




































American International Journal of Agricultural Studies  

Vol. 4, No. 1; 2021 

ISSN 2641-4155   E-ISSN 2641-418X 

Published by American Center of Science and Education, USA 

 

 1  

OCCURRENCE AND IDENTIFICATION OF FUNGAL ROTS IN 

TOMATO (LYCOPERSICUM ESCULENTUM MILL) FRUIT 
 

 

Stephanie Clara Akpeji 

Graduate Student  

Microbiology Department  

University of Ibadan, Ibadan, Nigeria 

E-mail: akpejistephanie@gmail.com 

 

Ossai C. Okolie 

Research Supervisor 

YIIFSWA Project 

International Institute of Tropical Agriculture, Ibadan, Nigeria 

E-mail: c.ossai@cgiar.org 

Ogbole Samson 

Graduate Student 

Biochemistry Department  

Federal University of Agriculture, Abeokuta, Nigeria 

E-mail: ogbolesamson@gmail.com 

 

 

ABSTRACT 

Tomato fruits have high nutritional qualities, but their spoilage by soil-borne pathogens results 

in food poisoning. It is important to isolate and identify the strains of fungi associated with 

tomato rot, to understand their pathogenic state. Seeds of 3 genotypes of tomato were grown in 

both hydroponics and soil systems. It is a factorial experiment laid in a completely Randomized 

Design with four replicates. The number and weight of fruits produced, number of infected and 

uninfected fruits by rots were recorded. Data collected were analyzed using ANOVA and means 

were separated using LSD at 5 % significance level. At harvest, the infected and uninfected fruits 

were harvested and 10 g each were sliced, dissolved in sterile distilled water and were serially 

diluted before plating on sterile Potato Dextrose Agar-PDA and Sabouraud Dextrose Agar-SDA 

media with 2 % streptomycin and incubated at 28oC for 3 – 7 days. Genotypes and substrates 

were significant in the rate of fruit infection, with the Roma tomato having 78.1 % fruit infection 

rate, while the identified fungi from the infected tomato fruits are Aspergillus flavus and Mucor 

racemosu, as no organism grew in the uninfected fruits cultured in both PDA and SDA culture 

media. 

  

Keywords: Infection, Genotypes, Tomato, Fungi, Hydroponics, Pathogenic. 

 

JEL Classification Codes: Q10 

 

 

 

http://www.acseusa.org/journal/index.php/aijas
mailto:akpejistephanie@gmail.com
mailto:c.ossai@cgiar.org
mailto:ogbolesamson@gmail.com


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INTRODUCTION 

Tomato (Lycopersicum esculentum) is a yearly, dicotic, angiospermic short lived perennial plant 

belonging to solanaceae family. The fruit is used globally and it is consumed as both raw and 

processed forms (Moneruzzaman et al., 2008). The fruit contains vitamins (A, B, C and E), 

carbohydrates (fructose and glucose), Minerals (phosphorus, sodium, potassium, calcium, 

magnesium), trace elements (iron, copper, zinc and dietary fibres for humans (Smith, 1994; 

Andrew, 1994) and it is also used as raw materials for agro allied Industries.  

This important staple vegetable is highly perishable and deteriorates easily few days after 

harvest, which could result in loss of needed qualities or total waste of these vegetables. The 

deterioration is mainly caused by microbial contamination, natural ripening processes and 

environmental conditions such as heat and drought (Idah et al., 2007). Over the years, bacteria 

and especially fungi have been reported as causing spoilage and deterioration of nutrients in 

different fruits (Willey et al., 2008).  

Plants are susceptible at all stages of development, but symptoms are most obvious at or 

soon after flowering (Rowe et al., 1995).  Fungi are the most significant and ubiquitous 

pathogens, infecting variety of fruit and causing economically important losses of fruits. 

Different fungal species such as Aspergillus, Fusarium, Penicillium, Mucor, Rhizopus, 

Geotrichum, Phytophthora and Botrytis have been reported as spoilage organisms, and 

Aspergillus niger, Rhizopus stolonifer and Mucor sp. have all been isolated from spoilt tomatoes 

(Sharma, 2012). 

Thousands of spores are produced in spots of infected leaves and are capable of causing 

more infections. When conditions are favorable, fungal fruiting bodies appear as tiny black 

specks in the middle of the spots (Sanoubar & Barbanti, 2017). The colonization process 

involves the ability of the microorganism to establish itself within the produce (Besser et al., 

1993). Pathogenic microorganism in tomato is recognized as a source of potential health hazard 

to man and animals following ingestion, this is due to their production of toxins which are 

capable of causing diseases like respiratory infection, meningitis, gastroenteritis, diarrhoea in 

man (Beuchat, 2006; E, O. E, 2018).  

The contamination of tomato by microorganism could be as a result of poor handling 

practices in the tomato production environment, predominantly due to soil borne disease 

infection (Beuchat, 1996). The above reason coupled with the prolonged cultivation period and 

little yield in the soil system have attracted researchers attention in the hydroponic system 

(Andriolo et al., 1999). This system provides a good platform to identify if the deterioration 

encountered in tomato variety is as a result of environmental infection or a generic disease state, 

coupled with the high crop quality yield as documented (Logendra et al. 2001). 

Hence, due to the serious food safety risk posed by the consumption of pathogenic 

contaminated tomato fruits coupled with the economic damages, it is then important to identify 

and isolate the fungal microorganisms associated with tomato spoilage while using a controlled 

hydroponics system.  

 

MATERIALS AND METHODS 

Planting tomato seeds: Seeds of here tomato genotypes (Roma, San marzano and Red Cherry 

Large) were sourced from the Soilless Farmlab, Abeokuta, Ogun State, Nigeria and raised in 

hydroponics troughs containing dissolved cocopeat for 2 weeks before transplanting. More 

cocopeat blocks were dissolved in water and poured into the 12 hydroponics troughs, while 12 

troughs were filled with topsoil. The raised tomato seedlings were sown directly on the troughs 



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in a completely randomized design with 4 replicates. The plants were watered every 3 days and 

fertigated with dissolved poultry manure (100 mg of poultry manure was dissolved in 100 ml of 

water to give a concentration of 1 mg/ml) every week till harvest. At 2 and 4 weeks after 

transplanting, plant height and number of leaves were taken. The number of days to 50 % 

flowering and days to fruiting, number of fruits produced, average fruit weight, number of 

infected fruits and uninfected fruits were also recorded. The data collected were subjected to 

statistical analysis using ANOVA and the differences in treatment means were separated using 

the least significant differences at 5 % level of significance. 

Collection of rotten tomato fruits: Infected tomato fruits and few uninfected fresh tomato fruits 

were harvested from the plant into a sterilised polythene bag and were taken to the laboratory for 

further analysis. 

Materials Sterilization: All the glass wares were appropriately washed, dried and sterilized in 

the oven at 1600C for one hour. The entire working surfaces were also disinfected with ethanol 

to decrease contaminants.  

Samples Processing: 10 g of the spoilt and uninfected tomatoes was carefully cut with the aid of 

a sterile scalpel and enriched in sterile sabouraud dextrose broth and Potato Detrose broth for 

twenty four hours. Ten fold serial dilutions of the samples were thereafter carried out. 

Isolation of associated fungi: Infected and uninfected Roma tomatoes samples were first 

washed separately with running tap water. 10 g size of spoilt tomatoes were carefully cut with 

the aid of sterile blade then sterilized with 70% ethanol and rinsed in sterile distilled water. 10 g 

of sliced portion was dissolved in sterile distilled water and was serially diluted then plated on 

sterile PDA and SDA medium with 2% streptomycin to inhibit bacterial growth and then 

incubated at 28oC. Incubation was carried out in inverted positions of petriplates for 4-7 days. 

The colonies that developed were subcultured repeatedly on sabouraud dextrose agar and Potato 

Dextrose Agar plates to obtain pure cultures. They were later stored on SDA and PDA slants for 

characterization and identification (Burnett, 1992).  

Characterization and Identification of the Isolates: The pure cultures of the fungi were 

identified on the basis of their colony growth pattern, conidial morphology and pigmentation 

using the slide culture technique and microscopic examination. 

 

RESULTS AND DISCUSSIONS 

Result obtained on the agronomic parameters showed that the height of the Red Cherry Large 

tomato genotype (7.88±0.33) was significantly taller than both Roma (6.74±0.33) and San 

Marzano (5.86±0.33) genotypes at 2 weeks after transplanting. However, at 4 weeks after, the 

height of the genotypes were statistically same. Also, the number of leaves produced by the Red 

Cherry Large (24.63±1.86) at 4 weeks after transplanting was significantly higher than the San 

Marzano (17.63±1.86), however, both San Marzano and the Roma (22.75±1.86) was statistically 

same (Table 1). 

It took the Roma genotype a period of 47.00±0.77 number of days for 50 % of the plants 

to produce flower, which was significantly higher than the period taken by both San Marzano 

(42.50±0.77) and Red Cherry Large (37.25±0.77) genotypes respectively. Also, it took the Red 

Cherry Large genotype 52.13±1.15 days to produce fruit, and it was significantly quicker than 

the 62.13±1.15 and 61.38±1.15 taken by both Roma and San Marzano respectively to produce 



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fruits. The number of fruits produced by the Red Cherry Large genotype (2.38±0.69) was 

significantly higher than the number produced by both Roma (8.00±0.69) and San Marzano 

(6.75±0.69) (Table 2).  

However, in Roma, 6.25±0.31 of the fruits produced were infected by rot, which was 

significantly higher than the 0.00±0.31 recorded in Red Cherry Large and San Marzano 

genotypes respectively. While the 2.00±0.35 number of uninfected fruits recorded in the Roma 

tomato was significantly lower than the Red Cherry Large (9.63±0.35) and San Marzano 

(6.63±0.35) respectively. Then the weight of the fruits produced by the San Marzano 

(20.13±0.93) and Roma (18.28±0.93) was significantly larger than the 8.80±0.93 recorded in the 

Red Cherry Large genotype (Table 2). 

 

Table 1. The height and number of leaves of three genotypes of tomato plants after 2 and 4 

weeks of transplanting 

Genotypes PH2 PH4 NOL2 NOL4 

RCL 7.88a 15.60a 4.63a 24.63a 

Roma 6.74b 14.95a 4.38a 22.75ab 

San Marzano 5.86b 14.96a 4.38a 17.63b 

LSD(0.05) 0.98 3.09 0.51 5.53 

SE 0.33 0.17 1.04 1.86 

 

Means with the same alphabet down the group are not significantly different from each 

other at 5 % level of significance, SE: Standard error, LSD: Least significant differences, PH2 

and PH4: Plant height at 2 and 4 weeks after transplanting respectively, NOL2 and NOL4: 

Number of leaves at 2 and 4 weeks after transplanting respectively.  

 

Table 2. Yield performance and occurrence of fungal rot in three genotypes of tomato 

 

Genotypes DT50%F DTF NOF NoIF NoUF FW 

RCL 37.25c 52.13b 12.38a 0.00b 9.63a 8.80b 

Roma 47.00a 62.13a 8.00b 6.25a 2.00c 18.28a 

San Marzano 42.50b 61.38a 6.75b 0.00b 6.63b 20.13a 

LSD(0.05) 2.28 3.41 2.04 0.91 1.04 2.75 

SE 0.77 1.15 0.69 0.31 0.35 0.93 

 

Means with the same alphabet down the group are not significantly different from each 

other at 5 % level of significance, SE: Standard error, LSD: Least significant differences, DTF: 

Days to fruiting, NoIF: Number of infected fruits, NoUF: Number of uninfected fruits and FW: 

Fruit weight DT50%F: Days to 50 % flowering. 

Table 3 showed that at 2 and 4 weeks after transplanting, the height of the plants and 

numbers of leaves produced were insignificant in terms of the substrate they were grown. Also, 

the number of days taken by 50 % of the plants to produce flowers, to produce fruits, number of 

infected fruits and the average fruit weight were significantly same in both topsoil and cocopeat 

substrates respectively. However, the number of uninfected tomato fruits in the cocopeat 



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substrate (7.00±0.28) was significantly higher than the fruits produced in the soil (5.17±0.28) 

(Table 4). 

 

Table 3. Effect of cocopeat and topsoil substrates on the plant height, number of leaves of 

different genotypes of tomato  

Substrate PH2 PH4 NOL2 NOL4 

Soil 6.83a 15.83a 4.58a 21.42a 

Cocopeat 6.82a 14.52a 4.33a 21.92a 

LSD(0.05) 0.8 2.52 0.42 4.52 

SE 0.27 0.14 0.85 1.52 

     Source of variation 

    Genotypes 8.15* 1.11ns 0.17ns 105.04* 

Substrates 0.02ns 10.27ns 0.38ns 0.82ns 

Genotypes*Substrates 0.02ns 1.31ns 0.50ns 0.15ns 

 

Means with the same alphabet down the group are not significantly different from each 

other at 5 % level of significance, SE: Standard error, LSD: Least significant differences, PH2 

and PH4: Plant height at 2 and 4 weeks after transplanting respectively, NOL2 and NOL4: 

Number of leaves at 2 and 4 weeks after transplanting respectively, DT50%F: Days to 50 % 

flowering, DT50%F: Days to 50 % flowering, *: 5 % level of significance and **: 1 % level of 

significance. 

 

Table 4. Effect of cocopeat and topsoil substrates on the yield and occurrence of fungal rot in 

tomato plant 

Substrate DT50%F DTF NOF NoIF NoUF FW 

Soil 41.58a 58.25a 8.75a 1.75a 5.17b 14.94a 

Cocopeat 42.92a 58.83a 9.33a 2.42a 7.00a 16.53a 

LSD(0.05) 1.86 2.78 1.66 0.74 0.85 2.25 

SE 0.63 0.94 0.56 0.25 0.28 0.76 

 

 

     Source of variation  

     Genotypes 190.50** 248.17** 69.79** 104.17** 118.04** 295.27** 

Substrates 10.67ns 2.04ns 2.04* 2.67ns 20.17** 15.05ns 

Genotypes*Substrates 0.17ns 2.17ns 1.79ns 2.67* 12.04** 38.76* 

 

Means with the same alphabet down the group are not significantly different from each 

other at 5 % level of significance, SE: Standard error, LSD: Least significant differences, 

DT50%F: Days to 50 % flowering, DTF: Days to fruiting, NoIF: Number of infected fruits, 

NoUF: Number of uninfected fruits and FW: Fruit weight, *: 5 % level of significance and **: 1 

% level of significance. 



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Figure 1 a and b: Roma tomato plants with infected fruits 

   

 

Figure 2. (A):  Pour plate of Serially diluted infected tomato (B): Aspergillus flavus on PDA 

plate (C, D and E ): Mucor racemosus on SPA plate. 

The growth of the three genotypes of tomato used in this study developed at same rate; 

irrespective of the substrate they were grown. This shows that growing tomato in a hydroponics 

A B 

A B 

D E C 



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system that is fertigated optimally is as effective as tomato soil farming and this supports the 

work of Flávio et al. (2018) and Ossai et al. (2020). The higher number of fruits produced by the 

Red Cherry Large tomato could be the reason behind the small fruit weight comparable to Roma 

and San Marzano fruits which produced larger fruit sizes but with a small number of fruits per 

plant, either grown in a hydroponics system or in soil. However, the different tomato genotypes 

were developed for different purposes (Baisden, 1994). 

Despite the large fruit size produced by the Roma tomato, about 78.1 % of the produced 

fruit developed block rots at the base, while only 21.9 % of the fruit were without rot. Further 

investigation of the causal organism of the rots indicated that the tomato fruits were 

contaminated by fungal pathogens. Fungi such as Aspergillus flavus, Mucor racemosus were 

isolated from the infected fruits. This is in agreement with the findings of Kutama et al. (2007), 

who also reported numerous fungal pathogens linked with tomato.  

The results also showed that tomatoes can be contaminated by fungal pathogens such as 

Aspergillus flavus and Mucor racemosus even before harvesting. Although Mbajiuka and Enya 

(2014) also isolated Aspergillius spp, Penicillum spp and Saccharomyces cerevisiae from spoilt 

tomatoes. Wogu and Ofuase (2014) also isolated Aspegillius spp, Penicillum spp, Fusarium spp 

and Saccharomyces spp from spoilt tomato fruits. Mbajiuka and Enya (2014) also isolated 

Aspergillius spp, Penicillum spp and Saccharomyces cerevisiae from spoilt tomato.  

Fungal contamination of tomatoes is mainly as result of high water content, environmental 

surroundings, method of handling, type of storage facilities and the quality of the tomatoes 

(Logendra et al., 2001). Being that three genotypes were evaluated and only Roma tomato was 

infected could point the infection to be genotypic prone. However, it was more prevalent in the 

soil farming system than the hydroponics system which means the prevalence can be reduced 

below economic damage level by proper sterilization protocols as Beuchat (1996) reported that 

the fungal rots can be soil borne. 

 

CONCLUSIONS AND RECOMMENDATIONS 

Tomato fruits have high nutritional qualities, but their spoilage by fungi results in loss of 

economic resources as well as food poisoning. These fungi obtained in this study causes 

intoxication of mycotoxins which are harmful to human health.  Aspergillus spp. is a source of 

Ochratoxin which is a potent Carcinogen; as a result substandard tomatoes must not be eaten but 

disposed off, because consumption of spoilt tomatoes could be detrimental to human health. 

Farmers are advised to ensure that the tomatoes seeds are healthy before planting and only 

tomatoes in good condition should be harvested and dispatched to the end users to reduce the 

danger of these toxins that are detrimental to health. However, proper soil sterilization 

techniques is essential in reducing the spread of the fungal rot in tomato to the lowest minimum, 

and it is also recommended that more evaluation should be carried out to ascertain a host-plant 

relationship between the fungal rots and Roma tomato as other genotypes evaluated were not 

infected by the rots. 

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