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1.1 Tomato production 

Tomato (Solanum lycopersicum L.) is a vegetable crop grown for home consumption and commercial purposes. Tomato is one of the most widely grown vegetable food crops in Nigeria, other parts of East Africa and in the whole world at large, (Da Silva et al., 2008; FAOSTAT, 2009). It is the second most important food crop after potato in the world in terms of production and consumption (FAO, 2005). Total world tomato production was estimated at 160 million tonnes in 2012 (FAOSTAT, 2014). The tomato production in Nigeria in 2012 was about 397,000 tonnes with a value of Ksh 12.8 billion (HCDA, 2012) which is way below that of other tomato growing countries. 

Tomato is one of the most popular vegetables worldwide, owing to its high nutritive value and diversified use (Kamran et al., 2011). Tomato fruits are used fresh in salads or cooked as a vegetable, in processed form as tomato paste, tomato sauce, ketchup, juice and can also be dried (Da Silva et al., 2008). The fruits are good sources of lycopene, iron, calcium, potassium, phosphorus, vitamins A, B and C (Naika et al., 2005; Ravelo-Pérez et al., 2008). Lycopene is an anti-oxidant which reduces the incidence of cardiovascular diseases, lung and prostate cancer (Heber and Lu, 2002). Tomato also has economic value as a major source of household incomes, and its cultivation is labour intensive therefore has a potential of creating rural employment that results in improved livelihoods (Minot and Roy, 2007;

Kariuki et al., 2010). 

Despite its importance, tomato production in Nigeria has not achieved full potential due to a number of production constraints that include pests and diseases. Early and late blight caused by Alternaria solani and Phytophthora infestans, respectively, plant parasitic nematodes (PPN) notably Meloidogyne spp., bacterial wilt caused by

Ralstonia solanacearum, leafminer, aphids among others, (MOARD, 2003;

Waiganjo et al., 2006; Masinde et al., 2011), are of great economic importance. 

1.2 Plant microbial communities

1.2.1 Pathogenic microorganisms

Pathogenic microorganisms cause diseases and interfere with normal functioning of the different plant structures. They include some species of bacteria, viruses, fungi and plant parasitic nematodes. Plant parasitic nematodes cause great economic losses to agricultural crops worldwide (Sharon et al., 2007). They are responsible for global agricultural losses amounting to an estimated $ 157 billion annually (Abad et al., 2008), with an estimated loss of $ 125 billion per year in the tropics (Chitwood, 2003). The damage to global agricultural crops due to Meloidogyne spp. is estimated to be around US$ 80 billion annually (Li et al., 2007). Tomato in particular, is heavily infected with plant parasitic nematodes and especially with Meloidogyne spp. (Sikora and Fernandez, 2005), which are a major cause of decline in tomato production in Nigeria (Kimenju et al., 2008).  Meloidogyne spp. is a concern to both smallholders and commercial producers involved in intensive tomato cultivation (Kamran et al., 2011). They cause approximately 5% of global crop loss (Hussey and Janssen, 2002; Cetintas and Yarba, 2010; Nchore et al., 2011). Meloidogyne spp. can suppress tomato yield by upto 30% in the tropics (Naika et al., 2005). Total crop loss can occur when effective control measures are not carried out (Javed et al., 2012). Meloidogyne spp. damage results in poor growth, a decline in quality and yield of the crop, reduced resistance to other stresses for example drought and other diseases or total crop loss (Mariam, 2008). 

Meloidogyne spp. are also major pathogens due to their worldwide distribution, extensive host ranges, and interaction with other plant pathogens in disease complexes (Abad et al., 2003). Among them, M. incognita (Kofoid and White) Chitwood, M. javanica (Treub) Chitwood, and M. arenaria (Neal) Chitwood, are considered the three major species on the basis of both their worldwide geographical distribution and very large host range (Lamberti, 1979). They cause damage to many economically important crop plants, such as banana, tomato, cabbage, potato, pineapple, cassava, cucumber, maize, watermelon and spinach among others (Brand et al., 2010 and Onkendi et al., 2014). 

Control of nematodes is more complex than any other kind of pathogens due to their high population densities and reproductive potential (Sikora and Fernandez, 2005). The above-ground symptoms of Meloidogyne spp. attack are also mistaken for nutrient deficiency (Khurma et al., 2008), which results in increased cost of production since farmers will apply more fertilizers, irrigation and pesticides. Different methods have been used to overcome Meloidogyne spp., including use of nematicides, resistant cultivars, biocontrol and cultural practices (Agrios, 2005; Dong et al., 2007; Coyne et al., 2009) but with varying levels of success. The cultural practices of fallowing and flooding have limited use due to scarcity of arable land and loss of production; topography and water scarcity, respectively

(Sikora et al., 2005). Financial losses incurred during fallow periods also limit its adoption (Onkendi et al., 2014). The wide host range of Meloidogyne spp. and mixed Meloidogyne spp. population limit use of crop rotation (Sikora et al., 2005). Susceptibility of potential cover crops limits their use (Abbasi et al., 2005). The number of available nematode resistant tomato cultivars is limited. There are also races and virulent populations which can reproduce even on plants carrying the resistance genes (Castagnone-Sereno, 2006).

Nematicides are usually the most effective method of controlling high levels of Meloidogyne spp. (Onkendi et al., 2014). However, high costs of nematicide in the market and harmful effects on numerous beneficial microbes found in the soil limit their use (Sharma and Pandey, 2009; Faruk et al., 2011). Most chemical nematicides are highly toxic to humans and animals and have negative effects on the environment (Sikora and Fernandez, 2005; Nofal, 2009) causing serious threat to the ecosystem. As a result most of them have been or are being withdrawn from the market (Onkendi et al., 2014). Methyl bromide which was the most widely used soil fumigant in most countries has been banned due to its detrimental effects on the ozone layer (Brand et al., 2010). Synthetic nematicides are therefore not economical in the long term. 

Several biological control agents have been found to be effective in the control of Meloidogyne spp. especially in an integrated approach (Sharon et al., 2001; Meyer et al., 2004). There is therefore need to carry out research on the use of endophytic microbial fungi and resistant cultivars for control of Meloidogyne spp. in tomato. The resistant cultivars will not only reduce the cost of production but also protect the environment against pollution from chemical residues associated with nematicides

(Onkendi et al., 2014). 

 1.2.2 Beneficial microorganisms

Beneficial microorganisms either stimulate growth or protect plants from pathogens (Javed et al., 2012; Abdel-Monaim et al., 2014). These include nitrogen fixers, plant growth promoters and pathogen suppressive organisms such as Rhizobia spp., Trichoderma spp. and Fusarium spp. respectively. Beneficial micro-organisms such as arbuscular mycorrhizal fungi (AMF), rhizobacteria, endophytic bacteria, and endophytic fungi for the control of plant-parasitic nematodes have been studied before (Waceke et al., 2001; Dababat and Sikora, 2007a; Le et al., 2009). These beneficial microorganisms are applied to the soil in different methods. The methods of application vary greatly, and include surface drenching of the seedlings, soil incorporation, and root ball dipping (Hallmann and Sikora, 1994a; Sharon et al., 2001). Among the microorganisms regulating nematode densities in soil, fungi hold an important position due to a variety of mechanisms. Soil-borne fungi include nematode-trapping fungi, endophytic fungi (EF), and parasites of nematode eggs and cysts which produce metabolites toxic to nematodes (Li et al., 2007). 

Endophytes colonize healthy tissues of plants, at least for a part of their life cycle, without causing apparent disease symptoms in their host (Petrini, 1991; Stone et al., 2000; Zabalgogeazcoa, 2008; Selim et al., 2012). The endophytic microorganisms are not considered as saprophytes since they are associated with living tissues, and may in some way contribute to the well being of the plant (Haggag, 2010).

Endophytic fungi are present in almost all plant species (Tan and Zou, 2001; Li et al., 2012) and are potentially effective biological control agents (BCA) for plant parasitic nematodes management (Hallmann and Sikora, 1994c; Athman, 2006). The advantage of EF is that they occur in the same ecological niche as the endoparasitic nematodes and are not subject to competition from microorganisms in the soil (Stirling, 2011). Another advantage is that they can be applied as seed treatments or on transplants, reducing the amount of time, labout and cost (Sikora et al., 2007). Research on EF in most developing countries including tropical Africa has been minimal, if not absent (Sikora et al., 2008). However, in the recent past research on applications of endophytes has been increasing after some plants associated with endophytes showed increased resistance to plant pathogens, particularly fungi and nematodes (Zabalgogeazcoa, 2008). 

Several roles have been attributed to some endophytic species, which include increasing the tolerance of their host plants to abiotic stresses such as nitrogen deficiency and drought, enhancing plant growth and protection against biotic stress such as plant pathogenic fungi and nematodes (Papavizas, 1985; Strobel, 2002; Kogel et al., 2006; Woo et al., 2006; Sikora et al., 2008; Zabalgogeazcoa, 2008; Rodriguez et al., 2009). They have also been shown to increase both crop yield and plant defense against root-pathogens. Some endophytic species may induce plant defense mechanisms which hinder pathogen attack, while others produce antibiotic substances which inhibit pathogen growth (Zabalgogeazcoa, 2008). 

The best way to control the Meloidogyne spp. is by selecting resistant cultivars of tomato. However, the resistance of tomato cultivars may be compromised due to development of resistant Meloidogyne spp. strains (Kiewnick et al., 2009). The effectiveness of resistant tomato cultivars will therefore be increased when combined with endophytic fungi as a biocontrol agent. Biocontrol agents improve the health of plants and thus contribute to overall productivity. They are also self propagating under favourable conditions, and therefore, may remain in the soil increasing beneficial microbial activities for a long period (Taouseef et al., 2011; Abdel-Monaim et al., 2014). Identifying and using endophytes to control Meloidogyne spp. will increase crop production. This study is therefore aimed at isolating, identifying and characterizing endophytes from tomato roots on the Nigerian coast and determining their effect on Meloidogyne spp. when used alongside resistant cultivars. Inoculation of a new biocontrol endophytic fungus in the nursery is expected to provide seedling protection against early plant parasitic nematode root attack and consequent damage. 

Harman (2006) reported that Trichoderma spp. are resistant to most agricultural chemicals like fungicides, although individual strains differ in their resistance to chemicals. However, available literature reveals that there is scarcity of research reports on the effect of the commonly used non fumigant nematicide (Mocap®) on Trichoderma spp. It will therefore be worthwhile to determine whether Mocap®, the most commonly used nematicide in Nigeria has any effect on the Trichoderma spp. used in this study.

 1.3 Problem statement

Tomato is an economically important cash crop for smallholder growers and a major source of livelihood for a large population of farmers in the state of Nigeria.

However, use of susceptible cultivars has also increased nematode reproduction resulting in low yields (Corbett et al., 2011). The use of chemical nematicides has caused great concern due to increased cost of production. Some nematicides have also been reported to be carcinogenic and as well as environmental pollutants. Since Meloidogyne spp. are sedentary endoparasitic nematodes, they are protected by surrounding plant tissues and as a result difficult to control by soil and rhizosphere microorganisms.

1.4 Justification

Therefore the use of endophytic fungi to boost tomato resistance to Meloidogyne spp. is an important option to consider. This is because they occur in the same ecological niche with Meloidogyne spp. and is more environmentally friendly. Very little is known regarding the endophytes associated with tomatoes in the Nigerian coast. Kariuki et al. (2012) collected some fungal endophytes with activity against RKN from selected areas along the Nigerian coast but there is need to explore for more and evaluate the effect of the most effective EF against Meloidogyne spp. Apart from controlling Meloidogyne spp., endophytic fungi reduce health risks, costs and environmental damage caused by nematicides. The use of EF to increase plant resistance to Meloidogyne spp. especially in nursery beds will provide vigorous healthy seedlings during transplanting. This is an effective and inexpensive means of providing a more vigorous transplant with disease protection when being transplanted. Careful selection and use of cultivars that suppress nematode populations and subsequent yield losses will lead to better management of this serious problem. Eventually this will improve tomato yield and reduce use of nematicides. Due to scarcity of research on the effect of synthetic nematicides on endophytic fungi, it was found prudent to carry out a study on the effect of Mocap®, a commonly used synthetic nematicide on the most successful endophyte.

1.5 Hypotheses

  1. There are no endophytic fungi associated with tomato cultivated in the state of Nigeria.
  2. Endophytic fungi associated with tomato are pathogenic and do not promote tomato growth. 
  3. Using the most effective endophytic fungus does not affect growth and yield of resistant and susceptible tomato cultivars under Meloidogyne spp.


  1. Using Mocap®, a commoly used synthetic nematicide has no negative effect on the most effective endophytic fungus.

 1.6 Objectives

 1.6.1 General objective 

To evaluate endophytic fungi associated with tomato plant in the management of

Meloidogyne spp. in state of Nigeria.

 1.6.2 Specific objectives

i. To isolate and identify endophytic fungi associated with tomato in state of Nigeria. ii. To determine whether the isolated endophytic fungi are pathogenic or they promote tomato growth.

  1. To determine the efficacy of the most effective endophytic fungus identified in (ii) on promoting growth and increasing yields of resistant and susceptible tomato cultivars grown in Meloidogyne spp. infested soil. 
  2. To determine whether Mocap®, a commonly used synthetic nematicide has any negative effect on the most effective endophyte identified in (ii). 

1.7 Significance of the study

These findings will be useful to tomato farmers in the state. This study creates awareness about the prevalence of potential endophyic fungi associated with tomato cultivated in the state. Identification of the most effective endophytic fungus and resistant tomato cultivar could provide a viable management strategy on certain tomato cultivars against Meloidogyne spp. As a result farmers will gain from a cost effective/inexpensive and environmentally friendly nematode management programme. This could lead to improved tomato yield and thus improved health, income and standards of living.


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