Türkiye’nin Eskişehir ilinden, Phaseolus vulgaris L.’den izole edilen rhizobial örneklerin moleküler karakterizasyonu

Cem Tolga Gürkanlı; İbrahim Özkoç; Merih Kıvanç

Molecular identifications of rhizobial samples isolated from Phaseolus vulgaris L. in Eskişehir province of Turkey

Year 2018, Volume: 11 Issue: 2, 106 - 114, 15.08.2018

Cem Tolga Gürkanlı İbrahim Özkoç Merih Kıvanç

Abstract

In this study three rhizobial samples R28, R51, R66 were anaysed using molecular phylogenetic methods. Rhizobial samples were isolated from P. vulgaris L. root nodules collected from Eskişehir province of Turkey and morphologically characterized in a previous study. Analyses were performed using a concatenated data set which composed of three housekeeping genes recA, atpD and glnII . Additionally two symbiotic genes, nodA and nifH, were sequenced and analysed to determine the symbiotic plasmid type. As a result of housekeeping gene phylogeny, isolate R28 was found to be related to R. laguerreae. Although other two isolates, R51 and R66, placed in the same lineage with R. sophoriradicis, they showed enough divergence to be considered as a new species. But this presumption need to be confirmed with further investigations. Network analyses of nodA and nifH genes clearly showed that R28 has a unique symbiotic plasmid. On the other hand, symbiotic plasmids of R51 and R66 found to be related to p42d which is the most common symbiotic plasmid in rhizobia nodulating P. vulgaris L. in Europe and also Turkey. In this study first report of R. laguerreae from Turkey is presented. More over, first report of a R. laguerreae isolate from P. vulgaris L. root nodules is also presented and suggested isolate R28 as R. laguerreae bv. phaseoli. Additionally, molecular hints for a potentially new rhizobial species have also given. But this presumption must be supported with some additional molecular and morphological investigations

Keywords

rhizobia, phylogeny, housekeeping genes, nodulation, nitrogen fixation

References

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Türkiye’nin Eskişehir ilinden, Phaseolus vulgaris L.’den izole edilen rhizobial örneklerin moleküler karakterizasyonu

Year 2018, Volume: 11 Issue: 2, 106 - 114, 15.08.2018

Cem Tolga Gürkanlı İbrahim Özkoç Merih Kıvanç

Abstract

Bu çalışmada üç rizobial örnek R28, R51, R66 moleküler filogenetik yöntemler kullanarak analiz edilmiştir. Rizobial örnekler önceki bir çalışmada izole edilmiş Türkiye’nin Eskişehir ilinden toplanmış P. vulgaris L. bitkisinin kök nodüllerinden ve morfolojik analizleri yapılmıştır. Analizler üç adet housekeeping genden recA, atpD and glnII oluşan birleştirilmiş bir veri seti kullanılarak yapılmıştır. Ek olarak, simbiyotik plazmit tipini belirlemek için nodA ve nifH olmak üzere iki simbiyotik genin dizilemesi yapılmış ve analizleri gerçekleştirilmiştir. Housekeeping gen filogenisin sonucu olarak izolat R28 R. laguerreae ile ilişkili olarak bulunmuştur. Diğer iki izolat R51 ve R66, R. sophoriradicis ile aynı soy hattında yer almasına rağmen yeni bir tür sayılabilecek kadar yeterli farklılık göstermiştir. Fakat bu öngörünün ileri araştırmalar ile doğrulanmaya gereksinimi vardır. NodA and nifH genlerinin network analizleri R28 in özgün bir simbiyotik plazmite sahip olduğunu açık bir şekilde göstermiştir. Diğer taraftan R51 ve R66’nın simbiyotik plazmitlerinin p42d ile ilişkili olduğu bulunmuştur, bu plazmit Avrupa ve Türkiye’de P. vulgaris L. ile kök nodülü oluşturan rhizobiadaki yaygın görülen simbiyotik plazmittir. Bu çalışmada R. laguerreae in Türkiye’den ilk kaydı sunulmuştur. Ötesinde, bir R. laguerreae izolatının P. vulgaris L. kök nodüllerinden ilk kaydıda verilmiştir ve izolat R28 R. laguerreae bv. phaseoli olarak önerilmiştir. Ek olarak yeni bir rizobial tür için moleküler ip uçlarıda sunulmuştur. Fakat bu öngörünün ilave bazı moleküler ve morfolojik araştırmalar ile desteklenmesi gerekmektedir

Keywords

rhizobia, filogeni, housekeeping genler, nodülasyon, azot fiksasyonu

References

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Bekler, F. M. (2016). Isolation and identification of a novel thermo-alkalophilic Anoxybacillus sp. strain KB4 from Kuşburnu hot spring in Turkey. Biological Diversity and Conservation, 9(2), 169-179.
Bustos, P., Santamaría, R. I., Pérez-Carrascal, O. M., Acosta, J. L.,Lozano, L., Juárez, S., Martínez-Flores, I., Martínez- Romero, E., Cevallos, M. A., Romero, D., Dávila, G., Vinuesa, P., Miranda, F., Ormeño, E., González, V. (2017). Complete genome sequences of three Rhizobium gallicum symbionts associated with common bean (Phaseolus vulgaris). Genome Announcements, 5(11).
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Debelle, F., Plazanet, C., Roche, P., Pujol, C., Savagnac, A., Rosenberg, C., Prome, J. C., Denarie, J. (1996). The NodA proteins of Rhizobium meliloti and Rhizobium tropici specify the N-acylation of Nod factors by different fatty acids. Molecular Microbiology, 22 (2), 303-314.
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Fischer, H. M. (1994). Genetic Regulation of Nitrogen Fixation in Rhizobia. Microbiological Reviews, 58, 352-386.
Gaunt, M. W., Turner, S. L., Rigottier-Gois, L., Lloyd-Macgilp, S. A., Young, J. P. (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.
Gepts, P. (1990). Biochemical evidence bearing on the domestication of Phaseolus (Fabaceace) beans. Economic Botany, 44, 28-38.
Gepts, P., Bliss, F. A. (1988). Dissemination pathways of common bean (Phaseolus vulgaris) deduced from phaseolin electrophoretic variability. II. Europe and Africa. Economic Botany, 42, 86-104.
Girard, M. L., Flores, M., Brom, S., Romero, D., Palacios, R., Davila,G. (1991). Structural complexity of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli. Journal of Bacteriology, 173 (8), 2411-2419.
Grange, L., Hungria, M. (2004) Genetic diversity of indigenous common bean (Phaseolus vulgaris) rhizobia in two Brazilian ecosystems. Soil. Biol. Biochem. 36, 1389–1398.
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Gurkanli, C. T., Ozkoc, I., Gunduz, I. (2013). Genetic diversity of rhizobia nodulating common bean (Phaseolus vulgaris L.) in the Central Black Sea region of Turkey. Annals of Microbiology, 63(3), 971-987.
Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
Han, S. Z., Wang, E. T., Chen, W. X. (2005). Diverse bacteria isolated from root nodules of Phaseolus vulgaris and species within the genera Campylotropis and Cassia grown in China. Systematic and Applied Microbiology, 28, 265-276.
Haukka, K., Lindstrom, K. and Young, J. P. W. (1998). Three Phylogenetic Groups of nodA and nifH Genes in Sinorhizobium and Mesorhizobium Isolates from Leguminous Trees Growing in Africa and Latin America. Applied and Enviromental Microbiology, 64, 419-426.
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Primary Language	Turkish
Journal Section	Research Article
Authors	Cem Tolga Gürkanlı This is me İbrahim Özkoç This is me Merih Kıvanç This is me
Publication Date	August 15, 2018
Published in Issue	Year 2018 Volume: 11 Issue: 2

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APA	Gürkanlı, C. T., Özkoç, İ., & Kıvanç, M. (2018). Türkiye’nin Eskişehir ilinden, Phaseolus vulgaris L.’den izole edilen rhizobial örneklerin moleküler karakterizasyonu. Biological Diversity and Conservation, 11(2), 106-114.

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