Microbiomes and Disease Suppressiveness of Soils from Managed and Abandoned Orchards in New Hampshire

Abstract

The soil microbiome is an essential component of ecosystem productivity. In agricultural systems, the soil microbiome significantly impacts plant health and the subsequent yield and productivity of those systems. Due to increasing demands on the food supply and the many challenges posed by climate change, soil fertility loss, and plant pathogens, modern agricultural systems often employ the use of chemical fertilizers and pesticides that can have detrimental effects on human health and the environment. These chemicals also significantly affect soil microbiomes, and although the extent of these effects are still unknown, changes in diversity or functionality of plant associated microbiomes may negatively affect agricultural production in ways that we do not fully understand. “Modern agricultural systems” is a very broad term – it can range from conventionally managed monocultures to small organic diversified systems to controlled-environment agriculture in greenhouses. Each system is managed with different practices – till or no till, inorganic fertilizers or organic fertilizers, pesticides, herbicides, biocontrol agents, etc. All these practices affect the soil microbiome. Despite a proliferation of studies comparing soil microbiome composition between managed and conventional systems, till and no till, and agricultural systems to nearby natural systems, the comparison of managed systems to abandoned agricultural systems has received less attention. Abandoned systems that contain the original agricultural crop offer a rare opportunity to study microbiomes after they have been released from the pressures of agriculture without the confounding effects of changing in the host plant, since plant associated microbes are often host specific. New Hampshire is full of small apple orchards, many of which were abandoned in the last 10-20 years as regional and national markets changed. When compared with orchards that still remain active in the small geographical area of Hillsborough County NH, these abandoned sites offer an opportunity to study how soil microbiomes are influenced by agricultural practices. The objectives of this study were to: (1) Compare abandoned and managed orchard soil microbiome composition and diversity using amplicon sequencing of prokaryotes and fungi (using 16S and ITS marker genes), and (2) study microbiome function as it relates to plant resilience to stress, by developing a high throughput radish damping-off microcosm assay to test the disease suppressiveness of microbial slurries from different orchard types. I hypothesized that the soil microbiomes would be different in terms of composition, richness, and evenness between managed and abandoned sites (Chapter 2) and that soil microbes from abandoned orchards would enhance plant growth and reduce soilborne plant disease severity compared to microbes collected from managed orchards (Chapter 3). For objective one, I found that for both prokaryote and fungal communities, beta diversity was significantly different between managed and abandoned orchards (p<0.001). Shannon diversity and Faith’s phylogenic diversity scores were generally higher in managed sites in the prokaryotic communities, but in fungal communities, none of the alpha diversity metrics were different between the two types of orchards. These results supported my hypothesis that the microbial communities were different between the managed and abandoned orchards, especially in terms of beta diversity metrics. For objective two, I found that microbial slurries from abandoned orchards significantly improved seedling emergence counts compared to the water controls (p=0.0126), and the abandoned slurries tended to have higher emergence counts than the slurries from managed orchards (p=0.11). Disease severity and biomass were not affected by slurry type. However, this could have been due to disease pressure being too severe and problems with the disease scale used to score disease severity in the seedlings. These results partially support my hypothesis that microbes from abandoned sites would reduce disease severity (in terms of successful emergence), but there was no significant effect on plant growth (as determined by biomass measurements). The soil microbiomes in abandoned orchards appear to be more disease suppressive to R. solani than the soils from managed orchards, though the mechanism of suppression is still unknown. This study is the first to indicated that abandoned orchards may be more disease suppressive than managed orchards, however, additional studies with more sample sites and different pathogens are required to confirm my preliminary findings. This research adds to the limited pool of literature regarding abandoned agroecosystems and provides evidence that management, or the lack thereof, effects soil microbiomes in such a way that it can have consequences for plant heath and productivity. Understanding more about the functionality of the soil microbiome in these systems will lead to new insights and ideas for utilizing the soil microbiome in future agricultural practices.

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