Influence of Groundcover Vegetation, Soil Physicochemical Properties, and Irrigation Practices on Soil Fungi in Semi-arid Vineyards

Although plants are known to have a strong influence on soil biota, the effect of groundcover vegetation in perennial cropping systems on soil fungi has been little explored. We surveyed extensively managed vineyards to determine how plant community functional characteristics, soil factors, and irrigation management related to the abundance of two guilds of soil fungi that may play a role in plant-soil feedback (entomopathogenic fungi represented by Beauveria bassiana, and the pathogenic species complex, Ilyonectria spp.). We found that plant community characteristics were related to fungal abundance for both fungi assayed. Beauveria bassiana increased with native species, annual plants, and legumes consistently across sampling periods. Ilyonectria spp. increased with the abundance of forbs and exotic species, though only the relationship with forbs was consistent across sampling periods. Both fungal guilds increased with increasing soil organic matter. The use of dual or sprinkler irrigation systems also increased B. bassiana and Ilyonectria spp. in vineyard soils. Overall, groundcover vegetation played a significant role in driving abundance of these important groups of soil fungi. Groundcover management may therefore be a viable tool to manipulate soil fungi with the potential for improving ecosystem services such as conservation biological control of soil dwelling insect pests and deterring pathogens in perennial cropping systems

The effect of vineyard ground cover vegetation on soil fungi and plant-soil feedback

Groundcover vegetation is managed in vineyards for many purposes including for soil quality, trafficability, and pest and fertility management. Because plants are major drivers of soil biota, groundcover identity could also cause changes in soil microbial communities that then influences vine health. Using greenhouse and field trials as well as a multi-year survey of Okanagan valley vineyards, I studied the effect of groundcover identity and management on soil fungi known to be important in influencing vine health and growth attributable to these plant-soil feedbacks. Overall, groundcover vegetation influenced abundances of each of the studied guilds of soil fungi in the drive row, with plant effects on the entomopathogenic Beauveria bassiana being the most consistent. Under vine living mulches, however, did not affect these same groups of fungi. When soil trained by different groundcovers from the same field were used as microbial inoculant in the greenhouse, they led to differences in arbuscular mycorrhizal (AM) communities in vine roots, but differences in vine growth were only seen when a pathogen was also included. Taken together, these results suggest that groundcover vegetation does influence soil fungi in drive rows of Okanagan vineyards. Certain groundcovers may provide ecosystem services such as conservation biological control of pest insects through increases in entomopathogenic fungi, improved carbon sequestration and soil structure through increases in AM fungi, and deterrence of soil-borne pathogens. However, feedback effects on vines in this dissertation were limited to abiotic competitive effects in the field and biotic responses in the greenhouse, suggesting a high degree of context-dependency of plant-soil feedbacks in this system.Arts and Sciences, Irving K. Barber School of (Okanagan)Biology, Department of (Okanagan)Graduat

Mycorrhizal fungi and soil factors influence toxic element uptake in urban grown produce

Abstract Despite the need for more urban‐grown produce, toxic elements contaminated soils continue to be a major barrier to food production and food sovereignty in urban areas and a continued health and environmental justice issue. Although the US EPA provides recommendations regarding levels of soil lead that are safe for gardening, soil abiotic and biotic factors as well as plant identity play a major role in determining the actual crop uptake of toxic elements. This study evaluated the role of crop identity, harvested tissue, and soil factors, including arbuscular mycorrhizal (AM) fungi on crop uptake of lead (Pb) and arsenic (As) in an urban community farm. Crop species varied in their Pb and As accumulations, both by crop identity and also by plant tissue. Crop uptake of lead increased with lower soil pH (range 5.3–6.9) and lower soil P (range 365–1771 mg kg−1 total P). For mycorrhizal crops, greater intensity of AM fungal colonization and the prevalence of arbuscules were associated with greater lead uptake, but the presence of more storage vesicles was related to less As uptake into leaves. These findings can help inform crop selection and soil management to improve soil stabilization of toxic elements in moderately contaminated soils while serving as a platform for community conversations about the importance of soil management in healthy urban food production

Cover crops to increase soil microbial diversity and mitigate decline in perennial agriculture. A review

International audienceAbstractCommercial perennial agriculture is prone to declining productivity due to negative plant-soil feedback. An alternative to costly and environmentally harmful conventional treatment such as soil fumigation could be to manipulate soil microbial diversity through careful selection and management of cover crop mixtures. Although cover crops are already used in these systems for other reasons, their capacity to influence soil biota is unexploited. Here, we examine the role of plant diversity and identity on plant-soil feedbacks in the context of perennial agriculture. We identify key microorganisms involved in these feedbacks and explore plant-based strategies for mitigating decline of perennial crop plants. We conclude that (1) increasing plant diversity increases soil microbial diversity, minimizing the proliferation of soil-borne pathogens; (2) populations of beneficial microbes can be increased by increasing plant functional group richness, e.g., legumes, C4 grasses, C3 grasses, and non-leguminous forbs; (3) brassicas suppress fungal pathogens and promote disease-suppressive bacteria; (4) native plants may further promote beneficial soil microbiota; and (5) frequent tillage, herbicide use, and copper fungicides can harm populations of beneficial microbes and, in some cases, contribute to greater crop decline. Non-crop vegetation management is a viable and cost-effective means of minimizing crop decline in perennial monocultures but is in need of more direct experimental investigation in perennial agroecosystems

Challenges Using Droplet Digital PCR for Environmental Samples

Droplet digital polymerase chain reaction (ddPCR) is a method used to detect and quantify nucleic acids even when present in exceptionally low numbers. While it has proven to be valuable for clinical studies, it has failed to be widely adopted for environmental studies but despite some limitations, ddPCR may represent a better option than classical qPCR for environmental samples. Due to the complexity of the chemical and biological composition of environmental samples, protocols tailored to clinical studies are not appropriate, and results are difficult to interpret. We used environmental DNA samples originating from field studies to determine a protocol for environmental samples. Samples included field soils which had been inoculated with the soil fungus Rhizophagus irregularis (environmental positive control), field soils that had not been inoculated and the targeted fungus was not naturally present (environmental negative control), and root samples from both field categories. To control for the effect of soil inhibitors, we also included DNA samples of an organismal control extracted from pure fungal spores (organismal positive control). Finally, we included a no-template control consisting only of the PCR reaction reagents and nuclease free water instead of template DNA. Using original data, we examined which factors contribute to poor resolution in root and soil samples and propose best practices to ensure accuracy and repeatability. Furthermore, we evaluated manual and automatic threshold determination methods and we propose a novel protocol based on multiple controls that is more appropriate for environmental samples.Science, Irving K. Barber Faculty of (Okanagan)Non UBCBiology, Department of (Okanagan)ReviewedFacultyResearche