Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
IFAS Soil & Water Sci
Non Technical Summary
High-intensity specialty fruit and vegetable crop production depend on fumigation to reduce disease, nematode, and weed pressure prior to planting. While the impacts of fumigants on targeted soilborne pathogens are well documented, they can also impact the abundance and diversity of non-target soil microorganisms. As the soil microbiome is a critical component of agricultural production, the broad modes of action of fumigation could influence crop production by reducing abundances of critical plant-growth-promoting organisms providing nutrient availability and natural biocontrol. However, while general responses of soil microbial diversity to fumigation have been examined, there is limited information regarding the impacts to soil microbiome functions, particularly as they relate to crop production, over multiple growing seasons, and in different soil environments.This project will assess the interactions between fumigants, the soil microbiome, with a focus on plant-growth-promoting bacteria involved in nitrogen cycling and biocontrol, and the impacts on crop production. Field trials will be established in university and commercial farms. Trials at the university farm will focus on determining short- and long-term impacts on the soil microbiome composition and function due to different fumigant mixtures. Trials at commercial farms will examine the influence of soil environment and management practices on fumigant impacts to soil microbiome functions.Our project will "help fill major knowledge gaps in characterizing agricultural microbiomes and microbiome functions across agricultural production systems" by "functionally characterizing microbiomes" that may be impacted by fumigation and influence processes that are critical for crop production, including nutrient cycling and pest and disease control.
Animal Health Component
60%
Research Effort Categories
Basic
40%
Applied
60%
Developmental
(N/A)
Goals / Objectives
The overarching goal is to determine the impact of fumigation on the soil microbiome related to N cycling, plant disease, and plant production to develop strategies that limit environmental impacts and improve the sustainability of high-intensity specialty crop production systems. Our supporting objectives (SO) are to:SO1:Determine how the relationships between fumigation mixtures and ratios and soil microbial diversity, composition, and function impact biological control of pests and tomato production over time.SO2:Quantify fumigation changes to specific soil microbial plant growth-promoting and biocontrol functions and their relationship with production over a range of commercial settings with varying soil environments.
Project Methods
Methods for Objective 1:We will conduct trials at two sites within the UF/IFAS Gulf Coast Research and Education Center farm. Treatments will consist of four common fumigant mixtures and a no-treatment control and will be repeated every year to assess both single season and multiple season impacts of fumigation. Fumigation concentrations will be measured at multiple intervals after fumigation. Fumigants will be applied in January, the tomato crop transplanted in February, and harvested in May. After planting we will maintain a bare ground fallow. The crop will be grown following industry standards.During the fallow period, weed density and biomass by species will be measured at multiple times. During the cropping period, nutsedge emergence on the plastic covered bed will be counted. Broadleaf and grass weeds emerging in the planting hole will be identified and counted at season end. Weeds emerging within the row middle will be counted at three time points. Tomato height and vigor and disease incidence will be rated in each plot as well as overall plant health. Tomatoes will be harvested and graded following industry standards.Soil samples will be collected every year at 4 time points: prior to fumigation, after fumigation at planting, at the end of the harvest, and during the fallow period.Basic soil physicochemical properties will be measured each year of the study in fall before fumigants are applied, including soil bulk density, organic matter content, total carbon (C), and total N, C:N ratio, texture, pore space, CEC, and pH.Due to budget constraints, the soil microbiome analyses will only be conducted during Year 1 and Year 4. For N dynamics, soil will be collected from three soil depths, and we will measure the following soil N concentrations: total N, inorganic N, N mineralization rate, nitrification rate, and denitrification.Soil DNA will be extracted from soil samples and sent to an outside facility for high throughput amplicon sequencing of the bacterial 16S rRNA gene using the Illumina MiSeq platform. Data will be analyzed in QIIME 2 andthe R package 'Phyloseq'.Potential bacterial functions in each sample will be predicted using PICRUSt2 and those related to PGP will be determined using the KEGG database. Bioinformatics analyses will be conducted to examine significant differences in predicted PGP functional capabilities, indicator species analysis, and identification of potential ¨keystone¨ taxa. PGPB will be isolated from soil by serial dilution plating. Random amplified polymorphic DNA (RAPD)-polymerase chain reactions will be performed to select for representative strains of each RAPD group. Representative strains will be selected and assayed for select PGPB activities. Genomic DNA isolated from bacterial cells will be used for PCR amplifications of 16S rRNA gene and sequenced at an outside facility. A "PGPB" database will be created with those isolated taxa matching taxonomic affiliations between databases. Isolates found to be positive for at least one PGP functional trait will be considered PGPB.To link potential changes in microbial communities to the biocontrol against specific fungal soil pathogens, we will use prepared inoculum ofF. oxysporumf.sp.lycopersici,M. phaeseolinaandS. rolfsiito bait potential biocontrol agents from fumigated soils. We will stagger testing of the two field trials over the four years of the project. Following retrieval, inoculum samples will be quantified using serial dilutions plated on semi-selective media. Representative isolates will be typed by 16S rRNA gene sequencing. Additional aliquots will be plated for the recovery ofTrichoderma,F. oxysporum,andM. phaseolina, andS. rolfsiiviability. Inoculum viability from field treatments will be compared to additional inoculum bags stored in the lab. Representative fungal biocontrol isolates will be typed based using sequencing.To evaluate potential biocontrol activity, representative fungal biocontrol isolates and PGPB strains will be tested for their ability to inhibit the growth ofF. oxysporumf.sp.lycopersici,M. phaeseolinaandS. rolfsiiin dual plating assays. Potential biocontrol activity will be based on the inhibition of mycelial growth, as well as inhibition of sclerotia formation forS. rolfsii, relative to a non-treated control.Multivariate statistical analyses will be performed to determine the influence of fumigant type, sampling point, and abiotic parameters on biotic variables and yield.Methods for Objective 2:Commercial strawberry and tomato farms will be selected for the trial. Site selection will be based on identification of growers that use Pic-Clor 60, generally have consistent fumigation and pest management programs over time and are at sites that reflect the range of soil types in Central and Southern Florida. Data will be collected from each site over a 3-year period with the fumigation treatment compared with a non-fumigated control each year at each site. All other management practices will be the same.Soil will be collected in the same manner and intervals as in Objective 1.Prior to fumigation each season, a sub-sample of the collected soil will be analyzed at theGCREC Soil and Water Quality labfor soil texture, organic matter, and water potential. Soil penetration resistance and the depth of the plow pan will be measured. At each soil sampling date, soil volumetric water content will be measured, and a subsample will be sent to a professional laboratory to measure soil pH and content of soil macro- and micronutrients. Changes in soil seedbanks over time will be measured each year.To determine if PGPB functions significantly impacted by fumigation with Pic-Clor 60 and correlated with plant production in Objective 1 are impacted in a similar manner in different soil environments, assessments of the soil microbial diversity and composition and function using high-throughput amplicon sequencing, bioinformatics assessments, and PGPB isolation, functional assessment, and identification as described in Objective 1 will be conducted on soil samples for one season at a select tomato and strawberry farm.Based on the results from these sequencing and bioinformatics analyses as well as the new contributions to the PGPB database, we will assay for the PGPB functions determined to be significantly impacted by fumigation in soils collected from each of the farms. These assays and identification will be conducted at the time points during the growing season determined to have the greatest differences based on results from Objective 1. Identified PGPB will be added to the PGPB database as described in Objective 1.Similar methods will be utilized as described in Objective 1 to evaluate potential changes in microbial communities to the biocontrol against specific fungal soil pathogens. As described, we will use prepared inoculum ofF. oxysporum f.sp. lycopersici, M. phaeseolina,andS. rolfsiito bait potential biocontrol agents from fumigated soils. However, due to the scale of commercial fields and reduced number of treatments (fumigated vs. non-fumigated), we will increase the number of buried bags to 6 per a set with 2 sets per farm. Processing, isolation, and characterization will be similar to what was described in Objective 1.Soil N cycling measurements at 3 soil depths will be conducted from each farm as described in Objective 1.Similarmultivariate statistical analyses as described for Objective 1 will be performed to determine the influence of fumigation, sampling point, and abiotic parameters on PGPB abundance, disease incidence, weed populations, and yield. In addition, multivariate statistical analyses will be conducted using the entire PGPB database generated from both Objectives to determine whether the impacts of PicClor 60 on all variables is crop specific.