Periodic Reporting for period 1 - NEM-EMERGE (An integrated set of novel approaches to counter the emergence and proliferation of invasive and virulent soil-borne nematodes)
Reporting period: 2024-01-01 to 2025-06-30
Nem-Emerge: An integrated set of novel approaches to counter the emergence and proliferation of invasive and virulent soil-borne nematodes
Soil-borne plant-parasitic nematodes are a biosecurity risk for global food production with an estimated annual loss of €110 billion worldwide. Root-knot nematodes (RKN) and potato cyst nematodes (PCN) rank 1 and 2 in the Top 10 of high-impact plant-parasitic nematodes with RKN alone accounting for ~5% of global crop losses. RKN and PCN are A2 quarantine pests or emerging species listed on the EPPO Alert List. The two PCN species are also included in EU Commission implementing regulation 2021/2285. Recent reports document the emergence of new RKN and PCN problems in tomato and potato cropping across Europe and beyond due to two independent drivers: global warming and genetic selection. For decades, environmentally harmful agrochemicals have been applied to manage RKN and PCN. The increasing awareness about their negative impact prompted the phasing out of most nematicides. Consequently, there is a need for novel, durable control strategies that enable adequate responses by stakeholders to prevent crop losses in the EU and beyond.
The overall aim of NEM-EMERGE is to support sustainable food production in the EU and Associated and Third Countries by the development of environmentally-sound, non-GMO solutions that counteract the effect of global warming and genetic host selection on the proliferation and increased virulence of the two most devastating plant-parasitic nematodes in major food crops.
Fig. 1. Nem-Emerge overall objectives.
Soil-borne plant-parasitic nematodes are a biosecurity risk for global food production with an estimated annual loss of €110 billion worldwide. Root-knot nematodes (RKN) and potato cyst nematodes (PCN) rank 1 and 2 in the Top 10 of high-impact plant-parasitic nematodes with RKN alone accounting for ~5% of global crop losses. RKN and PCN are A2 quarantine pests or emerging species listed on the EPPO Alert List. The two PCN species are also included in EU Commission implementing regulation 2021/2285. Recent reports document the emergence of new RKN and PCN problems in tomato and potato cropping across Europe and beyond due to two independent drivers: global warming and genetic selection. For decades, environmentally harmful agrochemicals have been applied to manage RKN and PCN. The increasing awareness about their negative impact prompted the phasing out of most nematicides. Consequently, there is a need for novel, durable control strategies that enable adequate responses by stakeholders to prevent crop losses in the EU and beyond.
The overall aim of NEM-EMERGE is to support sustainable food production in the EU and Associated and Third Countries by the development of environmentally-sound, non-GMO solutions that counteract the effect of global warming and genetic host selection on the proliferation and increased virulence of the two most devastating plant-parasitic nematodes in major food crops.
Fig. 1. Nem-Emerge overall objectives.
Activities and main achievement Nem-Emerge (Months 1-18). Below main achievements will be presented on a per Workpackage (WP) basis.
To counteract the impact of global warming:
WP1. Tropical RKN detection toolkit (Deliverable (D)1). In the past, tropical RKNs referred to three species: Meloidogyne incognita, M. arenaria and M. javanica. Currently, this group includes other species such as M. enterolobii, M. luci and M. ethiopica. Microscopic identification of tropical RKN species is very hard as they very much look alike. Due to the hybrid nature of ‘tropical RKNs’ the nuclear DNA of these hybrid species show the characteristics of multiple species. Alternatively, species-specific non-nuclear DNA motifs were shown to be suitable for RKN identification. Our solution allows for the correct identification of tropical RKN in four steps: triage, amplification, sequencing and bioinformatic analysis. Our results indicate that this solution is capable of identifying temperate RKN species as well.
WP2. Heat stability signatures of plant resistances (D4). The current effective and economically viable genetic resistance to Meloidogyne spp is based on tomato plants carrying the Mi1.2 gene, but this resistance is broken at 28C. Hence, global warming currently threatens this crucial source of RKN control in tomato. A closer look was taken into the sequence of the Mi-1.2 gene and its temperature stable functional ortholog Mi-9 from tomato. In this way, 35 amino acid differences were identified which could explain their difference in temperature. We could further reduce this number by sequence comparison with other R gene homologs. By integrating this in silico information, we could pinpoint amino acid residues in specific subdomains that may contribute to Mi-1/Mi-9 immune activation.
To counteract the impact of genetic selection
WP3. Research goal: identification of molecular markers to discriminate virulent and avirulent RKN populations. Using an INRAE institutional RKN collection, the genomes of two avirulent M. incognita populations and their progenitor avirulent populations were sequenced with both Nanopore long-reads and AVITI short reads. Convergent deletions in the genomes of the two virulent populations were identified as compared to the avirulent ones. We hypothesize that individuals without and with these deletions co-exist in the population but at different frequencies. This suggests quantitative rather than qualitative molecular markers might be more suitable for early detection of virulent populations.
WP4. Research goal: identification of molecular motifs to discriminate virulent and avirulent PCN populations. Whole genome sequencing of successive generations of two Globodera pallida populations selected for virulence on resistant potato cultivars led to a single locus in G. pallida significantly associated with virulence on resistant potato cultivars. We hypothesize that the breakdown of resistance in potato involves a nematode effector in G. pallida. We therefore used typical features of nematode effectors to reduce the list of genes in the virulence locus to a single candidate effector. Interestingly, multiple single nucleotide polymorphisms (SNPs) in the genome of G. pallida are associated with this effector offering several options for developing a SNP-based virulence assay.
To counteract the impacts of both global warming and genetic selection
WP5. Protocol for characterization of nematode antagonist communities (D13). To map the microbial antagonist community associated with range-expanding ‘tropical’ root-knot nematode (RKN) species, a method was developed that utilizes in-house long-read DNA sequencing technology. Mapping microbial nematode antagonists requires identification of bacteria and fungi at the species level, and long-read DNA sequencing provides the necessary taxonomic resolution. Nematode-antagonists do not share common DNA signatures. By integrating information from authoritative reviews, we compiled a list of known nematode antagonists. This list was used to identify and characterize the nematode-antagonistic microbial community present in any given soil sample collected along the two major latitudinal sampling swaths as defined in the Nem-Emerge DoA.
Towards the actual use of Nem-Emerge developed innovations:
WP6. In the first period of the project, the main aim of the social media activity has been to promote the project. Therefore, apart from single posts highlighting some specific aspect or activity of the project, two strategic approaches have been followed for this purpose. On the one hand, two promotional campaigns have been carried out, one explaining the project’s objectives and ambitions, and the other one presenting all the consortium members, in the “Who is who?” campaign. In addition, on several international days related to the project (Plant Health Day, World Environment Day, Biodiversity Day), small campaigns have been carried out.
To counteract the impact of global warming:
WP1. Tropical RKN detection toolkit (Deliverable (D)1). In the past, tropical RKNs referred to three species: Meloidogyne incognita, M. arenaria and M. javanica. Currently, this group includes other species such as M. enterolobii, M. luci and M. ethiopica. Microscopic identification of tropical RKN species is very hard as they very much look alike. Due to the hybrid nature of ‘tropical RKNs’ the nuclear DNA of these hybrid species show the characteristics of multiple species. Alternatively, species-specific non-nuclear DNA motifs were shown to be suitable for RKN identification. Our solution allows for the correct identification of tropical RKN in four steps: triage, amplification, sequencing and bioinformatic analysis. Our results indicate that this solution is capable of identifying temperate RKN species as well.
WP2. Heat stability signatures of plant resistances (D4). The current effective and economically viable genetic resistance to Meloidogyne spp is based on tomato plants carrying the Mi1.2 gene, but this resistance is broken at 28C. Hence, global warming currently threatens this crucial source of RKN control in tomato. A closer look was taken into the sequence of the Mi-1.2 gene and its temperature stable functional ortholog Mi-9 from tomato. In this way, 35 amino acid differences were identified which could explain their difference in temperature. We could further reduce this number by sequence comparison with other R gene homologs. By integrating this in silico information, we could pinpoint amino acid residues in specific subdomains that may contribute to Mi-1/Mi-9 immune activation.
To counteract the impact of genetic selection
WP3. Research goal: identification of molecular markers to discriminate virulent and avirulent RKN populations. Using an INRAE institutional RKN collection, the genomes of two avirulent M. incognita populations and their progenitor avirulent populations were sequenced with both Nanopore long-reads and AVITI short reads. Convergent deletions in the genomes of the two virulent populations were identified as compared to the avirulent ones. We hypothesize that individuals without and with these deletions co-exist in the population but at different frequencies. This suggests quantitative rather than qualitative molecular markers might be more suitable for early detection of virulent populations.
WP4. Research goal: identification of molecular motifs to discriminate virulent and avirulent PCN populations. Whole genome sequencing of successive generations of two Globodera pallida populations selected for virulence on resistant potato cultivars led to a single locus in G. pallida significantly associated with virulence on resistant potato cultivars. We hypothesize that the breakdown of resistance in potato involves a nematode effector in G. pallida. We therefore used typical features of nematode effectors to reduce the list of genes in the virulence locus to a single candidate effector. Interestingly, multiple single nucleotide polymorphisms (SNPs) in the genome of G. pallida are associated with this effector offering several options for developing a SNP-based virulence assay.
To counteract the impacts of both global warming and genetic selection
WP5. Protocol for characterization of nematode antagonist communities (D13). To map the microbial antagonist community associated with range-expanding ‘tropical’ root-knot nematode (RKN) species, a method was developed that utilizes in-house long-read DNA sequencing technology. Mapping microbial nematode antagonists requires identification of bacteria and fungi at the species level, and long-read DNA sequencing provides the necessary taxonomic resolution. Nematode-antagonists do not share common DNA signatures. By integrating information from authoritative reviews, we compiled a list of known nematode antagonists. This list was used to identify and characterize the nematode-antagonistic microbial community present in any given soil sample collected along the two major latitudinal sampling swaths as defined in the Nem-Emerge DoA.
Towards the actual use of Nem-Emerge developed innovations:
WP6. In the first period of the project, the main aim of the social media activity has been to promote the project. Therefore, apart from single posts highlighting some specific aspect or activity of the project, two strategic approaches have been followed for this purpose. On the one hand, two promotional campaigns have been carried out, one explaining the project’s objectives and ambitions, and the other one presenting all the consortium members, in the “Who is who?” campaign. In addition, on several international days related to the project (Plant Health Day, World Environment Day, Biodiversity Day), small campaigns have been carried out.
A main structure of data exploitation and protection has been created. The necessary communication channels are in place, and the WP leads and co-leads are aware of their roles and contributions. The two workflows were approved by the partners in the consortium. Two core components of workflows were created using MS Teams channels. These are used for the storage of NEM-EMERGE outputs considered; 1) public domain (poster presentations, talks, paper submissions, etc.) and; 2) sensitive outputs (sensitive datasets, markers, opportunities for exploitation, etc.). WP lead and co-lead are responsible for approaching their WP partners to approve public domain outputs as well as for identifying opportunities for exploitation.