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Root-knot nematodes (RKNs) are major threats to crops through attacking the roots, which induces an abnormal development of the plant. Meloidogyne hapla is of particular concern, as it is currently expanding its distribution area and displays a wide host range. Effective plant protection against this RKN requires early detection, as even a single individual can cause severe economic losses on susceptible crops. Molecular tools are of particular value for this purpose, and among them, quantitative PCR (qPCR) presents many advantages (i.e., sensitivity, specificity, and rapidity of diagnosis at a reduced cost). Although a few studies have already been proposed for detecting M. hapla through this technique, they lack experimental details and performance testing, suffer from low taxonomic resolution, and/or require expensive hydrolysis probes. Here, we propose a qPCR detection method that uses SYBR Green with developed primers amplifying a fragment of the cytochrome oxidase I mitochondrial region. The method was developed and evaluated following the minimum information for publication of quantitative real-time PCR experiments (MIQE) guidelines to ensure its quality (i.e., sensitivity, specificity, repeatability, reproducibility, and robustness). The results demonstrate that the newly developed method fulfills its goals, as it proved specific to M. hapla and allowed for a reproductible detection level as low as 1.25 equivalent of a juvenile individual. All criteria associated with the MIQE guidelines were also met, so the method is of general use for the reliable early detection of M. hapla.

International audience; Current restrictions on the use of chemical nematicides have led to an increase in root-knot nematode (RKN) damages in horticultural crops. The effects of two sorghums as summer cover crops, Sorghum sudanense sudan-grass cv. ‘Piper’ or sudangrass hybrid [S. bicolor x S. sudanense] ‘270911’, respectively with low and high dhurrin contents, were compared in their ability to suppress RKN in a vegetable production system. The use of both sorghums ‘Piper’ and ‘270911’ as a green manure was found to be an effective strategy for decreasing RKN infestation in the soil, thereby protecting the subsequent planting of RKN susceptible crops (chard, lettuce or melon). Analytical experiments were further conducted in growth chamber and greenhouse pot experiments to investigate and compare the susceptibility of the sorghums and the factors affecting their efficacy for RKN management, in order to better explain the results obtained in the field trial. The two sorghums were poor hosts of RKN, acted as trap crops and as a biofumigant releasing hydrogen cyanide. Time of planting, time of bio-fumigation, and type of soil affected their efficacy for RKN management. For best RKN suppression, the sorghum cover crops need to be cultivated during one month or less and biofumigated for one month prior to crop planting. The trapping effect of both sorghums in clayey soil was less efficient than in sandy or sandy-loamy soils. Combining less than 30-days of sorghum culture and 10-days soil incorporation with solarization mulch was particularly efficient in suppressing nematodes. No effect relative to the sorghum type was detectable as long as they were used appropriatel.

Root-knot nematodes (RKNs) are major threats to crops through attacking the roots, which induces an abnormal development of the plant.

International audience; Ancient ecological legacies and past land use changes may inform on the present structure of biological communities. However, regions providing such successive ecosystems are scarce. In France, the Landes de Gascogne area provides such ecological shifts since a few ancient moorland, peatland and oak areas prior the afforestation with maritime pine (Pinus pinaster) 160 years ago still remain. Focusing on soil-borne parasites such as plant-parasitic nematodes (PPN), because forests were recently increasingly impacted by the introduction of intensive agriculture, this study is therefore aimed at comparing the diversity and the community patterns of these organisms at different scales (intra- and intersites) and between different successive ecosystems. The understory vegetation as well as the pedoclimatic characterization of the sampled sites were also considered. Common diversity indices were not impacted by this transition from ancient to past ecosystems. Although the most colonizer nematodes prevailed in all the ecosystems, PPN community structures significantly diverged between both ecosystems. In the logged pine forests, the sediment legacy could have primarily impacted the diversity. Moreover, the PPN diversity would mainly respond to the soil hydromorphicity that determined the associated understory vegetation. Consequently, a significant shift in community structure from moorlands to logged pine to logged pine forests was observed, regarding especially high pathogenic species such as Pratylenchus spp. Thus, analyzing PPN community structure highlights the PPN potential risk to consider during the introduction of intensive cropping systems.

International audience; Plant-parasitic nematodes (PPN) are detected everywhere as mixed-species communities. Most non-chemical control strategies of PPN only target some species, thus raising questions about the consequences that this specificity may have on the residual community. In this respect, the long-term ecological sustainability of such strategies is challenged. In order to evaluate the impacts of agronomical practices on PPN communities, two four-year experiments that differed by the presence or absence of root-knot nematodes (RKN - Meloidogyne spp.) were carried out under cold shelters in the south of France, under native field conditions of vegetable cropping systems that included a nematicidal sorghum green manure and a pepper variety carrying a RKN resistance gene. At the site with RKN, RKN populations developed on susceptible vegetables. They were controlled by the green manure but not by the R-pepper, and were also vulnerable to low soil temperatures. At the site without RKN, Paratylenchidae populations developed on susceptible vegetables, but were controlled by both the green manure and the R-pepper, and not by low temperatures. At each site, populations of Telotylenchidae exhibited dynamics suggesting competition with RKN or Paratylenchidae. Hypotheses about competition models are discussed according to the specific life traits of the PPN involved, including ecto- vs. endoparasitism and sedentary vs. free-living behaviour, and to the antagonist mechanisms of the cover and resistant crops that must be introduced in vegetable cropping systems.

Meloidogyne javanica is considered as the most damaging nematode of vegetables in Morocco. Eco-friendly bionematicides are urgently required for its control. In vitro experiments were carried out to assess the direct effect of bioproducts of Peganum harmala against M. javanica. The bioassay showed extracts to be nematotoxic. Aqueous extracts of P. harmala exhibited reversible nematostatic activity. The estimated ID50 of the most active product in methanolic extracts was 368ppm. HPLC-MS of the methanolic extract revealed that total content of major alkaloids of P. harmala was approximately 12.162±0.637mg/g. Harmine (8.514±0.521mg/g) is the dominant alkaloid. In conclusion, Peganum harmala has a reversible nematostatic activity on second stage juveniles of M. javanica. The effect of P. harmala is due to its possession of a high content of β-carboline alkaloids, which warrant further experimentation. Bioproducts from P. harmala should be exploited through formulations for management of the root knot nematode.

International audience; Plant-parasitic nematodes (PPN) are key impediments to efficient global crop production and impair the quality of susceptible plants in nurseries as well. In this context, nematode communities were determined in 305 solid substrate samples collected from 25 olive (Olea. europaea. subsp. europaea) nurseries in Morocco. Taxonomical and functional diversity as well as the structures of PPN communities were described and then compared between regions, cultivars as well as according to biotic and abiotic factors. A high diversity of PPN was observed, with the detection of 63 species and 26 genera. The most dominant taxa detected were spiral nematodes (Helicotylenchus spp. and Rotylenchus spp.), stunt nematodes (Tylenchorhynchus spp.), grazer nematodes (Tylenchus spp.) and root-knot nematodes (Meloidogyne spp.). Hoplolaimidae nematodes (Helicotylenchus spp. and Rotylenchus spp.) and Tylenchus spp. were better adapted to rainy conditions that prevailed in the northern regions of Morocco. Multiblock analyses demonstrated that functional diversity (cp and trophic groups) was more affected by the environment than taxonomical diversity (total number, species richness, locale diversity and evenness). They also indicated that PPN communities were more impacted by climatic variables (rainfall and minimum temperature) and nursery substrate origins than by soil physic-chemical factors. Nevertheless, a co-inertia analysis showed that N, P and K amendments in olive nurseries enhanced the development of harmful PPN, especially root-knot nematodes.

Background Root-knot nematodes (RKN) are major pest of olive tree (Olea europaea ssp. europaea), especially in nurseries and high-density orchards. Soil samples were collected from main olive growing areas of Morocco, to characterize Meloidogyne species and to discuss the contribution of biotic and abiotic factors in their spatial distribution. Results RKN were found in 159 soil samples out of 305 from nurseries (52.1% occurrence) and in 11 out of 49 soil samples from orchards (23.2% occurrence). Biochemical and molecular characterisation (PAGE esterase and SCAR) revealed the dominance of M. javanica both in nurseries and orchards with minor presence of M. incognita only in nurseries, and M. arenaria in only one nursery. RKN were distributed on aggregated basis. Frequent presence of M. javanica in orchards might have come from nurseries. In contrast, the detection of M. incognita in nurseries alone suggests that this species could not reproduce in orchards because of either the competition with other plant-parasitic nematodes or unfit local habitats. The impact of environmental variables (climate, habitat origin and physicochemical characteristics of the substrates) on the distribution of Meloidogyne species is also discussed. Conclusion Olive nurseries in Morocco are not able to guarantee the safety of rooted plants. As a result, olive production systems are exposed to strong RKN invasion risks. Consequently, the use of healthy substrates in nurseries may prevent plant-parasitic nematode induction in orchards.

Plant-parasitic nematodes are major pests in agriculture. Microbial antagonists such as nematophagous fungi are of great interest for developing alternative biocontrol strategies to replace nematicide use. This study aims to isolate, identify and assess the diversity and the in vitro predatory activity of nematophagous fungi from various olive nurseries in Morocco. A total of 305 soil samples were collected in 25 nurseries in Moroccan olive-producing areas (Jbala, Guerouane, Haouz and Souss). Seventy-three pure fungal strains from nematophagous fungi were recovered from nursery substrates infested with root-knot nematodes. Diversity indices showed that fungi were more numerous in southern regions, whereas fungal communities were more numerically alike in northern regions, partly depending on the occurrence of root-knot nematodes. One fungal strain, Talaromyces assiutensis , killed all Meloidogyne javanica juveniles during in vitro predation tests. Orbiliaceae ( Arthrobotrys spp., Drechslerella brochopaga , Monacrosporium spp.) trapped 50 to 80% of juveniles. Purpureocillium and Trichoderma species killed 30 to 50% of juveniles. The diversity of nematophagous communities could be affected by the north-south climate gradient of Morocco, by their nematode prey expansion, and, to a lesser extent, by the habitat origin of the substrates used. Talaromyces assiutensis was the most efficient nematophagous species against M. javanica . The use of native nematophagous fungi is a promising alternative strategy for nematode control in olive nurseries and to prevent nematode introduction into olive orchards.

International audience; Knowing which factors affect the distribution of organisms provides useful insights for the management of biodiversity. For root-knot nematodes Meloidogyne (RKN), a critical threat in agriculture, an understanding of the constraints that impact their diversity is a fundamental prerequisite for their control. RKN are reported to be major pests on olive trees, mainly in high-density orchards and in nurseries. This study was undertaken in order to characterise the Meloidogyne species associated with olive trees in Morocco and to consider how anthropogenic stresses and some edaphic and climatic factors may be involved in their spatial distribution. A soil sampling was conducted in the main olive growing areas in Morocco, including wild, feral and cultivated olive trees. RKN were detected in 12.2% of the samples. The analysis of biochemical (esterase patterns) and molecular (SCARS, D2D3) markers revealed the occurrence of M. javanica (as the predominant species), M. arenaria, M. hapla,M. spartelensis and of an undescribed species Meloidogyne n.sp. Some esterase variability was detected in M. javanica and M. hapla populations. The RKN species were distributed everywhere on an aggregated basis. However, M. javanica was recorded in high abundance throughout the cultivated areas in Morocco in high-density and traditionally cultivated olive orchards and rarely on some feral olive, while the other species were detected in low abundance on wild olive in mountain plant refuge areas in northern and southern Morocco. Nevertheless, the large distribution of M. javanica in cultivated areas could be primarily due to widespread introductions from nurseries, followed by multiple founder processes favoured by local conditions such as irrigation and planting density. In contrast, the detection of the other species hosted by wild olive only in plant refuge areas suggest that these areas host ancestral nematode species that did not disperse in the absence of human activities.

Farming activities that are likely to induce the development of emerging pests increasingly disturbs the Argan Biosphere in Morocco. Considering that plant-parasitic nematodes strongly contribute to the decrease in plant growth production, a survey was conducted in the Argan Biosphere in order to assess nematode diversity and distribution. It was established that the parasitic nematofauna was rich, with 70 species belonging to 34 genera and 12 families. Species with high plant decay potential belonging to Longidoridae, Heteroderidae, Hoplolaimidae, Meloidogynidae, Paratylenchidae and Pratylenchidae are present in the argan forest. Telotylenchus sp., Paratylenchus microdorus and Paratylenchus veruculatus , Xiphinema italiae and Xiphinema pachtaicum (virus-transmitting nematodes), and Helicotylenchus crassatus are the most dominant species. Populations of root-knot ( Meloidogyne spp.) and lesion ( Pratylenchus spp.) nematodes are also present. Climate forces have driven the structuration of the argan forest to topoclimatic landscapes that led the diversity of the plant-parasitic nematodes communities. The north–south typology of the arid climate affects the richness and the taxonomic and functional diversity of nematodes, while the west–east temperature typology mainly affects the abundance of nematodes, especially of colonizing species. The emergence of plant-parasitic nematode problems as a consequence of intensive agroforestry or argan orchard development is considered.

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International audience; Plant-parasitic nematodes affect significantly the production of susceptible plants, including olive trees. In this context, nematode communities were determined in soil samples collected from 23 olive growing sites in the Haouz and Souss regions (southern Morocco). These sites corresponded to various modalities: wild (Olea europaea L. ssp. sylvestris) or cropped olive (Olea. europaea L. ssp. europaea), traditional or high-density cropping, rainfed or irrigated. Even free-living nematodes prevailed in most of the sites, high population levels of plant-parasitic nematodes were observed in rainfed cropping systems than in irrigated systems. Ten nematode families and 14 genera were identified. The most important plant-parasitic nematodes detected, in order decreasing frequency of infestation (percentage of samples), were spiral nematodes Helicotylenchus spp. (100%) and Rotylenchus spp. (87%), lesion nematodes Pratylenchus spp. (100%) and root-knot nematodes Meloidogyne spp. (40%). Most of the nematode species were assigned to more or less colonizer nematodes, whereas only one family (Longidoridae) was assigned to persistent nematodes. Considering the two producing areas, plant-parasitic nematodes were significantly more abundant in the Souss region than in the Haouz region, but nematode diversity was higher in the second one. The prevalence of Meloidogyne spp. in the Haouz region would be related to the predominance of irrigated cropping systems in this region. Hoplolaimidae nematodes (Helicotylenchus spp. and Rotylenchus spp.) are better adapted to rainfed conditions that prevail in the Souss region. Co-inertia analysis showed the importance of soil physic-chemical characteristics (e.g., pH, texture and nutrients) on the structure of the plant-parasitic nematode community patterns. The high occurrence of Helicotylenchus spp. in olive orchards may be induced by fertilization. Aphelenchoides spp., Gracilacus spp., Pratylenchus spp., Rotylenchidae and Tylenchidae were supported by coarse textures as it was observed in the Souss region.

Human activities increasingly frequent and persistent in ecosystems on one hand, and cropping system intensification on the other hand partly with radical methods to control pests and diseases of crops, raise questions about the ecological risks related to biotop changes, including disturbances of living organism communities. Plant-parasitic nematodes (PPN), microscopic round soil-borne worms that cause significant losses of crop production, are everywhere present in communities. They respond quickly to external forces (e.g. human and environmental) by changing the structure of their communities. In this thesis, we seek to better understand the effect of the factors involved in the assemblage of PPN species in communities associated with the Mediterranean olive tree and to determine the response of these communities to forces imposed by olive domestication, by crop intensification and by various environmental factors. The study was conducted in all olive-growing regions in Morocco (traditional low density and high density orchards), in refugia areas for wild olive (oleaster) and on feral olive trees. The soil and climatic factors that characterize the sampling sites were also considered. The analysis of the nematofauna revealed a wide species diversity, many species being described for the first time on olive tree, and a new species (Meloidogyne spartelensis) have been discovered. The diversity, the species / trophic / functional structure of the communities, the dominance of the taxa, and the community patterns are strongly affected by the various forces considered. The increasing anthropogenic gradient (wild vs feral vs traditional cultivation vs high-density cultivation) is the variable that mostly impacts the diversity by reducing the species richness and increasing the abundance of PPN. A particular attention was attributed in this study to the diversity of root-knot nematodes Meloidogyne, a major pest of the olive tree. It revealed that M. javanica is widespread in orchards and olive feral, while other species (M. arenaria, M. hapla and M. spartelensis) are confined in oleaster refuge areas. In order to analyse the genetic diversity, morphological and molecular markers have revealed a significant diversity between and within different Meloidogyne populations. These thesis studies confirm that both the diversity and the structure of the PPN communities could be relevant indicators to assess soil health in agro and ecosystems, by correlating diversity and pathogenicity of communities. They therefore emphasize the importance of parasite diversity as a main variable to consider for inspiring pest control strategies based on the concept of diversity resilience (even if it concerns parasites) for sustainable management of PPN communities and for environment preservation., Les interventions humaines de plus en plus fréquentes et persistantes dans les écosystèmes d'une part, et l'intensification des systèmes de cultures d'autre part qui s'accompagne pour partie de méthodes radicales pour combattre les bio-agresseurs des cultures, nous posent de multiples questions au sujet des risques écologiques liés aux changements des milieux, dont les perturbations induites sur les communautés d'organismes vivants. Les nématodes phytoparasites (NPP), vers ronds microscopiques telluriques qui occasionnent des pertes de production végétale importantes, sont partout présents en communautés. Ces nématodes répondent rapidement aux forçages extérieurs (e.g. anthropiques et environnementaux) par des modifications de la structure de leurs communautés. Par ce travail de thèse, nous cherchons à mieux comprendre l'effet des facteurs impliqués dans l'assemblage des espèces de NPP en communautés associées à l'olivier méditerranéen et à déterminer la réponse de ces communautés aux forçages imposés par la domestication de l'olivier, par l'intensification de sa culture et par différents facteurs environnementaux. L'étude a été réalisée au Maroc dans toutes les régions oléicoles (vergers traditionnels à faible densité et vergers à haute-densité), dans les zones refuge d'olivier sauvage (oléastre) et sur olivier féral. Les facteurs pédoclimatiques qui caractérisent les sites d'échantillonnage ont également été pris en considération. L'analyse de la nématofaune a révélé d'une grande diversité spécifique, de nombreuses espèces étant décrites pour la première fois sur olivier, et une nouvelle espèce (Meloidogyne spartelensis) ayant été découverte. La diversité, la composition taxonomique, trophique et fonctionnelle, la dominance des taxons, les patrons de communautés sont fortement affectés par les différents forçages pris en compte. Le gradient d'anthropisation croissante (sauvage vs féral vs cultivé traditionnel vs cultivé haute-densité) est la variable qui impacte le plus la diversité par réduction de la richesse spécifique et l'augmentation de l'abondance en NPP. L'étude a également porté une attention particulière sur la diversité des nématodes à galles des racines du genre Meloidogyne, un des principaux ravageurs de l'olivier. Elle a indiqué la dispersion de M. javanica dans les vergers et sur olivier féral, alors que d'autres espèces (M. arenaria, M. hapla et M. spartelensis) sont confinées dans les zones refuge des oléastres. Afin d'analyser la diversité génétique, des marqueurs morphologiques et moléculaires ont dévoilé d'une diversité importante entre et au sein des différentes populations de Meloidogyne. Les études diligentées dans le cadre de cette thèse confirment que la diversité et la structure des communautés de NPP pourraient être des indicateurs pertinents pour évaluer la santé des sols dans les agro et écosystèmes, en corrélant diversité et pathogénicité des communautés. Elles soulignent donc l'importance de la diversité parasitaire comme variable prioritaire à prendre en compte pour inspirer des stratégies de gestion des parasites basées sur le concept de résilience de la diversité (même s'il s'agit de parasites), pour une gestion durable des communautés de NPP et la préservation des milieux.