Root-knot nematodes: abundance in organic farming, differentiation among populations, microbes attached to juveniles in soil, and bacterial antagonists

Abstract

Two surveys were conducted to determine the frequency and abundance of plantparasitic nematodes associated with different crops at an organic farm in Egypt, during autumn 2009 and 2011. Eleven genera of plant-parasitic nematodes were detected. Root-knot nematodes (Meloidogyne spp.) showed the highest abundance and frequency of all plant-parasitic nematodes during the two surveys. Commonly detected genera were Tylenchorhynchus, Rotylenchulus, Helicotylenchus and Pratylenchus. Further studies on Meloidogyne were carried out with regard to discrimination among populations, attachment of microbes to juveniles (J2) in soil, and biocontrol through bacterial strains which were known as antagonists of fungal pathogens. Meloidogyne incognita populations and/or races that showed differential pattern of reproduction on a set of host plants, could be differentiated based on a newly developed PCR-DGGE system to electrophorecically separate variants of the pathogenicity gene msp1. Three arable soils from different regions of Germany were shown to vary in the suppressiveness of their indigenous microbial communities against Meloidogyne hapla. Attachment of microbes to J2 in these three soils was investigated by cultivation-independent methods to identify those which specifically interacted with J2 in the most suppressive soil (Kleinwanzleben). The three soils differed in the microbes attached to J2. PCR-DGGE fingerprints of amplified ITS fragments or 16S rRNA genes showed many fungi and bacteria that were abundant on J2 but not in the surrounding soil, some of which seemed to be present in all three soils while most were soil type specific. Many bacteria associated with J2 from the most suppressive soil were closely related to infectious species like Shigella spp., while most abundant were Malikia spinosa and Rothia amarae as determined by 16S rRNA gene amplicon pyrosequencing. Nematode-fungus disease complexes can cause dramatic synergistic yield losses. Bacterial strains known as antagonists of phytopathogenic fungi were evaluated with respect to their biocontrol potential towards M. incognita. Seed inoculation with most of the strains significantly reduced propagation of nematode on tomato roots. The best strains Bacillus subtilis Sb4-23, Mc2-Re2, and Mc5- Re2 were further studied for their mode-of-action. The strains were able to affect the nematodes directly by metabolites present in culture supernatants and indirectly by induced systemic resistance of the plant. Experimental comparison of direct and plantmediated effects suggested that the latter was the major control mechanism of these antagonists. Overall, these findings may improve the basis for integrated management strategies of root-knot nematodes in organic farming.