Abstract
Under more intensified cropping conditions agriculture will face increasing incidences of soil-borne plant pests and pathogens, leading to increasingly higher yield losses world-wide. Soil-borne disease complexes, in particular, are especially difficult to control. In order to better understand soil-borne Meloidogyne-based disease complexes, we studied the volatile-based control mechanism of associated bacteria as well as the rhizospheric microbiome on Ugandan tomato plants presenting different levels of root-galling damage, using a multiphasic approach. The experimental design was based on representative samplings of healthy and infected tomato plants from two field locations in Uganda, to establish species collections and DNA libraries. Root galling symptoms on tomato resulted from a multispecies infection of root-knot nematodes (Meloidogyne spp.). Results revealed that 16.5% of the bacterial strain collection produced nematicidal volatile organic compounds (nVOC) active against Meloidogyne. Using SPME GC-MS, diverse VOC were identified, including sulfuric compounds, alkenes and one pyrazine. Around 28% of the bacterial strains were also antagonistic toward at least one fungal pathogen of the disease complex. However, antagonistic interactions appear highly specific. Nematicidal antagonists included Pseudomonas, Comamonas, and Variovorax and fungicidal antagonists belonged to Bacillus, which interestingly, were primarily recovered from healthy roots, while nematode antagonists were prominent in the rhizosphere and roots of diseased roots. In summary, all antagonists comprised up to 6.4% of the tomato root microbiota. In general, the microbiota of healthy and diseased root endospheres differed significantly in alpha and quantitative beta diversity indices. Bacteria-derived volatiles appear to provide a remarkable, yet wholly unexploited, potential to control Meloidogyne-based soil-borne disease complexes. The highly specific observed antagonism indicates that a combination of volatiles or VOC-producing bacteria are necessary to counter the range of pathogens involved in such complexes.
Highlights
Agriculture causes long-lasting anthropogenic environmental impacts as it replaces natural vegetation, alters biogeochemical cycles, and decreases biodiversity; this defined a new humandominated geological epoch, the Anthropocene
Sequences of the 16S rRNA genes identified the nematicidal bacteria as Pseudomonas koreensis, Comamonas sediminis, Variovorax paradoxus, P. soli and two strains of P. monteilii
Our novel VOC-based screening method toward RKN resulted in the identification of several nematicidal antagonists, namely Comamonas sediminis, P. koreensis, P. monteilii, P. soli, and Variovorax paradoxus
Summary
Agriculture causes long-lasting anthropogenic environmental impacts as it replaces natural vegetation, alters biogeochemical cycles, and decreases biodiversity; this defined a new humandominated geological epoch, the Anthropocene. Bacteria occupy important niches and roles, linking plant microbial diversity and ecosystem functioning, such as productivity, host plant fitness and resilience (Bais et al, 2004; Tilman et al, 2012; Vandenkoornhuyse et al, 2015; Laforest-Lapointe et al, 2017). Among the most striking direct consequences of agricultural intensification is the elevated presence and impact of soil-borne pests and pathogens (Mendes et al, 2012). Soil-borne diseases are often “microbiome diseases”; they signify the result of a loss of microbial diversity and dysbiosis in soil and in the rhizosphere and endosphere of plants (van Elsas et al, 2012). The soil environment is a complex arena, the biological permutations of which are little understood (Bais et al, 2004), especially in areas such as Africa, where assessments and understanding of the microflora and microbiota remain negligible
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