Suppressive compost provides an environment in which plant disease development is reduced, even in the presence of a pathogen and a susceptible host. Despite the numerous positive reports, its practical application is still limited. The main reason for this is the lack of reliable prediction and quality control tools for evaluation of the level and specificity of the suppression effect. Plant disease suppression is the direct result of the activity of consortia of antagonistic microorganisms that naturally recolonize the compost during the cooling phase of the process. Thus, it is imperative to increase the level of understanding of compost microbial ecology and population dynamics. This may lead to the development of an ecological theory for complex ecosystems as well as favor the establishment of hypothesis-driven studies.

Suppressive Composts: Microbial Ecology Links Between Abiotic Environments and Healthy Plants

Bacterial food-borne pathogens use plants as vectors between animal hosts, all the while following the life cycle script of plant-associated bacteria. Similar to phytobacteria, Salmonella, pathogenic Escherichia coli, and cross-domain pathogens have a foothold in agricultural production areas. The commonality of environmental contamination translates to contact with plants. Because of the chronic absence of kill steps against human pathogens for fresh produce, arrival on plants leads to persistence and the risk of human illness. Significant research progress is revealing mechanisms used by human pathogens to colonize plants and important biological interactions between and among bacteria in planta. These findings articulate the difficulty of eliminating or reducing the pathogen from plants. The plant itself may be an untapped key to clean produce. This review highlights the life of human pathogens outside an animal host, focusing on the role of plants, and illustrates areas that are ripe for future investigation.

Interrelationships of Food Safety and Plant Pathology: The Life Cycle of Human Pathogens on Plants

Biological control of phytopathogenic fungi and insects continues to inspire the research and development of environmentally friendly bioactive alternatives. Potentially lytic enzymes, chitinases can act as a biocontrol agent against agriculturally important fungi and insects. The cell wall in fungi and protective covers, i.e. cuticle in insects shares a key structural polymer, chitin, a β-1,4-linked N-acetylglucosamine polymer. Therefore, it is advantageous to develop a common biocontrol agent against both of these groups. As chitin is absent in plants and mammals, targeting its metabolism will signify an eco-friendly strategy for the control of agriculturally important fungi and insects but is innocuous to mammals, plants, beneficial insects and other organisms. In addition, development of chitinase transgenic plant varieties probably holds the most promising method for augmenting agricultural crop protection and productivity, when properly integrated into traditional systems. Recently, human proteins with chitinase activity and chitinase-like proteins were identified and established as biomarkers for human diseases. This review covers the recent advances of chitinases as a biocontrol agent and its various applications including preparation of medically important chitooligosaccharides, bioconversion of chitin as well as in implementing chitinases as diagnostic and prognostic markers for numerous diseases and the prospect of their future utilization.

Chitinases: in agriculture and human healthcare

Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.

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Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region.

Clubroot caused by Plasmodiophora brassicae is an emerging threat to canola (Brassica napus) production in western Canada, and a serious disease on crucifer vegetable crops in eastern Canada. In this study, seven biological control agents and two fungicides were evaluated as soil drenches or seed treatments for control of clubroot. Under growth cabinet conditions, a soil-drench application of formulated biocontrol agents Bacillus subtilis and Gliocladium catenulatum reduced clubroot severity by more than 80% relative to pathogen-inoculated controls on a highly susceptible canola cultivar. This efficacy was similar to that of the fungicides fluazinam and cyazofamid. Under high disease pressure in greenhouse conditions, the biocontrol agents were less effective than the fungicides. Additionally, all of the treatments delivered as a seed coating were less effective than the soil drench. In field trials conducted in 2009, different treatments consisting of a commercial formulation of B. subtilis, G. catenulatum, fluazinam or cyazofamid were applied as an in-furrow drench at 500 L ha−1 water volume to one susceptible and one resistant cultivar at two sites seeded to canola in Alberta and one site of Chinese cabbage in Ontario. There was no substantial impact on the susceptible canola cultivar, but all of the treatments reduced clubroot on the susceptible cultivar of Chinese cabbage, lowering disease severity by 54–84%. There was a period of 4 weeks without rain after the canola was seeded, which likely contributed to the low treatment efficacy on canola. Under growth cabinet conditions, fluazinam and B. subtilis products became substantially less effective after 2 weeks in a dry soil, but cyazofamid retained its efficacy for at least 4 weeks.

Potential biological control of clubroot on canola and crucifer vegetable crops

Clonostachys rosea f. catenulata (syn. Gliocladium catenulatum) is an effective fungal biological agent against Fusarium root and stem rot and Pythium damping-off diseases on cucumber plants. Both chitinase and beta-1,3-glucanase enzymes were produced when C. rosea was grown on a synthetic medium containing chitin or laminarin as a sole carbon source, respectively. Chitinase production was also induced by Fusarium cell walls, while beta-1,3-glucanase activity was induced by both Fusarium and Pythium cell walls, as well as by growth on homogenized cucumber roots and on low-carbon media. Mycelial growth of Fusarium and Pythium, when exposed to C. rosea culture filtrates that contain glucanase activity, was significantly reduced compared with the controls, and cell walls of both pathogens were degraded. On excised cucumber roots, hyphae of C. rosea formed appressorium-like structures and coiled around hyphae of Pythium. In culture, C. rosea caused localized degradation of Fusarium hyphae. Cucumber root tissues colonized by C. rosea showed higher levels of beta-1,3-glucanase activity at 7 days post-application compared with untreated controls. To determine if this activity was derived from C. rosea, glucanase isoforms were separated on activity gels. Fungal culture filtrates and root extracts contained the same predominant 20 kDa isoform. Reverse-transcription polymerase chain reaction (RT-PCR) using primers designed to amplify a beta-1,3-glucanase gene in C. rosea confirmed glucanase expression on roots. These results show that C. rosea produces beta-1,3-glucanase in situ, which can degrade hyphae of Fusarium and Pythium and contribute to biological control efficacy.

Chitinase and β-1,3-glucanase enzyme production by the mycoparasite Clonostachys rosea f. catenulata against fungal plant pathogens

Three composts (Ball, dairy, and greenhouse) were tested for the ability to suppress the development of Fusarium root and stem rot (caused by Fusarium oxysporum f. sp. radicis-cucumerinum) on greenhouse cucumber. Dairy and greenhouse composts significantly reduced disease severity (P = 0.05), while Ball compost had no effect. Assessment of total culturable microbes in the composts showed a positive relationship between disease suppressive ability and total population levels of pseudomonads. In vitro antagonism assays between compost-isolated bacterial strains and the pathogen showed that strains of Pseudomonas aeruginosa exhibited the greatest antagonism. In growth room trials, strains of P. aeruginosa and nonantagonistic Pseudomonas maculicola, plus 2 biocontrol strains of Pseudomonas fluorescens, were tested for their ability to reduce (i) survival of F. oxysporum, (ii) colonization of plants by the pathogen, and (iii) disease severity. Cucumber seedlings grown in compost receiving P. aeruginosa and P. ...

Composts containing fluorescent pseudomonads suppress fusarium root and stem rot development on greenhouse cucumber.

Fusarium oxysporum causes root browning and crown infection on marijuana (Cannabis sativa L.) plants, resulting in stunted growth, yellowing of leaves, and plant death. Pathogen presence and divers...

Epidemiology of Fusarium oxysporum causing root and crown rot of cannabis (Cannabis sativa L., marijuana) plants in commercial greenhouse production

The objective of this study was to assess harvested dried inflorescences (buds) of cannabis (Cannabis sativa L., marijuana) for fungal presence and diversity. Samples from drying rooms of three lic...

https://www.tandfonline.com/doi/pdf/10.1080/07060661.2020.1758959

The diverse mycoflora present on dried cannabis (Cannabis sativa L., marijuana) inflorescences in commercial production

Cannabis (Cannabis sativa L., marijuana) plants grown under greenhouse or controlled environments with symptoms of leaf yellowing, leaf necrosis and defoliation were observed during 2018–2019. Addi...

Zamir K. Punja

Papers

Chitinase and β-1,3-glucanase enzyme production by the mycoparasite Clonostachys rosea f. catenulata against fungal plant pathogens

Composts containing fluorescent pseudomonads suppress fusarium root and stem rot development on greenhouse cucumber.

Epidemiology of Fusarium oxysporum causing root and crown rot of cannabis (Cannabis sativa L., marijuana) plants in commercial greenhouse production

The diverse mycoflora present on dried cannabis (Cannabis sativa L., marijuana) inflorescences in commercial production

First report of Fusarium proliferatum causing crown and stem rot, and pith necrosis, in cannabis (Cannabis sativa L., marijuana) plants