizae n. sp. (Ciliophora, Nassophorea, Colpodidiidae), from Van, Turkey. Turkish Journal of Zoology, 45, 304 - 313. doi:10.3906/zoo-2101-20
There are 33 citations in total.

Details

Primary Language Turkish
Subjects Hydrobiology
Journal Section Natural Sciences and Mathematics / Fen Bilimleri ve Matematik
Authors

N. Fırat Dicle 0000-0002-2864-8461

İsmail Yıldız 0000-0001-9986-0358

Project Number FYL-2019-7960
Publication Date August 31, 2023
Submission Date January 20, 2023
Published in Issue Year 2023 Volume: 28 Issue: 2

Cite

APA Dicle, N. F., & Yıldız, İ. (2023). Van Gölü Kıyı Kumlarından İzole Edilen Spathidiid Siliyatlar (Ciliophora, Spathidiida) Üzerinde Morfolojik ve Moleküler Filogenetik Araştırmalar. Yüzüncü Yıl Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 28(2), 345-358. https://doi.org/10.53433/yyufbed.1239915
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