Optimizing crop rotations for soil health and plant disease management in California processing tomatoes

This project will take place at the UC Davis Plant Pathology Experiment Station. We plan to replicate a winter cash/cover crop/fallow/weedy fallow rotation cycle in a field study.  The selected field will be infested with Fusarium falciforme and planted to tomatoes for the summer of 2023. .  This field will then be planted to plots containing cool season cash/cover crops, chemical fallow, and weedy fallow for winter 2023 to spring 2024, and then back to tomatoes for summer 2024.

The trial will be set up in a complete randomized block design.  The winter trial will be divided into three blocks, each containing 5, 240ft rows divided into three 80ft plots.  Within each block, each randomized 80ft plot will be planted to a different crop. The cash and cover crops tested will be selected based off current winter crops grown in areas where processing tomatoes are also grown. Chemical fallow plots will be treated with herbicide both pre and post planting as needed. The location of each crop will be marked and disease development assessed in summer 2024 tomato and compared to the different crop treatments.  

Objective 1: Developing avoidance, rotation crop and weed management strategies which minimize losses from soil borne Fusarium falciforme in annual crops, particularly the highly susceptible keystone annual, processing tomatoes.

Obj 1a: Assess disease development of Fusarium falciforme in common California winter cash crops to determine highly susceptible crops to avoid planting in infested fields

In September 2023, the previous tomato crop will be mowed and incorporated.  Beds will be formed and inline dip and micro sprinklers will be set up to irrigate the winter crops if seasonal rains are insufficient.

            Some cool season crops that might be included are as follows:  hairy vetch, mustard, triticale, parsley, alfalfa, romaine, onion, garlic, and broccoli.  These will be transplanted or direct sown in the field depending on the agronomic practices for each crop. Crops that need to be transplanted will be started in the greenhouse four weeks prior to transplantation. The crops will be watered and fertilized as needed.  The crops will be planted out in late fall 2023.  Cash crops will be harvested when needed to mimic a typical agronomic field. 

After planting, a 15 ft monitoring plot will be established in each crop plot to rate canopy symptoms.  After the plants have reached maturity (approximately 12 weeks in), disease assessment will occur every 3 weeks. Plants in the monitoring plot will be rated for one of four canopy ratings; healthy, early decline, advanced decline, and dead.  Then, 3 random plants from each row will be dug up and assessed for foot rot, crown rot, and stem rot.  This data will be used to build an Area Under the Disease Pressure Curve (AUDPC). Any symptomatic plants will be taken back to our lab and isolated from to extract the causative pathogen using aseptic technique and standard de-infestation protocol.  Identification will be done based on morphologic fungal structures and DNA sequencing of the Elongation Factor genes.  Sequences will be matched to our known sequence that has been deposited on NCBI BLAST.    

At the end of the season (late spring 2024), the final evaluation of disease will occur.  This will consist of pulling 15 random plants per plot and rating for canopy and rot symptoms as stated above.  Any symptomatic plants will be isolated from to confirm disease as stated above.

Host status of each crop will be determined if the crop develops symptoms and F. falciforme presence is confirmed by DNA sequencing.

Obj 1b: Evaluate common California winter cash and cover crops for their ability to reduce disease incidence in tomato when compared to chemical fallow:

After all winter disease evaluations are complete, the winter cash and cover crops will be mowed and incorporated into their respective plots and beds.  Care will be taken to make sure the placement of the plots is known so that when tomatoes are planted, differential disease development can be recorded.

Tomato transplants donated from industry will be machine transplanted into the field.  Once the plants are established, disease monitoring plots containing 15 plants will be established for each treatment plot (the plots previously containing the different winter crops). 

40 days after transplant, the first disease assessment will take place.  This will consist of rating the plants in the monitoring plot as healthy, early decline, advanced decline, or dead.  3 plants outside of the monitoring plots will be randomly selected for destructive sampling and rated for decline symptoms as described above and for incidence of rot in the foot, crown, and stem.  This disease evaluation will be repeated every 3 weeks after for a total of 3 times, plus a final disease evaluation at harvest.  Five symptomatic plants per plot from the final evaluation will be collected for pathogen confirmation in our lab as mentioned above. 

120 days from transplant, the 15 plant monitoring plots will be harvested using a small scale mechanical harvester.  Average fruit weight will be gathered per plot.  A subsample of fruit from each plot will be sorted for fruit quality to quantify disease effect on fruit quality.  Total yield per acre will be extrapolated from the total plot yield.

Disease development in each treatment plot will be compared to the chemical fallow treatment plot as the negative control.  If tomato plants in a particular treatment crop develop more severe disease than plants planted in the chemical fallow plot, then that treatment is likely a poor winter cover crop.  If tomato plots in a particular treatment crop develop less severe disease than plants planted in the chemical fallow plot, then that treatment is likely a good winter cover crop and possibly reduces soil innoculum.

Obj 1c: Assess cool season weed hosts, to determine weed management targets.   

            Within the field trial described above, we will leave one plot per block empty to become a weedy fallow plot.  Midwinter, we will identify, and catalog all weed species in theses plots. We will then use the same disease evaluation method described in Obj1a to determine the host status of each weed species.  Weed species that are confirmed hosts will be recommended targets of weed management.

Objective 2: Assessing the effect of common California rotation and cover crops on soil physiochemistry, carbon cycling, and associated decomposition of pathogen-infested litter.

The field will be prepared and planted as described in objective 1.

Obj 2a. Characterize soil nutrition, structure and compaction, and organic matter under different winter cash and cover crops. 

            Soil samples will be taken from the field at the following time points; post-harvest/pre summer 2023, mid-winter 2023, mid spring 2024, pre-plant summer 2024, mid-season 2024, and post-harvest 2024. 

            Soil sampling timeline

Soil samples will be collected by taking 3 random soil cores per crop plot down to 6 inches depth aimed near the root zone of the plants.  Soil will then be bulked for each plot and sent to Dellavalle Soil Testing to get a metric of soil macro and micronutrients.  Nutrients to be tested and their units are as follows: 

Water retention and soil infiltration rates will be measured using tensiometers and infiltrometers.  Three sites per crop plot will be selected and tested with the tensiometer.

            Soil organic matter will be measured using a loss of ignition assay.  Soil will be collected from 4 random locations within each crop plot and bulked.  Each sample will be weighed, baked at 900C in a furnace to remove any organic material, allowed to cool, and reweighed.  The difference in weight is organic matter content.  This will be done following the timeline above to get a pretreatment baseline.

Obj 2c: Measure the decomposition rates of different pathogen-infested crop residues in order to compare the level of organic matter addition, rates of carbon cycling, as well as effects on persistence of infested tissue residing in the soil

            In August 2023, tomato plant material (leaves stems, roots, crowns etc) will be gathered and stored in a ventilated barn at ambient air temperature and humidity to initiate plant drying.  After two weeks in the barn, the plant material will be shredded into 1inch pieces and left to dry for a further 2 weeks.  Once dry, mesh draw string bags will be filled with 10 grams of dried litter material. We will need enough bags for 3 time points: mid-winter season, late spring/pre summer plant, and mid-summer season.  Three pouches will be made per crop plot (12), per block (3), per time point (3) for a total of 324 bags of tomato litter. These bags will be then buried in the crop plots at 20ft, 40ft, and 60ft from the front of the plot, 4inches deep.

            After 2 months in the field, the first set of 3 bags will be removed from the field and dried in an oven at 60C for 3 days and then weighed to see how much material has decomposed.  After another 2 months, the second set of 3 bags will be removed, oven dried, and weighed for the second time point. The third and final time point will occur in the summer of 2024 after the field has been replanted to tomato.

            At the end of the winter trial in the spring of 2024, plant materials will be gathered from each winter crop and prepared using the same method above.  We will need enough litter bags for 2 time points: planting and end of summer season. Three pouches will be made per crop, per block (3), per time point (2) for a total of 18 bags per crop.  These bags will be then buried 3 per crop plot at 20ft, 40ft, and 60ft from the front of the plot at a depth of 4 inches.

            After 2 months in the field, the first set of bags will be removed from the field and dried in an oven at 60C for 3 days.  They will then be weighed to see how much material has decomposed.  After another 2 months, the second set of bags will be removed, oven dried, and weighted again for the final time point.

Objective 3: Work with growers to quantify the benefits of rotation and cover crops for crop health and disease control in annual crops, with an emphasis on tomatoes.

Obj 3a: Work with growers who are currently utilizing a rotation plan to assess the effects on soil health and disease losses

Working with statewide farm advisors, we have identified five grower fields that have implemented a rotation program that involves processing tomatoes, including our collaborating producer.  These growers have agreed to work with us and allow us to visit the fields, take plant samples to looks for disease, and give us yield data so that we can compare rotation effects. These fields started in tomato and rotated through the following crops (not necessarily in this order): Alfalfa, sunflower, cucumber, wheat, tomato.  For the summer of 2023, we have confirmation that two fields will be planted to wheat and alfalfa, and one might be tomato.  We are still waiting on information for the fourth and fifth fields. 

During the summer of 2024, we plan to visit these five fields at pre-harvest and take a random 100ft transect of 10 rows in the field.  We will look for any disease symptoms (such as necrotic leaves, vine decline, root/crown rot) to quantify general plant health.  We will also take soil samples from these rows to be used for nutrient and soil health analysis as discussed above.  The growers will supply us with historical yield data to compare tomato yields from before and after this rotation program.