Novel Strategies for Soil-Borne Diseases: Exploiting the Microbiome and Volatile-Based Mechanisms Toward Controlling Meloidogyne-Based Disease Complexes

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.

Mixed bacterial fermentation can control the growth and development of Verticillium dahliae

“…In the years that followed, in most of China's cotton growing areas, including Xinjiang province, the damage has continued to grow: annual occurrence area of about 3 million hm 2 , the annual economic loss amounting to about 200 million yuan [25,26]. These non-specific above-ground symptoms, however, lead to the excess overuse of fertilizers and ineffective treatments with pesticides [27].…”

The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato

“…are very harmful plant parasites due to their high pathogenicity and their ability to overcome resistance in many hosts (Jones et al, 2013;Elling, 2013). Interactions of root-knot nematodes (RKN) with other phytopathogenic microorganisms can cause syndromes known as Meloidogyne-based disease complex (MDC), severely affecting world agricultural production (Wolfgang et al, 2019). MDC symptoms are characterized by the initial infection of RKN, causing the typical root swellings and knots.…”

“…MDC symptoms are characterized by the initial infection of RKN, causing the typical root swellings and knots. As the infection progresses, the concomitant presence of fungi and bacteria is observed along with nematodes in root tissues, which present more severe symptoms such as hyperplasia with deep and cracked cortical root tissues, having a cork-like appearance, leading to necrosis and atrophy of the root system (Koike et al, 2006;Taher et al, 2017;López-Lima et al, in press;Wolfgang et al, 2019). These symptoms, in the advanced stages of infection, are also commonly known as corky-root disease in coffee (Bertrand et al, 2000;Lopez-Lima et al, 2015;Villain et al, 2018).…”

The bacterial community structure dynamics inMeloidogyne incognitainfected roots and its role in worm-microbiome interactions

“…The interaction of M. incognita virulence and microbial taxa in the various niches they occupy, have been studied in the context of biological control, revealing complex relationships, which efficacy diminishes with the transfer from lab to field [20] . Common themes in this line of research include the isolation of Meloidogyne pathogens from the cuticle of second stage juveniles (J2) [21][22][23] , or the identification of soil microbes and bacterial volatile compounds with antagonistic effects [24,25] , key taxa including Rhizobia [26] , Trichoderma and Pseudomonas [27,28] , Pasteuria [29] , Pochonia [30,31] and some mycorrhiza [31][32][33] .…”