Van Topraklarından İzole Edilen Colpoda (Ciliophora, Colpodea) Türleri Üzerinde Morfolojik ve Moleküler Filogenetik Araştırmalar

Year 2023, Volume: 28 Issue: 3, 830 - 842, 29.12.2023

Pelin Erişen İsmail Yıldız

https://doi.org/10.53433/yyufbed.1285464

Abstract

Bu makalede Van topraklarından izole edilen Colpoda Ö. F. Müller 1773 cinsine ait dört siliyat siliyat türünü hem morfolojik hem de 18S rDNA gen dizisine dayalı filogenetik olarak inceledik. C. lucida, C. magna ve C. maupasi morfolojik olarak literatür verileri ile uyumludur. Morfolojik karakterleri bakımından daha önce tanımlanmış herhangi bir popülasyon ile eşleşmeyen bir popülasyon ise Colpoda sp. olarak sunuldu. C. lucida ve C. magna Türkiye siliyat faunasına ilk kez bu çalışma ile kaydedilmiştir. Filogenetik analizlerde (ML ve BI) Colpoda cinsi üyeleri dış grup olarak kullanılan türlerden tam destek ile ayrılmıştır. Bu çalışmada izole edilen C. lucida ve C. magna filogenetik ağaçlarda daha önce tanımlanmış türdeşleri ile birlikte konumlanırken C. maupasi popülasyonunun morfolojik olarak benzer olmamasına karşın C. eucaudata ile daha yakın konumlanmıştır. C. lucida türdeşlerinin bazal pozisyonunda onlardan genetik olarak farklılaşmış olarak yer almaktadır. Colpoda sp. ise diğer hemcinslerinden farklı bir kol üzerinde Colpoda sp. (JF747216) popülasyonu ile kardeş pozisyonda ve ondan genetik olarak uzak pozisyonda konumlanmıştır. Colpoda sp.’nin filogenetik pozisyonu ve genetik farklılığı onun yeni tür olmaya aday olduğuna işaret etmektedir.

Keywords

Colpoda, Filogeni, Morfoloji, Toprak siliyatları, Van

Morphological and Molecular Phylogenetic Investigations on Colpoda (Ciliophora,Colpodea) Species Isolated from Van Soils

Abstract

In the present paper, we have investigated four ciliate species belonging to the genus Colpoda O. F. Müller, 1773 isolated from Van soil and examined both morphologically and molecular phylogenetically based on the 18S rDNA gene sequence. C. lucida, C. maupasi and C. magna are compatible morphologically with literature data. One population, which did not match any previously defined species in terms of morphological characters, was presented as Colpoda sp. C. lucida and C. magna were recorded for the first time in the ciliate fauna of Turkey with this study. In the phylogenetic analyses (ML and BI), the members of the genus Colpoda separated from the species used as the outgroup with full support. In the phylogenetic trees, the C. lucida and C. magna species isolated in this study clustered together with the same species described previously, while the C. maupasi population was more closely located with C. eucaudata, although not morphologically similar. C. lucida was located in the basal position of the other populations of the same species and slightly genetically differentiated from them. The Colpoda sp. isolated in this study is located on a different arm from its congeners, in a sister position with the Colpoda sp. (JF747216) population and in a genetically distant position from it. It's phylogenetic position and genetical difference from other populations of the Colpoda sp. from other populations indicating a candidate to be a new species.

Keywords

Colpoda, Morpholohy, Phylogeny, Soil ciliates, Van

References

• Chen, L., Liu, Y., Long, Y., Lyu, J., Feng, C., Ning, Y., & Yi, Z. (2021). Morphology and molecular phylogeny of two new soil ciliates, Hemiurosomoida warreni nov. spec. and Hemiurosoma clampi nov. spec. (Ciliophora, Hypotrichia) from Tibet. European Journal of Protistology, 77, 125746. doi:10.1016/j.ejop.2020.125746
• Çınar, H. (2011). Van’daki ceviz ağacı (Juglans regia L.) kabuklarında bulunan kolpodit siliyat (Protista: Ciliophora: Colpodea) faunası. (Yüksek Lisans tezi), Van Yüzüncü Yıl Üniversitesi, Fen Bilimleri Enstitüsü, Van, Türkiye.
• 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
• Díaz, S., Martín Gonzåles, A., Rico, D., & Gutiérrez, J. C. (2003). Morphogenesis of the division and encystment process of the ciliated protozoan Colpoda minima. Journal of Natural History, 37(20), 2395-2412. doi:10.1080/00222930210144325
• Foissner, W. (1993). Colpodea (Ciliophora). New York, USA: Gustav Fischer Verlag.
• Foissner, W. (1999). Protist diversity: Estimates of the near-imponderable. Protist, 150(4), 363-368. doi:10.1016/S1434-4610(99)70037-4
• Foissner, W., Agatha, S., & Berger, H. (2002). Soil ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa), with emphasis on two contrasting environments, the Etosha Region and the Namib Desert. Denisia, 5, 1-1459.
• Foissner, W., & Xu, K. (2007). Monograph of the Spathidiida (Ciliophora, Haptoria) Vol. I: Protospathidiidae, Arcuospathidiidae, Apertospathulidae. Monographiae Biologicae, 81, 1-485.
• Foissner, W., Stoeck, T., Agatha, S., & Dunthorn, M. (2011). Interaclass evolution and classification of the Colpodea (Ciliophora). Journal of Eukaryotic Microbiology, 58(5), 397-415. doi:10.1111/j.1550-7408.2011.00566.x
• 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., Bourland, W. A., Wolf, K. W., Stoeck, T., & Dunthorn, M. (2014). New SSU-rDNA sequences for eleven colpodeans (Ciliophora, Colpodea) and description of Apocyrtolophosis nov. gen. European Journal of Protistology, 50(1), 40-46. doi:10.1016/j.ejop.2013.09.003
• Göçmen, B. (2014). Protozooloji (Ökaryotik Mikrobiyoloji). Ankara, Türkiye: Palme Yayıncılık.
• 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
• Hofmann-Munz, A. H. (1991). The oral apparatus of Colpoda variabilis (Ciliophora, Colpodidae): II. Ultrastructure of the oral ciliature and its implications on ciliate phylogeny. European Journal of Protistology, 26, 288-302. doi:10.1016/S0932-4739(11)80150-1
• 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, 939-974. doi:10.1080/00222933.2017.1319520
• Kaya, Z., & Şenler, N. G. (2012). Van ili, Türkiye, topraklarinda yaşayan bazi Colpoda türleri (Protista: Ciliophora: Colpodea) hakkinda. Erciyes Üniversitesi, Fen Bilimleri Enstitüsü Dergisi, 28(3), 183-197.
• Kim, K. S., & Min, G. S. (2015). New record of three colpodean ciliates (Ciliophora: Colpodea) from Korea. Korean Journal of Environmental Biology, 33(4), 375-382. doi:10.11626/KJEB.2015.33.4.375
• 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
• Li, J., Li, L., Wang, J., Zhu, E., & Shao, C. (2021). Morphology, morphogenesis and molecular phylogeny of a novel soil ciliate, Afrokahliella paramacrostoma n. sp. (Ciliophora, Hypotrichia). European Journal of Protistology, 77, 125748. doi:10.1016/j.ejop.2020.125748
• Lynn, D. H. (2008). The Ciliated Protozoa: Characterization, Classification, and Guide to the Literature. Dordrecht: Springer.
• 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.
• Medlin, L., Elwood, H. J., Stickel, S., & Sogin, M. L. (1988). The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene, 71(2), 491-499. doi:10.1016/0378-1119(88)90066-2
• 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
• Posada, D. (2008). jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25(7), 1253-1256. doi:10.1093/molbev/msn083
• 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
• 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’ačný, P., & Foissner, W. (2012). Monograph of the dileptids (Protista, Ciliophora, Rhynchostomatia). Denisia, 31, 1-529.
• Vd'acny, P., & Foissner, W. (2019). Re-analysis of the 18S rRNA gene phylogeny of the ciliate class Colpodea. European Journal of Protistology, 67, 89-105. doi:10.1016/j.ejop.2018.11.003
• Wang, J., Ma, J., Qi, S., & Shao, C. (2017). Morphology, morphogenesis and molecular phylogeny of a new soil ciliate Paragonostomoides xianicum n. sp. (Ciliophora, Hypotrichia, Gonostomatidae). European Journal of Protistology, 61, 233-243. doi:10.1016/j.ejop.2017.07.001
• 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