The threat of root-knot nematodes (Meloidogyne spp.) in Africa: a review



Meloidogyne species pose a significant threat to crop production in Africa due to the losses they cause in a wide range of agricultural crops. The direct and indirect damage caused by various Meloidogyne species results in delayed maturity, toppling, reduced yields and quality of crop produce, high costs of production and therefore loss of income. In addition, emergence of resistance-breaking Meloidogyne species has partly rendered various pest management programmes already in place ineffective, therefore putting food security of the continent at risk. It is likely that more losses may be experienced in the future due to the on-going withdrawal of nematicides. To adequately address the threat of Meloidogyne species in Africa, an accurate assessment and understanding of the species present, genetic diversity, population structure, parasitism mechanisms and how each of these factors contribute to the overall threat posed by Meloidogyne species is important. Thus, the ability to accurately characterize and identify Meloidogyne species is crucial if the threat of Meloidogyne species to crop production in Africa is to be effectively tackled. This review discusses the use of traditional versus molecular-based identification methods of Meloidogyne species and how accurate identification using a polyphasic approach can negate the eminent threat of root knot nematodes in crop production. The potential threat to Africa posed by highly damaging and resistance-breaking populations of ‘emerging’ Meloidogyne species is also examined.


In the recent past, the use of nematicides has led to a significant reduction of Meloidogyne spp. populations in crop production. However, due to their toxicity and adverse effects on the environment, many nematicides have been or are currently being withdrawn from the market. This has now propelled Meloidogyne spp. to the forefront as important pathogens of many crops and other plants. In fact, in a 2013 survey for the journal Molecular Plant Pathology of the top ten plant parasitic nematodes, Meloidogyne spp. collectively were voted at the top of the list (Jones et al., 2013). This article assesses the current threat of Meloidogyne spp. to crop production, with a specific focus on Africa. The importance of an integrated approach towards accurate species identification is also discussed, together with current and future Meloidogyne spp. management strategies.

Meloidogyne Species Present in Africa

There are currently nearly 100 recognized Meloidogyne spp., with 22 of these species reported to be present in Africa (Table 1). Historically, Meloidogyne spp. have been divided into major and emerging species. According to Moens et al. (2009), Marenaria, Mincognita, M. javanica (occurring in tropical regions) and M. hapla (occurring in temperate regions) are considered to be the four major Meloidogyne spp. However, these authors consider a further five species as emerging species. These are: Meloidogyne chitwoodi, M. fallax, M. enterolobii, M. minor and Mparanaensis. In Africa, M. arenaria, M. javanica and M. incognita are regarded as the most dominant species, reported in 26, 36 and 37 different countries across the continent, respectively (IITA, 1981; De Waele & Elsen, 2007). Collectively, these three species have been reported to cause damage in economically important crop plants such as sweet potato, banana, tomato, cabbage, potato, pineapple, cassava, maize, tobacco and cowpea, as well as others such as okra (Abelmoschus esculentus), papaya, buchu (Agathosma betulina) and African spinach (for a full list of reported hosts refer to Table 1). Three of the five emerging species, M. chitwoodi, M. enterolobii and M. fallax, are also reported from Africa (Table 1). For example, the resistance-breaking apomictic species M. enterolobii has been isolated from Burkina Faso, the Democratic Republic of Congo, Malawi, Mozambique, Senegal, South Africa and Togo, causing damage in potato and guava (M. Marais, unpublished data; Onkendi & Moleleki, 2013b). Meloidogyne chitwoodi and M. fallax have been reported to cause damage of various crop plants in South Africa and Mozambique. Other Meloidogyne spp. affecting economically important crop plants in Africa include those that infect coffee (Mafricana, Mdecalineata, Mmegadora and Moteifai); cassava (Mexigua, Mchitwoodi, Mmegadora and Mnaasi); sugarcane (Mhispanica and Mkikuyensis); and cotton (Macronea). A number of Meloidogyne spp. have also been reported on trees and woody shrubs, such as Methiopica infecting black wattle (Acacia mearnsii); Mmorocciensis infecting peach trees; Mpartityla infecting pecan and walnut trees; Mpropora reported on black nightshade (Solanum nigrum); and Mvandervegtei, which has been reported on woody plants and coastal forests. Finally, two Meloidogyne species, Mgraminicola and Mkikuyensis, were reported to affect members of the Poaceae family, Paspalum spp. and kikuyu grass (Pennisetum clandestinum), respectively.

Table 1. Meloidogyne species reported from various parts of Africa
Meloidogyne sp.Country/regionCrop(s) affectedReferences
  1. a

    The SAPPNS database was made available courtesy of M. Marais (ARC, South Africa).

M. acronea Kenya, South Africa, MalawiCotton, pigeon pea, sorghum, millet, grasses, pea, bulrush, okra, potato, tomatoWhitehead & Kariuki (1960); Hunt & Handoo (2009)
M. africana Kenya, Sudan, TanzaniaCoffeeWhitehead (1959); Eisenback (1997)
M. arenaria Algeria, Cote d'Ivoire, Egypt, Gambia, Ghana, Liberia, Libya, Madagascar, Malawi, Mauritius, Morocco, Mozambique, Nigeria, Sao Tome and Principé, Senegal, South Africa, Sudan, Tanzania, Uganda, ZimbabweDate palm, peach, potato, tobacco, tea, carrot, tomato, lettuce, cucumber,aubergine, cotton, soybean, pineapple,pyrethrum, banana, papaya, pepper, cowpea, okra, velvet beanIITA (1981); CABI (2003)
M. chitwoodi South Africa, MozambiquePotato, cassava, groundnut, wheat soilKleynhans et al. (1996); Fourie et al. (2001b);Coyne et al. (2006b)
M. decalineata Tanzania, Sao TomeCoffeeWhitehead (1968); Lordello & Fazuoli (1980)
M. enterolobii Malawi, Senegal, South Africa, Cote d'Ivoire, Burkina Faso, Democratic Republic of CongoPotato, guavaM. Marais (unpublished data); Onkendi & Moleleki (2013a,b)
M. exigua MozambiqueCassavaCoyne et al. (2006b)
M. ethiopica Ethiopia, Mozambique, Tanzania, Zimbabwe, South AfricaTomato, bean, black wattle (Acacia mearnsii), cabbage, tobacco, pumpkin, pepper, macadamia, pineapple, carrot, home gardens, natural veld, potatoWhitehead (1968, 1969); CABI (2005)
M. fallax South AfricaGroundnutFourie et al. (2001b)
M. graminicola South AfricaPaspalum spp.Kleynhans (1991)
M. hapla Algeria, Cote d'Ivoire, Egypt, Kenya, Libya, Malawi, Morocco, Nigeria, South Africa, Tanzania, Uganda, ZimbabwePotato, date palm, groundnut, native plants and numerous cropsFourie et al. (2001b); CABI (2002a)
M. hispanica Burkina Faso, Malawi, South AfricaGranadilla, sugarcane, Ficus spp., ornamental crops, grapevineKleynhans (1991)
M. incognita Algeria, Angola, Botswana, Burkina Faso, Cameroon, Congo, Democratic Republic ofCongo, Cote d'Ivoire, Egypt, Ethiopia, Gambia, Ghana, Guinea, Kenya, Liberia, Libya, Madagascar, Malawi, Mauritania, Mauritius, Morocco, Mozambique, Namibia, Niger, Nigeria, Reunion, Senegal, Seychelles, Somalia, South Africa, Sudan, Tanzania, Tunisia, Uganda, Zambia, ZimbabwePotato, grapevine, maize, date palm, tomato, tobacco, cowpea, upland rice, soybean, papaya, pepper, aubergine, cauliflower, okra, cabbage, Chinese cabbage, onion, watermelon, African spinach, coconut, mango, citrus, guava, yam, cassava and numerous cropsIITA (1981); CABI (2002b); Kwerepe & Labuschagne (2004); SAPPNS databasea
M. javanica Aldabra, Algeria, Angola, Botswana, Burundi, Comoros, Democratic Republic of Congo, Cote d'Ivoire, Egypt, Eritrea, Gabon, Gambia, Ghana, Kenya, Liberia, Libya, Madagascar, Malawi, Mauritania, Mauritius, Morocco, Mozambique, Namibia, Nigeria, Reunion,Rwanda, Senegal, South Africa, Sudan, Tanzania, Tunisia, Uganda, Zambia, ZimbabwePotato, buchu (Agathosma betulina), sugarcane, banana, yam, sweet potato, date palm, tobacco, broad bean, celery,tomato, upland rice, aubergine, cabbage, Chinese cabbage, cassava and numerous cropsIITA (1981); CABI (2002b); SAPPNS databasea
M. kikuyensis Kenya, South Africa, TanzaniaKikuyu grass, sugarcaneDe Grisse (1960); Kleynhans (1991)
M. megadora Angola, SudanCoffee, carrot, bananaWhitehead (1968); Eisenback (1997)
M. morocciensis MoroccoPeachRammah & Hirschmann (1990)
M. naasi MozambiqueCassavaCoyne et al. (2006b)
M. oteifai Democratic Republic of CongoCoffeeElmiligy (1968)
M. partityla South AfricaPecan, walnutKleynhans (1991)
M. propora Aldabra AtollBlack nightshade (Solanum nigrum), Cyperus obtusiflorusSpaull (1977)
M. vandervegtei South AfricaUnidentified woody plant from coastal forestKleynhans et al. (1996)

The number of Meloidogyne species listed in Table 1 is most certainly not exhaustive, due to paucity of data in many regions in the continent. Because the three major species (M. arenaria, M. incognita and M. javanica) are widespread and well-studied, this could have led to bias against accurate identification of the emerging species. Consequently, it is possible that many of the species listed as one of the major species could have been incorrectly diagnosed. Hence, it is conceivable that the potential impact of new and emerging species has been grossly understated. Similar problems of misidentified Meloidogyne species have been previously reported. For instance, for many years both M. paranaensis and M. enterolobii were misidentified as Mincognita (Yang & Eisenback, 1986; Carneiro et al., 1996). The wide adoption of molecular diagnostic tools in the future is anticipated to lead to an increase in the number of species as more cases of misidentification are made known, or new species are recorded. It is important that the different Meloidogyne species are accurately identified in order to be able to evaluate their impact. It is also important to determine which quarantined Meloidogyne spp. are currently present in Africa and the extent of their distribution. If present, are they being accurately identified? Can new diagnostic tools based on molecular technology be employed together with classical methods to carry out accurate identification? For instance, Onkendi & Moleleki (2013a,b) have recently demonstrated the use of molecular approaches in accurately identifying various Meloidogyne spp. present in potatoes from South Africa. This information will enhance knowledge of the current population densities and distribution of different Meloidogyne species, and guide farmers in the implementation of integrated pest management strategies.

Economic Impact

Meloidogyne spp. cause an estimated annual loss of $157 billion globally (Abad et al., 2008). However, in most cases, the impact of Meloidogyne spp. is grossly underestimated. This is more so in Africa than anywhere else in the world. Hence it is probable that the overall annual losses due to these pathogens are much higher. In many crop producing regions in Africa, there has been no comprehensive assessment that focuses specifically on the economic impact of Meloidogyne spp. (Coyne et al., 2006a). There are several factors that have led to the scanty availability of information on the economic impact of Meloidogyne spp. across Africa. First, there is a general lack of awareness of the effect of Meloidogyne spp. in crop production. As a result, these pathogens tend to be overlooked. Secondly, the long-term use of nematicides has led to an underestimated effect of Meloidogyne spp. However, with diminishing options for use of nematicides, Meloidogyne spp. problems are steadily beginning to resurface. Finally, the lack of information can be attributed to the acute lack of resources (both financial and human) to initiate large-scale projects necessary to fully assess the Meloidogyne spp. situation in Africa (De Waele & Elsen, 2007). Even though in general there is limited information on the impact of Meloidogyne spp. in crop production in Africa, there is growing evidence that suggests that the problem of Meloidogyne spp. in most farms across the continent is a significant threat to crop production. Furthermore, through several projects, among others the International Meloidogyne Project (IMP), it is evident that Meloidogyne spp. cause considerable damage to various crops (Fig. 1; Jones, 2005; Coyne et al., 2006b).

Figure 1.

Galls and other symptoms caused by various Meloidogyne species on select crops. (a) Galls on tomato roots caused by Meloidogyne enterolobii. (b) Galls on grenadella roots caused Meloidogyne incognita. (c) Galls on cucumber roots caused by Meloidogyne javanica. (d) Galls and damage symptoms on carrot caused by Meloidogyne arenaria and M. incognita. (e) Galls on beetroot roots caused by M. javanica and M. incognita. Pictures (d) and (e) represent damage caused by Meloidogyne species during co-infection.

Based on the level of nematode populations, Meloidogyne spp. can cause high levels of crop loss during growth, increase the cost of production through increased fertilizer application and control programmes, and also significantly reduce post-harvest yields (Fig. 2). Crop losses of 30% or more in tobacco farms in some parts of Tanzania have been reported (Whitehead, 1969). In addition, crop losses of 50% in pyrethrum flower yields and a decrease in pyrethrin content in Kenya has also been attributed to Meloidogyne spp. infection (IITA, 1981). During surveys carried out by Fourie et al. (2001a) on soybean in South Africa, Meloidogyne spp. that significantly hamper soybean production were observed in 16 of the 17 different localities sampled by the authors. In South Africa alone, potato production losses associated with plant parasitic nematode species in 1989 were estimated to be 16·7%, accounting for $7 million annually (Keetch, 1989). Speijer & Kajumba (2000) identified Meloidogyne spp. and other plant parasitic nematodes as the phytoparasites that are responsible for 50% of banana loss in Uganda. Coyne et al. (2006a) also found that 14·4% of galling on the yam tubers on sale in Mali was as a result of Meloidogyne spp. infection. Rejection of inferior quality crop produce both locally and internationally, increased scarcity of clean and healthy propagating materials and predisposing of crops to secondary infections by other organisms, especially soilborne pathogens, are also some of the problems associated with Meloidogyne spp. infection (Powers et al., 2005). For example, interactions between Meloidogyne spp. and pathogens such as Fusarium spp. are well documented, while there may still be many other interactions which are less well studied (Siddiqui et al., 2010; Mongae et al., 2013).

Figure 2.

Damage caused by Meloidogyne spp. in a tomato field in Mwea, Kenya.

The presence of Meloidogyne spp. populations puts agricultural production in Africa at a significant risk given the fact that most farmers do not have accurate information on the actual Meloidogyne spp. present on their farms (Onkendi & Moleleki, 2013a). This, coupled with the ban and restrictions on some of the effective chemical compounds (such as methyl bromide) against a wide range of Meloidogyne spp. and lack of alternative strategies which are effective, may greatly contribute to incidents of food crisis across the continent. Meloidogyne fallax and M. chitwoodi are listed as quarantine organisms in Europe as per the EC Directive of 2000/29/EC and EPPO region (Viaene et al., 2007; EPPO, 2009; Wesemael et al., 2011). Furthermore, M. enterolobii is also listed as a quarantine organism across Europe (EPPO, 2011). This compounds the problems farmers in African countries face when exporting their farm produce, especially to the European markets, as the presence of these pathogens in their produce leads to rejection at international markets (Powers et al., 2005). Resistance-breaking species such as M. enterolobii may also contribute to a reduction in forest cover which may affect water catchment zones and therefore access to water in the long term. This may happen in isolation or in conjunction with highly damaging forestry pathogens. Forest cover cushions various countries from adverse environmental conditions such as floods and drought.

Species Identification

Many African countries have inadequate diagnostic capabilities to carry out reliable pathogen diagnostic services (Ogundiran, 2005). This has led to fragmented data on the presence and distribution of Meloidogyne spp. which has serious implications on various aspects of agriculture. There is the threat of introduction of new and possibly aggressive Meloidogyne spp. to an area, higher cost implications through management strategies that target the wrong organism, and loss of revenue due to produce being denied entry into other countries based on the presence of a quarantine organism. Historically, nematologists have relied solely on morphological and morphometrical characters to identify Meloidogyne spp. The earliest use of isozymes as biochemical methods to identify Meloidogyne spp. was published by Esbenshade & Triantaphyllou (1985), and according to Blok & Powers (2009), isozymes are a convenient first stage approach in determining Meloidogyne spp. biodiversity. Antibodies, both polyclonal and monoclonal, have been produced for Meloidogyne spp. diagnostics, but the use of antibodies is limited to a few examples as it has, according to Blok & Powers (2009), been superseded by DNA-based diagnostics (Davies et al., 1996; Tastet et al., 2001). In recent years, identification methods that are DNA-based have gained popularity and this has led to a combination of both morphological, biochemical and molecular methods to describe and identify nematodes (Karssen et al., 2004; Castillo et al., 2009).

Morphological and morphometric characteristics

The use of morphological and morphometric characters has traditionally been the most common method used by diagnosticians as the preliminary and routine method of identifying Meloidogyne spp. These methods rely heavily on the shape of body, labial region, stylet length, shape of stylet cone, basal knobs and nature of perineal pattern in female labial region and characteristics of size, stylet length, distance of the dorsal gland orifice (DGO) from the stylet base for males and J2 juveniles (Kleynhans, 1991; Hunt & Handoo, 2009). According to Hunt & Handoo (2009), clear interspecific boundaries that all Meloidogyne spp. diagnosticians yearn for are becoming increasingly obscure due to factors such as existence of obscure species and an increasing occurrence of new or emerging species. These authors also cite variable morphometrics, conserved morphology host effects, intraspecific variation, and parthenogenetic mode of reproduction as obscuring factors. This problem is best illustrated by the fact that the existence of what is known as the incognita type perineal pattern is now acknowledged to occur in a number of species (Hunt & Handoo, 2009). Hence, this underscores the importance of an integrated diagnostic approach in identification of Meloidogyne spp. (Landa et al., 2008; Blok & Powers, 2009).

Isozyme phenotypes

Isozymes are variants of a particular enzyme. Isozyme phenotypes have been used for routine identification of various Meloidogyne spp. in several parts of Africa despite the fact that they are restricted to the adult female stage of development (Esbenshade & Triantaphyllou, 1990; Muturi et al., 2003). The adult female is the suitable stage because it is associated with the expression of a given gene product. The procedure is easy and quick to perform, and given the fact that reference standards for certain Meloidogyne spp. (usually M. javanica) are used, it is easy to identify various common Meloidogyne spp.

The limitations of diagnostic tests based entirely on isozyme phenotypes include lack of capacity to use other stages of development (second stage juveniles and eggs) and lack of a wide array of standards to compare results (Molinari et al., 2005; Wesemael et al., 2011). In some cases, it is difficult to determine and differentiate band sizes between different species during identification. This has necessitated the use of more than one enzyme. Malate dehydrogenase (mdh) is known to separate M. hapla from M. incognita, M. arenaria and M. javanica, whereas glutamate dehydrogenase can separate M. incognita from M. javanica, M. arenaria and M. hapla (Esbenshade & Triantaphyllou, 1990; Muturi et al., 2003). As a result of these limitations, isozymes may be used as an initial step in surveys aimed at the identification of Meloidogyne spp.

Molecular-based identification methods

Molecular-based methods used in nematode diagnostics are usually based on nucleic acid studies. Most of these methods, particularly the DNA-based ones, are known to be robust, sensitive, specific and reliable in detecting and distinguishing various Meloidogyne spp. compared to morphological or biochemical methods (Powers et al., 2005; Berry et al., 2007). Based on this, several molecular methods have been employed to accurately identify various Meloidogyne spp. For the purpose of this review, these will be grouped into gel or sequence-based methods, and other methods that do not strictly fall into either of these categories.

Gel-based molecular diagnostic methods include random amplified polymorphic DNA (RAPD), sequence characterized amplified region markers (SCAR-PCR), restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLP) and microsatellites. The RAPD method employs short sequence RAPD primers to distinguish several Meloidogyne spp. on the basis of species characteristic patterns. These characteristic patterns can be harnessed to design species-specific markers and/or primers (SCAR-PCR) (Zijlstra, 2000; Fourie et al., 2001b). Using RFLPs, genomic (g) DNA is digested with restriction endonucleases followed by probe hybridization to generate polymorphisms. AFLPs generate unique fingerprints of gDNA through selective PCR amplification of restriction digested gDNA fragments that have been ligated to specific adaptors. Both RFLP and AFLP have previously been used for identification of different Meloidogyne spp. (Curran et al., 1986; Williamson et al., 1997; Fargette et al., 2005). Microsatellites are high tandem repeats of short sequences which are often located in the heterochromatin, centromeric and telomeric regions of the chromosomes. Polymorphisms generated using microsatellites are due to differences in copy numbers or sequence lengths (Mestrovic et al., 2006). The use of microsatellites (satDNA) to discriminate various Meloidogyne spp. has been explored in a number of studies (Piotte et al., 1994; Castagnone-Sereno et al., 1998; Mestrovic et al., 2006).

The advantages of gel-based methods are that they are simple to perform and they are not limited to a certain stage of development (Blok & Powers, 2009). Despite being simple, there are some challenges associated with these methods including low sensitivity, poor band visibility in some cases, lack of reproducibility between different laboratories and the need to use large amounts of DNA to achieve desired results (Adam et al., 2007; Blok & Powers, 2009). A further challenge, especially in the case of RFLP and AFLP, is the need to, at times, use radioactive materials. These challenges are not just limited to Africa. This is a global problem that would require global cooperation between researchers for cross-validation of samples if these methods are to be used effectively. However, given the stated lack of financial and other resources, this is a particularly big challenge for African researchers, as validation would incur huge costs of shipping DNA samples across the globe.

Sequenced-based diagnostics rely, although not exclusively, on obtaining sequences of specific gene regions and comparing them with reference sequences deposited in public databases. Sequence-based methods include the use of mitochondrial DNA (mtDNA) and ribosomal DNA (rDNA) (Blok & Powers, 2009). The mtDNA is one of the regions usually targeted for identifying various Meloidogyne spp. (Hyman, 1990; Hugall et al., 1994; Hyman & Whipple, 1996). Multiple copies present in the mtDNA in each cell offer a ready template for PCR assays and other molecular studies (Brown et al., 1979). The low level of recombination associated with mtDNA, coupled with high rates of evolution, provides a unique region that has also been used for phylogenetic studies and for studying different Meloidogyne spp. (Blouin, 2002; Blok & Powers, 2009). The cytochrome oxidase subunit I (COI) within the mitochondrial DNA is currently being viewed as a potential gene for barcoding all Meloidogyne spp. and for studying evolutionary trends and intraspecific variations within Meloidogyne populations (Powers, 2004; Blok, 2005). Based on this barcoding concept, other studies have suggested the clustering of nematodes into molecular operational taxonomic units (MOTUs) which have individuals with highly similar sequence homology. These sequences are based on a specific gene which may not necessarily be the COI of the mtDNA (Floyd et al., 2002).

Molecular sequence-based identification can also be based on the ribosomal DNA (rDNA) to identify various Meloidogyne spp. The 18S, 28S (26S), 5·8S coding genes, the internal transcribed spacer (ITS), the external transcribed spacer (ETS) and the intergenic spacer (IGS) regions are usually employed in diagnostics and phylogenetic studies (Blok et al., 1997). The repetitive nature of rDNA provides a better template for PCR work due to more variations among Meloidogyne spp. than other regions such as the D2–D3 (Palomares-Rius et al., 2007). Variations in sequence occur between regions of the rDNA that code for 18S, 28S (26S) and 5·8S, and these repetitions and sequence variations can be exploited for identification of Meloidogyne spp.

The use of sequence-based methods coupled with depositing of these sequences into publicly available databases presents huge opportunities for many African researchers for the identification of Meloidogyne spp. The advantage of this is that obtaining and shipping voucher specimens or reference DNA from all over the world is not required for comparisons because analysis can be done using platforms linked to international databases through the internet. This is also a huge benefit to other researchers who may identify new Meloidogyne spp. and may need to compare their unique sequences with those deposited in databases for similar Meloidogyne spp. identified in other countries. For an African researcher, one of the major factors hindering the wide adoption of sequence-based technologies would be easy access and affordability of sequencing.

The final category of molecular-based diagnostic methods discussed is that which, for the purpose of the review, has been deemed to be neither gel- nor sequence-based. These include microarrays, qPCR and high resolution melt curves (HRMC). Microarrays consist of oligonucleotide probes that have been spotted onto a solid support (microarray chip) to which fluorescently labelled gDNA samples are hybridized for diagnosis. The first study to demonstrate the use of microarray chips for Meloidogyne spp. identification was reported by François et al. (2006). Although not yet widely adopted for identification of Meloidogyne spp., microarrays are useful in Meloidogyne spp. diagnostics due to their potential for high throughput sample analysis. However, the major challenge with microarrays is that they are costly for non-established, resource-poor laboratories. There are also other global challenges associated with microarrays such as sensitivity and specificity which will need to be properly optimized before they can be widely used (Blok & Powers, 2009).

As molecular technology continues to advance, the entry of real-time PCR (qPCR) has significantly improved identification of Meloidogyne spp. This method has increased sensitivity and specificity, and simultaneous detection of more than one Meloidogyne spp. can be performed within a single qPCR assay. In addition, the method can be performed within a short period due to the fact that there are no post-PCR procedures. Apart from detection, qPCR can be used in the quantification of the amount of nucleic acid present, and in genotyping through the generation of high resolution melt curves (HRMC) that are only specific to certain species (Bates et al., 2002; Holterman et al., 2012). To this end, some progress involving different Meloidogyne spp. has been made in using this approach (Zijlstra & Van Hoof, 2006; Berry et al., 2008; De Weerdt et al., 2011; Holterman et al., 2012). All these studies have demonstrated that the use of qPCR in Meloidogyne spp. identification is highly specific and efficient.

It would be futile to attempt to make specific recommendations regarding the appropriateness of each of the three categories of molecular-based methods discussed here for laboratories within the region. However, it would appear that of all the methods discussed, gel-based methods such as SCAR-PCR provide a low cost and effective method of Meloidogyne spp. delineation. Nevertheless, because there are a number of new and/or emerging Meloidogyne spp., some of which cannot be accurately identified using gel-based methods, the choice of diagnostic methods will ultimately have to be decided by each individual laboratory. This choice will be further influenced by the resources available to the various laboratories as well as the level of accuracy of identification required.

Management Strategies

The ultimate goal of controlling various Meloidogyne spp. in the soil is to protect the crop from attack, cushion it from being predisposed to secondary infections and achieve maximum crop yield at the end of the growing season at a low cost (Coyne et al., 2006a; Norshie et al., 2011). Pest management strategies that have been adopted in most parts of Africa can be categorized broadly as chemical, biological or cultural. These are either practised singly or in combination to achieve desired results.

Chemical control methods

Chemical methods of control involve the application of different inorganic formulations to kill or interfere with the reproduction of Meloidogyne spp. in infested soils. In Meloidogyne spp. control programmes, nematicides are usually the most effective method of controlling high levels of Meloidogyne spp. in various farms. Nematicides containing active ingredients of methyl bromide, Aldicarb (Temik) and other harmful compounds have been banned in various parts of the world. Other nematicides which are known to control various Meloidogyne spp. include fenamiphos, oxamyl, 1, 3 dichloropropene (1, 3-D), dazomet and metam-sodium. Nematicides reduce high populations of various Meloidogyne spp. in the soil, but once symptoms have developed, they are incapable of completely eliminating those Meloidogyne species already in plant tissue (Sirias, 2011). They can be applied either as pre-plant nematicides, fumigants or as contact nematicides (Strajnar & Širca, 2011). Breaking of large lumps of soil, good soil humidity and removing crop remains of the previous season from the soil are essential for maximum effectiveness of these nematicides. The disadvantages of using chemical methods to control these Meloidogyne spp. are that some of these chemicals are toxic to humans and animals as a result of residues in the food chain, they contribute to environmental pollution through the pollution of the ozone layer (such as methyl bromide), and they are expensive to small-scale farmers. Furthermore, their continued use can lead to some level of resistance in plant parasitic nematode species. This resistance can be mainly as a result of mutation, given the fact that the phylum Nematoda is associated with high evolution rates (Blouin et al., 1995).

Biological control methods

Biological methods entail the use of living organisms either in pure cultures or in mixtures to control Meloidogyne spp. Some biological products such as those developed by Pasteuria Inc. and Koppert Biological Systems against certain Meloidogyne spp. have demonstrated significant effects in the control of these plant parasitic nematodes. These products are usually developed from microorganisms such as Pasteuria penetrans, Pasteuria hartismeri, Pochonia chlamydosporia, Bacillus firmus, Paecillomyces lilacinus and Trichoderma spp. The mode of action of these microorganisms is to attach to the nematode cuticle or to parasitize female eggs, subsequently killing the nematodes (Bishop et al., 2007; Kariuki & Dickson, 2007). In addition, some studies have also shown another biological strategy where endophytes such as Fusarium oxysporum (FO162) can induce systemic resistance against Meloidogyne spp. in some crops such as tomato (Walters, 2009). Colonization of roots by F. oxysporum (FO162) leads to the accumulation of root exudates in tomato roots which have a repelling effect on M. incognita (Mohamed, 2010).

Soil amendment procedures involving the application of organic materials such as farm manure and extracts from marigold (Tagetes spp.) to release toxic compounds that can kill plant parasitic nematodes have also been explored as a form of biological control (McSorley & Duncan, 1995). Antagonistic bacteria such as Pseudomonas aeruginosa in these decomposing organic materials either act as competitors or release metabolic toxins which may change the nature of root exudates (aimed at reducing the population of Meloidogyne spp. colonizing the roots) or kill various Meloidogyne spp. To achieve better results from soil amendments, organic materials should be applied at high rates to have a significant effect on nematode populations (Putten et al., 2006). In general, the use of organic material is not only cheap but also improves the efficiency of these antagonistic bacteria by offering them ready nutrients which are essential for their growth and survival.

Cultural control methods

Cultural practices include the development and use of resistant crop cultivars, the use of clean planting materials, intercropping, crop rotation and cleaning of farm implements (Brown et al., 2006). Many of these practices have been employed successfully in various parts of Africa to reduce the spread of Meloidogyne spp. in different crop fields for many years. However, the cost and availability of clean planting material can at times be a hindrance to many small-scale growers. A further challenge for small-scale growers is the limited amount of land they have for agricultural production. Subsequently, there are limitations to employing crop rotation as a control strategy. For example, crop rotation is at times not economically feasible due to financial losses which may be incurred during fallow periods or during establishment of a new crop to large-scale production levels over successive years. Growth challenges associated with the human population also make crop rotation virtually impractical in certain parts of the continent. Prior to the use of methods such as crop rotation, the identity of Meloidogyne spp. should be understood, and its host range and the cropping history of the field evaluated. This is critical in decision-making to avoid indiscriminate use of nematicides and to scale down management costs. Physical methods such as heat treatment and solarization of the soil before planting can be combined with cultural methods for effective control of various Meloidogyne spp. (Ioannou, 2000). Solarization of nursery soil up to 40 cm for a period of 3 weeks has been found effective in reducing egg infectivity (Nico et al., 2003).

Resistant cultivars

The basis of using resistant cultivars to control Meloidogyne spp. relies on knowing exactly which species is being targeted. Several studies are underway to develop crops with resistance genes against various Meloidogyne spp. (Norshie et al., 2011). There are certain cases of known resistant crops such as tomatoes (due to the Mi-1 gene) and wild potato (Solanum bulbocastunum). Initially, the resistance gene Rmc-1, located on chromosome 11 of wild potatoes, was found to confer resistance against M. chitwoodi and other Meloidogyne spp. such as M. fallax and M. hapla (Gebhardt & Valkonen, 2001; Brown et al., 2006). With the entry of resistance-breaking Meloidogyne spp., some of these crops have been rendered susceptible (Janssen et al., 1998; Brown et al., 2009; Kiewnick et al., 2009). Interestingly, the Mexigua resistance gene Mex-1 was identified in one coffee species, Coffea canephora, but not in the popularly used species Carabica (Souza, 2008). Undoubtedly, the success of current and future prospects of using resistant cultivars to manage Meloidogyne spp. will require intensified research. In this respect, Norshie et al. (2011) recently showed that certain potato lines are capable of partially resisting Mchitwoodi during infection. Furthermore, with the enormous amount of information being generated from the expressed sequence tags (ESTs), genome, transcriptome and proteomic sequences and attempts to introduce genes into plants to code for protein inhibitors such as chitinases, collagenases, cytotoxins, lectins and monoclonal antibodies against plant parasitic nematodes, it is anticipated that there will be an increase in transgenic crops with resistance to Meloidogyne spp. in the future (Fuller et al., 2008). This increase in GM plants coupled with a generally positive attitude by African growers, governments and consumers towards GM technology, is likely to go a long way in alleviating Meloidgyne spp. problems in crop production within the continent.

Resistant cultivars will not only reduce the cost of production but also safeguard the environment against pollution from chemical residues associated with nematicides. Resistance of various crops to Meloidogyne spp. infection is important because a resistant crop can allow little or no Meloidogyne spp. reproduction, thus providing a better way of controlling nematodes in the field (Norshie et al., 2011). In order to achieve promising results with the use of resistant cultivars, there is need to constantly carry out accurate species identification and surveillance. It is also important to educate growers on the importance of containing resistance-breaking Meloidogyne spp. such as M. enterolobii to areas where they have been detected. Ultimately the cost and availability of resistant genotypes will be a huge influencing factor on whether these benefits will trickle down to small-scale growers in Africa.

Concluding Remarks

The recent identification of ‘emerging’ highly damaging and resistant Meloidogyne spp. in certain parts of Africa poses a considerable challenge to formulation of effective management strategies. Lack of accurate and current data on various Meloidogyne spp. present in different parts of the continent and the polyphagous nature of these pathogens also poses a greater risk to the future of food production in Africa. To adequately address emerging and other Meloidogyne spp., it is imperative that resources are harnessed to drive more research aimed at assessing and understanding the species identity, genetic diversity, population structure, parasitism mechanisms and the overall threat posed by them (Fargette et al., 2010). Therefore, there is a need to embrace modern technology in conjunction with classical methods while carrying out Meloidogyne spp. identification.

It is imperative to have platforms that will allow those involved in research projects focusing on Meloidogyne spp. identification to share information with other projects targeting other phytoparasitic nematodes of economic importance. This is particularly vital for understanding the parasitism mode of these pathogens, because they share some traits (Curtis, 2007). The training of more scientists in the field of plant parasitic nematodes and molecular biology should also be a key priority to various agricultural stakeholders if food sustainability and income generation is to be achieved (Barker et al., 1994; Barker, 2003).

To effectively manage these highly damaging pathogens and other Meloidogyne spp., application of biological, cultural and chemical methods should be used in line with integrated pest management (IPM) practices. This should be preceded by a thorough survey of farms in context and an accurate diagnosis of Meloidogyne spp. present. Molecular-based methods of diagnosis should be used together with classical methods for accurate identification (Oliveira et al., 2011). This will lead to gradual management of Meloidogyne spp., and finally reduction in the high levels of damage that they cause on various crops. This strategy will eventually benefit growers and avoid high production costs. With the phasing out of various effective nematicides such as methyl bromide, the search for effective and environmentally friendly alternative methods should be pursued. At the same time, more robust diagnostic techniques should be adopted to correctly identify and avoid further spread of the highly damaging, resistance-breaking and emerging Meloidogyne spp. Growers should also be educated on proper phytosanitary procedures to avert the introduction of Meloidogyne spp. into their farms.


The authors wish to thank the Nematology Unit, ARC-PPRI for the use of data from the South African Plant-Parasitic Nematode Survey (SAPPNS) database. They acknowledge Professor Piet Hammes (Plant Production, University of Pretoria) for many fruitful discussions on the effect of Meloidogyne spp. in South African Potato production. They would like to apologise to their colleagues whose relevant publications have not been cited due to space and other restraints. This work was funded by the National Research Foundation (NRF). E. M. Onkendi's studentship was funded by the University of Pretoria.