Sensitive quantitative detection of Ralstonia solanacearum in soil by the most probable number-polymerase chain reaction (MPN-PCR) method

Construction of a TRFIC strip for rapid and sensitive detection of Ralstoniasolanacearum

The development of a sensitive and rapid screening method for Ralstonia solanacearum is critical for the control of tobacco wilt. In the present study, tissue homogenates of three tobacco varieties (Honda, Yunnan 87 and K326) with different resistance to R. solanacearum, were individually used as additives to the bacteria culture medium. The changes in R. solanacearum secretome were investigated and one of the most abundant secretary proteins with increased expression, polygalacturonase (PG), was selected as a marker for R. solanacearum identification. Then PG gene was cloned into E. coli, and the expressed protein was used as the immunogen to develop monoclonal antibodies. Subsequently, the monoclonal antibody against PG was coupled with synthesized polystyrene microspheres, and a rapid test strip system was developed for the detection of R. solanacearum based on time-resolved fluorescent immunochromatographic (TRFIC) method. Under optimal conditions, the detection limit of the strips could reach 72 cells/mL; while it was 422 cells/mL with a linear range from 4 × 10² to 5.12 × 10⁴ cells/mL when testing tobacco samples, which is 1000 times lower than that of colloidal gold-labeled strips. Notably, no cross-reactivity was observed with nine tobacco-related pathogens. Finally, this TRFIC strips was applied to detect R. solanacearum existed in the tobacco and soils of fields with or without bacterial wilt. The results demonstrated that this TRFIC strips could distinguish the difference in bacterial concentration existed in tobacco and soil between the two fields. In summary, this test strip is suitable for sensitive, quick screening of R. solanacearum in tobacco.

Rapid quantification of fecal indicator bacteria in water using the most probable number - loop-mediated isothermal amplification (MPN-LAMP) approach on a polymethyl methacrylate (PMMA) microchip

Fecal contamination of water and its associated pathogens are a major public health concern in both developing and industrialized areas. Fecal indicator bacteria (FIB) are commonly used to assess microbial water quality, but they require a relatively long period of incubation time. Currently, molecular techniques have been applied to rapidly detect FIB. However, these molecular techniques require expensive and sophisticated equipment. In this study, we developed a rapid on-chip gene quantification method based on loop-mediated isothermal amplification (LAMP) PCR. The LAMP assays can measure the target genes of the fecal indicator bacteria (FIB), including E. coli and Enterococcus spp, using the most probable number (MPN) approach. The colorimetric LAMP assay allows for naked-eye observation of the PCR reaction as few as 4 gene copies / well. When the reaction ends, MPN measurement of positive outcomes on the white-based PMMA (polymethacrylic acid) microchips provides the concentrations of the target genes of FIB with a confidence interval. We validated the feasibility of the MPN-LAMP approach by obtaining a strong correlation between the results of the MPN estimations and the qPCR analysis. Moreover, the MPN-LAMP approach was used to quantify the FIB in different environmental water collected from the freshwater reservoirs, beach, agriculture farm, and sewage. Our research demonstrates that the MPN- LAMP method enables us to easily and quickly quantifying FIB genes isolated from the environment without expensive qPCR instruments.

Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields

Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics. Soil samples were collected from three fields and two depths because bacterial wilt pathogens were present in soil at a depth greater than 40 cm. We classified soil samples based on the presence or absence of the bacterial phcA gene, a key gene for bacterial wilt pathogenicity and tomato disease symptoms. Pyrosequencing of the prokaryotic 16S rRNA gene and eukaryotic internal transcribed spacer region sequences showed that the diversity and richness of the communities mostly did not correlate with disease symptoms. Prokaryotic and eukaryotic community structures were affected more by regional differences than the appearance of disease. Several prokaryotes and eukaryotes were more abundant in soil that lacked disease symptoms, and eight prokaryotes and one eukaryote of this group were commonly detected among the three fields. Some of these taxa were not previously found in disease-suppressive soil. Our results suggest that several prokaryotes and eukaryotes control plant disease symptoms.

Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse

The characterization of microbial communities that promote or suppress soil-borne pathogens is important for controlling plant diseases. We compared prokaryotic communities in soil with or without the signs of tomato bacterial wilt caused by Ralstonia solanacearum. Soil samples were collected from a greenhouse at two different depths because this pathogen is present in deep soil. We used samples from sites in which we detected phcA, a key gene regulating R. solanacearum pathogenicity. The pyrosequencing of prokaryotic 16S rRNA sequences in four soil samples without disease symptoms but with phcA and in two soil samples with disease symptoms indicated that community richness was not significantly different between these two soils; however, microbial diversity in the lower soil layer was higher in soil samples without disease symptoms but with phcA. A difference in prokaryotic community structures between soil samples with and without bacterial wilt was only observed in the upper soil layer despite apparent similarities in the communities at the phylum level. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and several Archaea were more abundant in soil samples without disease symptoms, whereas taxa in another eight phyla were more abundant in soil samples with disease symptoms. Furthermore, some prokaryotic taxa were abundant specifically in the lower layer of soil, regardless of whether disease was present. These prokaryotic taxa may suppress or accelerate the pathogenesis of bacterial wilt and are good targets for future studies on disease control.

Tube-Wise Diagnostic Microarray for the Multiplex Characterization of the Complex Plant Pathogen Ralstonia solanacearum

Ralstonia solanacearum is a well-known agricultural and ecological threat worldwide. The complexity of the R. solanacearum species complex (Rssc) represents a challenge for the accurate characterization of epidemiological strains by official services and research laboratories. The majority of protocols only focus on a narrow range of strains; however, this species complex includes strains that represent major constraints and are under strict regulation. The main drawback associated with the current methods of detecting and characterizing Rssc strains is their reliance on combining different protocols to properly characterize the strains at the ecotype level, which require time and money. Therefore, we used microarray technology (ArrayTube) to develop a standard protocol, which characterizes 17 major groups of interest in the Rssc, in a single multiplex reaction. These 17 majors groups are linked with a phylogenetic assignation (phylotypes, sequevars), but also with an ecotype assignation associated with a range of hosts (e.g., brown rot, Moko). Probes were designed with a 50-mer length constraint and thoroughly evaluated for any flaws or secondary structures. The strains are characterized based on a DNA extraction from pure culture. Validation data showed strong intra-repeatability, inter-repeatability, and reproducibility as well as good specificity. A hierarchical analysis of the probe groups is suitable for an accurate characterization. Compared with single marker detection tests, the method described in this paper addresses efficiently the issue of combining several tests by testing a large number of phylogenetic markers in a single reaction assay. This custom microarray (RsscAT) represents a significant improvement in the epidemiological monitoring of Rssc strains worldwide, and it has the potential to provide insights for phylogenetic incongruence of Rssc strains based on the host of isolation and may be used to indicate potentially emergent strains.

Identification and Management Challenges Associated with <I>Ralstonia solanacearum </I> (Smith), Causal Agent of Bacterial Wilt Disease of Tomato in Sub-Saharan Africa

Tomato is the world's most consumed vegetable crop after potato and it is source of vitamins, minerals, fiber, lycopene, β-carotene and income. Despite its significant importance tomato can heavily be attacked by different pathogens including Ralstonia solanacearum that incites bacteria wilt disease. The disease is very devastating causing a considerable yield loss worldwide. The pathogen can survive in plant debris, infected plants and host weeds and spread from one field to another by irrigation or flood water, soil, farm equipment and workers and weeds which usually grow along waterways and it is difficult to manage due to complication in biology, nature of infestation and wide host range. In areas like the Sub-Saharan Africa where there exists a wide diversity of plant species, the pathogen becomes even more difficult to manage. It is on this basis that this review article, clearly discusses challenges for bacterial wilt disease identification and management in tomato farming systems with respect to the diagnosis methods used, pathogen genetic diversity and host range and pathogen survival mechanisms under different environment. The information will empower the responsible personnel involved in tomato production chain to have clear information about the pathogen and management options available against the disease in Sub-Saharan Africa.

Recent trends in control methods for bacterial wilt diseases caused by Ralstonia solanacearum

Previous studies have described the development of control methods against bacterial wilt diseases caused by Ralstonia solanacearum. This review focused on recent advances in control measures, such as biological, physical, chemical, cultural, and integral measures, as well as biocontrol efficacy and suppression mechanisms. Biological control agents (BCAs) have been dominated by bacteria (90%) and fungi (10%). Avirulent strains of R. solanacearum, Pseudomonas spp., Bacillus spp., and Streptomyces spp. are well-known BCAs. New or uncommon BCAs have also been identified such as Acinetobacter sp., Burkholderia sp., and Paenibacillus sp. Inoculation methods for BCAs affect biocontrol efficacy, such as pouring or drenching soil, dipping of roots, and seed coatings. The amendment of different organic matter, such as plant residue, animal waste, and simple organic compounds, have frequently been reported to suppress bacterial wilt diseases. The combined application of BCAs and their substrates was shown to more effectively suppress bacterial wilt in the tomato. Suppression mechanisms are typically attributed to the antibacterial metabolites produced by BCAs or those present in natural products; however, the number of studies related to host resistance to the pathogen is increasing. Enhanced/modified soil microbial communities are also indirectly involved in disease suppression. New promising types of control measures include biological soil disinfection using substrates that release volatile compounds. This review described recent advances in different control measures. We focused on the importance of integrated pest management (IPM) for bacterial wilt diseases.

Enhanced soil washing process for the remediation of PBDEs/Pb/Cd-contaminated electronic waste site with carboxymethyl chitosan in a sunflower oil-water solvent system and microbial augmentation

An innovative ex situ soil washing technology was developed to remediate polybrominated diphenyl ethers (PBDEs) and heavy metals in an electronic waste site. Elevated temperature (50 °C) in combination with ultrasonication (40 kHz, 20 min) at 5.0 mL L(-1) sunflower oil and 2.5 g L(-1) carboxymethyl chitosan were found to be effective in extracting mixed pollutants from soil. After two successive washing cycles, the removal efficiency rates for total PBDEs, BDE28, BDE47, BDE209, Pb, and Cd were approximately 94.1, 93.4, 94.3, 99.1, 89.3, and 92.7 %, respectively. Treating the second washed soil with PBDE-degrading bacteria (Rhodococcus sp. strain RHA1) inoculation and nutrient addition for 3 months led to maximum biodegradation rates of 37.3, 52.6, 23.9, and 1.3 % of the remaining total PBDEs, BDE28, BDE47, BDE209, respectively. After the combined treatment, the microbiological functions of washed soil was partially restored, as indicated by a significant increase in the counts, biomass C, N, and functioning diversity of soil microorganisms (p < 0.05), and the residual PBDEs and heavy metals mainly existed as very slow desorbing fractions and residual fractions, as evaluated by Tenax extraction combined with a first-three-compartment model and sequential extraction with metal stability indices (I R and U ts). Additionally, the secondary environmental risk of mixed contaminants in the remediated soil was limited. Therefore, the proposed combined cleanup strategy is an environment-friendly technology that is important for risk assessment and management in mixed-contaminated sites.