Nematode pests of some major cereals in Nigeria: Need for integration of morphological/morphometrical,biochemical, and molecular diagnostic approaches for accurate identification

Plant-parasitic nematodes pose a major threat to crop production in Nigeria. Comprehensive data on yield losses for most cereal crops are not readily available. Research on maize (Zea mays), rice (Oryza sativa), and sorghum (Sorghum bicolor) has shown an 18%–67% reduction in yield linked to the destructiveness of parasitic nematodes, particularly root-knot and root-lesion nematodes. Continuous monoculture and a conservative approach to agriculture increase the incidence and population density of nematodes, leading to higher levels of damage and losses in most cultivated cereal crops. These losses affect the food security of the growing population of Nigeria and many African countries that are heavily dependent on cereals. The accurate identification of nematodes is fundamental for effective management strategies. Nematode taxonomy based on morphology has been difficult due to intraspecific character variations coupled with the limited expertise of indigenous nematologists. Biochemical and molecular marker-based tools and approaches have allowed efficient diagnosis of most nematode species affecting cereal production globally. These approaches have proved useful due to their practicality, rapidness, accuracy, and cost-effectiveness. This review describes the important economic effects of these parasitic nematodes on cereal production and highlights the need for integrative approaches to taxonomy for accurate species identification that will improve nematode diagnosis, thereby contributing to the increase of food production in Nigeria.     

The Basis of Predictive Modelling for Estimating Yield Loss and Planning Potato Cyst Nematode Management

The basis of modelling yield loss and population dynamics relations of potato cyst nematodes is that both are strongly density-dependent. Potato cyst nematodes (PCN; Globodera pallida and G. rostochiensis) are particularly suitable for analysing such relationships because they have only one generation per year, potato is their only field host, the juvenile nematodes within the egg are very durable (up to 20 years persistence), and they hatch mainly in response to specific chemicals exuded from host roots. Small populations increase the most, up to 50-fold, when a potato crop is grown. Multiplication rates decrease as the population density increases because damage decreases root system size and increases competition so that very large populations may actually be decreased when potatoes are grown. The newly formed eggs have a ‘half-life’ of c.two years when non-host, rotational crops are being grown. Control is achieved largely by the use of rotation, the application of nematicidal chemicals, and growing resistant cultivars. As rotations are shortened, so PCN populations will be increased, and crop damage becomes more likely. Thresholds for damage vary with both soil type (greatest on sandy soils) and potato cultivar. Cultivars differ in their tolerance of PCN damage depending on how vigorously they grow, on their root sensitivity to damage from the PCN juveniles which invade close to root tips, on cultivar resistance which decreases the parasitic effect by reducing the numbers of developing PCN females, and on various environmental factors such as the amounts of fertiliser applied. The dependence of the yield-loss relationship on population density, soil type and cultivar effects has been described in a simple equation and assessed using field-trial data. Effects on yield are described in proportion to the PCN-free yield but the addition of information on expected yield (in tonnes ha⁻¹) in the absence of PCN renders this equation predictive. Nematicides are widely applied to infestations of potato cyst nematodes, both to prevent the crop from being damaged and to prevent population increase which could hazard the next potato crop in the rotation, but they are generally more effective at preventing the former than the latter. A complex equation has also been developed to model the population dynamics of PCN. This equation incorporates a factor for host-crop growth and tolerance (from the yield-loss equation) and also the effects of host resistance. This latter is particularly relevant to G. pallida, where all the resistance currently available is determined by minor genes and hence is ‘quantitative’ or ‘partial’. Effects of rotation and of nematicides can also be incorporated into this model. To provide a realistic prediction also requires accurate information on PCN population densities, species composition and distributions, and rates of PCN population decline between potato crops.     

Molecular variability and phylogenetic relationships among different species and populations of <Emphasis Type="Italic">Pratylenchus</Emphasis> (Nematoda: Pratylenchidae) as inferred from the analysis of the ITS rDNA

Sequence comparisons and molecular phylogenetic analyses were used to describe the nucleotide variability of the ITS containing regions of eighteen Pratylenchus species and several populations. Comparative analysis of nucleotide sequences of the rDNA internal transcribed spacers (ITS1 and ITS2) among Pratylenchus species used in the present study demonstrates that ITS sequences can widely vary in primary sequence and length. Alignment of eighty-seven Pratylenchus sequences and one outgroup taxon reveals the presence of ambiguous regions that have the greatest effect on phylogeny reconstruction. Phylogenetic analyses using Bayesian Inference, Neighbour Joining-LogDet, Maximum Likelihood and Maximum Parsimony, distinguished twelve highly or moderately supported major clades within Pratylenchus. Our results support the taxonomic usefulness of the ITS region to identify root-lesion nematode species of the genus Pratylenchus but the high nucleotide variability, sometimes, can preclude its use to resolve relationships among all members of the genus. In addition, the phylogenetic groupings are not congruent with those defined by characters derived by lip patterns and numbers of lip annuli.     

Assessment of the pest status of Pratylenchus curvicauda and ultrastructural changes in roots of infected wheat and barley

Pratylenchus curvicauda, which was first described in metropolitan Perth in 1991, was recently identified in grain-growing areas in Western Australia. The biology of this root-lesion nematode, and especially its pest status, is unknown. We investigated its life cycle and interaction with host plants, because such information is essential for its management. The life cycle took 45 days to complete in a wheat cultivar maintained at 23°C. Over 10 weeks, the nematode multiplied in 26 of 61 genotypes; these host plants were all cereals and included widely grown cultivars of wheat and barley. Eighteen other cereal genotypes and 13 cultivars including canola, chickpea, ryegrass, lupin, soybean, and tomato, sustained the nematodes to different degrees without multiplication. Four cover crops were not suitable hosts. The patterns of attraction of the nematodes and penetration into roots of the host and tolerant plants were similar. The nonhosts attracted fewer nematodes, none of which penetrated the roots. Browning of infected roots was atypical—it occurred late in some roots, 55 days after inoculation, and in the presence of a fungus. The nematodes were confined to, and fed from, cortical cells. The ultrastructure of infected wheat and barley cells showed typical signs of damage caused by Pratylenchus spp. and included cell disorganization and lack of membrane integrity, disintegration of cytoplasm, hypertrophy of some nuclei, and deposition of tannin-like granules. This detailed characterization of P. curvicauda–host interaction indicates the nematode is likely to be a pest of major crops, and attention should be given to its management.     

Cropping systems for the management of phytonematodes

Damage caused by nematodes is one of the limiting factors in crop production. Traditional nematode management is based on the use of crop rotations, resistant cultivars, nematicides, or combinations of these methods. For a crop like peanut (Arachis hypogaea), cultivars resistant to root-knot nematodes are not available. There are soybean (Glycine max) cultivars resistant to some of the species of root-knot nematodes (Meloidogyne spp.); however, most fields have nematode infestations composed of mixtures of species. Research at Auburn has shown that tropical crops can be used effectively in rotation to manage nematode problems. Rotations with American jointvetch (Aeschynomene americana), castor (Ricinus communis), hairy indigo (Indigofera hirsuta), partridge pea (Cassia fasciculata), sesame (Sesamum indicum), and velvetbean (Mucuna deeringiana) have resulted in good nematode control and increased yields of peanut and soybean. Some crops (castor, sesame) are considered ‘active’ in that they produce compounds that are nematicidal, whereas others (e.g. corn, sorghum) are simply non-host, that is, ‘passive’.     

Potato cyst nematodes in the Canary Islands: an epidemiologic model for the Mediterranean region1

This work describes studies done on the Canary Islands in order to support the elaboration of quarantine and control legislation for potato cyst nematodes which take into account the special agroecological characteristics of the Mediterranean region. The interest of the islands for epidemiological studies is based on the occurrence of the oldest potato crops in the Old World and the use of several local cultivars and traditional management cropping systems. Also, the environmental conditions allow field experiments to be performed throughout the year. The phytonematological problems of the potato crop on the Canary Islands is reported and the absence of Ditylenchus destructor, D. dipsaci, Nacobbus aberrans, Rotylenchulus reniformis and trichodorids pointed out. The cyst nematodes, Globodera rostochiensis and G. pallida were found to cause severe damage to the crop and were studied in detail by field trials at Tenerife. Continuous growing of the cv. Cara, with the H1 gene conferring resistance to G. rostochiensis (pathotypes Ro1 and Ro4), exerted selection pressure for G. pallida. Under the edaphic and climatic conditions of Tenerife, nematicide application was found to be inefficient for controlling potato cyst nematodes. Alternative control techniques based on traditional management systems and on the use of environmentally adverse conditions were investigated.     

Pratylenchus species of soybean in Croatia1

The numbers and species of phytoparasitic nematodes on soybean were studied over several years in Croatia, especially in the regions of Slavonija and Baranja. 19 phytoparasitic species were found, and of these Pratylenchus spp. predominated. These nematodes were found in mixed populations and their numbers were, at times, enormous. The average number per 100 ml of soil was about 100 individuals, with a maximum of 3348. The relationship between the number of nematodes and yield of soybean was calculated by a single regression equation. The soybean cultivars Sava and OS-88 apparently possess tolerance to relatively high numbers of Pratylenchus spp. in the rhizosphere.     

<Emphasis Type="Italic">Solanum sisymbriifolium</Emphasis> - a new approach for the management of plant-parasitic nematodes

Plant-parasitic nematodes are serious pests causing important crop losses worldwide. After extensive screening of non-tuber-bearing Solanaceae, a resistant trap crop, Solanum sisymbriifolium, with a high production level of hatching agents, seemed an ideal control method for potato cyst nematodes (PCN), Globodera spp. Recently, root-knot nematodes (RKN), Meloidogyne spp., were found coexisting with PCN. Therefore, it is important to find alternative methods to control both nematode genera. The chemical properties of S. sisymbriifolium turns this plant into an excellent candidate for further nematicidal studies and to develop new crop production models. Studies concerning the effects of this plant on plant-parasitic nematodes are presented. Pathogenicity studies with four S. sisymbriifolium cvs (Domino, Pion, Sis 4004 and Sharp) and five Meloidogyne species showed that all cultivars of S. sisymbriifolium studied were resistant to M. chitwoodi and hypersusceptible to M. arenaria and M. hapla. For M. hispanica only cv Pion was susceptible. M. javanica induced different responses: cvs Pion and Sharp were susceptible; cv Domino resistant and Sis 4004 hypersusceptible. The studies of the hatching effects of root exudates from these cvs showed that they had an influence on the hatching inhibition of second stage juveniles of the five Meloidogyne species tested.     

Comparison of the sequences of the D3 expansion of the 26S ribosomal genes reveals different degrees of heterogeneity in different populations and species of <Emphasis Type="Italic">Pratylenchus</Emphasis> from the Mediterranean region

Plant parasitic nematodes belonging to the genus Pratylenchus, also known as root lesion nematodes, cause serious economic damage to different crop plants. In order to explore genetic structures in different isolates, we investigated several P. thornei, P. neglectus and P. penetrans populations of different geographic origins. The analysis at the species level was also extended to P. penetrans, P. pinguicaudatus, P. vulnus and P. mediterraneus. Sequence analysis of a specific portion of DNA was carried out. In particular, the sequences of the D3 region of the 26S gene were obtained and compared with similar sequences available in databases. The results support the hypothesis that P. penetrans may represent a species complex, while in P. neglectus the intra-species heterogeneity observed is due to intra-individual variability. Furthermore, the specific conservation of some nucleotides in different P. thornei populations indicates their fixation in the rDNA repeats in this species. The presence of these nucleotides, the molecular signature of P. thornei, may assist in determining the nature of nematode infections.     

Plant parasitic nematodes as pests of potatoes in Poland1

Only two plant parasitic nematode species have practical importance in potato crops in Poland. They are Ditylenchus destructor and Globodera rostochiensis pathotype Ro1. Control of D. destructor is done permanently by the elimination of infested seed potatoes and sowing of cereals in the infested fields. Damage to potatoes is observed rather seldom. G. rostochiensis is widely distributed throughout Poland. It is controlled by non-host crops and by resistant potato cultivars. Chemical control of potato nematodes is not put into practice in Poland.     

Identification of <Emphasis Type="Italic">Pratylenchus thornei</Emphasis>, the cereal and legume root-lesion nematode,based on SCAR-PCR and satellite DNA

Two different molecular tools for the diagnosis of the cereal and legume root-lesion nematode Pratylenchus thornei were developed. A randomly amplified DNA (RAPD) fragment specific to P. thornei was identified. After sequencing the fragment, longer primers were designed that complement the terminal sequences of the RAPD fragment, and this pair of specific primers was used to amplify the sequence-characterized amplified region (SCAR). Using the developed pair of SCAR primers, the SCAR fragment specific to P. thornei was easily amplified with DNA extracts obtained from different life stages of the nematode. The described SCAR-PCR-based assay has the potential to be optimized for routine practical diagnostic tests. In addition, the use of a species-specific satellite DNA sequence to distinguish P. thornei from other Pratylenchus spp. is discussed.     

Genotypic and phenotypic characterization of Streptomyces species associated with potato crops in the central part of Colombia

In Colombia, Streptomyces scabiei (syn. S. scabies) is commonly believed to be the causal organism of scab disease in local potato crops. However, very little is known about this organism and about the diversity and pathogenicity of the Streptomyces species associated with potato crops in Colombia. This study, therefore, aimed to elucidate aspects regarding the diversity of these bacteria associated with potato crops in a particular region of Colombia and evaluate their pathogenicity. We obtained 33 isolates of Streptomyces from netted, superficial and deep-pitted potato scab lesions from two main potato-producing regions in Colombia. Of these, 17 were pathogenic based on in vitro and in planta assays. None of these isolates carried the txtA, txtB, or nec1 genes, commonly associated with pathogenicity in Streptomyces, and characteristic of the pathogenicity island (PAI). We also characterized all isolates based on phenotypic characteristics and analysed their phylogenetic relationships using the 16S rRNA, atpD, recA, rpoB, and trpB genes. The isolates were highly diverse, placed in nine clades with 15 different phenotypes. The 17 pathogenic isolates were placed into three clades, namely S. pratensis, S. xiamenensis, and unknown species. This study is a preliminary investigation towards understanding scab disease in Colombia through the study of both pathogenic and nonpathogenic species present in scab disease lesions in potatoes. Also, this is the first report of Streptomyces species associated with potato tubers in Colombia.     

Detection of the root lesion nematode Pratylenchus penetrans in potato tubers

The root lesion nematode Pratylenchus penetrans parasitizes a wide range of economically important crops, including potato (Solanum tuberosum). Damage by P. penetrans impacts not only the potato yield but can also reduce the tuber quality. Detailed information on tuber infection by P. penetrans is scarce for most cultivars and molecular detection of nematodes from infected tubers is needed. The objective of this study was to assess tuber symptomatology due to P. penetrans infection in 10 potato cultivars and to provide an accurate molecular methodology for nematode detection using tuber peels. Sprouts of certified potato seed from cultivars Agata, Agria, Camel, Désirée, Dirosso, Kennebec, Laura, Picasso, Royata, and Stemster were planted in 2 L pots, and soil was inoculated with 4 P. penetrans/g of soil. Sixty days after inoculation, tubers were harvested, inspected for lesions, and the number of nematodes/g of potato peel assessed. Observations of tubers with symptoms showed the presence of P. penetrans in superficial layers of peels around the lenticels and injured necrotic tissue. Different nematode stages were detected in tubers of all inoculated cultivars, varying from 4 to 46 nematodes/g of potato peel. Species-specific primers showed suitable sensitivity and reproducibility for the detection of P. penetrans in tuber potato peel samples. The molecular detection of P. penetrans directly from tuber peels can facilitate routine nematode inspections of potato seed tubers or cull potatoes for nematode detection, and prevent further dissemination of this species.     

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.     

Effects of fosthiazate and aldicarb on populations of plant-growth-promoting bacteria, root-lesion nematodes and bacteria-feeding nematodes in the root zone of potatoes

A 2-year study investigated the relationship between the nematicides aldicarb and fosthiazate and populations of plant growth-promoting (PGP) and plant-growth-inhibiting (PGI) bacteria, and root-lesion nematodes and bacteria-feeding nematodes in the root-zone soils of potatoes. Fewer ( P  < 0.05) bacterial genera and species were recovered from aldicarb-treated soils than from the fosthiazate and untreated soils but bacterial population densities were greatest in the aldicarb-treated soils. In potato plantlet bioassays using root-zone bacteria from the three soil sources, bacteria from the aldicarb-treated soils reduced ( P  < 0.01) the mean wet and dry weight of shoots and roots compared with those from the fosthiazate and untreated soils. In the field, fosthiazate (but not aldicarb) significantly increased tuber yields and reduced nematode population densities of Pratylenchus penetrans in roots and soil. Population densities of bacteria-feeding nematodes (primarily Diplogaster lheritieri ) were not affected by either nematicide. Aldicarb appeared to suppress the populations of plant-growth-promoting bacteria that contribute to enhanced growth in potatoes. This is attributed to the long-term use of aldicarb at the trial site, which may have encouraged the selection, or adaptation, of soil microorganisms that degrade carbamate pesticides but do not enhance potato growth.     

玉米矮化病株及其根际土壤内线虫的分离与分子鉴定

为探究玉米矮化病的病原,采用Ludox TM悬浮法对从吉林和辽宁采集的玉米矮化病株及其根际土壤和健康株根际土壤分离的线虫进行了鉴定和种群比较,并对矮化病株茎基组织PCR产物进行测序分析。结果表明:玉米健康株根际土壤分离出29属线虫,特有线虫是角咽线虫属Actinolaimus和木盾移线虫属Peltamigratus,矮化玉米病株根际土壤分离出28属线虫,特有线虫为锥线虫属Dolichorus,二者相同的线虫属有27个。矮化玉米病株根际土壤中植物线虫种类和数量明显比健康株根际土壤中高,线虫种群数量差异明显的主要是矮化线虫属Tylenchorhynchus、短体线虫属Pratylenchus和刺线虫属Belonolaimus,病株根际土壤中这3个属线虫总数约占病株土壤分离线虫总数的20.23%、11.27%和10.40%。玉米矮化病株茎基组织中短体线虫属和矮化线虫属数量占优势,2个属的线虫数量分别占测序总数的22%、14%(吉林长岭)和16%、20%(辽宁黑山)。表明玉米矮化病的发生与植物线虫相关,很可能是多种线虫共同引起的病害。     

SSR assessment of Phytophthora infestans populations on tomato and potato in British gardens demonstrates high diversity but no evidence for host specialization

Phytophthora infestans populations can differ in composition as a result of host specialization on tomato and potato hosts. In Great Britain many amateur gardeners grow outdoor tomatoes but there is little or no commercial tomato production outdoors. This study analysed isolates of P. infestans from British gardens with 12 multiplexed simple sequence repeat markers that are used to monitor the disease on commercial potato crops. Samples of P. infestans from tomato hosts were collected in 3 years and from potato in 1 year from across Great Britain. Seven previously unreported clonal lineages were detected in garden populations and higher frequencies of unique clonal lineages (28–40%) were present compared with populations from British commercial potato crops reported elsewhere. Garden populations had a lower proportion (11–48% less) of the most common lineages (13_A2 and 6_A1) that together made up at least 86% of the commercial potato populations during the sampling period. Host species accounted for only 2·0% of molecular variance detected between garden potato‐ and tomato‐hosted samples. No significant difference in clonal lineage composition was found between host species in Great Britain and this could be due to the whole P. infestans population overwintering on potato. British garden populations on both hosts were much more diverse than those on commercial potato crops; this finding may be influenced by less frequent fungicide use by gardeners and a higher diversity of unsprayed susceptible potato cultivars, enabling metalaxyl‐sensitive and less aggressive genotypes to survive in gardens.     

Biological control of Meloidogyne spp. with Pasteuria penetrans1

Pasteuria penetrans, an endospore-forming obligate parasite of root-knot nematodes, can be an effective biological control agent, particularly when used in pots, small plots or container-grown crops. The absence of adequate mass-production techniques prevents its deployment on a field scale. The spores are not mobile and their concentration and distribution influence parasitism since attachment of spores to free-living juvenile root-knot nematodes depends upon chance contact. Efficacy can also be influenced by the specificity of the population of P. penetrans to the root-knot nematode population. If these problems can be overcome, the use of P. penetrans in integrated management systems developed over several crop cycles would appear to have good prospects for decreasing root-knot nematodes in intensively cultivated soils.     

Characterization and pathogenicity assessment of Plectosphaerella species associated with stunting disease on tomato and pepper crops in Italy

This study follows a survey carried out in 2012 and 2013 on tomato and pepper crops in the Foggia province (southern Italy), for morphological, molecular and pathogenicity analyses of Plectosphaerella fungi. The Plectosphaerella genus includes several species that are pathogens of horticultural plants. The survey identified tomato and pepper crops that showed abundant wilt, leaf yellowing, and discolouration and necrosis of roots, plus collar and stem symptoms. Different fungi including Plectosphaerella spp. were isolated from tissues with and without symptoms. Subsequent molecular and morphological studies identified first records of P. citrulli infecting tomato and pepper, and P. pauciseptata and P. ramiseptata infecting pepper. Pathogenicity testing confirmed that most isolated species of Plectosphaerella caused symptoms on tomato and pepper, with P. ramiseptata the most aggressive. On the basis of these data, it is considered that Plectosphaerella species may cause stunting disease in tomato and pepper.     

Resistance to root-lesion nematode Pratylenchus neglectus identified in a new collection of two wild chickpea species (Cicer reticulatum and C. echinospermum) from Turkey

Chickpea (Cicer arietinum) is a major legume crop, with Australia being the second largest producer worldwide. Pratylenchus neglectus is a root-lesion nematode that invades, feeds and reproduces in roots of pulse and cereal crops. In Australia, chickpea and wheat (Triticum aestivum) are commonly grown in rotation and annual damage by P. neglectus accounts for large economic losses to both crops. Cultivated chickpea has narrow genetic diversity that limits the potential for improvement in resistance breeding. New collections of wild chickpea species, C. reticulatum and C. echinospermum, have substantially increased the previously limited world collection of wild Cicer germplasm and offer potential to widen the genetic diversity of cultivated chickpea through the identification of accessions with good resistance. This research assessed 243 C. reticulatum and 86 C. echinospermum accessions for response to P. neglectus in replicated experiments under controlled glasshouse conditions from 2013 and 2014 collection missions that were received, tested and analysed in two experimental sets. Multi-experiment analyses showed lower P. neglectus population densities in both sets of wild Cicer accessions tested than Australia's elite breeding cultivar PBA HatTrick at the significance level p < 0.05. Provisional resistance ratings were given to all genotypes tested in both experimental sets, with C. reticulatum accessions CudiB_008B and Kayat_066 rated as resistant in both Set 1 and Set 2. New sources of resistance to P. neglectus observed in this study can be introgressed into commercial chickpea cultivars to improve their resistance to this nematode.