Rapid and sensitive methods for detection of Allorhizobium vitis, causal agent of grapevine crown gall

A rapid method and sensitive methods for extraction of bacterial DNA from pure culture and directly from plant materiel were compared in polymerase chain reaction with specific primers VCF3/VCR3 to see the reliable method that can used in the detection of tumorigenic strain of Allorhizobium vitis causal agent of grapevine crown gall. From the three tested methods of DNA extraction from pure culture, the alkaline method is the most effective technique for the extraction presenting a high sensitivity with a detection threshold equal to 5.104 CFU/ml. Five different protocols for extracting bacterial DNA from plant tissues of infected tomato, based on the use of an extraction buffer, were tested to see its usefulness in detecting pathogenic strain of A. vitisS4. Two protocols based on the use of Triton X-100 and Tween 20 were efficient for detecting A. vitis S4 directly from tomato tumors with a sensitivity of 103 CFU/ml for the both protocols. Consequently, these protocols were proposed as specific protocols for the detection of tumorigenic strain of A. vitis from symptomatic and asymptomatic plants.


INTRODUCTION
Crown gall of grapevine caused by Allorizobium vitis (Moussavi et al., 2014(Moussavi et al., , 2015, previously named Agrobacterium vitis (Ophel and Kerr 1990);is an economically important disease and one of the most serious bacterial disease affecting grape production in several countries (Burr and Otten, 1999). The tumorigenicity of A. vitis is an encogenes transfer into plant cells of the T-DNA (transferred DNA), part of a large tumor-inducing (Ti) plasmid (Thomashow et al. 1984).The T-DNA integrated into the plant cell genome, contains gens responsible for the biosynthesis of hormones (auxins and cytokines) leading to gall development and genes coded for biosynthesis of opines used as specific carbon and nitrogen sources for A. vitis development (Lacroix and Citovsky, 2013). The development of galls obstruct vascular tissue and restrict movement of water and nutrients into the vine above the gall, which affect grapevine growth and yield (Schroth et al., 1988). A. vitis is adapted to survive in the plants tissues without causing tumors until conditions becomes favorable for gall development. Therefore, the disease spreads out by asymptomatic propagating materials (Kuzmanovic et al., 2014) which is necessary to develop a reliable detection methods of the pathogen in both symptomatic and asymptomatic plant materials and in the soil to efficiently prevent the disease (Bini et al., 2008). Generally, the detection methods of A. vitis are based on their isolation on the semiselective culture media and pathogenicity tests but these methods can take many weeks for results (Johnson et al., 2013, Shams et al., 2012. Polymerase chain reaction (PCR) it's the most reliable technique improve sensitivity, specificity and rapidity for the detection of bacteria which targets gens that is found only in A. vitis by the use of specific primers (Johnson et al., 2013;Shams et al., 2012Shams et al., , 2013. Several PCR protocols have been developed and successfully used for detection of tumorigenic strains of A. vitis directly from plant hostswith the use of primers, which target gens localized on Ti plasmid,vir or T-DNAregions (Bini et al., 2008). Generally,the methods of extraction of bacterial DNA from plant tissues are based to the use of a DNA purification Kit specific to A. vitis and characterized to inhibit the action of plant polyphenols that inhibit the PCR reaction (Bini et al., 2008). This method is very expansive and need several steps for purification of the DNA; for this reason, many study work was conducted to develop others techniques of DNA extraction directly from infected plants (Llop et al., 1999, Szegedi andBottka, 2002). The main purpose of this study was to compare the extraction procedures of DNA from pure culture for efficient routine detection of A. vitis and to evaluate and optimize protocols of detection of A. vitis used Bio-PCR and PCR reaction directly for infected plant with the study of threshold of detection of the pathogen.

Pathogenicity and hypersensibility tests
The pathogenicity of strains A. vitis S4 was studied by inoculating-plants of tomato (Solanum lycopersicum L.). The inoculation was made by 10 µl of suspension (10 7 CFU/mL) of 24 hours bacterial culture in stem internodes of tomato 2-3 weeks after transplanting. Inoculated plants were maintained in greenhouse at 27°C during 3-4 weeks. The hypersensibility reaction was determined on tobacco (Nicotiana tabacum cv. Xanthi). 200 µl of bacterial suspensions (10 7 CFU/ml) were infiltrated ontobacco leaf by a needleless syringe. Sterile water was used as a negative control. The tobacco plants were kept in a growth greenhouse. Development of necrosis was scored over a period of 4 to 5 days. DNA extraction from pure culture Three extraction procedures were used to obtain DNA for Bio-PCR analysis: The first protocol was based to use alkaline method (Shams et al., 2013). From bacteria grown overnight at 28°C in MG medium, one colony of A. vitis S4 was mixed with 10µl of NaOH (20 mM) and incubated at 37°C for 5 minutes. The A. vitis lyses cells were stored at 4°C until they use. The second protocol was based on the lysis of the bacterial cells by heating a bacterial suspension of 10 8 CFU/ml at 100 °C for 15 min. the lyses cells were stored at 4°C until they use (Hannou et al., 2013). The third protocol is based on the lysis of the cells by thermal shock by heating the bacterial suspension for 15 min at 100 °C then cooling in ice for 5 min and centrifuging at 10000 g for 1 min. The resulting supernatant was used for PCR (Pastrick and Rainay, 1999; Ameur et al., 2014). Bio PCR-pTi Specific primers VCF3 (GGCGGGCGYGCYGAAAGRAARACYT) and VCR3 (AAGAACGYGGNATGTTGCATCTYAC) were used to identify pathogenic strains of A. vitisby the detection of plasmids (pTi); they amplify a DNA fragment of 414bp of the virC1 and virC2 genes (Kawaguchi, 2009). Standard PCR was carried out in a 60µl reaction volume containing 38.6µL H2O, 6µl (2mM) DNTPs, 1.2µl (2mM) MgCl2, 3µl DMSO (Dimethyl sulfoxide), 1µl (10 µM) of each primer, 0.2µl Taq DNA polymerase (Invitrogen, France) and 3µl of lyses cells from each extraction protocols were tested. In order to test the possibility to detect A. vitis without carring extraction of the DNA, two others methods were tested; the first was to add a small colony directlyin master mix using toothpick; and the second method was to add 3µl of a bacterial suspension of (10 8 CFU/ml) into the mix. In all five protocols were tested to detect A. vitis. The PCR was performed using the following program: initial denaturation at 95°C for 5min, followed by 35 cycles of denaturation at 95°C for 1min, annealing at 57°C for 1min and extension at 72°C for 1min, followed by an additional extension at 72°C for 3min. Electrophoresis was performed in 1.5 % agarose gel. The gel was soaked with ethidium bromide. Fragments were visualized with an ultraviolet (UV) transilluminator, and the gel was photographed. Bacterial DNA extraction from tomato tumors Five protocols were tested to obtain DNA from tomato tumors for PCR analysis. The samples used in this test was made from the tumors obtained during the production of symptoms on tomato plants. Firstly, the tumors were washed in running water and tumor fragment surface were disinfected with 70 % ethanol. The necrotic tissues were removed; and tumor was cut in small fragment. The pieces of tumor were ground in 2µl of sterile distilled water using a mortar and pestle to isolate the pathogen from plant tissues. After incubation during 30min, the macerates were filtered using sterile filter paper.
The first protocol used in this study to extract the DNA from the macerates was been described by Bereswill et al. (1992). The macerates were shaken for two hours in a 0.9% NaCl solution. The supernatant was centrifuged during 10min at 10000g, the pellet was resuspended in 0.1ml of sterile water, and 10µl was used for PCR-pTi analysis. The second protocol was described in the study work of Llop et al. (1999). 500µl of macerates were placed into an Eppendorf and centrifuged at 10000g for 10min. The pellet was resuspended in 500µl extraction buffer (200 mM Tris HCL pH 7.5, 250 mM NaCl, 25 mM EDTA, 0.5% SDS, 2% PVP), vortexed and left for 1 hour at room temperature with continuous shaking. Then it was centrifuged at 5000g for 5min, 450 µl of the supernatant were taken 450µl isopropanol added, mixed and left for 1 hour at room temperature. The mixture was centrifuged and the pellet dried under vacuum. Finally, it was responded in 100 µl water. For the third protocol, we use the modified extraction technic by Taylor et al. (2001). 500µl of macerates were placed into an Eppendorf and centrifuged at 10000g for 10min. the pellet was suspended in 500 µl of plant extraction buffer (140 mM NCL, 50 mM KCl, 0.05% Tween 20, 2% PVP and 0.4% BSA). The mixture was left at room temperature during 15min and stored in 4°C until use. The fourth technic tested in this study was described in the study work of Szegedi and Bottka (2002). 1ml of the macerate was placed in Eppendorf and centrifuged at 18000g in 4°C for 15 min. the pellet was suspended in 100µl of sterile water in mixture with Triton X-100 (1%) (V:V) and heated at 95°C for 10 min. The last protocol tested in this study was the same protocol described previously but with some modifications. The Triton X-100 solution was replaced with Tween 20 (0.1%). This protocol is based on the work of Bini et al. (2008).

PCR analysis
For all extraction protocols from tumors, PCR analysis was made using specific primers of VircC1 and VirC2 gens (VCF3 and VCR3). The reactional mix was prepared separately for each protocol (Table 1). PCR program was performed with the same condition as before.

Determination of the detection threshold of A. vitis
In order to evaluate the sensitivity of detection protocols of A. vitis by Bio-PCR, two bacterial suspension of 10 9 CFU/ml were prepared, one in sterile water and the other in lysis solution of NaOH (20 mM). From the two bacterial suspensions, serial dilutions were made to a concentration of 10 2 CFU/ml. The detection threshold of A. vitis was also made for the macerates obtained from the previous tests. The PCR was performed using specific primers VCF3 and VCF3 and according to the same condition as before.

III. RESULTS & DISCUSSION Pathogenicity and hypersensibility tests
A. vitis strain S4 was tested for the ability to induce hypersensitive response (HR) on tobacco and tumors in tomato. The tested strain is capable to cause HR in leaf of tobacco after 2 days of inoculation ( Figure 1A) and able to induce tumor on stems of inoculated tomato within 20 days of incubation in greenhouse ( Figure 1B). The capacity of this strain to induce gall development in tomato is related to the presence of pTi plasmid, which is an important element for the pathogenicity and tumorigenicity of A. vitis strains (Shams et al., 2012). The necrosis in leaf of tobacco results in rapid cell death and it is a part of the plant defense response against pathogens (Rodriguez-Palenzuela et al., 1991, Heath, 1998). The HR induced in leaf of tobacco it resembles a disease reaction in grape tissues infected with A. vitis in natural conditions. It has been demonstrated that several plant pathogenic bacteria that cause necrosis on host plant are able to induce HR to another plants ( Alfano and Collmer, 1996).The ability of A. vitis to induce HRis due to the capacity of this strain to produce specific enzyme, Plygalacturonase (PG) (Rodriguez-Palenzuela et al., 1991). Other research have demonstrated that when the concentration of A. vitisis greater than approximately 10 6 CFU/ml, the A. vitis was able to cause necrosis (Herlache, 1999).

Bio PCR-pTi
The effectiveness of three protocols of the DNA extraction and two others methods without the extraction of the DNA, used for detection of A. vitis S4 from pure culture, was evaluated by molecular test with the primers VCF3/VCR3 (Figure 2). The results show that a 414 bp fragment of virC1-virC2 gene (Sawada and Tsuchiya, 2003) was amplified with all the tested protocols of DNA extraction and without extraction using only a colony or a bacterial suspension; therefore, these protocols can be used for the different molecular tests to characterize and detect A. vitis strains. Moreover, the use of virC primers are able to detect pathogenic strains of A. vitis possessing pTi plasmid (Kawaguchi, 2009;Kumagai and Fabritius, 2008); and were used in several study work to identify tumorigenic strain of A. vitis in several countries (Kuzmanovic and al., 2012;Lamovšek et al., 2014).

Detection of A. vitis S4 from tomato tumors
The detection of A. vitis directly from infected plant represents an important technique for the diagnostic of the disease. In this work, five different protocols were used to extract the DNA from tumors produced in tomato plants.

International Journal of Environment, Agriculture and Biotechnology (IJEAB)
Vol -2, Issue-4, July-Aug-2017  http://dx.doi.org/10.22161/ijeab/2.4.45  ISSN: 2456-1878 www.ijeab.com Page | 1817 Moreover, to compare these protocols the macerate, the enriched macerate with the PBS and pure colonies were used as a DNA template. The obtained results show the presence an expected size amplicon (414 bp) which amplified using the protocols 3 (Taylor et al In the research work of Eastwell et al. (1995) they found that the bacterial lysis cells in situ in grapevine followed by DNA purification was more effective to detect A. vitis than then analysis of bacteria suspended in water. This observation may be due to the fixation of the bacteria to the cell walls of the grapevine cell. Moreover, in the study work of Kaufmann et al. (1996) they showed that the use of immunocapture culture of plant extract improve the sensibility and reliability of the method.

Determination of the detection threshold of A. vitis
For a large application of PCR for the detection of A. vitis, it is necessary to develop a rapid and simple protocol for the extraction of DNA for amplification and in the same time, the protocol must be sensitive for the detection of bacteria on low concentrations. For this reason, an evaluation test of the detection threshold of each protocol (from pure culture and macerate) was mad to know the minimum concentration detectable by various protocols applied to the A. vitis strain. Different concentrations of DNA ranging from 10 9 CFU/ml to 10 2 CFU/ml were test for the evolution of the detection threshold. The determination of detection threshold by Bio-PCR of different protocols of DNA extraction indicate that the three protocols of lysis cell from pure culture show different results. For the alkaline method of DNA extraction, the detection threshold was determinate in a concentration equal to 5.10 4 CFU/ml ( figure 4A). For the protocol of heating bacterial suspension, the detection threshold correspond to the concentration equal to 5.10 6 CFU/ml ( Figure 4B). Moreover, for the third protocol of thermal shock the detection threshold correspond to the concentration 10 5 CFU/ml ( Figure 4C). From the three tested protocols, the alkaline method was the more sensitive method for detection of A. vitis from pure culture. The alkalinity and high temperature cause the lysis of well cells and therefore the liberation of the DNA in the solution. The sensitivity of alkaline protocol can be explained by the additional NaOH property of the hydrogen bond perturbation between the DNA base pairs, which denatures genomic and plasmid DNA and allow their amplification. However the alkaline method is only used for the pure culture and isolated bacterial cells and cannot be used for the detection of A. vitis from plant material. In the study work of Burr et al. (1999) and Cubero et al. (1999) the detection threshold was determinate for 150 to 200 cells. Szegedi and Bottka (2002) were demonstrated that the detection threshold is equal to 10 5 CFU/ml using the protocol of heating bacterial suspension in sterile distillated water and in Triton X-100. The Triton X-100 solution was more effective than sterile distillated water. For the determination of detection threshold, theprotocol 4 and 5 used for the extraction of DNA of A. vitis from plant material and based on the use of Triton X-100 and Tween 20 were selected due to the simplicity and rapidity of these techniques. Therefore, it is necessary to determinate their sensitivity in order to identify their detection threshold. The sensitivity evaluation test of each protocol was carried using a decimal dilution of the macerate solution. The obtained results of specific PCR-pTi show that tested protocols are able to detect bacteria with concentration equal to 10 3 CFU/ml ( Figure 5). These techniques can identify A. vitis with a low concentration from macerate that contain different bacterial species.

IV. CONCLUSION
In conclusion, results obtained in the present work show that use of alkaline method for the extraction of DNA from pure culture are the reliable and sensitive method can be used in several study for molecular characterization and detection of A. vitis isolates. Moreover, the use of direct techniques to detect A. vitis from plant materials by specific PCR are important issues that can be used for the detection of the pathogens from symptomatic and asymptomatic grapevines.