Microbiomes associated with infective stages of root-knot and lesion nematodes in soil

Abstract

Endoparasitic root-knot (Meloidogyne spp.) and lesion (Pratylenchus spp.) nematodes cause considerable damage in agriculture. Before they invade roots to complete their life cycle, soil microbes can attach to their cuticle or surface coat and antagonize the nematode directly or by induction of host plant defenses. We investigated whether the nematode-associated microbiome in soil differs between infective stages of Meloidogyne incognita and Pratylenchus penetrans, and whether it is affected by variation in the composition of microbial communities among soils. Nematodes were incubated in suspensions of five organically and two integrated horticultural production soils, recovered by sieving and analyzed for attached bacteria and fungi after washing off loosely adhering microbes. Significant effects of the soil type and nematode species on nematode-associated fungi and bacteria were revealed as analyzed by community profiling using denaturing gradient gel electrophoresis. Attached microbes represented a small specific subset of the soil microbiome. Two organic soils had very similar bacterial and fungal community profiles, but one of them was strongly suppressive towards root-knot nematodes. They were selected for deep amplicon sequencing of bacterial 16S rRNA genes and fungal ITS. Significant differences among the microbiomes associated with the two species in both soils suggested specific surface epitopes. Among the 28 detected bacterial classes, Betaproteobacteria, Bacilli and Actinobacteria were the most abundant. The most frequently detected fungal genera were Malassezia, Aspergillus and Cladosporium. Attached microbiomes did not statistically differ between these two soils. However, Malassezia globosa and four fungal species of the family Plectosphaerellaceae, and the bacterium Neorhizobium galegae were strongly enriched on M. incognita in the suppressive soil. In conclusion, the highly specific attachment of microbes to infective stages of phytonematodes in soil suggested an ecological role of this association and might be involved in soil suppressiveness towards them.

Nematode‐associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats

“…In the present study, we used two rRNA genes to evaluate nematode–microbiome associations (i.e., 16S for bacteria/archaea and 18S for other microbial eukaryotes). Hypervariable rRNA gene regions have been broadly used for microbiome investigations, with previous applications in nematodes showing specific host–microbiome patterns (Derycke et al., ; Dirksen et al., ; Elhady et al., ). However, despite strict laboratory and bioinformatics protocols that were designed to maximize the recovery of nematode microbiomes, our results from free‐living marine species showed no clear patterns in host‐associated prokaryotic or eukaryotic taxa corresponding to nematode morphology, ocean region or feeding ecology (Figures and ).…”

“…Among plant parasitic nematodes, Elhady et al. () found not only that the microbiome of Meloidogyne incognita and Pratylenchus penetrans differed, but also that the soil types nematode species were exposed to had a significant effect on structuring their microbiomes. In natural habitats on Réunion Island, Meyer et al.…”

Apple Replant Disease: Causes and Mitigation Strategies

“…Indirectly, (Freckman, 1988;Wang and McSorley, 2005) or activation of specific microbial growth by the release of growth limiting nutrients (Wang and McSorley, 2005). Recent findings by Adam et al (2014) and Elhady et al (2017) confirm specific bacteria and fungi to be attached to infective stages of Meloidogyne incognita and P. penetrans in different soil types indicating an ecological role of the association. Four way interaction between fungi, oomycetes, bacteria and nematodes was supposed to increase the ARD severity when these organisms were present at the same time Mazzola and Mullinix, 2005).…”

Isolation and molecular characterization of Malassezia pachydermatis from a cutaneous lesion in a California sea lion (Zalophus californianus)

“…Several metagenomic studies have reported the presence of the Malassezia genome on the surface of soil nematodes (RENKER et al, 2003;ELHADY et al, 2017), marine sponges, seawater (GAO, 2003) and corals (AMEND at al., 2012). In this study, sampling the environment as a possible source of the Malassezia yeast, and culturing of the swabs from the pool walls and water samples did not yield any Malassezia growth.…”