Effects of Soil Chemistry, Belowground Microbiota, and Disease Management on Health and Yield of Field-Grown Processing Tomatoes in California

Processing tomatoes are a major crop in the central valley of California with a farm gate value of 1.38 billion dollars. Soilborne pathogens are a serious threat to production, yet little is known about the microbial and pathogen communities in these soils and on the roots of field-grown processing tomatoes, and the effect soil inputs have on these communities, plant health, and yield. To address this knowledge gap we undertook a study with the following objectives: (1) to demonstrate the effect of soil chemistry, incorporated manures, soil-delivered nutrients, and chemical and biological fungicides on tomato plant health and fruit yield at harvest; (2) to describe the tomato field soil and root microbial and pathogen communities, and to assess the effect of the above mentioned treatments on those communities; and (3) to demonstrate the antifungal, biocontrol, and synergistic properties of the bacterium Collimonas and its effect on the root microbiota of field-grown processing tomatoes. We performed a 3-year field study in 6 commercial fields in Yolo and Solano counties with a history of premature vine decline (PVD), a phenomenon characterized by the loss of plant vigor and canopy cover at the onset of fruit ripening. Higher yielding fields also had lower levels of leaf necrosis and sunburnt fruit. Pre-plant levels of soil potassium and cation exchange capacity (CEC) correlated positively with fruit yield and negatively with leaf necrosis and sunburn at time of harvest. Soil amendments of composted poultry manure or other nutrient supplements increased yields in 3 of the 6 fields. None of the soil amendments, including chemical and biological fungicides, significantly or consistently reduced disease incidence or severity. We used next generation high throughput Illumina sequencing to profile the bacterial (16S) and fungal (ITS1) communities of bulk (n = 630) and rhizosphere (n = 169) soil samples, and of tomato crown tissue (n = 192) from the same 6 fields. We found a rhizosphere effect for both communities in terms of beta and alpha diversity, culturable populations, and pathogen enrichment. In the rhizosphere fungal community, the 6 most dominating species, representing 48.2% of the community, all are known to have representatives that are pathogenic to tomato. These included Pyrenochaeta lycopersici, Plectosphaerella cucumerina, Fusarium oxysporum, Colletotrichum coccodes, Fusarium solani, and Rhizoctonia solani. In tomato crown tissue we found the above mentioned pathogens together with Verticillium dahliae. P. cucumerina was identified as a hereto unknown root parasite of tomato in the continental US using community data and pathogenicity tests. Three cucurbit species including watermelon, melon, and pumpkin were determined to be asymptomatic hosts. There was no effect of treatment on microbial community composition and structure at any time point and soil compartment combination with the exception of composted poultry manure at one field. In a comparison of Collimonas isolates, we identified the Californian isolate Collimonas arenae Cal 35 as the best performer in confrontation assays against a wide range of plant pathogenic fungi and oomycetes including Fusarium oxysporum f. sp. lycopersici (Fol). In greenhouse and field experiments, neither C. arenae Cal35 nor the commercially available Bacillus-based biofungicide Serenade Soil reduced Fusarium wilt severity. However, a mixture of the two (referred to as Collinade) reduced vascular discoloration and prevented biomass loss. Roots of Collinade treated plants had less F. oxysporum compared to untreated plants. There was no effect of Collinade on the root bacterial communities