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Soil biota plays an essential role in ecosystem services such as carbon fixation, nitrogen and phosphorous cycling, and disease suppressiveness. Conventional soil management with large inputs of mineral fertilizers and pesticides have a significant impact on primary decomposer communities (bacteria and fungi), as well as on protists and metazoa, representatives of the next trophic level. Organic soil management is thought to contribute to a more diverse and stable soil food web. However, information to pinpoint this supposed beneficial effect is sparse and fragmented. Keeping in mind that a substantial fraction of the soil biota is dormant, we set out to map both the resident and the active the bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as main crop. For all four organismal groups, the contrast between resident (rDNA-based) and active (rRNA-based) was the most important explanatory variable explaining 22%, 14%, 21% and 25% of the variance among bacterial, fungal, protozoan, and metazoan communities. Less prominent were the effects of soil management and soil type, however significant as well for all four organismal groups. LEfSe was used to identify indicator taxa for both the contrasts between resident and active communities, and the effects of soil management. Our results suggest that - next to DNA-based community characterisation - mapping of the active microbial community could provide essential insights in the effects of variables such as crop and soil management on the soil living community.

Soil-borne cyst nematodes are obligatory sedentary parasites that cause severe losses to cultivation of major crops such as potato and soybean. Cyst nematodes establish specialised permanent feeding sites within the roots of their host by manipulating plant morphology and physiology through secreted effectors. Here we identified host targets of effector GpRbp-1 and studied their roles in plant-nematode interactions. GpRbp-1 was found to interact in yeast and in planta with the potato and Arabidopsis homologues of Siz/PIAS-type E3 SUMO ligase SIZ1. Our results show that a pathogen effector targets the master regulator SIZ1 in plant cells, which has not been demonstrated earlier to our knowledge. The interaction of GpRbp-1 and SIZ1 localizes to the plant nucleus, suggesting that the nuclear functions of SIZ1 as regulator of plant immunity and physiology may be modulated by GpRbp-1. Furthermore, nematode infection assays and transcriptomic profiling indicate that SIZ1 is required for susceptibility to cyst nematodes. So, these data indicate that E3 SUMO ligases may play an important role in plant-nematode interactions. Based on the prediction of SUMO acceptor and interaction sites in GpRbp-1, a model is proposed in which the effector may recruit SIZ1 to be SUMOylated for full functionality in host cells.

The present invention relates to a method for determining the presence of a cyst nematode in a sample comprising the steps of : providing a pair of bidirectional oligonucleotide primers or an oligonucleotide probe that hybridizes specifically, under stringent hybridization conditions, to a nucleic acid sequence encoding the SSU rRNA or LSU rRNA, or the complement or transcript thereof, of a sub genus-cluster of nematodes, said subgenus-cluster comprising cyst nematodes belonging to at least one species of nematode, and wherein said primers or probe do not hybridize to a nucleic acid sequence encoding the LSU rRNA, or the complement or transcript thereof, of cyst nematodes not part of said subgenus-cluster of cyst nematodes; providing a sample in which the presence of the cyst nematode is to be detected, and performing a nucleic acid detection assay on said sample using said pair of bidirectional oligonucleotide primers or said oligonucleotide probe.

Nematodes – “eel worms”; members of the phylum Nematoda – can be considered as a success story within the Metazoa (multicellular, heterotrophic eukaryotes in which cells lack cell walls): they are speciose and – probably - the most numerous group of multicellular animals on our planet. Nematodes are present in virtually all terrestrial, freshwater and marine habitats. Nematodes are trophically diverse; they may feed on bacteria, fungi/oomycetes, algae and protozoa, other nematodes or on a combination of these (omnivores), or live as facultative or obligatory parasites of plants or animals. As they are abundant, ubiquitous and occupy several trophic levels, they play an important role in the soil food web. Nematode parasites of animals affect billions of humans and livestock, while plant parasites such as cyst, root knot and lesion nematodes cause large agricultural losses worldwide. Despite their undisputed ecological and economical relevance, the systematics of the phylum Nematoda is far from established. One of the aims of this research was to further elucidate nematode phylogeny using molecular data. First a phylogenetic tree was constructed of 349 taxa, spanning the entire phylum Nematoda, on the basis of full length small subunit ribosomal DNA (SSU rDNA) sequences. A series of mostly well-supported bifurcations defined twelve major clades, whereas the most basal clade was defined by representatives of the Enoplida and Triplonchida. Our analysis confirmed the paraphyly of the Adenophorea. Furthermore it was found that the SSU rDNA from representatives of the distal clades evolved at a higher rate than the SSU rDNA from the basal clades. In the meantime, a substantial number of sequences was added to our overall SSU rDNA nematode alignment - both public data (GenBank) and data generated by ourselves (≈ 1,500 sequences in total; February 2008). It is noted that the clade division as proposed in 2006 on the basis of “only” 349 taxa still seems to be valid. Subsequent research focused on three specific groups; Dorylaimia, Chromadoria and Tylenchomorpha. Within the suborder Dorylaimina, the SSU rDNA provided an exceptionally low phylogenetic signal, and - therefore – a part (≈ 1,000 bp) of the more variable large subunit ribosomal DNA (LSU rDNA) was analyzed. In most cases nematode relationships could be elucidated with good support, although some areas in the trees remained unresolved. Generally speaking the results of molecular phylogenetics corresponded fairly well with classical nematode taxonomy. The main exception was the order Dorylaimida where twelve subclades could be distinguished which bore little resemblance to classical taxonomy. Furthermore the suitability of ribosomal DNA for a (semi-) quantative molecular identification method was demonstrated using quantitative PCR (q-PCR) and primers designed to specifically amplify members of the order Mononchida and the potato cyst nematodes Globodera pallida and G. rostochiensis. Plant parasitism has arisen several times within the phylum Nematoda (once in the Triplonchida, at least three times in the Dorylaimida and at least twice in the Tylenchomorpha). The long-standing and generally accepted hypothesis states that plant parasites evolved from fungal feeding ancestors. However, while in most cases plant parasites were associated with fungal feeding nematodes, this hypothesis could neither be confirmed nor denied with the results of our phylogenetic analyses. In the case of two Dorylaimida (Pungentus and Longidorella), however, the ancestor was probably an omnivore. The analysis of this problem was substantially hampered by the lack of knowledge on feeding behavior of basal Tylenchomorpha. Presumably, the common ancestor of the nematodes lived in a marine environment and - if this assumption is correct - the transition to a limnoterrestrial environment must have taken place at least once. Surprisingly, analysis of the Chromadoria (minus the Rhabditida) revealed that transitions from a thalassic to a limnoterrestrial habitat (and vice versa) have taken place at least 11 times in the Chromadoria. Given their frequency these transitions are apparently fairly easy to achieve for nematodes and the possible adaptations involved were discussed. Nematodes vary widely in their responses to environmental disturbance, making them good bio-indicators of soil health. Yet it is not known with certainty which traits are responsible for tolerance to stress in nematodes. A framework was laid out to study correlations between nematode traits and stress tolerance. Furthermore the importance of accounting for the confounding effects of phylogeny was demonstrated. This is a first step towards a transparent, ecological grouping of free-living nematodes. It is worthwhile mentioning that - on the basis of the rDNA-based molecular framework described in this PhD thesis - DNA sequences signatures were identified for nearly all North-West European terrestrial and freshwater nematodes families. The relationship between quantitative PCR signal and numbers of individuals has been established for nearly all families and a first testing of DNA barcode-based community analysis is planned for spring 2008.

Nematoden vormen één van de meestgevarieerde en succesvolle diergroepen ter wereld. Ze zijn waarschijnlijk de meest talrijke dieren op aarde, komen in uiteenlopende milieus voor (zowel terrestrische als marien) en spelen een belangrijke rol in het ecosysteem. De verscheidenheid van voedingstypes en habitats maken deze groep ook erg interessant vanuit een evolutionair oogpunt. Ons onderzoek richt zich op het uitzoeken van de evolutionaire verwantschappen tussen nematoden aan de hand van het ribosomaal DNA - een neutraal gen dat niets te maken heeft met dier- of plantparasitisme - en de evolutie van kenmerken als voedingstypen, stresstrolerantie en de overgang van een marien leefmilieu naar het land. Nematodentaxonomie is een onderzoeksveld dat sinds het begin in beweging is geweest. De geconserveerde morfologie en de vaak moeilijk waarneembare kenmerken bemoeilijken de reconstructie van de evolutie van de nematoden. Dit heeft tot gevolg gehad dat de nematodensystemetiek steeds veranderde en er bijna net zoveel classificaties als taxonomen zijn. De laatste jaren is er veel veranderd door de opkomst van de moleculaire fylogenie. Het gebruik van DNA-sequenties - in het geval van vaak het small subunit ribosomal DNA (SSU rDNA)-gen - om de evolutie te traceren heeft geleid tot nieuwe inzichten en een hernieuwde interesses in nematodenevolutie

The present invention relates to a method method of testing a sample for the presence of a Meloidogyne nematode, said method comprising the step of analyzing the nucleic acid in said sample for the presence of an rRNA gene of a Meloidogyne nematode, or the transcription product thereof, or a fragment thereof, comprising at least one single nucleotide polymorphism (SNP) and/or at least one oligonucleotide polymorphism (OP) that is essentially unique on phylum level to a specific group of Meloidogyne nematode species of which said Meloidogyne nematode is a member, wherein said step of analyzing said nucleic acid involves a nucleic acid hybridization assay, and wherein said group comprises (a) the species M. chitwoodi, M. fallax