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Mutai JC, Stewart JE, Medvecky B, Dobbs JT, Vanek SJ, Ojiem J, Chege G, Fonte SJ. Assessing performance of simplified bioassays for soil-borne pathogens in smallholder systems of western Kenya. FRONTIERS IN PLANT SCIENCE 2024; 15:1389285. [PMID: 39211840 PMCID: PMC11360875 DOI: 10.3389/fpls.2024.1389285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
Introduction Soil-borne pathogens cause considerable crop losses and food insecurity in smallholder systems of sub-Saharan Africa. Soil and crop testing is critical for estimating pathogen inoculum levels and potential for disease development, understanding pathogen interactions with soil nutrient and water limitations, as well as for developing informed soil health and disease management decisions. However, formal laboratory analyses and diagnostic services for pathogens are often out of reach for smallholder farmers due to the high cost of testing and a lack of local laboratories. Methods To address this challenge, we assessed the performance of a suite of simplified soil bioassays to screen for plant parasitic nematodes (e.g., Meloidogyne, Pratylenchus) and other key soil-borne pathogens (Pythium and Fusarium). We sampled soils from on-farm trials in western Kenya examining the impact of distinct nutrient inputs (organic vs. synthetic) on bean production. Key soil health parameters and common soil-borne pathogens were evaluated using both simple bioassays and formal laboratory methods across eleven farms, each with three nutrient input treatments (66 samples in total). Results and Discussion The soil bioassays, which involved counting galls on lettuce roots and lesions on soybean were well correlated with the abundance of gall forming (Meloidogyne) and root lesion nematodes (e.g., Pratylenchus) recovered in standard laboratory-based extractions. Effectiveness of a Fusarium bioassay, involving the counting of lesions on buried bean stems, was verified via sequencing and a pathogenicity test of cultured Fusarium strains. Finally, a Pythium soil bioassay using selective media clearly distinguished pathogen infestation of soils and infected seeds. When examining management impact on nematode communities, soils amended with manure had fewer plant parasites and considerably more bacterivore and fungivore nematodes compared to soils amended with synthetic N and P. Similarly, Pythium presence was 35% lower in soils amended with manure, while the Fusarium assays indicated 23% higher Fusarium infection in plots with amended manure. Our findings suggest that relatively simple bioassays can be used to help farmers assess soil-borne pathogens in a timely manner, with minimal costs, thus enabling them to make informed decisions on soil health and pathogen management.
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Affiliation(s)
- Joyce C. Mutai
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Jane E. Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Beth Medvecky
- Innovations in Development, Education and the Mathematical Sciences (IDEMS) International, Reading, United Kingdom
| | - John T. Dobbs
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Steven J. Vanek
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - John Ojiem
- Kenya Agricultural & Livestock Research Organization, Kibos Centre, Kisumu, Kenya
| | - Gabriel Chege
- Kenya Agricultural & Livestock Research Organization, Kibos Centre, Kisumu, Kenya
| | - Steven J. Fonte
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
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Batson AM, Woodhall JW, du Toit LJ. Real-Time PCR Assays for Races of the Spinach Fusarium Wilt Pathogen, Fusarium oxysporum f. sp. spinaciae. PLANT DISEASE 2023; 107:2633-2642. [PMID: 36734942 DOI: 10.1094/pdis-11-22-2658-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is a significant limitation for producers of vegetative spinach and spinach seed crops during warm temperatures and/or on acid soils. Identification of isolates of F. oxysporum f. sp. spinaciae, and distinction of isolates of the two known races, entails time-intensive pathogenicity tests. In this study, two real-time PCR assays were developed: one for a candidate effector gene common to both races of F. oxysporum f. sp. spinaciae, and another for a candidate effector gene unique to isolates of race 2. The assays were specific to isolates of F. oxysporum f. sp. spinaciae (n = 44) and isolates of race 2 (n = 23), respectively. Neither assay amplified DNA from 10 avirulent isolates of F. oxysporum associated with spinach, 57 isolates of other formae speciales and Fusarium spp., or 7 isolates of other spinach pathogens. When the assays were used to detect DNA extracted from spinach plants infected with an isolate of race 1, race 2, or a 1:1 mixture of both races, the amount of target DNA detected increased with increasing severity of wilt. Plants infected with one or both isolates could be distinguished based on the ratio in copy number for each target locus. The real-time PCR assays enable rapid diagnosis of Fusarium wilt of spinach and will facilitate research on the epidemiology and management of this disease, as well as surveys on the prevalence of this understudied pathogen in regions of spinach and/or spinach seed production.
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Affiliation(s)
- Alex M Batson
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273
| | - James W Woodhall
- University of Idaho Parma Research and Extension Center, Parma, ID 83360
| | - Lindsey J du Toit
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273
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Batson AM, Gyawali S, du Toit LJ. Shedding Light on Races of the Spinach Fusarium Wilt Pathogen, Fusarium oxysporum f. sp. spinaciae. PHYTOPATHOLOGY 2022; 112:2138-2150. [PMID: 35621310 DOI: 10.1094/phyto-03-22-0107-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Two pathogenicity groups of Fusarium oxysporum f. sp. spinaciae, the causal agent of Fusarium wilt of spinach (Spinacia oleracea), were described recently based on virulence of isolates on proprietary spinach inbreds. In this study, a wide range in severity of wilt was observed for 68 spinach cultivars inoculated with an isolate of each pathogenicity group, with 22 (32.4%) cultivars displaying differential responses to the isolates. In a second set of trials, seven spinach cultivars were inoculated with five isolates of each pathogenicity group. The cultivars had similar wilt responses to isolates within each group. In both sets of trials, the most severe wilt developed on cultivars inoculated with pathogenicity group 2 isolates when daylength was shorter and light intensity lower. To test whether light intensity exacerbates severity of Fusarium wilt, three spinach cultivars were inoculated with two isolates of each pathogenicity group and grown with or without shading. Shaded plants developed more severe wilt than nonshaded plants. This difference in wilt severity was greatest for plants inoculated with pathogenicity group 2 isolates. We propose naming isolates of pathogenicity groups 1 and 2 as races 1 and 2 of F. oxysporum f. sp. spinaciae, respectively, and recommend the cultivars Kiowa (susceptible to both races) and Magnetic (susceptible to race 2 and highly resistant to race 1) as differentials. Results of this study should help breeders screen spinach germplasm for resistance to both races of F. oxysporum f. sp. spinaciae.
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Affiliation(s)
- Alex M Batson
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273, U.S.A
| | - Sanjaya Gyawali
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273, U.S.A
| | - Lindsey J du Toit
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273, U.S.A
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Batson AM, Fokkens L, Rep M, du Toit LJ. Putative Effector Genes Distinguish Two Pathogenicity Groups of Fusarium oxysporum f. sp. spinaciae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:141-156. [PMID: 33103963 DOI: 10.1094/mpmi-06-20-0145-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is an important disease during warm conditions in production regions with acid soils, yet little is known about what confers pathogenicity to spinach in F. oxysporum f. sp. spinaciae genetically. To identify candidate fungal genes that contribute to spinach Fusarium wilt, each of 69 geographically diverse F. oxysporum isolates was tested for pathogenicity on each of three spinach inbreds. Thirty-nine isolates identified as F. oxysporum f. sp. spinaciae caused quantitative differences in disease severity among the inbreds that revealed two distinct pathogenicity groups of F. oxysporum f. sp. spinaciae. Putative effector gene profiles, predicted from whole-genome sequences generated for nine F. oxysporum f. sp. spinaciae isolates and five nonpathogenic, spinach-associated F. oxysporum (NPS) isolates, distinguished the F. oxysporum f. sp. spinaciae isolates from the NPS isolates, and separated the F. oxysporum f. sp. spinaciae isolates into two groups. Five of the putative effector genes appeared to be unique to F. oxysporum f. sp. spinaciae, as they were not found in 222 other publicly available genome assemblies of F. oxysporum, implicating potential involvement of these genes in pathogenicity to spinach. In addition, two combinations of the 14 known Secreted in Xylem (SIX) genes that have been affiliated with host pathogenicity in other formae speciales of F. oxysporum were identified in genome assemblies of the nine F. oxysporum f. sp. spinaciae isolates, either SIX8 and SIX9 or SIX4, SIX8, and SIX14. Characterization of these putative effector genes should aid in understanding mechanisms of pathogenicity in F. oxysporum f. sp. spinaciae, developing molecular tools for rapid detection and quantification of F. oxysporum f. sp. spinaciae, and breeding for resistance to Fusarium wilt in spinach.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Alexander M Batson
- Washington State University Northwestern Washington Research and Extension Center Mount Vernon, Mount Vernon, WA 98273, U.S.A
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands
| | - Lindsey J du Toit
- Washington State University Northwestern Washington Research and Extension Center Mount Vernon, Mount Vernon, WA 98273, U.S.A
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Gatch EW, du Toit LJ. Limestone-Mediated Suppression of Fusarium Wilt in Spinach Seed Crops. PLANT DISEASE 2017; 101:81-94. [PMID: 30682316 DOI: 10.1094/pdis-04-16-0423-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium wilt of spinach is caused by the soilborne fungus Fusarium oxysporum f. sp. spinaciae and occurs in most regions of spinach production. The disease is favored by acid soils and warm temperatures, and the fungus can survive extended periods as chlamydospores or by asymptomatic colonization of the roots of nonhost plant species. The 10- to 15-year rotation required to minimize losses to Fusarium wilt is the primary constraint on spinach seed production in the maritime Pacific Northwest, the only region of the United States suitable for this cool-season, daylength-sensitive crop. Raising soil pH with agricultural limestone (97% CaCO3) results in a transitory, partially suppressive effect on spinach Fusarium wilt. A field trial was completed from 2009 to 2012 to assess the potential for annual applications of agricultural limestone at 0, 2.24, and 4.48 tons/ha for 3 years prior to a spinach seed crop to improve Fusarium wilt suppression compared with the level of suppression attained from a single limestone amendment at 4.48 tons/ha. Three proprietary female spinach lines were planted that ranged from highly susceptible to partially resistant to Fusarium wilt. Three successive annual applications of limestone at 4.48 tons/ha reduced midseason wilt incidence by an average of 20%, increased spinach biomass by 33%, and increased marketable spinach seed yield by 45% compared with plots amended once with the same rate of limestone in the spring of planting. The suppressive effect increased with increasing rate of limestone amendment, with the greatest difference observed when limestone was applied at between 0 and 2.24 tons/ha annually for 3 years. The effects on seed yield were greatest for the partially resistant female line, followed by the moderately susceptible and highly susceptible female lines. Overall, the results demonstrate that annual applications of agricultural limestone on acid soils of the maritime Pacific Northwest of the United States can enhance suppression of spinach Fusarium wilt, potentially reducing the required rotation interval by as much as 50%, thereby doubling the capacity for spinach seed production in the United States.
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Affiliation(s)
- Emily W Gatch
- Washington State University, Mount Vernon Northwestern Washington Research & Extension Center, Mount Vernon 98273-4768
| | - Lindsey J du Toit
- Washington State University, Mount Vernon Northwestern Washington Research & Extension Center, Mount Vernon 98273-4768
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Alcala AVC, Paulitz TC, Schroeder KL, Porter LD, Derie ML, du Toit LJ. Pythium Species Associated with Damping-off of Pea in Certified Organic Fields in the Columbia Basin of Central Washington. PLANT DISEASE 2016; 100:916-925. [PMID: 30686151 DOI: 10.1094/pdis-07-15-0774-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Organic vegetable production accounted for 19% of the total organic acreage in Washington State in 2013, with 1,700 ha of certified organic vegetable pea. However, production is challenged constantly with the threat of poor emergence after planting due to damping-off caused by Pythium spp. A survey of Pythium spp. in organic vegetable production areas of the semiarid Columbia Basin of central Washington was carried out in fall 2009 to identify species associated with damping-off during early spring planting. Of 305 isolates baited from soil sampled from 37 certified organic fields, 264 were identified to 16 Pythium spp. by sequencing the internal transcribed spacer region of ribosomal DNA. A soil DNA-CFU regression curve was developed using real-time quantitative polymerase chain reaction assays for each of the three predominant pathogenic species (Pythium abappressorium, the P. irregulare complex, and P. ultimum var. ultimum) found in soil sampled from the 37 fields. The P. irregulare complex, P. abappressorium, and P. ultimum var. ultimum were detected in 57, 78, and 100% of the fields sampled, respectively. A regression analysis was used to determine that P. ultimum var. ultimum ranged from 14 to 332 CFU/g of soil in the 37 fields, the P. irregulare complex ranged from 25 to 228 CFU/g of soil, and P. abappressorium DNA was below the quantifiable limit. In summary, P. ultimum var. ultimum was the most prevalent pathogenic Pythium sp. detected in certified organic fields in the semiarid Columbia Basin of central Washington but multiple Pythium spp. may be associated with damping-off in cool and wet, early spring planting conditions.
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Affiliation(s)
- Ana Vida C Alcala
- Washington State University Mount Vernon NWREC, Mount Vernon 98273-4768
| | - Timothy C Paulitz
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Pullman, WA 99164-6430
| | - Kurtis L Schroeder
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Pullman, WA 99164-6430
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