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Yıl 2020, Cilt: 5 Sayı: 4, 475 - 483, 31.12.2020
https://doi.org/10.35229/jaes.744909

Öz

Kaynakça

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  • Gaunt, M.W., Turner, S.L., Rigotier-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.
  • Goodner, B., Hinkle, G., Gattung, S., Miller, N., Blanchard, M., Qurollo, B., Gold-man, B.S., Cao, Y., Askenazi, M., Halling, C., Mullin, L., Houmiel, K., Gordon, J.,Vaudin, M., Iartchouk, O., Epp, A., Liu, F., Wollam, C., Allinger, M., Doughty,D., Scott, C., Lappas, C., Markelz, B., Flanagan, C., Crowell, C., Gurson, J., Lomo,C., Sear, C., Strub, G., Cielo, C. & Slater, S. (2001). Genome sequence of the plantpathogen and biotechnology agent Agrobacterium tumefaciens C58. Science, 294, 2323-2328.
  • Guindon, S. & Gascuel, O. (2003). A simple, fast and accurate algorithm to estimate large phylogenies by maximum-likelihood. Systematic Biology, 52, 696-704.
  • 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, 971-987.
  • Gülümser, A. (2016). Dünyada ve Türkiye’de yemeklik dane baklagillerin durumu. Tarla Bitkileri Merkez Araştırma Enstitüsü Dergisi, 25, 292-298.
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  • Karakaya, A. & Özcan, S. (2000). Susceptibility of chickpea (Cicer arietinum L.) cultivars to Agrobacterium tumefaciens (Smith and Townsend) Conn. Turkish Journal Biology, 24, 285-289.
  • Kuzmanovic, N., Puławska, J., Prokic, A., Ivanovic, M., Zlatković, N., Jones, J.B. & Obradovic, A. (2015a). Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum. Systematic and Applied Microbiology, 38, 373-378.
  • Kuzmanovic, N., Prokic, A., Ivanovic, M., Zlatkovic, N., Gasic, K. & Obradovic, A. (2015b). Genetic diversity of tumorigenic bacteria associated with crown gall disease of raspberry in Serbia. European Journal of Plant Pathology, 142, 701-713.
  • Kuzmanovic, N., Puławska, J., Smalla, K. & Nesme, X. (2018). Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops. Systematic and Applied Microbiology, 41, 191-197.
  • 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.
  • Mafakheri, H., Taghavi, S.M., Pulowska, J., de Lajudie P., Lassalle, F. & Osdaghi, E. (2019). Two novel genomospecies in the Agrobacterium tumefaciens species complex associated with rose crrown gall. Phytopathology, 109, 1859-1868.
  • 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.
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  • 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.
  • Mrabet, M., Mnasri, B., Romdhane, S.B., Laguerre, G., Aouani, M.E., Mhamdi, R. (2006). Agrobacterium strains isolated from root nodules of common bean specifically reduce nodulation by Rhizobium gallicum. FEMS Microbiology Ecology, 56, 304-309.
  • Otağ, F., Tezcan, S., Özturhan, H., Aslan, G., Kuyucu, N. & Emekdaş, G. (2007). Emerging non-fermenter Gram negative pathogens in paediatric patients: Rhizobium radiobacter bacteremia. Journal of Pediatric Infection, 1, 143-146.
  • Panday, D., Schumann, P. & Das, S.K. (2011). Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.). International Journal of Systematic and Evolutionary Microbiology, 61, 2632-2639.
  • Pulawska, J., Willems, A. & Sobiczewski, P. (2012). Rhizobium skierniewicense sp. nov., isolated from tumours on chrysanthemum and cherry plum. International Journal of Systematic and Evolutionary Microbiology, 62, 895-899.
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Molecular Characterization of Some Saprophyte Agrobacterium spp. Strains Isolated from Root Nodules of C. arietinum L. Cultivated in Central Anatolia Region of Turkey

Yıl 2020, Cilt: 5 Sayı: 4, 475 - 483, 31.12.2020
https://doi.org/10.35229/jaes.744909

Öz

ABSTRACT
In the present study twelve plant associated bacteria which isolated from root nodules of C. arietinum L. collected from Central-Anatolia region of Turkey were identified with current molecular techniques. None of the isolates were produced root nodules or showed pathogenic effects (gall or hairy root) on the original host as the result of authentication and pathogenicity tests, respectively. These results have suggested that all these isolates are root endophytic bacteria. Additionally, PCR amplifications for nodD and virA genes did not revealed any bands. These results showed that these isolates have not harbour symbiotic (pSym) or pathogenicity (Ti: Tumor inducing or Ri: Root inducing) plasmids which are necessary for nodulation or virulence, respectively. TP-RAPD analysis revealed three patterns indicating three genetically distinct group within the isolate collection. From each pattern one representative isolate was selected for further molecular analyses. Phylogenetic analyses depending on nucleotide sequences of 16S rDNA and recA genes assigned representative isolates of Pattern-A (n: 4) and Pattern-B (n: 6) to A. radiobacter. On the other hand, the representative isolate of Pattern-C (n: 2) appeared as related to A. nepotum. As a result, this study presents the first phylogenetically identified root-endophytic Agrobacterium radiobacter and A. nepotum isolates from root nodules of C. arietinum L. grown in Central Anatolia part of Turkey. Additionally the first molecular data of A. radiobacter for Turkey also presented.

ÖZ
Bu çalışmada Türkiye’nin İç Anadolu bölgesinden toplanan C. arietinum L. bitkisinin kök nodüllerin’den izole edilmiş on iki bitki ilişkili bakteri moleküler teknikler kullanılarak teşhis edilmiştir. Bu izolatların hiç birisi otantikasyon ve patojenite testlerinin sonucunda orijinal konak üzerinde nodül oluşturmamış veya patojenik etki (gall oluşumu veya saçak kök oluşumu) göstermemiştir. Bu sonuçlar bütün bu izolatların kök endofitik bakteriler olduğunu ortaya koymuştur. Ek olarak nodD ve virA genleri için yapılan PCR amplifikasyonları herhangi bir bant ortaya koymamıştır. Bu sonuçlar bu izolatların nodülasyon veya virülans için gerekli olan sırasıyla simbiyotik (pSym) veya patojenite (Ti: Tümör oluşturan veya Ri: Saçak kök oluşturan) pilazmitlerini taşımadıklarını göstermiştir. TP-RAPD analizi izolat kolleksiyonu içerisinde genetik olarak ayrı üç gruba işaret eden üç şablon ortaya koymuştur. İleri moleküler analizler için her şablondan bir temsilci izolat seçilmiştir. 16S rDNA ve recA genlerinin nükleotid dizilerine dayalı filogenetik analizler Şablon-A (n: 4) ve Şablon-B’nin (n: 6) temsilci izolatlarını Agrobacterium radiobacter türü ile ilişkilendirmiştir. Diğer taraftan, Şablon-C’nin (n: 2) temsilci izolatı A. nepotum olarak ortaya çıkmıştır. Sonuç olarak bu çalışma Türkiye’nin İç Anadolu Bölgesinde yetiştirilen C. arietinum L.’nin kök nodüllerin’den filogenetik olarak tanımlanmış ilk kök endofitik Agrobacterium radiobacter and A. nepotum izolatlarını sunmaktadır. Ek olarak, A. radiobacter için Türkiye’den ilk moleküler verileri de sunmaktadır.

Kaynakça

  • REFERENCES Akbulut, M., Yücel, M. & Öktem, H.A. (2008). Analysis and optimization of DNA delivery into chickpea (Cicer arietinum L.) seedlings by Agrobacterium tumefacience. African Journal of Biotechnology, 7, 1011-1017.
  • Argun, N., Momol, M.T., Maden, S., Momol, E.A., Reid, C.L., Çelek, H. & Burr, T.J. (2002). Characterization of Agrobacterium vitis strains isolated from Turkish grape cultivars in the Central Anatolia Region. Plant Disease, 86, 162-166.
  • Aysan, Y., Sahin, F., Mirik, M., Donmez, M.F. & Tekman, H. (2003). First report of crown gall of apricot (Prunus armeniaca) caused by Agrobacterium tumefaciens in Turkey. Plant Pathology, 52, 793.
  • Aysan, Y. & Sahin, F. (2003). An outbreak of crown gall disease on rose caused by Agrobacterium tumefaciens in Turkey. Plant Pathology, 52, 780.
  • Bautista-Zapanta, J.N., Arafat, H.H., Tanaka, K., Sawada, H. & Suzuki, K. (2009). Variation of 16S-23S internally transcribed spacer sequence and intervening sequence in rDNA among the three major Agrobacterium species. Microbiological Research, 164, 604-612.
  • Ben Romdhane, S., Trabelsi, M., Aouani, M.E., de Lajudie, P., Mhamdi, R. (2009). The diversity of rhizobia nodulating chickpea (Cicer arietinum) under water deficiency as a source of more efficient inoculants. Soil Biology and Biochemistry, 41, 2568-2572.
  • Bouzar, H., Chilton, W.S., Nesme, X., Dessaux, Y., Vaudequin, V., Petit, A., Jones, J.B. & Hodge, N.C. (1995). A new Agrobacterium strain isolated from aerial tumors on Ficus benjamina L. Applied and Environmental Microbiology, 61, 65-73. Conn, H.J. (1942). Validity of the genus Alcaligenes. Journal of Bacteriology, 44, 353–360.
  • 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. Ditta, G., Virts, E., Palomares, A. & Kim, C.H. (1987). The nifA gene of Rhizobium meliloti is oxygen regulated. Journal of Bacteriology, 169: 3217-3223. FAOSTAT (2016). http://faostat.fao.org/faostat/
  • Flores-Felix, J.D., Menendez, E., Peix, A. & Gracia-Fraile, P. (2020). History and current taxonomic status of genus Agrobacterium. Systematic and Applied Microbiology, 43, 126046.
  • Gaunt, M.W., Turner, S.L., Rigotier-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.
  • Goodner, B., Hinkle, G., Gattung, S., Miller, N., Blanchard, M., Qurollo, B., Gold-man, B.S., Cao, Y., Askenazi, M., Halling, C., Mullin, L., Houmiel, K., Gordon, J.,Vaudin, M., Iartchouk, O., Epp, A., Liu, F., Wollam, C., Allinger, M., Doughty,D., Scott, C., Lappas, C., Markelz, B., Flanagan, C., Crowell, C., Gurson, J., Lomo,C., Sear, C., Strub, G., Cielo, C. & Slater, S. (2001). Genome sequence of the plantpathogen and biotechnology agent Agrobacterium tumefaciens C58. Science, 294, 2323-2328.
  • Guindon, S. & Gascuel, O. (2003). A simple, fast and accurate algorithm to estimate large phylogenies by maximum-likelihood. Systematic Biology, 52, 696-704.
  • 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, 971-987.
  • Gülümser, A. (2016). Dünyada ve Türkiye’de yemeklik dane baklagillerin durumu. Tarla Bitkileri Merkez Araştırma Enstitüsü Dergisi, 25, 292-298.
  • Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Serie, 41, 95-98.
  • Hao, X., Xie, P., Johnstone, L., Miller, S.J., Rensing, C. & Wei, G. (2012). Genome sequence and mutational analysis of plant-growth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286 isolated from a zinc-lead mine tailing. Applied and Environmental Microbiology, 78, 5384-5394.
  • Karakaya, A. & Özcan, S. (2000). Susceptibility of chickpea (Cicer arietinum L.) cultivars to Agrobacterium tumefaciens (Smith and Townsend) Conn. Turkish Journal Biology, 24, 285-289.
  • Kuzmanovic, N., Puławska, J., Prokic, A., Ivanovic, M., Zlatković, N., Jones, J.B. & Obradovic, A. (2015a). Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum. Systematic and Applied Microbiology, 38, 373-378.
  • Kuzmanovic, N., Prokic, A., Ivanovic, M., Zlatkovic, N., Gasic, K. & Obradovic, A. (2015b). Genetic diversity of tumorigenic bacteria associated with crown gall disease of raspberry in Serbia. European Journal of Plant Pathology, 142, 701-713.
  • Kuzmanovic, N., Puławska, J., Smalla, K. & Nesme, X. (2018). Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops. Systematic and Applied Microbiology, 41, 191-197.
  • 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.
  • Mafakheri, H., Taghavi, S.M., Pulowska, J., de Lajudie P., Lassalle, F. & Osdaghi, E. (2019). Two novel genomospecies in the Agrobacterium tumefaciens species complex associated with rose crrown gall. Phytopathology, 109, 1859-1868.
  • 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.
  • Mhamdi, R., Mrabet, M., Laguerre, G., Tiwari, R. & Aouani, M.E. (2005). Colonization of Phaseolus vulgaris nodules by Agrobacterium-like strains. Canadian Journal of Microbiology, 51, 105-111.
  • 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.
  • Mrabet, M., Mnasri, B., Romdhane, S.B., Laguerre, G., Aouani, M.E., Mhamdi, R. (2006). Agrobacterium strains isolated from root nodules of common bean specifically reduce nodulation by Rhizobium gallicum. FEMS Microbiology Ecology, 56, 304-309.
  • Otağ, F., Tezcan, S., Özturhan, H., Aslan, G., Kuyucu, N. & Emekdaş, G. (2007). Emerging non-fermenter Gram negative pathogens in paediatric patients: Rhizobium radiobacter bacteremia. Journal of Pediatric Infection, 1, 143-146.
  • Panday, D., Schumann, P. & Das, S.K. (2011). Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.). International Journal of Systematic and Evolutionary Microbiology, 61, 2632-2639.
  • Pulawska, J., Willems, A. & Sobiczewski, P. (2012). Rhizobium skierniewicense sp. nov., isolated from tumours on chrysanthemum and cherry plum. International Journal of Systematic and Evolutionary Microbiology, 62, 895-899.
  • Pulawska, J., Willems, A., De Meyer, S.E. & Sule, S. (2012). Rhizobium nepotum sp. nov. isolated from tumors on different plant species. Systematic and Applied Microbiology, 35, 215-220
  • Posada, D. (2008). jModel test: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
  • Rivas, R., Velázquez, E., Valverde, A., Mateos, P.F., Martínez- Molina, E. (2001). A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species. Electrophoresis, 22, 1086-1089.
  • Romdhane, S.B., Trabelsi, M., Aouani, M.E., de Lajudie, P. & Mhamdi, R. (2009). The diversity of rhizobia nodulating chickpea (Cicer arietinum) under water deficiency as a source of more efficient inoculants. Soil Biology and Biochemistry, 41, 2568-2572.
  • Rouhrazi, K. & Khodakaramian, G. (2015). Phenotypic and genotypic diversity of root-nodulating bacteria isolated from chickpea (Cicer arietinum L.) in Iran. Annals of Microbiology, 65, 2219-2227.
  • Saidi, S., Mnasri, B. & Mhamdi, R. (2011). Diversity of nodule-endophytic agrobacteria-like strains associated with different grain legumes in Tunisia. Systematic and Applied Microbiology, 34, 524-530.
  • Salmassi, T.M., Venkateswaren, K., Satomi, M., Nealson, K.H., Newman, D.K. & Hering, J. (2002). Oxidation of arsenite by Agrobacterium albertimagni, AOL15, sp. nov., isolated from Hot Creek, California. Geomicrobiology journal, 19, 53-66.
  • Shams, M., Vial, L., Chapulliot, D., Nesme, X. & Lavire, C. (2013). Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR. Systematic and applied microbiology, 36, 351-358.
  • 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, 2nd ed. Nobel Tıp Kitabevleri, İstanbul.
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  • Trimble, W.L., Phung le, T., Meyer, F., Gilbert, J.A. & Silver, S. (2012). Draft Genome Sequence of Agrobacterium albertimagni Strain AOL15. Journal of Bacteriology, 194, 6986-6987.
  • Velázquez, E., Peix, A., Zurdo-Piñeiro, J.L., Palomo, J.L., Mateos, P.F., Rivas, R., Muñoz-Adelantado, E., Toro, N., García-Benavides, P. & Martínez-Molina, E. (2005). The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy Roots in Plants. Molecular Plant Microbe Interactions, 18, 1325-1332.
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  • Wei, G.H., Wang, E.T., Tan, Z.Y., Zhu, M.E. & Chen, W.X. (2002). Rhizobium indigoferae sp. nov. and Sinorhizobium kummerowiae sp. nov., respectively isolated from Indigofera spp. and Kummerowia stipulacea. International Journal of Systematic and Evolutionary Microbiology, 52, 2231-2239.
  • Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Sczcepanowski, R., Goesmann, A., Setubal, J.C., Schmitt, R., Puhler, A. & Schluter, A. (2011). Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology, 155, 50-62.
  • Willems, A. & Collins, M.D. (1993). Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. International Journal of Systematic Bacteriology, 43, 305-313.
  • Yan, J., Li, Y., Han, X., Chen, W.F., Zou, W., Xie, Z. & Li, M., (2017a). Agrobacterium deltaense sp. nov., an endophytic bacteria isolated from nodule of Sesbania cannabina. Archives of microbiology, 199, 1003-1009.
  • Yan, J., Li, Y., Yan, H., Chen, W.F., Zhang, X., Wang, E.T., Han, X.Z. & Xie, Z.H. (2017b). Agrobacterium salinitolerans sp. nov., a saline-alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina. International Journal of Systematic and Evolutionary Microbiology, 67, 1906-1911.
  • Zahradnik, J., Nunvar, J., Pařízková, H., Kolářová, L., Palyzová, A., Marešová, H., Grulich, M., Kyslíková, E. & Kyslík, P. (2018). Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in Central Bohemia. Systematic and Applied Microbiology, 41, 184-190.
  • Zeze, A., Mutch, L.A. & Young, J.P.W. (2001). Direct amplification of nodD from community DNA reveals the genetic diversity of Rhizobium leguminosarum in soil. Environmental Microbiology, 3, 363-370.
  • Zhang, X.X., Guo, X.W., Terefework, Z., Paulin, L., Cao, Y.Z., Hu, F.R., Lindstrom, K., Li, F.D. (1999). Genetic diversity among rhizobial isolates from field-grown Astragalus sinicus of Southern China. Systematic and Applied Microbiology, 22, 312-320.
Toplam 52 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm Makaleler
Yazarlar

Cem Tolga Gürkanlı 0000-0001-8378-7109

Yayımlanma Tarihi 31 Aralık 2020
Gönderilme Tarihi 29 Mayıs 2020
Kabul Tarihi 23 Eylül 2020
Yayımlandığı Sayı Yıl 2020 Cilt: 5 Sayı: 4

Kaynak Göster

APA Gürkanlı, C. T. (2020). Molecular Characterization of Some Saprophyte Agrobacterium spp. Strains Isolated from Root Nodules of C. arietinum L. Cultivated in Central Anatolia Region of Turkey. Journal of Anatolian Environmental and Animal Sciences, 5(4), 475-483. https://doi.org/10.35229/jaes.744909


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