Development of PCR-based molecular marker for screening of disease-suppressive composts against Fusarium wilt of tomato (Solanum lycopersicum L.)

Abstract

The present study was carried out to develop a PCR-based molecular marker suitable for screening of disease-suppressive composts against Fusarium wilt of tomato. An effective uncultured bacterial community was screened from our previous study on investigation of microbial communities in composts for their potential for biocontrol of Fusarium wilt. Based on available sequence information (Accession no. HQ388491) of selective community, PCR-based molecular markers were designed and tested for their specificity in different compost sample. To confirm specificity of designed marker, real-time reverse transcription-PCR (qRT-PCR) analysis was performed. Selective marker efficacy was further tested for different set of composts and results were cross-verified by conducting bioassay of same composts against Fusarium wilt in tomato crop. Results showed that out of two designed set of primers (i.e., PAC1F/PAC1R and PAC4F/PAC4R), primer set PAC4F/PAC4R resulted in successful amplification of 199 bp in highly disease-suppressive compost (i.e., CPP); however, no/below detection level amplification was observed in non-suppressive compost (JC). qRT-PCR analysis confirmed the specificity of selective marker by representing single peak in melting curve. A clear difference was observed in relative population of selective community in different set of composts. It was observed maximum in the most effective compost, i.e., CPP followed by other disease-suppressive composts. Cross-examination of results with bioassay confirmed that composts with presence of selective bacterial community having no/very less disease incidence of Fusarium. It is clearly evident from the study that such kind of molecular markers can be developed and used in future research focusing on compost-based disease suppression.

Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane

“…An effort towards predicting disease suppression of composts against various pathogens has been made before (Chen, Hoitink and Madden 1988 ; Mehta et al . 2018 ). For example, microbial activity determined as hydrolysis of fluorescein diacetate and biomass measured as extractable phospholipid phosphate content have been proposed as prediction tools for suppression against damping-off caused by P. ultimum (Chen, Hoitink and Madden 1988 ); however, contradicting results, in which fluorescein diacetate hydrolysis was not related to suppression of P. ultimum , have questioned these results later on (Pane et al .…”

“…Mehta et al . ( 2018 ) have developed a PCR-based tool for screening suppression of composts against Fusarium based on the presence of a specific 16S rRNA gene fragment, which was determined using DGGE community profiling, indicating the potential of molecular marker-based diagnostic tools. In the present study, we focused on bacterial communities in composts as compared with those in the rhizoplanes.…”

Alpha and Beta-diversity of Microbial Communities Associated to Plant Disease Suppressive Functions of On-farm Green Composts

“…In the current study a proper involvement of specific healthy microbial community structures [27] in defining disease-suppressive properties of the examined on-farm composts has been revealed. Accordingly, in a previous report, Metha et al [28] categorized specific selective bacterial structures into compost communities associated with suppressiveness against the Fusarium wilt of tomato.…”