United States 

Department of 

Agriculture 

Forest 

Service 

Northern 

Region 

200 East Broadway 

P.O. Box 7669 

Missoula, MT 59807 

Forest Health

Protection

Report 03-3 March 2003 

COMPARING THREE METHODS OF ASSAYING SOIL 

FUSARIUM AND TRICHODERMA POPULATIONS FOR 

INTEGRATED PEST MANAGEMENT IN FOREST NURSERIES 

R. L. James 

Plant Pathologist 

ABSTRACT 

Three methods for assaying soil populations of potentially pathogenic Fusarium spp. and potentially 

antagonistic Trichoderma spp. were compared at the USDA Forest Service Lucky Peak Nursery near 

Boise, Idaho. Standard soil dilutions and estimates of colonization of residual roots within soil and roots 

from healthy-appearing seedlings were compared at the end of the first growing season of 1-0 ponderosa 

pine. Tested areas had undergone four different pre-plant treatments (methyl bromide/chloropicrin 

fumigation, fallowing with periodic cultivation, and incorporation of two different Brassica green manure 

crops). The three assay methods were similar in their ability to estimate treatment effects on soil 

populations of both Fusarium and Trichoderma. However, all three methods did not give adequate 

predictions of disease potential because they estimated overall Fusarium populations instead of 

elaborating pathogenic isolates. Improved assay methods for implementing integrated pest management 

should include molecular markers for pathogenic strains of Fusarium to supplement soil and seedling 

root colonization assays. 

INTRODUCTION 

Most disease control in forest nurseries involves 

preventing disease rather than treating disease 

once it becomes apparent. To prevent disease, 

cultural manipulations are made on the 

pathogen itself and/or on the conditions 

conducive to disease. Because of this emphasis 

on prevention, fairly high levels of pesticides 

have traditionally been used. In particular, preplant soil fumigants have become common in 

bare root nurseries due to improved stock 

quantity and quality that normally results from 

such treatments (Boone 1988; Boyd 1971; 

James 1989). Chemical soil fumigants are nonspecific biocides that kill all organisms within 

treated fields (Ebben et al. 1983; Fuller et al. 

1980; Johnson and Zak 1977). Although 

pathogen levels are usually eliminated or 

reduced by fumigation, beneficial microbes are 

also adversely affected (Ibarbia 1995; James 

1989; Munnecke et al. 1978). As a result, 

biological balances of microorganisms are 

disrupted and growers often have to repeat 

fumigations for each subsequent seedling crop 

(James 1989; Miller and Norris 1970). If 

fumigations are not conducted, high pathogen 

populations usually develop and often maintain 

themselves for several years until biological 

balances are naturally restored (Danielson and 

Davey 1969; Marois et al. 1983; Vaartaja 1967). 

Some nurseries have continually produced highquality bare root seedlings without pre-plant 

chemical soil fumigation (James 1989). In these 

situations, soil microbial populations may 

become suppressive to pathogens (Amir and 

Alabouvette 1993; James 1989). Under 
2 

suppressive conditions, pathogens may be 

present, even at relatively high levels, but do not 

elicit disease (Alabouvette et al. 1979; Amir and 

Alabouvette 1993). Many factors may affect soil 

suppressiveness, but one of the most important 

is quantity and makeup of microbes that are 

antagonistic toward pathogens (Abdul Wahid et 

al. 1998; Alabouvette et al. 1979, 1984). 

Disease suppressiveness is eliminated with soil 

fumigation (James 1989). 

If efforts to reduce or eliminate use of chemical 

pesticides, including pre-plant soil fumigation, 

are successful, growers will have to adopt a 

system of integrated pest management that will 

combine several different approaches to keep 

pest populations low (Linderman et al. 1994). 

However, for effective integrated pest 

management, good systems of pest population 

monitoring are essential (Bruehl 1989; Delahaut 

and Koval 1994). Monitoring is necessary to 

ascertain when population thresholds are 

exceeded so that satisfactory control measures 

may be instituted (Bruehl 1989; Heinz and 

Parrella 1991). 

Since one of the major problems confronting 

production of high-quality forest tree seedlings in 

bare root nurseries is soilborne pathogens 

inciting root disease (Bloomberg 1976; Smith 

and Bega 1966), monitoring soil populations of 

potentially-pathogenic organisms is a necessary 

prelude to effective integrated pest management 

(Bruehl 1989). The standard procedure for 

estimating soil populations of pathogenic fungi is 

soil dilution analysis from samples onto a 

selective agar medium for the group of targeted 

organisms (James and Beall 1999, 2000; James 

et al. 1996). This procedure requires laboratory 

analysis of soil fungi enumerated onto agar 

plates. Also, it assays all propagules within the 

target group rather than focusing on those 

isolates capable of eliciting disease (James et 

al. 2000). Other laboratory approaches include 

assaying for potential pathogens residing within 

residual roots that may be left from either 

previous seedling crops or produced from root 

pruning during crop production (James and 

Perez 1999). This procedure narrows the assay 

to those microorganisms capable of colonizing 

root tissues (James and Perez 1999), since 

these are of more concern from a disease 

potential standpoint (Bloomberg 1976; 

Bloomberg and Lock 1972; Booth 1966; James 

et al. 1991). Another approach is to assay for 

root colonization on seedlings that do not display 

disease symptoms (James 2002a, 2002b; 

James and Gilligan 1988a, 1988b). Since many 

potentially pathogenic fungi routinely colonize 

root cortical cells prior to initiating disease 

(Booth 1966; James et al. 1991, 1994), assaying 

of attached seedling roots limits the population 

sampling to those organisms most likely capable 

of causing disease. 

These three approaches to pathogen population 

monitoring have been utilized in the past at 

different nurseries. However, their efficacy in 

determining disease control treatment effects 

within a single area has not been compared. 

Therefore, the three methods were applied to 

same field and seedlings and quantitatively 

compared for the elucidation of potential 

pathogen populations. 

MATERIALS AND METHODS 

Three methods of assaying for potentiallypathogenic fungi in a bare root nursery were 

compared at the USDA Forest Service Lucky 

Peak Nursery, near Boise, Idaho. This nursery 

has been the site of several previous 

evaluations of the effectiveness of various 

treatments to reduce impacts caused by 

soilborne pathogens in general and Fusarium

spp. in particular (James and Beall 1999, 2000). 

Fusarium spp. are important causes of both 

damping-off and root diseases within conifer 

seedling crops grown at the nursery (James 

2001, 2002b). 

All assay methods were conducted from 

samples collected from the same fields that had 

undergone four different pre-plant soil 

treatments. These treatments included: (1) 

standard soil fumigation with methyl 

bromide/chloropicrin (67% methyl bromide 33% 

chloropicrin – applied at 350 lbs./acre), (2) bare 

fallowing with periodic cultivation for one 
3 

growing season prior to sowing, (3) Brassica

(dwarf essex) green manure crop grown during 

the fall and winter prior to sowing (incorporated 

at least 14 days before sowing), and (4) 

Brassica (mustard) green manure crop grown 

during the fall and winter prior to sowing 

(incorporated at least 14 days before sowing). 

All sampling was conducted during the fall at the 

end of the first seedling growing season (figure 

1). 

Soil Populations 

Six soil samples were collected within plots from 

each treatment. Samples were collected about 

in the middle of each plot between seedling 

rows. At each sample point, a soil core was 

taken to a depth of about 8 in. (20 cm). Soil was 

placed in plastic bags, kept refrigerated, and 

transported to the laboratory for analysis. 

Standard soil dilutions (James and Beall 1999, 

2000, James et al. 1996) were conducted to 

estimate populations of Fusarium and 

Trichoderma. Soil from each sample was initially 

sieved (2 mm sieve) to remove rocks, pieces of 

organic matter, and soil aggregates. From each 

sample, an approximate 5g subsample was 

oven-dried at about 100o

C for at least 24 hrs. 

until sample weight stabilized. Oven-dry weight 

was then calculated to provide a standard for 

sample comparison. For assays of Fusarium

and Trichoderma populations, 0.05g of fieldmoist soil was combined with 10 ml of 0.3% 

water agar and thoroughly mixed. One ml of the 

solution was then placed on each of three plates 

of a selective agar medium for Fusarium and 

closely-related fungi (Komada 1975) and spread 

uniformly. Plates were incubated 5-7 days at 

about 24o

C under diurnal cycles of cool, 

fluorescent light. Fusarium and Trichoderma

colonies were identified by their morphology on 

the selective medium; populations were 

expressed as colony-forming units (cfu) per g of 

oven-dried soil. Selected Fusarium isolates were 

transferred to potato dextrose (PDA) and 

carnation leaf (CLA) agar (Fisher et al. 1982) for 

identification using the taxonomy of Nelson et al. 

(1983). Average populations for each of the four 

pre-plant treatments were calculated. 

In addition, average ratios of Trichoderma to 

Fusarium populations (T/F ratio) were calculated 

to give an rough estimate of potential disease 

suppressiveness (James 2002a, 2002b). In 

general, the higher the T/F ratio, the less 

Fusarium-incited disease can be expected. 

Average soil populations of Fusarium and 

Trichoderma were statistically compared among 

the four pre-plant treatments using an analysis 

of variance. Significantly different (P≤0.05) 

means were located using Tukey’s HSD. 

Residual Root Colonization 

Assaying residual (detached) roots within soil 

has previously been done to enumerate 

populations of Fusarium within soil that might be 

capable of causing disease (James and Perez 

1999). Detached roots within soil were extracted 

from collected soil samples during sieving (see 

above). The roots were washed thoroughly to 

remove adhering soil particles, surface sterilized 

for 1 min in a 10% bleach solution (0.525% 

aqueous sodium hypochlorite) and rinsed in 

sterile, distilled water. Roots were cut into pieces 

approximately 3-5 mm in length and placed on 

Komada’s medium and incubated as described 

above. One hundred twenty root pieces were 

assayed from each of the four treatment areas. 

Selected Fusarium isolates were reisolated and 

identified as described above. Percentage of 

root pieces colonized by Fusarium, 

Trichoderma, other (unidentified) fungi or no 

fungi were determined. Percent root colonization 

by the different groups of fungi among the four 

pre-plant soil treatments were compared 

statistically with an analysis of variance. 

Significantly different (P≤0.05) means were 

located using Tukey’s HSD. All percentages 

underwent arc-sin conversion prior to analysis. 
4 

Seedling Root Colonization 

Seedling root colonization by potentially 

pathogenic fungi has been a useful measure of 

pathogen populations and an estimate of 

disease potential (James 2002a, 2002b; James 

and Gilligan 1988a, 1988b). Fifteen nondiseased 

seedlings were randomly collected at the end of 

the first growing season from each pre-plant 

treatment area. Seedlings were carefully 

extracted to make sure most of their roots were 

collected and transported to the laboratory for 

analysis. Root systems were washed thoroughly 

under running tap water to remove adhering soil 

particles. Ten root pieces located at the terminal 

ends of lateral roots were randomly selected and 

excised from roots; pieces were approximately 

3-5 mm in length. Root pieces were surface 

sterilized, rinsed and incubated on Komada’s 

medium as described above. Selected Fusarium

isolates were reisolated and identified as 

described above. Percentage of root pieces 

colonized by Fusarium, Trichoderma, 

Cylindrocarpon and other (unidentified) fungi 

were determined. Percent root colonization by 

the different groups of fungi among the four preplant soil treatments were compared statistically 

with an analysis of variance. Significantly 

different (P≤0.05) means were located using 

Tukey’s HSD. All percentages underwent arc-sin 

conversion prior to analysis. 

RESULTS 

Soil Populations 

Soil populations of Fusarium and Trichoderma 

spp. among the four pre-plant treatments are 

summarized in table 1. Treatment with methyl 

bromide/chloropicrin resulted in significantly 

(P=0.05) lower Fusarium and significantly higher 

Trichoderma populations by the end of the first 

seedling growing season. Likewise, the other 

three treatments resulted in high (> 1000) or 

very high (> 3000) populations of Fusarium and 

corresponding low populations of Trichoderma. 

This resulted in very low T/F ratios for all 

treatments except soil fumigation (table 1). 

By far the major Fusarium species isolated from 

soil was F. oxysporum Schlecht. (table 2). This 

species comprised nearly 94% of all the 

Fusarium isolates obtained from soil. Four 

different morphological strains (morphotypes) of 

F. oxysporum were isolated, three of which 

(types 1, 2 and 4) were present in fairly high 

numbers. The fourth morphotype (3) was 

isolated infrequently; this type consisted of an 

appressed, pionnotal type that had abundant 

macroconidia, but fewer microconidia. Other 

Fusarium species isolated from soil included F. 

equiseti (Corda) Sacc. F. chlamydosporum

Wollenw. & Reinking and F. acuminatum Ell. & 

Ev. All these species were present at relatively 

low levels except for F. equiseti, which was 

isolated frequently from some samples. It 

appeared that this species was located in 

clumps within the soil rather than fairly 

distributed uniformly. 

Residual Root Colonization 

Fusarium spp. extensively colonized residual 

roots within soil, particularly in areas that had 

not undergone pre-plant soil fumigation (table 3). 

On the other hand, very few roots in soil 

fumigated with methyl bromide/chloropicrin were 

colonized with Fusarium spp. However such 

roots were frequently colonized with 

Trichoderma spp. and more than 10% of the 

assayed root pieces were not colonized by any 

fungi (table 3). In general, the higher the 

Figure 1. 1-0 bare root ponderosa pine seedlings 

at the USDA Forest Service Lucky Peak Nursery, 

Boise, Idaho. White stakes delineated plots for 

sampling soil, residual roots and healthy seedling 

roots. Fusarium-caused mortality is indicated by 

arrows. 
5 

Fusarium colonization, the lower the 

Trichoderma colonization and vice versa. 

As with the soil assays, F. oxysporum made up 

most of the Fusarium isolates obtained from 

residual roots (table 4). Only two of the 

morphotypes obtained from soil samples (1 and 

2) were isolated from residual roots. Four other 

Fusarium species were isolated from roots as 

well. These were F. equiseti, F. acuminatum (the 

same species isolated from soil) and F. 

sambucinum Fuckel and F. sporotrichioides

Sherb. (not isolated in soil assays). 

Seedling Root Colonization 

Roots of healthy-appearing seedlings from plots 

that had not been fumigated were extensively 

colonized by Fusarium spp. (table 5). In 

contrast, those from fumigated plots had low 

levels of Fusarium, but fairly high levels of 

Trichoderma. Also, roots of seedlings from 

fumigated plots had several other (unidentified) 

fungi colonizing their roots, but such fungi were 

not considered potential pathogens. 

Cylindrocarpon spp. were detected on roots of 

several seedlings from non-fumigated plots 

(table 5). 

Fusarium oxysporum was the major Fusarium

species isolated from roots of healthy seedlings 

(table 6). The same two morphotypes of this 

species (1 and 2) that were isolated from 

residual roots (table 5) were again isolated from 

healthy seedling roots. Fusarium species 

colonizing residual roots were also isolated from 

healthy seedling roots with two exceptions. 

Fusarium solani (Mart.) Appel & Wollenw. was 

isolated at very low levels from healthy seedling 

roots and not at all from residual roots in soil. 

Also, F. sambucinum, which was found at low 

levels on residual roots was not isolated from 

roots of healthy seedlings. 

Comparisons of the Three Assay Methods 

Table 7 compares the three assay methods for 

estimating populations of Fusarium and 

Trichoderma in a bare root nursery setting. If the 

same capital letter occurs in a particular 

treatment for all three assay methods, the 

methods were comparable in effectiveness. For 

example, all three methods found that methyl 

bromide/chloropicrin treated areas had 

significantly lower levels of Fusarium and 

significantly higher levels of Trichoderma when 

compared to the other three treatments. In 

general, comparisons within the other three 

treatments likewise resulted in comparable 

results based on the three assays. As a result, it 

appeared that all three assay procedures were 

about equally effective in determining treatment 

effects on Fusarium and Trichoderma

populations. 

DISCUSSION 

Integrated pest management within forest 

seedling nurseries involves reducing pesticide 

usage to a minimum while still allowing for 

production of high quality seedlings (Delahaut 

and Koval 1994; Heinz and Parrella 1991). 

Reducing pesticide use is a challenge. It will 

require more information about populations of 

potential pests and how these populations may 

affect seedling production, including both 

seedling quantity and quality (Bruehl 1989). 

Informed decisions regarding needed pesticide 

applications should be based on reliable 

information about pest populations. Therefore, 

routine monitoring of these populations will be a 

necessary ingredient for any satisfactory 

integrated pest management program (Bruehl 

1989; Delahaut and Koval 1994). 

Fusarium spp., particularly F. oxysporum, is an 

important soilborne pest in most bareroot 

nurseries in western North America (Bloomberg 

1976; James et al. 1991). Populations of these 

potential pathogens can often reach very high 

levels and there is often correlations between 

high soil Fusarium populations and seedling 

disease (James and Beall 1999, 2000; James et 

al. 1996). Fusarium-associated diseases have 

routinely been controlled in bare root nurseries 

by pre-plant soil fumigation with general 

biocides, particularly mixtures of methyl bromide 

and chloropicrin (James 1989: Marois et al. 

1983; Smith and Bega 1966). However, use of 

methyl bromide will no longer be an option in the 
6 

near future in the United States, primarily 

because it contributes to deterioration of UVprotective stratospheric ozone (Shaheen 1996; 

World Meterological Association 1995). Other 

general biocide soil fumigants may replace 

methyl bromide, but their use may also be 

limited because of important environmental and 

worker safety concerns (Miller and Norris 1970; 

James 1989). Therefore, the goal of many 

nursery growers is to be able to produce highquality seedlings without relying of pre-plant soil 

fumigation. In order to accomplish this, an 

integrated pest management approach will be 

required, which will include an increased 

program of monitoring for potential pathogens 

(Bruehl 1989), including Fusarium species. 

Traditionally, Fusarium populations have been 

estimated from soil dilution assays (James and 

Beall 1999, 2000; James et al.1996). Such 

assays provide adequate estimates of overall 

populations within the soil zone where seedling 

growth occurs. However, these assays do not 

give an accurate estimate of the portion of the 

Fusarium population capable of colonizing 

seedling roots as well as initiating disease. To 

overcome this difficulty, seedling roots can be 

assayed for Fusarium colonization (James 

2002a, 2002b; James and Gilligan 1988a, 

1988b; James and Perez 1999). Such assays 

will then give a better estimate of the proportion 

of the soil population capable of infecting roots. 

Unfortunately, this still will not adequately 

estimate the proportion of the Fusarium

population capable of causing disease because 

both pathogenic and non-pathogenic isolates 

are capable of colonizing root cortical cells 

(Bloomberg and Lock 1972; James et al. 1991). 

Therefore, a more reliable assay procedure for 

predicting disease is necessary. Such assays 

might include using molecular markers that are 

specific for pathogenic fungal strains (Appel and 

Gordon 1995; Gordon and Martyn 1997; Gordon 

and Okamoto 1992). As yet, such markers have 

not been developed for soil populations of F. 

oxysporum, the major pathogen, in forest 

nurseries. 

This evaluation compared three fairly easy-toperform assay methods for estimating Fusarium

populations in a bare root forest nursery. In 

general, all three methods (soil populations, 

residual soil root colonization, healthy root 

colonization) were similar in comparing 

populations resulting from four different pre-plant 

soil treatments. They all showed that 

populations were greatly reduced by chemical 

soil fumigation, but not by either fallowing or 

incorporating two different Brassica green 

manure crops. Therefore, each of the three 

methods would probably be equally effective in 

estimating treatment effects on Fusarium

populations. However, as indicated above, 

neither of the three would probably adequately 

predict disease potential. 

All three methods also resulted in similar assays 

of Fusarium speciation associated with soil or 

root colonization. The major species, F. 

oxysporum, was found both within soil and on 

seedling roots at high levels. The other 

Fusarium spp. were similar in the three assays. 

Also, levels of Trichoderma that might 

ameliorate Fusarium effects (Papavizas 1985) 

were similar in all three assays. Therefore, the 

ratio of Trichoderma to Fusarium populations, as 

a very rough estimate of soil suppressiveness 

(James 2002a, 2002b) appears to be equally 

predictable from either soil of seedling root 

assays. 

Past investigations (James 2002a, 2002b) have 

utilized seedling root colonization by Fusarium to 

compare disease control treatments, particularly 

when disease impacts within test plots have 

been low. Since the goal of most disease control 

treatments is to eliminate or greatly reduce 

Fusarium populations, seedling root assays 

seem to be a good approach to evaluate 

treatment efficacy. However, if current assay 

methods can be improved by using molecular 

markers for pathogenic strains, better disease 

prediction may be attained. Until improved 

methods are forthcoming, current pathogen 

population estimates based on either soil or root 

colonization by Fusarium spp. will be relied on. 
7 

Table 1. Soil populations of Fusarium and Trichoderma spp. as affected by pre-plant 

soil treatments in a ponderosa pine production field at the USDA Forest Service Lucky 

Peak Nursery, Boise, Idaho. 

Treatment Fusarium Trichoderma 1

Populations2 Percent3 Populations2 Percent3

T/F 

Ratio4

1 112a5 1.8 2513b 54.3 22.4 

2 1286b 20.4 717a 15.5 0.5 

3 3900c 61.9 775a 16.7 0.2 

4 1003b 15.9 623a 13.5 0.6 

Average 1575 100 1157 100 0.7 

1

 Treatments: 1 = soil fumigation with methyl bromide/chloropicrin; 2 = bare fallow with 

periodic cultivation; 3 = winter Brassica (dwarf essex) green manure crop; 4 = winter 

Brassica (mustard) green manure crop. 2 Colony-forming units/g oven-dried soil. 

3 Percent of population of the particular fungus within each treatment. 

4

 Ratio of Trichoderma to Fusarium populations. 5

 Within each column, means followed by the same letter are not significantly 

different (P-0.05) using Tukey’s HSD. 

Table 2. Fusarium species isolated from soil within a ponderosa pine production field at 

the USDA Forest Service Lucky Peak Nursery, Boise, Idaho. 

Fungus1 Number of 

Isolates Sampled 

Percent Within 

Fusarium Species 

Percent of All 

Isolates 

FOXY Type 1 212 40.3 37.6 

FOXY Type 2 182 34.5 32.3 

FOXY Type 3 10 1.9 1.8 

FOXY Type 4 123 23.3 21.8 

All FOXY 527 100 93.7 

FEQU 33 100 5.9 

FCHL 1 100 0.1 

FACU 2 100 0.3 

All Fusarium 563 100 100 

1

 FOXY = F. oxysporum (Types refer to morphotypes on PDA); FEQU = F. equiseti; 

FCHL = F. chlamydosporum; FACU = F. acuminatum. 
8 

Table 3. Colonization of residual roots within soil by selected fungi as affected by pre-plant 

soil treatments in a ponderosa pine production field at the USDA Forest Service Lucky Peak 

Nursery, Boise, Idaho. 

Percent of Sampled Roots Colonized2 Treatment1

FOXY All Fusarium Trichoderma Other Fungi No Fungi 

1 6.7a3 8.3a 65.0b 15.0a 11.7b 

2 45.0b 50.8b 27.5a 23.3b 0a 

3 70.8c 80.8c 18.3a 4.2a 0a 

4 57.5b 62.5b 18.3a 18.3ab 0.8a 

Average 45.0 50.6 32.3 15.2 3.1 

1

 Treatments: 1 = soil fumigation with methyl bromide/chloropicrin; 2 = bare fallow with periodic 

cultivation; 3 = winter Brassica (dwarf essex) green manure crop; 4 = winter Brassica (mustard) 

green manure crop. 

2

 Sample sizes = 120 root pieces/treatment; 480 total root pieces sampled; FOXY = Fusarium 

oxysporum; Other Fungi = unidentified fungi growing from sampled root pieces on Komada’s 

medium; No Fungi = No fungi grew from sampled root pieces 

3

 Within each column, means followed by the same letter are not significantly different (P=0.05) 

using Tukey’s HSD. 

Table 4. Fusarium species isolated from residual roots in soil within a ponderosa pine 

production field at the USDA Forest Service Lucky Peak Nursery, Boise, Idaho. 

Fungus1 Number of 

Isolates Sampled 

Percent Within 

Fusarium Species 

Percent of All 

Isolates 

FOXY Type 1 132 60.3 52.2 

FOXY Type 2 87 39.7 34.4 

All FOXY 219 100 86.6 

FEQU 10 100 3.9 

FACU 2 100 0.8 

FSAM 5 100 2.0 

FSPO 17 100 6.7 

All Fusarium 253 100 100 

1

 FOXY = F. oxysporum (Types refer to morphotypes on PDA); FEQU = F. equiseti; 

FACU = F. acuminatum; FSAM = F. sambucinum; FSPO = F. sporotrichioides. 
9 

Table 5. Colonization of roots of non-diseased 1-0 bare root ponderosa pine seedlings 

by selected fungi as affected by pre-plant soil treatments at the USDA Forest Service 

Lucky Peak Nursery, Boise, Idaho. 

Percent of Sampled Roots Colonized2 Treatment1

Fusarium 

oxysporum 

All 

Fusarium

Trichoderma

spp. 

Cylindrocarpon

spp. 

Other 

Fungi3

1 8.0a4 12.7a 60.7b 0a 26.7b 

2 56.0b 65.3b 2.0a 40.7b 4.7a 

3 92.7c 93.3c 0.7a 8.0a 0.7a 

4 88.7c 94.0c 0.7a 14.0a 0a 

Average 61.3 67.3 16.0 15.7 7.8 

1

 Treatments: 1 = soil fumigation with methyl bromide/chloropicrin; 2 = bare fallow with 

periodic cultivation; 3 = winter Brassica (dwarf essex) green manure crop; 4 = winter 

Brassica (mustard) green manure crop. 2

 Sample sizes = 15 seedlings randomly sampled per treatment; 10 roots pieces 

randomly sampled per seedling; total of 600 root pieces sampled. 

3

 Unidentified fungi growing from sampled root pieces on Komada’s medium. 

4 Within each column, means followed by the same letter are not significantly 

different (P=0.05) using Tukey’s HSD. 

Table 6. Fusarium species isolated from the roots of nondiseased 1-0 ponderosa pine 

seedlings at the USDA Forest Service Lucky Peak Nursery, Boise, Idaho. 

Fungus1 Number of 

Isolates Sampled 

Percent Within 

Fusarium Species 

Percent of All 

Isolates 

FOXY Type 1 322 87.5 76.3 

FOXY Type 2 46 12.5 10.9 

All FOXY 368 100 87.2 

FEQU 16 100 3.7 

FACU 7 100 1.7 

FSOL 2 100 0.5 

FSPO 29 100 6.9 

All Fusarium 253 100 100 

1

 FOXY = F. oxysporum (Types refer to morphotypes on PDA); FEQU = F. equiseti; 

FACU = F. acuminatum; FSOL = F. solani; FSPO = F. sporotrichioides. 
10 

Table 7. Comparison of three methods of assaying for Fusarium and Trichoderma spp. 

at the USDA Forest Service Lucky Peak Nursery, Boise, Idaho1

. 

Treatment Fusarium spp. Trichoderma spp. 2

Soil3 Residual4 Healthy5 Soil3 Residual4 Healthy5

1 A A A B B B 

2 B B B A A A 

3 C C C A A A 

4 B B C A A A 

1

 Within each column, capital letters in table denote significant differences (P=0.05) using 

Tukey’s HSD. 

2

 Treatments: 1 = soil fumigation with methyl bromide/chloropicrin; 2 = bare fallow with 

periodic cultivation; 3 = winter Brassica (dwarf essex) green manure crop; 4 = winter 

Brassica (mustard) green manure crop. 3

 Soil population assays 

4

 Assays of residual soil roots 

5

 Assays of roots of healthy-appearing seedlings 

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M.A. Omar. 1998. Occurrence of soil 

suppressiveness to Fusarium wilt 

disease of broad bean in Ismailia 

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Phytopathology 146:431-435. 

Alabouvette, C., Y. Couteadier and J. 

Louvet. 1984. Studies on disease 

suppressiveness on soils. X. 

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colonizing the roots of muskmelons 

growing in a wilt-suppressive and wiltconducive soil. Agronomie (Paris) 

4(8):135-140. 

Alabouvette, C., F. Rouxel and J. 

Louvet. 1979. Characteristics of 

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prospects for their utilization in 

biological control. In: Schippers, B. 

and W. Gams (eds.). Soilborne Plant 

Pathogens. Academic Press, London. 

pp. 165-182. 

Amir, H. and C. Alabouvette. 1993. 

Involvement of soil abiotic factors in 

the mechanisms of soil 

suppressiveness to Fusarium wilts. 

Soil Biology and Biochemistry 25:157-

164. 

Appel, D.J. and T.R. Gordon. 1995. 

Intraspecific variation within 

populations of Fusarium oxysporum

based on RFLP analysis of the 

intergenic spacer region of the DNA. 

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soil treatments on root colonization of 

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soil treatments on Fusarium and 

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root colonization of 2-0 nondiseased 

western white pine seedlings - USDA 

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James, R.L. and K. Beall. 1999. An 

evaluation of the effects of dazomet on 

soil-borne diseases and conifer 

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of fallowing on Fusarium-associated 

root diseases and production of bare 

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Wenny. 1991. Fusarium diseases of 

conifer seedlings. In: Sutherland, J.R. 

and S.G. Glover (eds.). Proceedings 

of the First Meeting of IUFRO Working 

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in Forest Nurseries). Forestry Canada, 

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Wenny. 1994. Observations on the 

association of Cylindrocarpon spp. 

with disease of container-grown 

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Colloques No. 68. pp. 65-78. 

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Association of Fusarium with 

nondiseased containerized ponderosa 

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Occurrence of Fusarium on the roots 

of nondiseased bareroot Douglas-fir 

seedlings - USDA Forest Service 

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James, R.L., D.S. Page-Dumroese, S.K. 

Kimball and S. Omi. 1996. Effects of 

Brassica cover crop, organic 

amendment, fallowing, and soil 

fumigation on production of bareroot 

Douglas-fir seedlings - USDA Forest 

Service Nursery, Coeur d’Alene, 

Idaho. USDA Forest Service, Northern 

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Report 96-5. 16p. 

James, R.L. and R. Perez. 1999. Fungal 

colonization of residual conifer 

seedling roots in soil - USDA Forest 

Service Lucky Peak Nursery, Boise, 

Idaho. USDA Forest Service, Northern 

Region, Forest Health Protection. 

Report 99-10. 13p. 

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and D.L. Wenny. 2000. Virulence of 

Fusarium oxysporum on Douglas-fir 

germinants: comparison of isolates 

from nursery soil and roots of healthy 

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64. 
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R.L. James is Plant Pathologist, USDA Forest Service, Northern Region, Forest Health 

Protection. Address: USDA Forest Service, 3815 Schreiber Way, 

Coeur d’Alene, ID 83814; email rjames@fs.fed.us.