Performing Department
(N/A)
Non Technical Summary
There are some critical knowledge gaps on how the integration of various agricultural practices affects the dynamics and functions of soil and tomato-associated microbiome, soil and tomato health, and productivity. Therefore, the proposed research project will pursue four objectives: (1) assess the effects of the integration of cover crop cereal rye and arbuscular mycorrhizal fungi (AMF) practices on tomato yield and disease control against the soil-borne fungal pathogen, Fusarium oxysporum; (2) characterize and identify functional elements of soil and tomato root-associated microbiome affected by cereal rye and AMF that contribute to tomato health and yield; (3) identify the critical soil health indicators (i.e., soil aggregation, bulk density, soil organic matters, and enzyme activities) associated with cereal rye and AMF practices and elucidate their associations with soil and tomato root-associated microbiomes to improve tomato soil-borne disease control and yield efficiency; (4) develop extension activities for improving tomato and soil health management. The project will address the following program priorities: 1) evaluate how multiple management components of agricultural production systems can be integrated to enhance plant disease control and productivity; 2) investigate how production systems can alter the microbiome and determine how alterations can affect plant resistance to pathogen infections and productivity, and 3) assess how changes in the production system and biodiversity affect soil and plant health. The long-term goals of the proposed research are to develop sustainable agronomic management systems for improving soil and tomato health while enhancing tomato productivity, reducing inputs of chemicals, and benefitting the environment and human health.
Animal Health Component
30%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
(N/A)
Goals / Objectives
Our long-term goals for the proposed research are to develop agronomic management systems for improving soil and tomato health for sustainable productivity; and deliver knowledge-based information and approaches to educators, students, farmers, and the other stakeholders to enhance tomato and soil health with the reduced chemical application to benefit human health and environment. The goals are based on the integration of the holistic, innovative, and ecologically sound agricultural management components, which includes arbuscular mycorrhizal fungi (AMF) and cover crop (ryegrass) to decipher the indicators of soil health and tomato soil-borne disease control, by connecting tomato and soil-associated microbial communities.?Objective 1: Assess the effects of the integration of cover crop cereal rye and arbuscular mycorrhizal fungi (AMF) practices on enhancing tomato yield and disease control caused by one destructive soil-borne fungal pathogen, Fusarium oxysporum.Objective 2: Characterize and identify the functional elements of the soil and tomato root-associated microbiome affected by the integration of the cereal rye and AMF that contributes to tomato health and yield.Objective 3: Identify core soil health indicators (i.e., soil aggregation, bulk density, soil organic matters, and enzyme activity) associated with the integration of the cereal rye and AMF practices and elucidate their associations with soil and tomato root-associated microbiome to improve the tomato soil-borne disease control and yield.Objective 4: Develop extension activities for improving plant and soil health management.
Project Methods
For Objective 1: Assess the effects on tomato disease incidence and severity as well as fruit yield by the interactions of different agricultural practices, including the cover crop cereal rye and beneficial AMF.AMF application: Inoculation with AMF will be performed one week after the tomato transplanting by using the commercially available inoculum product.Fusarium oxysporum inoculation and disease evaluation: Fusarium oxysporum pathogen will be applied to the bed soil before tomato transplanting.Tomato growth and yield evaluationGrowth development: Tomato plant heights and leaf chlorophyll levels will also be measured using the SPAD & CI-340 photosynthesis system at different stages as mentioned above.Yield: Tomato plants in each plot will be harvested at the mature stage and the fruits will be graded into marketable yield size categories in the field using a portable grading table.The yield and disease control capability will be further evaluated in relation to soil properties and the soil health index based on the critical soil properties as described in objective 3. The least Significant Differences at probability level 0.10 (LSD 0.10) will be reported for plant height, yield, and other agronomic characteristics.For Objective 2: Characterize and identify functional elements of soil and tomato root-associated microbiome affected by different agricultural practices contributing to tomato health and yield. For analyzing the whole microbial community including the unculturable fungi and bacteria in soil and roots,the sequencing approach will be applied: The total microbial community DNA will be extracted from the soil and plant roots by using a FastDNA Spin Kit for Soil (MPBio) according to the manufacturer's instructions. The bacteria small-subunit 16s rDNA (eg. V5 and V7 region primersand fungal internal transcribed spacer ITs primers will be used for bacterial and fungal rDNA amplification by using PCR. The libraries for the 16s and ITs regions will be set up based on the previously developed protocols (Caporaso et al., 2012; McGuire et al., 2013). The amplicon library preparation will be performed using a two-step amplification protocol, individual samples will be indexed using a double-indexing approach. Samples will be pooled in equimolar concentration. And the amplicon libraries will be sequenced in an Illumina MiSeq 2 x300 sequencing platform. The sequencing data will be analyzed by the software Mothur for the microbial community composition, abundance, and diversity analysis (Debenport et al., 2015; Lebeis, S. L., et al., 2015). The analyses will be also performed using R program software (R Core Team, 2019).For Objective 3: Identify the core soil health indicators associated with different agricultural practices and elucidate their associations with soil and tomato root-associated microbiome to influence plant disease control and yield efficiency.Soil health indicator analysis: In each replicated plot the soil will be collected prior to the establishment of the cover crop as the baseline. Soil samples will also be collected at tomato seedling and harvesting in two stages. The collected soil samplings from 0 to 20 cm depths will be analyzed for biological, chemical, and physical properties as core soil health indicators from all the plots. There will be four replicates, for each replicate, around 500 g from 10 cores (2.5 dia. probes) will be combined as one sample for the final analysis. The experiments will be carried out for three years. The samples will be stored at -80 ?C or air-dried at room temperature for further diverse analysis. The data from soil physical, chemical, and biological properties will be used to compute soil health index (Moebius -Clune et al., 2017). Commonly accepted indicators of soil health will be analyzed, which include a combination of soil organic carbon concentration and stock, microbial biomass, bio-diversity and efficiency, aggregate stability, bulk density, water drainage infiltration and water retention, nutrient cycling, active and passive pools of soil organic matters, and soil enzyme activities (Dane and Topp,2002).1. The phospholipid fatty acid (PLFA) analysis2. Soil chemical properties: (1) Soil pH value will be measured on a 1:2 soil/water suspension (Thomas, 1996). (2) Soil organic carbon and nitrogen concentration will be measured by the dry combustion method using CN Analyzer (Nelson and Sommers,1996; Bonin and Lal, 2014).3. The soil enzyme activity with different functions will be tested: a) Carbon cycle, β-glucosidase is the last step in cellulose degradation, releasing glucose. β-glucosidase activity will be done as it is an established soil quality indicator being very sensitive to disturbance, such as C inputs and heavy metal pollution in soils (Knight and Dick, 2004; Hinjosa et al., 2004; Ochiai et al., 2008); b) P Cycle -acid phosphatase-releases PO4, which is plant available form (Margalef et al., 2017); c) N cycle: Urease and Amidase, as described by Tabatabai (1994), Parham and Deng (2000), and Deng et al (2017).d) Disease suppression: Hydrolytic enzymes known to attack pathogen membranes will include: β-glucosaminidase which hydrolyzes chitin chains (according to Parham and Deng, 2000); protease (according to Alef and Nannipieri, 1995), and b-1,3,glucanase (according to Lethbridge et al., 1978). Additionally, integrative enzyme assays that have potential to be calibrated for routine soil testing to identify or quantify disease suppressive soils will be run: fluorescein diacetate hydrolysis (FDA) activity (Chen et al., 1988; Boehm et al., 1992; Workneh et al., 1993; Drinkwater et al., 1995; van Bruggen, 2000); arlysulfatase activity (according to Green et al., 2006) which has been shown to be sensitive for detecting disease suppressive soil for Verticillium dahlia (Ochai et al., 2008) and Aphanomyes euteiches (Cespedes Leon et al., 2006).4. Soil physical properties: Water stable aggregation will be assessed as described by Kemper and Rosenau (1986) because soil structure governs water retention and transmission, aeration, biological habitat, rooting environment, and porosity (water holding capacity).5. Soil aggregate size distribution will be determined by wet sieving method. Aggregate size fractions (2000, 1000, 500, 250, 125, and 53 µm) retain in each sieve will be collected, oven-dried, weighted, and expressed as percent of soil on a sand-free basis. The data on aggregate size fractions will be used for the calculation of mean weight diameter (MWD), macro- and microaggregates, and aggregate stability. Bulk density will be determined by using the standard core methods (Kempers and Rosenau, 1986; Sundermeier et al. 2011).6. Soil water retention and infiltration measurement: Soil moisture retention at different potential will be measured on undisturbed cores for 0,0.06,0.1, and 0.3 bar; and on disturbed and sieved soil for 15 bar pressures. The plant available water capacity will be computed as the difference in moisture retention between 0.3 bar and 15 bar (Dane and Hopmans,2002). Water infiltration rate will be measured by the double ring infiltrometer (Reynolds et al., 2002) and the data will be analyzed to compute infiltrability, soil water sorptivity, and transmissivity (Philip,1957).Objective 4: Develop extension activities for improving tomato and soil health management.(a) Develop soil and tomato-associated microbiome and productivity production and management training curriculums following the scientific development research results and through DACUM analysis.(b) Carry out the soil and plant health, soil and plant-associated microbiome, and plant resilience-related workshops, field days, field trials, and surveys:(c) eXtension Foundation Website, social media, and radio/TV talk shows.