Challenges in tropical plant nematology

A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes

The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and <1 in LD 24, in comparison with >100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus.

Agricultural nematology in East and Southern Africa: problems, management strategies and stakeholder linkages

By 2050, Africa's population is projected to exceed 2 billion. Africa will have to increase food production more than 50% in the coming 50 years to meet the nutritional requirements of its growing population. Nowhere is the need to increase agricultural productivity more pertinent than in much of Sub-Saharan Africa, where it is currently static or declining. Optimal pest management will be essential, because intensification of any system creates heightened selection pressures for pests. Plant-parasitic nematodes and their damage potential are intertwined with intensified systems and can be an indicator of unsustainable practices. As soil pests, nematodes are commonly overlooked or misdiagnosed, particularly where appropriate expertise and knowledge transfer systems are meager or inadequately funded. Nematode damage to roots results in less efficient root systems that are less able to access nutrients and water, which can produce symptoms typical of water or nutrient deficiency, leading to misdiagnosis of the underlying cause. Damage in subsistence agriculture is exacerbated by growing crops on degraded soils and in areas of low water retention where strong root growth is vital. This review focuses on the current knowledge of economically important nematode pests affecting key crops, nematode control methods and the research and development needs for sustainable management, stakeholder involvement and capacity building in the context of crop security in East and Southern Africa, especially Kenya, Tanzania, Uganda and Zimbabwe.

The role of thionins in rice defence against root pathogens

Thionins are antimicrobial peptides that are involved in plant defence. Here, we present an in-depth analysis of the role of rice thionin genes in defence responses against two root pathogens: the root-knot nematode Meloidogyne graminicola and the oomycete Pythium graminicola. The expression of rice thionin genes was observed to be differentially regulated by defence-related hormones, whereas all analysed genes were consistently down-regulated in M. graminicola-induced galls, at least until 7 days post-inoculation (dpi). Transgenic lines of Oryza sativa cv. Nipponbare overproducing OsTHI7 revealed decreased susceptibility to M. graminicola infection and P. graminicola colonization. Taken together, these results demonstrate the role of rice thionin genes in defence against two of the most damaging root pathogens attacking rice.

Intraspecific variability of the facultative meiotic parthenogenetic root-knot nematode (Meloidogyne graminicola) from rice fields in Vietnam

Twenty years ago, the facultative meiotic parthenogenetic root-knot nematode (RKN), Meloidogyne graminicola, was recognised as an important rice pathogen in South Vietnam. Although this country is one of the most important rice exporters worldwide, a comprehensive picture of the occurrence of M. graminicola in Vietnamese rice fields is still not available. Therefore a nematode survey was carried out with the aim of better understanding the geographical distribution, and the pathogenic and genetic variability of the RKN in Vietnam. From the fields surveyed in a range of ecosystems, 21 RKN populations were recovered from infected rice roots. A diagnostic SCAR marker was developed showing that all Vietnamese populations belong to M. graminicola. Furthermore, sequencing of the Internal Transcribed Spacer (ITS) of the rDNA genes confirmed this identification. These populations were then characterised using morphometrics and pathogenicity tests (host plant range diversity, reproduction and virulence diversity) revealing intraspecific variability. We showed that morphometric traits are mainly genetically heritable characters with significant differences among the studied populations. Finally, a distinctive trait signature was found for the populations isolated from the upland rice cultures. All together, our study reveals the prevalence of M. graminicola populations in Vietnamese rice. Further investigations need to be developed to explore the population dynamics and evolutionary history of this species in South East Asia.

Mitochondrial haplotype-based identification of ethanol-preserved root-knot nematodes from Africa

The asexual root-knot nematodes (RKNs) (Meloidogyne spp.) exemplified by Meloidogyne incognita are widespread and damaging pests in tropical and subtropical regions worldwide. Comparison of amplification products of two adjacent polymorphic regions of the mitochondrial genome using DNA extracts of characterized RKN strains, including 15 different species, indicate that several species are derived from the same or closely related female lineages. Nevertheless, M. javanica, M. enterolobii, M. incognita, and other key species could each be assigned unique mitochondrial haplotypes based on polymerase chain reaction fragment size and restriction cleavage patterns. M. arenaria isolates did not group as a single haplotype, consistent with other reports of diversity within this species. To test the utility of this assay, we characterized ethanol-preserved samples from 103 single-species isolates from four countries in sub-Saharan Africa (Benin, Nigeria, Kenya, and Tanzania). Mitochondrial haplotypes corresponding to M. javanica and M. incognita were the most prevalent. Samples from western Africa included several instances of M. enterolobii but this species was not detected in samples from East Africa. This protocol provides progress toward a standardized strategy for identification of RKN species from small, preserved samples and a rational starting point for classifying species present in regions where previous knowledge has been limited.

Range-expanding pests and pathogens in a warming world

Crop pests and pathogens (CPPs) present a growing threat to food security and ecosystem management. The interactions between plants and their natural enemies are influenced by environmental conditions and thus global warming and climate change could affect CPP ranges and impact. Observations of changing CPP distributions over the twentieth century suggest that growing agricultural production and trade have been most important in disseminating CPPs, but there is some evidence for a latitudinal bias in range shifts that indicates a global warming signal. Species distribution models using climatic variables as drivers suggest that ranges will shift latitudinally in the future. The rapid spread of the Colorado potato beetle across Eurasia illustrates the importance of evolutionary adaptation, host distribution, and migration patterns in affecting the predictions of climate-based species distribution models. Understanding species range shifts in the framework of ecological niche theory may help to direct future research needs.

Meloidogyne incognita - rice (Oryza sativa) interaction: a new model system to study plant-root-knot nematode interactions in monocotyledons

BACKGROUND

Plant-parasitic nematodes developed strategies to invade and colonize their host plants, including expression of immune suppressors to overcome host defenses. Meloidogyne graminicola and M. incognita are root-knot nematode (RKN) species reported to damage rice (Oryza sativa L.) cultivated in upland and irrigated systems. Despite M. incognita wide host range, study of the molecular plant - RKN interaction has been so far limited to a few dicotyledonous model plants. The aim of this study was to investigate if the rice cv. Nipponbare widely used in rice genomic studies could be used as a suitable monocotyledon host plant for studying M. incognita pathogenicity mechanisms. Here we compared the ability of M. graminicola and M. incognita to develop and reproduce in Nipponbare roots. Next, we tested if RKNs modulates rice immunity-related genes expression in galls during infection and express the Mi-crt gene encoding an immune suppressor.

RESULTS

Root galling, mature females, eggs and newly formed J2s nematodes were obtained for both species in rice cultivated in hydroponic culture system after 4-5 weeks. Meloidogyne graminicola reproduced at higher rates than M. incognita on Nipponbare and the timing of infection was shorter. In contrast, the infection characteristics compared by histological analysis were similar for both nematode species. Giant cells formed from 2 days after infection (DAI) with M. graminicola and from 6 DAI with M. incognita. Real-time PCR (qRT-PCR) data indicated that RKNs are able to suppress transcription of immune regulators genes, such as OsEDS1, OsPAD4 and OsWRKY13 in young galls. Four M. incognita reference genes (Mi-eif-3, Mi-GDP-2, Mi-Y45F10D.4, and Mi-actin) were selected for normalizing nematode gene expression studies in planta and in pre-parasitic J2s. Meloidogyne incognita expressed the immune suppressor calreticulin gene (Mi-crt) in rice roots all along its infection cycle.

CONCLUSION

RKNs repress the transcription of key immune regulators in rice, likely in order to lower basal defence in newly-formed galls. The calreticulin Mi-CRT can be one of the immune-modulator effectors secreted by M. incognita in rice root tissues. Together, these data show that rice is a well suited model system to study host- M. incognita molecular interactions in monocotyledons.

Discrimination of plant-parasitic nematodes from complex soil communities using ecometagenetics

Many plant pathogens are microscopic, cryptic, and difficult to diagnose. The new approach of ecometagenetics, involving ultrasequencing, bioinformatics, and biostatistics, has the potential to improve diagnoses of plant pathogens such as nematodes from the complex mixtures found in many agricultural and biosecurity situations. We tested this approach on a gradient of complexity ranging from a few individuals from a few species of known nematode pathogens in a relatively defined substrate to a complex and poorly known suite of nematode pathogens in a complex forest soil, including its associated biota of unknown protists, fungi, and other microscopic eukaryotes. We added three known but contrasting species (Pratylenchus neglectus, the closely related P. thornei, and Heterodera avenae) to half the set of substrates, leaving the other half without them. We then tested whether all nematode pathogens-known and unknown, indigenous, and experimentally added-were detected consistently present or absent. We always detected the Pratylenchus spp. correctly and with the number of sequence reads proportional to the numbers added. However, a single cyst of H. avenae was only identified approximately half the time it was present. Other plant-parasitic nematodes and nematodes from other trophic groups were detected well but other eukaryotes were detected less consistently. DNA sampling errors or informatic errors or both were involved in misidentification of H. avenae; however, the proportions of each varied in the different bioinformatic pipelines and with different parameters used. To a large extent, false-positive and false-negative errors were complementary: pipelines and parameters with the highest false-positive rates had the lowest false-negative rates and vice versa. Sources of error identified included assumptions in the bioinformatic pipelines, slight differences in primer regions, the number of sequence reads regarded as the minimum threshold for inclusion in analysis, and inaccessible DNA in resistant life stages. Identification of the sources of error allows us to suggest ways to improve identification using ecometagenetics.

Histopathology of the rice root-knot nematode, Meloidogyne graminicola, on Oryza sativa and O. glaberrima

The root-knot nematode, Meloidogyne graminicola, can cause substantial rice yield losses. Understanding the mechanisms of resistance to this nematode species in known resistant rice genotypes may help to improve rice genotypes, aiming at developing and implementing environment-friendly and cost-effective nematode management strategies. Using susceptible and resistant rice genotypes, a comparative analysis of histological response mechanisms was made during two phases of the nematode colonisation: i) root penetration; and ii) subsequent establishment and development by M. graminicola second-stage juveniles (J2). Two types of defence response mechanisms could be distinguished in the resistant rice genotypes. The early defence response consisted of a hypersensitive response (HR)-like reaction in the early stage of infection characterised by necrosis of cells directly affected by nematode feeding. This HR-like reaction was observed only in the M. graminicola-resistant Oryza glaberrima genotypes and not in the M. graminicola-susceptible O. sativa genotypes. The late defence response took place after the induction of giant cells by the J2. Giant cells usually collapsed and degenerated before J2 developed into adults. Structural features of the roots of the susceptible O. sativa showed greater root and stele diam. and cortex thickness than the resistant O. glaberrima genotypes. Desired features of plants with resistance to M. graminicola elucidated in this study can be used for selection of plants for breeding programmes.

Plant-parasitic nematode infections in rice: molecular and cellular insights

Being one of the major staple foods in the world, and an interesting model monocot plant, rice (Oryza sativa L.) has recently received attention from molecular nematologists studying the cellular and molecular aspects of the interaction between this crop and plant-parasitic nematodes. In this review, we highlight recent advances in this field, with a focus on the best-studied root-knot nematodes. Histological studies have revealed the cellular changes inside root-knot nematode-induced feeding sites, both in the compatible interaction with Oryza sativa and the incompatible interaction with the related species Oryza glaberrima. After comparing the published data from transcriptome analyses, mutant studies, and exogenous hormone applications, we provide a comprehensive model showing the role and interaction of plant hormone pathways in defense of this monocot crop against root nematodes, where jasmonate seems to play a key role. Finally, recent evidence indicates that effectors secreted from rice-infecting nematodes can suppress plant defense.

The effect of root-knot nematode, Meloidogyne graminicola, on the quality and vigour of rice seed

The root-knot nematode, Meloidogyne graminicola, is a serious pest of rice known to reduce grain yield. The effects of a series of infestation levels of M. graminicola on the nutritional and seed quality parameters of the grain have been studied under pot and field conditions using two cultivars of rice, a basmati, cv. Pusa Sugandh-5 and a non-basmati, cv. Pusa-44. The 1000 grain weight was significantly reduced by as much as 44.5% in cv. Pusa Sugandh-5 and 50.7% in cv. Pusa-44 seed when the parent plants were grown in soil with very high levels of M. graminicola infestation. The protein and amylose contents of the grains were significantly reduced in both the rice cultivars. The seed germination percentages of both the rice cultivars were also reduced as the nematode inoculation rates increased from 1-8 second-stage juveniles (J2) cm−3 in a pot experiment. Similar trends were also observed in field conditions. There was a significant decrease in the seedling vigour indices of both the rice cultivars. These results showed that the rice grains produced on plants infected with the nematode M. graminicola were lighter in weight and had poorer nutrient qualities, such as amylose and protein content. Further, if these grains were used as seed, the germination percentage was lower and, even more importantly, seed vigour was poor compared to the seed obtained from plants grown in M. graminicola-free soil.

Top 10 plant-parasitic nematodes in molecular plant pathology

The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.

Identification of candidate effector genes in the transcriptome of the rice root knot nematode Meloidogyne graminicola

Plant-parasitic nematodes secrete so-called effectors into their host plant which are able to suppress the plant's defence responses, alter plant signalling pathways and, in the case of root knot nematodes, induce the formation of giant cells. Putative effectors have been successfully identified by genomics, transcriptomics and proteomics approaches. In this study, we investigated the transcriptome of the rice root knot nematode Meloidogyne graminicola by 454 sequencing of second-stage juveniles as well as mRNA-seq of rice infected tissue. Over 350 000 reads derived from M. graminicola preparasitic juveniles were assembled, annotated and checked for homologues in different databases. From infected rice tissue, 1.4% of all reads generated were identified as being derived from the nematode. Using multiple strategies, several putative effector genes were identified, both pioneer genes and genes corresponding to already known effectors. To check whether these genes could be involved in the interaction with the plant, in situ hybridization was performed on a selection of genes to localize their expression in the nematode. Most were expressed in the gland cells or amphids of the nematode, confirming possible secretion of the proteins and hence a role in infection. Other putative effectors showed a different expression pattern, potentially linked with the excretory/secretory system. This transcriptome study is a good starting point to functionally investigate novel effectors derived from M. graminicola. This will lead to better insights into the interaction between these nematodes and the model plant rice. Moreover, the transcriptome can be used to identify possible target genes for RNA interference (RNAi)-based control strategies. Four genes proved to be interesting targets by showing up to 40% higher mortality relative to the control treatment when soaked in gene-specific small interfering RNAs (siRNAs).

Identification of candidate effector genes in the transcriptome of the rice root knot nematode Meloidogyne graminicola

Plant-parasitic nematodes secrete so-called effectors into their host plant which are able to suppress the plant's defence responses, alter plant signalling pathways and, in the case of root knot nematodes, induce the formation of giant cells. Putative effectors have been successfully identified by genomics, transcriptomics and proteomics approaches. In this study, we investigated the transcriptome of the rice root knot nematode Meloidogyne graminicola by 454 sequencing of second-stage juveniles as well as mRNA-seq of rice infected tissue. Over 350 000 reads derived from M. graminicola preparasitic juveniles were assembled, annotated and checked for homologues in different databases. From infected rice tissue, 1.4% of all reads generated were identified as being derived from the nematode. Using multiple strategies, several putative effector genes were identified, both pioneer genes and genes corresponding to already known effectors. To check whether these genes could be involved in the interaction with the plant, in situ hybridization was performed on a selection of genes to localize their expression in the nematode. Most were expressed in the gland cells or amphids of the nematode, confirming possible secretion of the proteins and hence a role in infection. Other putative effectors showed a different expression pattern, potentially linked with the excretory/secretory system. This transcriptome study is a good starting point to functionally investigate novel effectors derived from M. graminicola. This will lead to better insights into the interaction between these nematodes and the model plant rice. Moreover, the transcriptome can be used to identify possible target genes for RNA interference (RNAi)-based control strategies. Four genes proved to be interesting targets by showing up to 40% higher mortality relative to the control treatment when soaked in gene-specific small interfering RNAs (siRNAs).

Nematicidal activity of terpenoids

Thirty four phytoterpenoids were evaluated for their nematicidal effect using the model nematode Caenorhabditis elegans. Nematicidal activities of the tested compounds at concentrations of 50 μg/mL showed wide variation in their effects ranging from no effect, weak, moderate and strong effects. Terpenoids exerting 50% or higher mortality at 50 μg/mL were further tested at five different concentrations to calculate the concentration that will kill 50% of the nematode population (LC(50)). Among the most effective terpenoids were carvacrol, thymol, nerolidol, α-terpinene, geraniol, citronellol, farnesol, limonene, pseudoionone and eugenol in a descending order. These compounds exhibited a dose-dependent effect. The results suggest that the selected monoterpenoids and essential oils with a high concentration of these compounds mayprovide potential natural nematicides and merit further study as botanical nematicides for the control of both plant and animal parasitic nematodes. In general, oxygenated terpenoids and phenolic terpenoids exhibited higher nematicidal activity than hydrocarbons terpenoids.

Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest

Comparisons of nematode communities among ecosystems have indicated that, unlike many organisms, nematode communities have less diversity in the tropics than in temperate ecosystems. There are, however, few studies of tropical nematode diversity on which to base conclusions of global patterns of diversity. This study reports an attempt to estimate nematode diversity in the lowland tropical rainforest of La Selva Biological Research Station in Costa Rica. We suggest one reason that previous estimates of tropical nematode diversity were low is because habitats above the mineral soil are seldom sampled. As much as 62% of the overall genetic diversity, measured by an 18S ribosomal barcode, existed in litter and understorey habitats and not in soil. A maximum-likelihood tree of barcodes from 360 individual nematodes indicated most major terrestrial nematode lineages were represented in the samples. Estimated 'species' richness ranged from 464 to 502 within the four 40 x 40 m plots. Directed sampling of insects and their associated nematodes produced a second set of barcodes that were not recovered by habitat sampling, yet may constitute a major class of tropical nematode diversity. While the generation of novel nematode barcodes proved relatively easy, their identity remains obscure due to deficiencies in existing taxonomic databases. Specimens of Criconematina, a monophyletic group of soil-dwelling plant-parasitic nematodes were examined in detail to assess the steps necessary for associating barcodes with nominal species. Our results highlight the difficulties associated with studying poorly understood organisms in an understudied ecosystem using a destructive (i.e. barcode) sampling method.

Emerging molecular knowledge on Radopholus similis, an important nematode pest of banana

TAXONOMY

Superkingdom Eukaryota; Kingdom Metazoa; Phylum Nematoda; Class Chromadorea; Order Rhabditida; Suborder Tylenchina; Infraorder Tylenchomorpha; Superfamily Tylenchoidea; Family Pratylenchidae; Subfamily Radopholinae; Genus Radopholus.

PHYSICAL PROPERTIES

Microscopic unsegmented worm; migratory endoparasite of plants. Strong sexual dimorphism; reproduction both by amphimixis and self-fertilization.

HOSTS

Over 250 different plant species, including citrus, black pepper and banana (main host plant).

SYMPTOMS

Purple to black lesions and extensive cavities in plant roots, leading to reduced uptake of water and nutrients. In banana, this may result in poor vegetative growth, reduced bunch weight and toppling of plants.

DISEASE CONTROL

Nematicides, alternative cropping systems, nematode-free planting material, some resistant cultivars.

AGRONOMIC IMPORTANCE

Major problem in banana plantations in tropical regions worldwide.

Natural organic compounds as alternative to methyl bromide for nematodes control

Thirty-three organic acids and furfural metabolites were examined for their nematicidal activity against plant-parasitic, free-living and predacious nematodes. Propionic acid, 2-methylhexanoic acid, lactic acid, maleic acid, and furic acid were the most effective nematicides among normal chain organic acids, branched organic acids, hydroxy/keto-acids, dicarboxylic acids and furfural metabolites, respectively. Seven of the tested compounds were found to have more than 90% mortality thus designating them as highly active nematicides. Of the highly active tested compounds, an average octanol/water log P of 0.97 was observed with a range from 0.28 to 2.64, and a Henry's Law constant averaging 2.6 x 10(- 7) atm.m3/mole. Tested chemicals with minor or low nematicidal activity showed an average log P of 1.76 with a range from 0.15 to 3.42 and a Henry's Law constant averaging 16.6 x 10(- 7) atm.m3/mole.