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By, Steven T. Koike, Director, TriCal Diagnostics and Tom Gordon, Professor, University of California at Davis


Introduction to Fusarium Wilt

Fusarium wilt diseases are well known problems that affect many crops and result in significant losses of yield and quality. In California’s central coast region, a number of Fusarium wilt diseases occur and affect crops such as celery, cilantro, lettuce, pepper, strawberry, and tomato (see Figure 1, column 3 for a list of some susceptible coastal crops).

Fusarium wilt diseases share a basic profile: (1) The pathogen can survive in the soil for a relatively long time, up to several years, without the presence of a susceptible crop; (2) In the presence of a susceptible plant, the Fusarium fungus penetrates the root, colonizes root tissue, enters the plant’s vascular tissue (xylem), and moves systemically into the plant stems via these vascular tubes; (3) Disease symptoms develop primarily due to the plugging up of the plant vascular tissue; (4) Symptoms include stunting and poor growth, yellowing of foliage, wilting of foliage, collapse of the plant, distinctive brown to red discoloration of the vascular tissue in roots and stems, and eventual death of the plant; (5) Because these pathogens are soilborne, Fusarium is readily spread in contaminated soil and crop residues that adhere to equipment and vehicles; (6) Fusarium wilt management is achieved by a combination of rotating to non-host crops, practicing field sanitation (avoid moving contaminated dirt on equipment), planting resistant cultivars, and in some cases applying pre-plant fumigants (example: conventional strawberry).

 Fusarium Fig1 Illustration

Fusarium wilt diseases are caused by one species of this fungus, Fusarium oxysporum. Researchers have shown that Fusarium wilt pathogens from different crops are genetically distinct from each other. A major implication of this genetic diversity is that each Fusarium wilt pathogen has a very narrow host range and usually causes disease on only one type of crop. The Fusarium wilt pathogen affecting celery causes disease in celery but does not cause symptoms in other crops such as lettuce or strawberry; the F. oxysporum that causes strawberry decline and death does so only to strawberry but not to lettuce or tomato. To help clarify this host specific phenomenon, plant pathologists give each Fusarium oxysporum pathogen the additional designation of “forma specialis” (abbreviated “f. sp.”) to indicate the host of that particular pathogen. The F. oxysporum that causes disease in celery becomes F. oxysporum f. sp. apii. Fusarium wilt of lettuce is caused by F. oxysporum f. sp. lactucae. See Figure 1, column 3 for a list of such designations for coastal crops. Pathogenic F. oxysporum in some cases can be further differentiated into distinct sub-populations such as races or somatic compatibility groups (Figure 1, column 4). These F. oxysporum pathogens persist in field soils for extended periods of time, thereby causing long-term concerns for a grower.

A factor that complicates Fusarium wilt diagnosis, however, is that the soil is home to a great diversity of Fusarium fungi. Agricultural soils are complex biological environments and may contain numerous Fusarium species, of which F. oxysporum is one of many (Figure 1, column 1). F. oxysporum fungi that are in agricultural soils can be either pathogenic or non-pathogenic to plants (Figure 1, column 2), which can create challenges regarding disease diagnostics and pathogen detection in soil. While non-pathogenic F. oxysporum strains do not cause disease symptoms in plants, these strains can still penetrate plant tissues and make their way into roots and other plant parts. Laboratory tests may detect these non-pathogenic F. oxysporum and report a false positive finding for Fusarium wilt. Likewise, soils that are tested for pathogenic F. oxysporum will likely also recover the non-pathogenic type of F. oxysporum, resulting in elevated counts and inaccurate test results.

Challenges and Errors in Confirming Fusarium Wilt Pathogens

Because of the economic impacts of Fusarium wilt diseases, confirmation of the respective F. oxysporum pathogens (the forma specialis sub-groups, Figure 1, column 3) isolated from plant samples is important. In addition, for some crops such as strawberry and lettuce, disease management decisions may depend on quantification of the true F. oxysporum pathogens in soil samples—i.e., how much inoculum is in the soil. However, such plant and soil confirmations are not straightforward. The following statements outline some of the challenges and errors inherent in Fusarium identification and detection.

  1. Identifying Fusarium fungi found in plant samples.

1. Because pathogenic F. oxysporum (forma specialis types), non-pathogenic F. oxysporum, and many other species of soilborne Fusarium can all enter plants via roots and damaged tissues and be recovered in lab culture tests, a laboratory result that lists “Fusarium species” is not a sufficiently detailed or useful report. A lab report that presents a diagnosis of “Fusarium wilt” based on the recovery of a “Fusarium species” does not have sufficient evidence to justify this conclusion.


2. Lab results for root tests can be especially ambiguous because many species of Fusarium, including non-pathogenic F. oxysporum and the primary F. oxysporum pathogens, can all invade and colonize roots. Isolations from xylem tissue in above-ground stems would reduce the likelihood of recovering non-pathogenic Fusarium fungi.

3. Most diagnostic labs cannot visually differentiate between colonies of pathogenic and non-pathogenic F. oxysporum recovered from plant samples. Some very experienced research labs can make this differentiation with a high degree of confidence (example: the Gordon program at University of California (UC) Davis can use Komada’s selective medium to visually differentiate between the pathogenic F. oxysporum f. sp. lactucae of lettuce from non-4StrawberryFusMay2014pathogenic F. oxysporum). Therefore, unless a lab has proven experience with such differentiation, visually identifying a Fusarium wilt pathogen from a culture plate generally is unreliable.

4. If a lab culture test recovers F. oxysporum from a plant’s vascular tissue, care must be taken before concluding that the sample is positive for Fusarium wilt. While such a conclusion is possibly correct, additional tests (molecular analysis, host inoculation experiments) must be completed to be sure scientifically. If a F. oxysporum-like fungus is consistently recovered from symptomatic vascular tissue, a conservative conclusion might be to call the sample “presumptive positive” or “provisionally positive” for Fusarium wilt.

  1. Identifying Fusarium fungi recovered from soil samples.


1. Tests that use non-selective culture media when attempting to quantify the amount of pathogenic (forma specialis types) F. oxysporum in soil samples will not provide any meaningful information. Pathogenic and non-pathogenic F. oxysporum as well as many other Fusarium species will all grow on such media and will be impossible to differentiate from each other.

2. When using semi-selective culture media (such as Komada’s selective medium), estimated counts of pathogenic F. oxysporum in soil samples may be of questionable accuracy because both pathogenic and non-pathogenic F. oxysporum can grow on this substrate. In general, it is difficult to differentiate between pathogenic and non-pathogenic colonies in culture. However, as indicated above, some very experienced research labs can make the distinction between these two groups.

3. On-going research may develop more accurate and useful soil tests using molecular methods. Such assays potentially will be specific for the particular forma specialis of concern and may eliminate the ambiguity and confusion caused by non-pathogenic F. oxysporum fungi that are very common in agricultural soils.



Positive identification and confirmation that a Fusarium isolate is truly a Fusarium wilt pathogen requires the involvement of a qualified lab that has the experience and tools necessary to make this determination. Lab test results that do not indicate which species was recovered provides little useful information to the submitter of the sample. If a lab confirms that F. oxysporum was recovered from symptomatic vascular tissue, a “presumptive” or “preliminary” statement could be made that the isolate is possibly a true wilt pathogen; however, to be rigorously correct, the isolate would need to be inoculated into a host plant so that pathogenicity can be confirmed. More specific tools under development may allow for conclusively identifying and quantifying this group of very important plant pathogens without recourse to time-consuming pathogenicity tests.