Progress 08/15/21 to 06/14/23
Outputs
Target Audience:The goal of the my postdoctoral fellowship, "Managing soil microbes to promote natural pest control" is to evaluate how soil management practices may enhance natural pest control by altering communities of soil microbes. My target audience is vegetable growers, who already work to build soil tilth and fertility, encouraging soil biodiversity. This is done, in part, to produce plants that are more resistant to pests. Growers need clear information about how particular soil management practices may enhance biocontrol and protect yield by shaping soil microbial communities. However, we currently have limited knowledge of the agriculturally-relevant impacts of soil microbes on biocontrol on working farms. Therefore, in the 2019-2020 field season, I performed a large field experiment evaluating how common soil amendments may enhance herbivore and disease suppression by altering soil microbial communities. I profiled the soil microbial communities using bioinformatic approaches and analyzed the nutrients in soil and leaf tissues. This dataset is providing important insights into how commonly used organic amendments shape soil microbial communities, influencing herbivore and disease resistance in hybrid and heirloom tomato varieties. To expand on this experimental work, I performed an on-farm survey evaluating how farm management practices shape soil microbial communities and the prevalence of soil-borne pathogens in tomato fields throughout the Southeast (Georgia, South Carolina, North Carolina) in the 2020-2021 field season. I interviewed each farmer about their soil management practices and surveyed the incidence common soil-borne diseases of tomato in each field. From the soils I collected from each farm, I sequenced the communities of bacteria and fungi using Illumina MiSeq to evaluate how on-farm management practices shape soil microbial communities across soils of distinct physicochemical properties (Mountains, Piedmont, Coastal Plains). In addition, I measured soil physical and chemical properties, the abundance of plant-parasitic nematodes, and the abundance of bacterial wilt and southern blight using qPCR. To consider the impacts of these on-farm, management-mediated microbial communities on the resistance of tomato plants to insect herbivores, I performed a growth room experiment in the 2021-2022 field season. I grew tomato plants in soil inoculated with microbial communities collected from a subset of my collaborating farmers and assessed the resistance of these plants to a specialist (Manduca sexta) or generalist (Spodoptera exigua) insect pest. These datasets will provide valuable information to growers in the Southeast about how on-farm management shapes soil microbial communities, affecting the suppression of soil-borne pathogens, plant-parasitic nematodes, and insect herbivores. Overall, the data from these experiments are critical for informing vegetable farmers' choice of soil management practices to not only provide nutrients to their plants, but also promote herbivore and disease resistance. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The postdoctoral researcher to whom this fellowship was provided, Amanda Meier, was trained on this project. Throughout the course of this fellowship, Amanda Meier also completed a position as a Visiting Assistant Professor at Davidson College and accepted a teure-track position as an Assistant Professor in the Biological Sciences Department at SUNY Plattsburgh.Amanda Meier performed the experiments and statistical analyses. In addition, Amanda was trained in bioinformatic analyses and analyzed the DNA sequencing data to determine how soil management practices shape rhizosphere fungal and bacterial communities. To gain professional development in pedagogy, Amanda took several pedagogy workshops, such as the Inclusive STEM Teaching Project, and taught Biostatistics for Life Scientists, Integrated Concepts in Biology II, Agroecology in a Changing World, and Ecologyat Davidson College. Overthe course of this project, six undergraduate students were trained on techniques ranging from insect rearing, to on-farm soil sampling, to DNA extraction. At the University of Goergia,Phoebe Scharle and Nicholas Miller utilized data from this large experiment to perform small, independent research projects for academic credit. Tatyanna Campbell and Kamaya Brantley have been participating in the project through the PeachState Louis Stokes Alliance for Minority Participation in Research. At Davidson College, Sam Van Horn worked on the project as a Research Assistant in Summer 2022 and Kayleigh participated in the project through the Research in Science Experience program at Davidson College. How have the results been disseminated to communities of interest?I have shared my preliminary findings, and the soil microbe and physicochemical property data from each farm, with the many farmers (> 50) I visited and interviewed in Summer 2020. I will be presenting my findings through an invited seminar at the EntomologicalSociety of America's annual conference in November 2023in the symposium "Trophic Interactions intheAgeoftheMicrobiome". I am currently finishing my analyses, and will soonbe submitting my papers for publication. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Farmers are faced with an increasing demand for reduced-input crops and need innovative tools to reduce pesticide use and strengthen natural control of insect pests and disease. Farmers already work to build soil tilth and fertility, and in doing so encourage soil biodiversity. One of their goals is to improve natural pest control by growing plants that can naturally defend themselves against insect pests and disease. By manipulating soil microbes through the addition of common soil amendments, there is the potential to improve biocontrol by enhancing plant defenses. However, we lack an understanding of how soil management practices may enhance herbivore and disease suppression by altering communities of soil microbes. Therefore, I performed a field experiment in the summer of 2019 to identify common soil amendments that enhance the resistance of heirloom and hybrid tomato plants to insect pests and a soil-borne pathogen (Southern Blight,Athelia rolfsii). In Summer 2020, I performed a complementary on-farm survey in collaboration with over fifty organic farmers throughout the Southeast to evaluate how farm management shapes soil microbial communities and physicochemical properties to affect the suppression of soil-borne diseases in tomato fields. To assess how these on-farm microbial communities may also affect the resistance of tomato plants to insect pests, I performed a growth room experiment in Summer 2022. I grew tomato plants in soil inoculated with microbes collected from a subset of my collaborating farms and assessed the resistance of these plants to common insect pests (hornworms,Manduca sexta; beet armyworms,Spodoptera exigua). Through the field experiment, I found that soil amendments that reduced soil microbial diversity, such as chicken manure and fish bone meal, increased the susceptibility of hybrid tomato plants to infection by Southern Blight (Athelia rolfsii), and increased the susceptibility of both hybrid and heirloom varieties to attack by insect herbivores, such as hornworms (Manduca sexta). While plants fertilized with chicken manure, fish bone meal, and mix of all amendments produced the greatest total yield, marketable yield was unaffected by amendments, likely due to the greater herbivore abundances on those plants. Through my complementary on-farm survey, I found that farm soils with greater fungal diversity had lower abundances of Bacterial Wilt (Ralstonia solanacearum), suggesting that management that increases soil fungal diversity may suppress this soil-borne pathogen. My findings demonstrate that common soil management practices alter soil microbial communities, influencing herbivore and disease resistance and resulting yield in tomato plants. These data are critical for informing vegetable farmers' choice of soil management to not only provide nutrients to their plants, but also to promote herbivore and disease resistance. Obj. 1a) Evaluate how soil management practices may enhance herbivore and disease suppression on farms In the 2019-2020 field season, I performed a manipulative field experiment, as described above. The addition of amendments, especially chicken manure and fish bone meal, increased the probability that hybrid, but not heirloom, tomato plants would be killed by Southern Blight (DF=12, x2=21.35, P=0.0455). Effects of soil amendments on herbivores were consistent across tomato varieties, but were herbivore-specific. For example, over the season, hornworms (M. sexta) were most abundant on plants of all varieties fertilized with chicken manure (F4,472=3.2, P=0.013), whereas aphids (Aphididae) were most abundant on plants fertilized with fish bone meal (F4,472=4.66, P=0.0011). While plants fertilized with chicken manure, fish bone meal, and mix of all amendments produced the greatest total yield (F4,425.6=3.75, P=0.0052), marketable yield was unaffected by amendments. To expand on my experimental work, I performed an on-farm survey in the 2020-2021 field season, as described above. From the soils I collected from each farm, I sequenced the microbial communities using Illumina MiSeq, measured the abundance of Bacterial Wilt and Southern Blight using qPCR, and measured soil physicochemical properties and the abundance of plant- parasitic nematodes. Management practices, such as growing tomatoes in the field compared to high tunnels, affected the prevalence of Bacterial Wilt, a soil-borne pathogen. Bacterial Wilt was more abundant in high tunnels than fields (F1,44.8=37.57, P<0.001). Obj. 1b) Determine management-mediated shifts in microbial communities and nutrients that are associated with the greatest suppression of insect pests and soil-borne pathogens Through the field experiment, I found that the addition of worm castings increased, and fish bone meal suppressed, the diversity of bacteria in the rhizosphere of plants across varieties (F4,134.3=6.86, P<0.0001). Similarly, fertilization with chicken manure or fish bone meal suppressed the diversity of fungi in the rhizosphere across varieties (F4,139.1=5.24, P=0.0006). Overall, amendments and varieties that promoted greater rhizosphere fungal diversity had a lower rate of infection by Southern Blight (F1,38=5.77, P=0.021). Through my on-farm survey, I found that soil fungal communities were shaped strongly by physiographic region and management (Physiographic Region: F2,64=2.22, P=0.001; Field or High Tunnel: F1,64=2.47, P=0.001). Importantly, farms using management practices that reduced soil fungal diversity, such as growing in high tunnels, had a greater abundance of Bacterial Wilt (F1,43=5.95, P=0.019). This suggests that management practices that increase soil fungal diversity may suppress soil-borne pathogens like Bacterial Wilt. Obj. 2) Investigate the chemical and molecular mechanisms by which particular soil management practices enhanced herbivore suppression in the field. Through the field experiment, I found that soil nutrients were shaped strongly by amendments (PERMANOVA: R2=0.32, F4,148=46.927, P<0.001). For instance, soils fertilized with chicken manure had the greatest pH (F4,148=13.01, P<0.001), while soils fertilized with fish bone meal had the greatest phosphorous concentration (Phosphorous F4,143.2=7.45, P<0.001). db-RDA indicated that soil physicochemical properties explained 12.8% of variation in the bacterial community and 5.5% of variation in the fungal community, with pH, magnesium, phosphorous, potassium, and manganese driving the bacterial community and pH, magnesium, phosphorous, and sodium shaping the fungal community. Plants fertilized with fish bone meal had the greatest, and plants fertilized with worm castings had the lowest, densities of Type VI trichomes (F4,193.2=3.17, P=0.015). Leaf toughness and foliar nutrient concentrations were unaffected by amendments. Herbivore abundances were not correlated with foliar nutrients, trichomes, or toughness, indicating that effects of amendments on herbivores may be driven by changes in other traits, such as plant chemical defenses. To evaluate how management-mediated, on-farm microbial communities may affect the resistance of tomato plants to insect pests, I performed a growth room experiment in Summer 2022 at Davidson College. I grew Sungold tomato plants in sterile soil inoculated with soil microbial communities collected from one of ten collaborating farms, or a mix of autoclaved farm soil (control). I subjected these plants to damage by either a specialist (M. sexta) or generalist (S. exigua) caterpillar, or no herbivore (11 farm treatments x 12 replicates x 3 herbivore treatments = 396 plants). I found that specific on-farm microbial communities suppressed damage by both specialist (M. sexta) and generalist (S. exgua) caterpillars (M. sexta:F9,110=2.98, P=0.003;S. exigua:F9,108=25.382, P<0.001).
Publications
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Progress 08/15/21 to 08/14/22
Outputs
Target Audience:The goal of the my postdoctoral fellowship, "Managing soil microbes to promote natural pest control" is to evaluate how soil management practices may enhance natural pest control by altering communities of soil microbes. My target audience is vegetable growers, who already work to build soil tilth and fertility, encouraging soil biodiversity. This is done, in part, to produce plants that are more resistant to pests. Growers need clear information about how particular soil management practices may enhance biocontrol and protect yield by shaping soil microbial communities. However, we currently have limited knowledge of the agriculturally-relevant impacts of soil microbes on biocontrol on working farms. Therefore, in the 2019-2020 field season, I performed a large field experiment evaluating how common soil amendments may enhance herbivore and disease suppression by altering soil microbial communities. I profiled the soil microbial communities using bioinformatic approaches and analyzed the nutrients in soil and leaf tissues. This dataset is providing important insights into how commonly used organic amendments shape soil microbial communities, influencing herbivore and disease resistance in hybrid and heirloom tomato varieties. To expand on this experimental work, I performed an on-farm survey evaluating how farm management practices shape soil microbial communities and the prevalence of soil-borne pathogens in tomato fields throughout the Southeast (Georgia, South Carolina, North Carolina) in the 2020-2021 field season. I interviewed each farmer about their soil management practices and surveyed the incidence common soil-borne diseases of tomato in each field. From the soils I collected from each farm, I sequenced the communities of bacteria and fungi using Illumina MiSeq to evaluate how on-farm management practices shape soil microbial communities across soils of distinct physicochemical properties (Mountains, Piedmont, Coastal Plains). In addition, I measured soil physical and chemical properties, the abundance of plant-parasitic nematodes, and the abundance of bacterial wilt and southern blight using qPCR. To consider the impacts of these on-farm, management-mediated microbial communities on the resistance of tomato plants to insect herbivores, I performed a growth room experiment in the 2021-2022 field season.I grew tomato plants insoil inoculated with microbial communities collected from a subset of my collaborating farmers and assesed the resistance of these plants to a specialist (Manduca sexta) or generalist (Spodoptera exigua) insect pest. Currently, I am sequencing the soil microbial communities and assessing foliar nutritive and defensive traits to determine which management-mediated microbial communities enhanced tomato plant resistance to these insect herbivores, and the mechanisms by which they do so. These datasets will provide valuable information to growers in the Southeast about how on-farm management shapes soil microbial communities, affecting the suppression of soil-borne pathogens, plant-parasitic nematodes, and insect herbivores. Overall, the data from these experiments are critical for informing vegetable farmers' choice of soil management practices to not only provide nutrients to their plants, but also promote herbivore and disease resistance. Changes/Problems:Due to starting a new position as a Visiting Assistant Professor at Davidson College in July 2021, and needing to have this fellowship transferred and converted to a grant, my final experiment and analyses were delayed, leading me to not yet complete my proposed project. I receieved a second no-cost extension to complete the project. What opportunities for training and professional development has the project provided?The postdoctoral researcher, and now visiting assistant professor, to whom this fellowship was provided, Amanda Meier, is currently being trained on this project. Amanda Meier performed the experiments and statistical analyses. In addition, Amanda was trained in bioinformatic analyses and analyzed the DNA sequencing data to determine how soil amendments shape rhizosphere fungal and bacterial communities. To gain professional development in pedagogy, Amanda took several pedagogy workshops, such as the Inclusive STEM Teaching Project, and taught Biostatistics for Life Scientists and Integrated Concepts in Biology II at Davidson College Two undergraduate students have been trained on this project on techniques ranging from insect rearing, to on-farm soil sampling, to DNA extraction. These students include Sam Van Horn and Kayleigh Davies. Sam worked on the project as a Research Assistant in Summer 2022 and Kayleigh participated in the project through the Research in Science Experience program at Davidson College. How have the results been disseminated to communities of interest?I have shared my preliminary experimental findings, and the soil microbe and physicochemical property data from each farm,with the many farmers (> 50) I visited and interviewed in Summer 2020. Similarly, I will be sharing my results, as well as the soil microbe and physicochemical property data from each farm, with the ten growers I collaborated with in my Summer 2022 experiments. I plan to share my findings at local conferences for growers, such as Georgia Organics, and national scientific conferences,such as the Ecological Society of America annual meeting. Once my analyses are complete, I will also submit my papers for publication. What do you plan to do during the next reporting period to accomplish the goals?Objectives 1 & 2: Evaluate how soil amendments may enhance herbivore and disease suppression on farms. Determine amendment-mediated shifts in soil microbial communities and nutrients, and resulting changes in foliar nutritive and defensive traits, that are associated with the greatest suppression of insect pests and disease. Amendment Field Experiment I will complete my bioinformatic and statistical analyses assessing how soil amendments, by altering soil microbial communities and physicochemical properties, influence foliar nutritive and defensive quality, affecting herbivore abundances, infection by Southern Blight, and tomato yield. I am currently writing up my results, which I will share through a publication and presentations at grower conferences, such as Georgia Organics. Complementary On-Farm Survey and Experiment I will finish performing bioinformatic analyses evaluating how on-farm management shaped bacterial and fungal communities in the Southeast. I will then relate grower practices with microbial communities, soil physicochemical properties, disease incidence, and pathogen and nematode abundances across farms using structural equation modelling. I will also perform network analyses to uncover which microbial communities may suppress soil-borne pathogens in each region of the Southeast. My undergraduate researchers and I will extract DNA from the rhizosphere soil samples we collected from our Summer 2022 experiment and use high-throughput sequencing and bioinformatic analyses to profile the bacterial and fungal communities.In addition, we will measure foliar physical defenses (e.g. trichome concentrations, leaf toughness), chemical defenses (e.g. protease inhibitors), and nutrient content from the leaf tissue we collected from the experimental plants. Once completing these chemical and molecular analyses, I will evaluate effects of on-farm microbial communities on foliar traits andherbivore performance. I will then use an information theoretic approach to identify the strongest microbial-based predictors of herbivore suppression, and microbial-mediated changes in plant traits that underlie suppression. I will share the results from both studies with my collaborating growers, as well as through publications and presentations at grower and scientific conferences.
Impacts
What was accomplished under these goals?
Farmers are faced with an increasing demand for reduced-input crops and need innovative tools to reduce pesticide use and strengthen natural control of insect pests and disease. Farmers already work to build soil tilth and fertility, and in doing so encourage soil biodiversity. One of their goals is to improve natural pest control by growing plants that can naturally defend themselves against insect pests and disease. By manipulating soil microbes through the addition of common soil amendments, there is the potential to improve biocontrol by enhancing plant defenses. However, we lack an understanding of how soil management practices may enhance herbivore and disease suppression by altering communities of soil microbes. Therefore, I performed a field experiment in the summer of 2019 to identify common soil amendments that enhance the resistance of heirloom and hybrid tomato plants to insect pests and a soil-borne pathogen (Southern Blight,Athelia rolfsii). In Summer 2020, I performed a complementary on-farm survey in collaboration with over fifty organic farmers throughout the Southeast to evaluate how farm management shapes soil microbial communities and physicochemical properties to affect the suppression of soil-borne diseases in tomato fields. To assess how these on-farm microbial communities may also affect the resistance of tomato plants to insect pests, I performed a growth room experiment in Summer 2022. I grew tomato plants in soil inoculated with microbes collected from a subset of my collaborating farms and assessed the resistance of these plants to common insect pests (hornworms,Manduca sexta; beet armyworms,Spodoptera exigua). Through the field experiment, I found that soil amendments that reduced soil microbial diversity, such as chicken manure and fish bone meal, increased the susceptibility of hybrid tomato plants to infection by Southern Blight (Athelia rolfsii), and increased the susceptibility of both hybrid and heirloom varieties to attack by insect herbivores, such as hornworms (Manduca sexta). While plants fertilized with chicken manure, fish bone meal, and mix of all amendments produced the greatest total yield, marketable yield was unaffected by amendments, likely due to the greater herbivore abundances on those plants. Through my complementary on-farm survey, I found that farm soils with greater fungal diversity had lower abundances of Bacterial Wilt (Ralstonia solanacearum), suggesting that management that increases soil fungal diversity may suppress this soil-borne pathogen. My findings demonstrate that common soil management practices alter soil microbial communities, influencing herbivore and disease resistance and resulting yield in tomato plants. These data are critical for informing vegetable farmers' choice of soil management to not only provide nutrients to their plants, but also to promote herbivore and disease resistance. Obj. 1a) Evaluate how soil management practices may enhance herbivore and disease suppression on farms In the 2019-2020 field season, I performed a manipulative field experiment, as described above. While the addition of amendments, especially chicken manure and fish bone meal, increased the probability that hybrid, but not heirloom, tomato plants would be killed by Southern Blight (DF=12, x2=21.35, P=0.0455). Effects of soil amendments on herbivores were consistent across tomato varieties, but were herbivore-specific. For example, over the season, hornworms (M. sexta) were most abundant on plants of all varieties fertilized with chicken manure (F4,472=3.2, P=0.013), whereas aphids (Aphididae) were most abundant on plants fertilized with fish bone meal (F4,472=4.66, P=0.0011). While plants fertilized with chicken manure, fish bone meal, and mix of all amendments produced the greatest total yield (F4,425.6=3.75, P=0.0052), marketable yield was unaffected by amendments. To expand on my experimental work, I performed an on-farm survey in the 2020-2021 field season, as described above. From the soils I collected from each farm, I sequenced the microbial communities using Illumina MiSeq, measured the abundance of Bacterial Wilt and Southern Blight using qPCR, and measured soil physicochemical properties and the abundance of plant-parasitic nematodes. Management practices, such as growing tomatoes in the field compared to high tunnels, affected the prevalence of Bacterial Wilt, a soil-borne pathogen.Bacterial Wilt was more abundant in high tunnels than fields (F1,44.8=37.57, P<0.001). Obj. 1b) Determine management-mediated shifts in microbial communities and nutrients that are associated with the greatest suppression of insect pests and soil-borne pathogens Through the field experiment, I found that the addition of worm castings increased, and fish bone meal suppressed, the diversity of bacteria in the rhizosphere of plants across varieties (F4,134.3=6.86, P<0.0001). Similarly, fertilization with chicken manure or fish bone meal suppressed the diversity of fungi in the rhizosphere across varieties (F4,139.1=5.24, P=0.0006). Overall, amendments and varieties that promoted greater rhizosphere fungal diversity had a lower rate of infection by Southern Blight (F1,38=5.77, P=0.021). Through my on-farm survey, I found that soil fungal communities were shaped strongly by physiographic region and management (Physiographic Region: F2,64=2.22, P=0.001; Field or High Tunnel: F1, 64=2.47, P=0.001). Importantly, farms with greater soil fungal diversity had a lower abundance of Bacterial Wilt (F1,43=5.95, P=0.019). Currently, I am using structural equation modelling to untangle how on-farm management shapes soil physicochemical properties and microbes to suppress of soil-borne pathogens. Obj.2) Investigate the chemical and molecular mechanisms by which particular soil management practices enhanced herbivore suppression in the field. Through the field experiment, I found that soil nutrients were shaped strongly by amendments (PERMANOVA: R2=0.32406, F4,148=46.927, P<0.001). For instance, soils fertilized with chicken manure had the greatest pH (F4,148=13.01, P<0.001), while soils fertilized with fish bone meal had the greatest phosphorous concentration (Phosphorous F4,143.2=7.45, P<0.001). db-RDA indicated that soil physicochemical properties explained 12.8% of variation in the bacterial community and 5.5% of variation in the fungal community, with pH, magnesium, phosphorous, potassium, and manganese driving the bacterial community and pH, magnesium, phosphorous, and sodium shaping the fungal community. Plants fertilized with fish bone meal had the greatest, and plants fertilized with worm castings had the lowest, densities of Type VI trichomes (F4,193.2=3.17, P=0.015). Leaf toughness and foliar nutrient concentrations were unaffected by amendments. Herbivore abundances were not correlated with foliar nutrients, trichomes, or toughness, indicating that effects of amendments on herbivores may be driven by changes in other traits, such as plant chemical defenses. To evaluate how management-mediated, on-farm microbial communities may affect the resistance of tomato plants to insect pests, I performed a growth room experiment in Summer 2022 at Davidson College. I grew Sungold tomato plants in sterile soil inoculated with soil microbial communities collected from one of ten collaborating farms, or a mix of autoclaved farm soil (control). I subjected these plants to damage by either a specialist (Manduca sexta) or generalist (Spodoptera exigua) caterpillar, or no herbivore (11 farm treatments x 12 replicates x 3 herbivore treatments = 396 plants). Currently, I am sequencing the soil microbial communities and analyzing foliar nutritive and defensive traits to determine which on-farm microbial communities enhance tomato plant resistance to insect herbivores, and the mechanisms by which they do so.
Publications
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