Development of a Species-Specific PCR for Detection and Quantification of Meloidogyne hapla in Soil Using the 16D10 Root-Knot Nematode Effector Gene

Tobacco Root Microbial Community Composition Significantly Associated With Root-Knot Nematode Infections: Dynamic Changes in Microbiota and Growth Stage

The root-knot nematode (RKN) is an important pathogen that affects the growth of many crops. Exploring the interaction of biocontrol bacteria-pathogens-host root microbes is the theoretical basis for improving colonization and controlling the effect of biocontrol bacteria in the rhizosphere. Therefore, 16S and 18S rRNA sequencing technology was used to explore the microbial composition and diversity of tobacco roots (rhizosphere and endophytic) at different growth stages in typical tobacco RKN-infected areas for 2 consecutive years. We observed that RKN infection changed the α-diversity and microbial composition of root microorganisms and drove the transformation of microorganisms from bacteria to fungi. The abundance of Sphingomonas decreased significantly from 18% to less than 3%, while the abundance of Rhizobiaceae increased from 4 to 15% at the early growth stage during the first planting year, and it promoted the proliferation of Chryseobacterium at the late growth stage in rhizosphere microorganisms with the highest abundance of 17%. The overall trend of rhizosphere microorganisms changed in the early growth stage with increasing growth time. The specific results were as follows: (1) Rhizobiaceae and Chryseobacterium increased rapidly after 75 days, became the main abundant bacteria in the rhizosphere microorganisms. (2) The dominant flora in fungi were Fusarium and Setophoma. (3) Comparing the root microbes in 2017 and 2018, RKN infection significantly promoted the proliferation of Pseudomonas and Setophoma in both the rhizosphere and endophytes during the second year of continuous tobacco planting, increasing the relative abundance of Pseudomonas from 2 to 25%. Pseudomonas was determined to play an important role in plant pest control. Finally, a total of 32 strains of growth-promoting bacteria were screened from tobacco rhizosphere bacteria infected with RKN through a combination of 16S rRNA sequencing and life-promoting tests. The results of this research are helpful for analyzing the relationship between RKNs and bacteria in plants, providing reference data for elucidating the pathogenesis of RKNs and new ideas for the biological control of RKNs.

GRAPHICAL ABSTRACT

Development of Loop-Mediated Isothermal Amplification Assay for Rapid Detection and Analysis of the Root-Knot Nematode Meloidogyne hapla in Soil

Soil analysis is crucial for estimating the risk of crop damage by the root-knot nematode Meloidogyne hapla. Here, we developed an analysis assay based on Loop-mediated Isothermal Amplification (LAMP). The LAMP primers were verified for specificity against 10 different nematode species. A manual soil DNA extraction, referred to as SKMM, was developed and compared with a FastDNA kit followed by DNA purification. DNA was extracted with both methods from artificially inoculated soils as well as from naturally infested soil collected from farm fields. The primers exclusively amplified DNA from M. hapla with both colorimetric and real-time LAMP. The detection limit was 193 gene copies and 0.0016 juveniles (12 pg µL−1) per reaction. DNA concentrations and purity (A260/A230) were significantly higher using the SKMM procedure compared with the kit. From the field samples collected in 2019, DNA was amplified from 16% of samples extracted with SKMM and from 11% of samples using the kit. Occurrence of M. hapla DNA was confirmed in soil samples from two out of six field soils in 2020 using both real-time LAMP and qPCR. In conclusion, the developed real-time LAMP is a fast and specific assay for detection and quantification of M. hapla DNA in soil.

Early Detection of the Root-Knot Nematode Meloidogyne hapla Through Developing a Robust Quantitative PCR Approach Compliant with the Minimum Information for Publication of Quantitative Real-Time PCR Experiments Guidelines

Root-knot nematodes (RKNs) are major threats to crops through attacking the roots, which induces an abnormal development of the plant. Meloidogyne hapla is of particular concern, as it is currently expanding its distribution area and displays a wide host range. Effective plant protection against this RKN requires early detection, as even a single individual can cause severe economic losses on susceptible crops. Molecular tools are of particular value for this purpose, and among them, quantitative PCR (qPCR) presents many advantages (i.e., sensitivity, specificity, and rapidity of diagnosis at a reduced cost). Although a few studies have already been proposed for detecting M. hapla through this technique, they lack experimental details and performance testing, suffer from low taxonomic resolution, and/or require expensive hydrolysis probes. Here, we propose a qPCR detection method that uses SYBR Green with developed primers amplifying a fragment of the cytochrome oxidase I mitochondrial region. The method was developed and evaluated following the minimum information for publication of quantitative real-time PCR experiments (MIQE) guidelines to ensure its quality (i.e., sensitivity, specificity, repeatability, reproducibility, and robustness). The results demonstrate that the newly developed method fulfills its goals, as it proved specific to M. hapla and allowed for a reproductible detection level as low as 1.25 equivalent of a juvenile individual. All criteria associated with the MIQE guidelines were also met, so the method is of general use for the reliable early detection of M. hapla.

Rapid and Visual Detection of Meloidogyne hapla Using Recombinase Polymerase Amplification Combined with a Lateral Flow Dipstick Assay

The northern root-knot nematode, Meloidogyne hapla, is a biotrophic parasite that infects many crops and causes severe economic losses worldwide. Rapid and accurate detection of M. hapla is crucial for disease forecasting and control. We developed a recombinase polymerase amplification combined with a lateral flow dipstick (RPA-LFD) assay for rapid detection of M. hapla. The primers and probe were designed based on the effector gene 16D10 sequence and were highly specific to M. hapla. The RPA reaction was performed at a wide range of temperatures from 25 to 45°C within 5 to 25 min, and the amplicon was visualized directly on the LFD within 5 min. The detection limits of the RPA-LFD assay were 10^-3 females and 10^-2 second-stage juveniles/0.5 g of soil, which was 10 times more sensitive than the conventional PCR assay. In addition, the RPA-LFD assay can detect M. hapla from infested plant roots and soil samples, and the entire detection process can be completed within 1.5 h. These results indicate that the RPA-LFD assay is a simple, rapid, specific, sensitive, and visual method that can be used for rapid detection of M. hapla in the field and in resource-limited conditions.

Development of Real-Time and Conventional PCR Assays for Identifying a Newly Named Species of Root-Lesion Nematode (Pratylenchus dakotaensis) on Soybean

A rapid and accurate PCR-based method was developed in this study for detecting and identifying a new species of root-lesion nematode (Pratylenchus dakotaensis) recently discovered in a soybean field in North Dakota, USA. Species-specific primers, targeting the internal transcribed spacer region of ribosomal DNA, were designed to be used in both conventional and quantitative real-time PCR assays for identification of P.dakotaensis. The specificity of the primers was evaluated in silico analysis and laboratory PCR experiments. Results showed that only P.dakotaensis DNA was exclusively amplified in conventional and real-time PCR assays but none of the DNA from other control species were amplified. Detection sensitivity analysis revealed that the conventional PCR was able to detect an equivalent to 1/8 of the DNA of a single nematode whereas real-time PCR detected an equivalent to 1/32 of the DNA of a single nematode. According to the generated standard curve the amplification efficiency of the primers in real-time PCR was 94% with a R2 value of 0.95 between quantification cycle number and log number of P.dakotaensis. To validate the assays to distinguish P.dakotaensis from other Pratylenchus spp. commonly detected in North Dakota soybean fields, 20 soil samples collected from seven counties were tested. The PCR assays amplified the DNA of P.dakotaensis and discriminated it from other Pratylenchus spp. present in North Dakota soybean fields. This is the first report of a species-specific and rapid PCR detection method suitable for use in diagnostic and research laboratories for the detection of P.dakotaensis.

Prediction of PCR amplification from primer and template sequences using recurrent neural network

We have developed a novel method to predict the success of PCR amplification for a specific primer set and DNA template based on the relationship between the primer sequence and the template. To perform the prediction using a recurrent neural network, the usual double-stranded formation between the primer and template nucleotide sequences was herein expressed as a five-lettered word. The set of words (pseudo-sentences) was placed to indicate the success or failure of PCR targeted to learn recurrent neural network (RNN). After learning pseudo-sentences, RNN predicted PCR results from pseudo-sentences which were created by primer and template sequences with 70% accuracy. These results suggest that PCR results could be predicted using learned RNN and the trained RNN could be used as a replacement for preliminary PCR experimentation. This is the first report which utilized the application of neural network for primer design and prediction of PCR results.

Sensitive, Accurate and Rapid Detection of the Northern Root-Knot Nematode, Meloidogyne hapla, Using Recombinase Polymerase Amplification Assays

Rapid and reliable diagnostics of root-knot nematodes are critical for selections of effective control against these agricultural pests. In this study, recombinase polymerase amplification (RPA) assays were developed targeting the IGS rRNA gene of the northern root-knot nematode, Meloidogyne hapla. The RPA assays using TwistAmp^® Basic, TwistAmp^® exo and TwistAmp^® nfo kits (TwistDx, Cambridge, UK) allowed for the detection of M. hapla from crude extracts of females, eggs and juveniles without a DNA extraction step. The results of the RPA assays using real-time fluorescence detection (real-time RPA) in series of crude nematode extracts showed reliable detection after 13 min with a sensitivity of 1/100 of a second-stage juvenile and up to 1/1000 of a female in reaction tubes. The results of the RPA assays using lateral flow dipsticks (LF-RPA) showed reliable detection within 30 min with a sensitivity of 1/10 of a second-stage juvenile and 1/1000 of a female in reaction tubes. The RPA assay developed here is a successful tool for quick, accurate and sensitive diagnostics of M. hapla. The application of the LF-RPA assay has great potential for diagnosing infestation of this species in the lab, field or in areas with a minimal laboratory infrastructure.