Türkiye’nin Samsun İlindeki Bazı Yabani Baklagil Türlerini Nodüle Eden Mesorhizobium Türlerinin Çeşitliliği
Yıl 2019,
, 401 - 408, 30.12.2019
Okan Kadir Nohut
Cem Tolga Gürkanlı
,
İbrahim Özkoç
Öz
Bu çalışmada Türkiye’nin Samsun
ilinden toplanan iki yabani Baklagil türünün (Argyrolobium biebersteinii (Ball in Feddes) and Lotus angustissimus
L.,)
mikrosimbiyontları geleneksel ve moleküler yöntemler kullanılarak incelenmiştir.
Toplamda orijinal konakçıları üzerinde aktif kök nodülleri oluşturan beş adet
rizobiyal izolat incelenmiştir. Bu izolatların teşhisleri 16S rDNA ve recA olmak üzere iki genin filogenetik
analizleri ile yapılmıştır. Sonuç olarak OKN-1 ve OKN-4 Mesorhizobium
tarimense ve OKN-3 M. japonicum
olarak teşhis edilmişlerdir. Diğer taraftan diğer iki izolatımız OKN-7 ve
OKN-10 potansiyel iki yeni Mesorhizobium türü olarak ortaya çıkmıştır. Sonuç olarak bu çalışmada Türkiye’den Mesorhizobium
cinsine ait ilk moleküler olarak tanımlanmış örnekleri sunmaktayız. Ayrıca M.
tarimense ve M. japonicum türleri için Türkiye’den ve Avrupa’dan ilk
kayıtları da vermekteyiz. Ek olarak M. tarimense ve M. japonicum izolatlarımız,
bu iki türün orijinal konaklarından ve lokalitelerinden tanımlanmasından sonra
bildirilen ilk izolatlardır. Bu çalışmada potansiyel olarak yeni iki Mesorhizobium
türü için de moleküler kanıtlar sunuyoruz.
Destekleyen Kurum
Ondokuz Mayıs Üniversitesi
Proje Numarası
PYO.FEN.1904.10.006
Kaynakça
- Akaike, H. (1974). A new look at statistical model identification. IEEE Transactions on Automatic Control, 19, 716-723.
- Adıguzel, A., Ogutcu, H., Baris, O., Karadayi, M., Gulluce, M.U., Sahin, F. (2010). Isolation and characterization of Rhizobium strains from wild vetch collected from high altitudes in Erzurum-Turkey. Romanian Biotechnological Letters, 15, 5017-5024.
- Alexandre, A., Laranjo, M., Young, J.P., Oliveira, S. (2008). dnaJ is a useful phylogenetic marker for alpha proteobacteria. International Journal of Systematic and Evolutionary Microbiology, 58, 2839-2849.
- Burdass, D. (2002). Rhizobium, root nodules and nitrogen fixation. http://biblio.teluq.ca/LinkClick.aspx?fileticket=Zt582qIwcMI5ljHgoneZIw%3D%3D&tabid=40831&language=fr-CA. Accessed: January 2018.
- Brewin, N.J., Beringer, J.E., Johnston, A.W.B. (1980). Plasmid mediated transfer of host-range specificity between two strains of Rhizobium leguminosarum. Journal of General Microbiology, 120, 413-420.
- De Lajudie, P., Willems, A., Pot, B., Dewettinck, D., Maestrojuan, G., Neyra, M., Collins, M.D., Dreyfus., B., Kersters, K., Gillis, M. (1994). Polyphasic taxomomy of Rhizobia: emendation of the genus Sinorhizobium and description of S. meliloti comb nov., S. saheli sp. nov., S. teranga sp. nov. International Journal of Systematic Bacteriology, 44, 715-733.
- De Meyer, S.E., Tan, H.W., Heenan, P.B., Andrews, M., Willems, A. (2015). Mesorhizobium waimense sp. nov. isolated from Sophora longicarinata root nodules and Mesorhizobium cantuariense sp. nov. isolated from Sophora microphylla root nodules. International Journal of Systematic and Evolutionary Microbiology, 65, 3419-3426.
- Gaunt, M.W., Turner, S.L., Rigottier-Gois, L., Lloyd-Macgilp, S.A., Young, J.P.W. (2001). Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. International Journal of Systematic and Evolutionary Microbiology, 51, 2037-2048.
- Graham, P.H., Sadowsky, M.J., Keyser, H.H., Barnet, Y.M., Bradley, R.S., Cooper, J.E., De Ley, D.J., Jarvis, B.D.W., Roslycky, E.B., Strijdom, B.W., Young, J.P.W. (1991). Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. International Journal of Systematic Bacteriology, 41, 582-587.
- Guan, S.H., Chen, W.F., Wang, E.T., Lu, Y.L., Yan, X.R., Zhang, X.X., Chen, W.X. (2008). Mesorhizobium caraganae sp. nov., a novel rhizobial species nodulated with Caragana spp. in China. International Journal of Systematic and Evolutionary Microbiology, 58, 2646-2653.
- Guindon, S., Gascuel, O. (2003). A simple, fast and accurate algorithm to estimate large phylogenies by maximum-likelihood. Systematic Biology, 52, 696-704.
- Gürkanli, C.T., Özkoç, İ., Gündüz, İ. (2013). Genetic diversity of rhizobia nodulating common bean (Phaseolus vulgaris L.) in the Central Black Sea region of Turkey. Annals of Microbiology, 63, 971-987.
- Gürkanli, C.T., Özkoç, İ., Gündüz, İ. (2014). Genetic diversity of Vicia faba L. and Pisum sativum L. nodulating rhizobia in the central Black Sea region of Turkey. Annals of Microbiology, 64, 99-112.
- Han, T.X., Han, L.L., Wu, L.J., Chen, W.F., Sui, X.H., Gu, J.G., Wang, E.T., Chen, W.X. (2008). Mesorhizobium gobiense sp. nov. and Mesorhizobium tarimense sp. nov., isolated from wild legumes growing in desert soils of Xinjiang, China. International Journal of Systematic and Evolutionary Microbiology, 58, 2610-2618.
- Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Research, 41, 95-98.
- Jarvis, B.D.W., Van Berkum, P., Chen, W.X., Nour, S.M., Fernandez, M.P., Cleyet-Marel, J.C., Gillis, M. (1997). Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov. International Journal of Systematic Bacteriology, 47, 895-898.
- Lloret, L., Ormeno-Orrillo, E., Rincon, R., Martinez-Romero, J., Rogel-Hernandez, M.A., Martinez-Romero, E. (2007). Ensifer mexicanus sp. nov. a new species nodulating Acacia angustissima (Mill.) Kuntze in Mexico. Systematic and Applied Microbiology, 30, 280-290.
- Lodwig, E.M., Hosie, A.H.F., Bourdes, A., Findlay, K., Allaway, D., Karunakaran, R., Downie, J.A., Poole, P.S. (2003). Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. Nature, 422, 722-726.
- Lu, Y.L., Chen, W.F., Wang, E.T., Han, L.L., Zhang, X.X., Chen, W.X., Han, S.Z. (2009). Mesorhizobium shangrilense sp. nov., isolated from root nodules of Caragana species. International Journal of Systematic and Evolutionary Microbiology, 59, 3012-3018.
- Martens, M., Delaere, M., Coopman, R., De, Vos P., Gillis, M., Willems, A. (2007). Multilocus sequence analysis of Ensifer and related taxa. International Journal of Systematic and Evolutionary Microbiology, 57: 489-503.
- Martinez-Hidalgo, P., Ramirez-Bahena, M.H., Flores-Felix, J.D., Rivas, R., Igual, J.M., Mateos, P.F., Martinez-Molina, E., Leon-Barrios, M., Peix, A., Velazquez, E. (2015). Revision of the taxonomic status of type strains of Mesorhizobium loti and reclassification of strain USDA 3471T as the type strain of Mesorhizobium erdmanii sp. nov. and ATCC 33669T as the type strain of Mesorhizobium jarvisii sp. nov. International Journal of Systematic and Evolutionary Microbiology, 65, 1703-1708.
- Martínez-Hidalgo, P., Ramírez-Bahena, M.H., Flores-Felix, J.D., Igual, J.M., Sanjuan, J., León-Barrios, M., Peix, A., Velazquez, E. (2016). Reclassification of strains MAFF 303099T and R7A into Mesorhizobium japonicum sp. nov. International Journal of Systematic and Evolutionary Microbiology, 66, 4936-4941.
- Moreira, FM.S., Haukka, K., Young, J.P.W. (1998). Biodiversity of rhizobia isolated from a wide range of forest legumes in Brazil. Molecular Ecology, 7, 889-895.
- Mousavi, S.A., Willems, A., Nesme, X., de Lajudie, P., Lindström, K. (2015). Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Systematic and Applied Microbiology, 38, 84-90.
- Nandasena, K.G., O'hara, G.W., Tiwari, R.P., Howieson, J.G. (2006). Rapid in situ evolution of nodulating strains for Biserrula pelecinus L. through lateral transfer of a symbiosis island from the original mesorhizobial inoculant. Applied and Environmental Microbiology, 72, 7365-7367.
- Nandasena, K.G., O’Hara, G.W., Tiwari, R.P., Willems, A., Howieson, J.G. (2009). Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia. International Journal of Systematic and Evolutionary Microbiology, 59, 2140-2147.
- Nour, S.M., Fernandez, M.P., Normand, P., Cleyet-Marel, J.C. (1994). Rhizobium ciceri sp. nov., consisting of strains that nodulate chickpeas (Cicer arietinum L.). International Journal of Systematic Bacteriology, 44, 511-522.
- Ogutcu, H., Adıguzel, A., Gulluce, M., Karadayı, M., Sahin, F. (2009). Molecular characterization of Rhizobium strains isolated from wild chickpeas collected from high altitudes in Erzurum-Turkey. Romanian Biotechnological Letters, 14, 4294-4300.
- Oyaizu, H., Matsumoto, S., Minamisawa, K., Gamou, T. (1993). Distribution of Rhizobia in leguminous plants surveyed by phylogenetic identification. Journal of General and Applied Microbiology, 39, 339-354.
- Posada, D. (2008). jModel test: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
- Raymond, J., Siefert, J.L., Staples, C.R., Blankenship, R.E. (2004). The Natural history of nitrogen fixation. Molecular Biology and Evolution, 21, 541-554.
- Sawada, H., Kuykendall, L.D., Young, J.M. (2003). Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. Journal of General and Applied Microbiology, 49, 155-179.
- Shamseldin, A., Abdelkhalek, A., Sadowsky, M.J. (2017). Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis, 71, 91-109.
- Somasegaran, P., Hoben, H.J. (1985). Methods in legume-Rhizobium technology. United States Agency for International Development, USA.
- Sprent, J.I. (2007). Evolving ideas of legume evolution and diversity: a taxonomic perspectiveon the occurrence of nodulation. New Phytologist, 174, 11-25.
- Swofford, D.L. (1998). PAUP* Phylogenetic analysis using parsimony (*and other methods). Version 4 beta 10. Sinauer Associates, Sunderland, Massachusetts.
- Temizkan, G., Arda, N. (2004). Moleküler biyolojide kullanılan yöntemler. Nobel Tıp Kitabevleri, İstanbul.
- Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997). The ClustalX-Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876-4882.
- Vidal, C., Chantreuil, C., Berge, O., Maure, L., Escarre, J., Bena, G., Brunel, B., Cleyet-Marel, J.C. (2009). Mesorhizobium metallidurans sp. nov., a metal-resistant symbiont of Anthyllis vulneraria growing on metallicolous soil in Languedoc, France. International Journal of Systematic and Evolutionary Microbiology, 59, 850-855.
- Vincent, J.M. (1970). A manual for the Practical Study of the Root-Nodule Bacteria. Blackwell Scientific Publications, Oxford and Edinburgh.
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Diversity of Mesorhizobium Species Nodulating Some Wild Legumes in Samsun Province of Turkey
Yıl 2019,
, 401 - 408, 30.12.2019
Okan Kadir Nohut
Cem Tolga Gürkanlı
,
İbrahim Özkoç
Öz
In this study microsymbionts of
two wild legumes, Argyrolobium
biebersteinii (Ball
in Feddes) and Lotus
angustissimus L.,
collected from Samsun province of Turkey were investigated using conventional
and molecular methods. A total of five rhizobial isolates which produced active
root nodules on their original hosts were considered. Identifications of the
isolates were depending on the phylogenetic analyses of two housekeeping genes,
16S rDNA and recA. As a result,
isolates OKN-1 and OKN-4 identified as Mesorhizobium
tarimense and OKN-3 identified as M.
japonicum. On the other hand, our other two isolates OKN-7 and OKN-10
appeared as two potentially new Mesorhizobium species. In this study we present the first Mesorhizobium isolates identified using valid molecular methods from Turkey. We also
give the first reports of M. tarimense and M. japonicum from Turkey
and Europe. Additionally, our M. tarimense and M. japonicum
isolates are the first isolates reported after the description of these two
species from their original hosts and locations. In this study we also present
molecular evidences for two potentially new Mesorhizobium species.
Proje Numarası
PYO.FEN.1904.10.006
Kaynakça
- Akaike, H. (1974). A new look at statistical model identification. IEEE Transactions on Automatic Control, 19, 716-723.
- Adıguzel, A., Ogutcu, H., Baris, O., Karadayi, M., Gulluce, M.U., Sahin, F. (2010). Isolation and characterization of Rhizobium strains from wild vetch collected from high altitudes in Erzurum-Turkey. Romanian Biotechnological Letters, 15, 5017-5024.
- Alexandre, A., Laranjo, M., Young, J.P., Oliveira, S. (2008). dnaJ is a useful phylogenetic marker for alpha proteobacteria. International Journal of Systematic and Evolutionary Microbiology, 58, 2839-2849.
- Burdass, D. (2002). Rhizobium, root nodules and nitrogen fixation. http://biblio.teluq.ca/LinkClick.aspx?fileticket=Zt582qIwcMI5ljHgoneZIw%3D%3D&tabid=40831&language=fr-CA. Accessed: January 2018.
- Brewin, N.J., Beringer, J.E., Johnston, A.W.B. (1980). Plasmid mediated transfer of host-range specificity between two strains of Rhizobium leguminosarum. Journal of General Microbiology, 120, 413-420.
- De Lajudie, P., Willems, A., Pot, B., Dewettinck, D., Maestrojuan, G., Neyra, M., Collins, M.D., Dreyfus., B., Kersters, K., Gillis, M. (1994). Polyphasic taxomomy of Rhizobia: emendation of the genus Sinorhizobium and description of S. meliloti comb nov., S. saheli sp. nov., S. teranga sp. nov. International Journal of Systematic Bacteriology, 44, 715-733.
- De Meyer, S.E., Tan, H.W., Heenan, P.B., Andrews, M., Willems, A. (2015). Mesorhizobium waimense sp. nov. isolated from Sophora longicarinata root nodules and Mesorhizobium cantuariense sp. nov. isolated from Sophora microphylla root nodules. International Journal of Systematic and Evolutionary Microbiology, 65, 3419-3426.
- Gaunt, M.W., Turner, S.L., Rigottier-Gois, L., Lloyd-Macgilp, S.A., Young, J.P.W. (2001). Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. International Journal of Systematic and Evolutionary Microbiology, 51, 2037-2048.
- Graham, P.H., Sadowsky, M.J., Keyser, H.H., Barnet, Y.M., Bradley, R.S., Cooper, J.E., De Ley, D.J., Jarvis, B.D.W., Roslycky, E.B., Strijdom, B.W., Young, J.P.W. (1991). Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. International Journal of Systematic Bacteriology, 41, 582-587.
- Guan, S.H., Chen, W.F., Wang, E.T., Lu, Y.L., Yan, X.R., Zhang, X.X., Chen, W.X. (2008). Mesorhizobium caraganae sp. nov., a novel rhizobial species nodulated with Caragana spp. in China. International Journal of Systematic and Evolutionary Microbiology, 58, 2646-2653.
- Guindon, S., Gascuel, O. (2003). A simple, fast and accurate algorithm to estimate large phylogenies by maximum-likelihood. Systematic Biology, 52, 696-704.
- Gürkanli, C.T., Özkoç, İ., Gündüz, İ. (2013). Genetic diversity of rhizobia nodulating common bean (Phaseolus vulgaris L.) in the Central Black Sea region of Turkey. Annals of Microbiology, 63, 971-987.
- Gürkanli, C.T., Özkoç, İ., Gündüz, İ. (2014). Genetic diversity of Vicia faba L. and Pisum sativum L. nodulating rhizobia in the central Black Sea region of Turkey. Annals of Microbiology, 64, 99-112.
- Han, T.X., Han, L.L., Wu, L.J., Chen, W.F., Sui, X.H., Gu, J.G., Wang, E.T., Chen, W.X. (2008). Mesorhizobium gobiense sp. nov. and Mesorhizobium tarimense sp. nov., isolated from wild legumes growing in desert soils of Xinjiang, China. International Journal of Systematic and Evolutionary Microbiology, 58, 2610-2618.
- Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Research, 41, 95-98.
- Jarvis, B.D.W., Van Berkum, P., Chen, W.X., Nour, S.M., Fernandez, M.P., Cleyet-Marel, J.C., Gillis, M. (1997). Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov. International Journal of Systematic Bacteriology, 47, 895-898.
- Lloret, L., Ormeno-Orrillo, E., Rincon, R., Martinez-Romero, J., Rogel-Hernandez, M.A., Martinez-Romero, E. (2007). Ensifer mexicanus sp. nov. a new species nodulating Acacia angustissima (Mill.) Kuntze in Mexico. Systematic and Applied Microbiology, 30, 280-290.
- Lodwig, E.M., Hosie, A.H.F., Bourdes, A., Findlay, K., Allaway, D., Karunakaran, R., Downie, J.A., Poole, P.S. (2003). Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. Nature, 422, 722-726.
- Lu, Y.L., Chen, W.F., Wang, E.T., Han, L.L., Zhang, X.X., Chen, W.X., Han, S.Z. (2009). Mesorhizobium shangrilense sp. nov., isolated from root nodules of Caragana species. International Journal of Systematic and Evolutionary Microbiology, 59, 3012-3018.
- Martens, M., Delaere, M., Coopman, R., De, Vos P., Gillis, M., Willems, A. (2007). Multilocus sequence analysis of Ensifer and related taxa. International Journal of Systematic and Evolutionary Microbiology, 57: 489-503.
- Martinez-Hidalgo, P., Ramirez-Bahena, M.H., Flores-Felix, J.D., Rivas, R., Igual, J.M., Mateos, P.F., Martinez-Molina, E., Leon-Barrios, M., Peix, A., Velazquez, E. (2015). Revision of the taxonomic status of type strains of Mesorhizobium loti and reclassification of strain USDA 3471T as the type strain of Mesorhizobium erdmanii sp. nov. and ATCC 33669T as the type strain of Mesorhizobium jarvisii sp. nov. International Journal of Systematic and Evolutionary Microbiology, 65, 1703-1708.
- Martínez-Hidalgo, P., Ramírez-Bahena, M.H., Flores-Felix, J.D., Igual, J.M., Sanjuan, J., León-Barrios, M., Peix, A., Velazquez, E. (2016). Reclassification of strains MAFF 303099T and R7A into Mesorhizobium japonicum sp. nov. International Journal of Systematic and Evolutionary Microbiology, 66, 4936-4941.
- Moreira, FM.S., Haukka, K., Young, J.P.W. (1998). Biodiversity of rhizobia isolated from a wide range of forest legumes in Brazil. Molecular Ecology, 7, 889-895.
- Mousavi, S.A., Willems, A., Nesme, X., de Lajudie, P., Lindström, K. (2015). Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Systematic and Applied Microbiology, 38, 84-90.
- Nandasena, K.G., O'hara, G.W., Tiwari, R.P., Howieson, J.G. (2006). Rapid in situ evolution of nodulating strains for Biserrula pelecinus L. through lateral transfer of a symbiosis island from the original mesorhizobial inoculant. Applied and Environmental Microbiology, 72, 7365-7367.
- Nandasena, K.G., O’Hara, G.W., Tiwari, R.P., Willems, A., Howieson, J.G. (2009). Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia. International Journal of Systematic and Evolutionary Microbiology, 59, 2140-2147.
- Nour, S.M., Fernandez, M.P., Normand, P., Cleyet-Marel, J.C. (1994). Rhizobium ciceri sp. nov., consisting of strains that nodulate chickpeas (Cicer arietinum L.). International Journal of Systematic Bacteriology, 44, 511-522.
- Ogutcu, H., Adıguzel, A., Gulluce, M., Karadayı, M., Sahin, F. (2009). Molecular characterization of Rhizobium strains isolated from wild chickpeas collected from high altitudes in Erzurum-Turkey. Romanian Biotechnological Letters, 14, 4294-4300.
- Oyaizu, H., Matsumoto, S., Minamisawa, K., Gamou, T. (1993). Distribution of Rhizobia in leguminous plants surveyed by phylogenetic identification. Journal of General and Applied Microbiology, 39, 339-354.
- Posada, D. (2008). jModel test: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
- Raymond, J., Siefert, J.L., Staples, C.R., Blankenship, R.E. (2004). The Natural history of nitrogen fixation. Molecular Biology and Evolution, 21, 541-554.
- Sawada, H., Kuykendall, L.D., Young, J.M. (2003). Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. Journal of General and Applied Microbiology, 49, 155-179.
- Shamseldin, A., Abdelkhalek, A., Sadowsky, M.J. (2017). Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis, 71, 91-109.
- Somasegaran, P., Hoben, H.J. (1985). Methods in legume-Rhizobium technology. United States Agency for International Development, USA.
- Sprent, J.I. (2007). Evolving ideas of legume evolution and diversity: a taxonomic perspectiveon the occurrence of nodulation. New Phytologist, 174, 11-25.
- Swofford, D.L. (1998). PAUP* Phylogenetic analysis using parsimony (*and other methods). Version 4 beta 10. Sinauer Associates, Sunderland, Massachusetts.
- Temizkan, G., Arda, N. (2004). Moleküler biyolojide kullanılan yöntemler. Nobel Tıp Kitabevleri, İstanbul.
- Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997). The ClustalX-Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876-4882.
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