Research Topic: Phylogenetics and evolution

Soil is one of the most densely populated, competitive & complex (and therefore interesting!) habitats. Bacteria, fungi and nematodes are among the main inhabitants, but it also includes arthropods, protozoa, algae etc. Because of their abundance, their central place in the soil food web, their trophic diversity, and their diversity in responses towards environmental stressors, nematodes have a high potential as soil health indicators.

“Never change a winning team” could have been the motto of nematodes, a group of worm-like animals that arose in the early Cambrian (more than 500 million years ago). The morphological diversity of nematodes is relatively low, and this is the main reason why microscopic analysis of nematode communities is time and labor intensive (and not particularly exciting).

Schematic overview of the evolution of the phylum Nematoda derived from SSU rDNA sequence data (based on Holterman et al., 2006). Three major lineages of plant parasites are indicated by dotted boxes (Tylenchomorpha, Dorylaimida and Triplonchida). It is noted that the infraorder Tylenchomorpha is a polyphyletic group; it includes the members of Clade 12 and the Aphelenchoididae, a family within Clade 10. » Click here for an enlargement of the schematic overview/Picture: Wim Bert, Gerrit Karssen en Johannes Helder
Schematic overview of the evolution of the phylum Nematoda derived from SSU rDNA sequence data (based on Holterman et al., 2006). Three major lineages of plant parasites are indicated by dotted boxes (Tylenchomorpha, Dorylaimida and Triplonchida). It is noted that the infraorder Tylenchomorpha is a polyphyletic group; it includes the members of Clade 12 and the Aphelenchoididae, a family within Clade 10. » Click here for an enlargement of the schematic overview/Picture: Wim Bert, Gerrit Karssen en Johannes Helder

Fortunately, the molecular diversity among nematodes is high, and this is offers great new opportunities. Nematodes contain just ≈ 0.2 ng of DNA, this may sound as a minor quantity but state of the art amplification methods allow us to detect less than 1/1.000 of a single nematode. We have created a data base that contains digital pictures from individual nematodes and molecular data - mostly full length small subunit ribosomal DNA (≈ 1.700 bp) - from that particular individual. The overall SSU rDNA alignment - the largest one in the world - includes at the moment (August 2010) over 2,000 specimen.

Currently, we are working on nematode phylogenetics and the evolution of plant parasitism (how did plant parasitism arise?). Apart from this we are developing a molecular tool for nematode community analysis at family level (see also Maturity Index). We have generated dozens of sets of family, genus or species specific PCR primers. The DNA barcoding tools make life of a soil ecologist and pathologists more pleasant than ever.

A parasitic life style accelerates evolution. Therefore and unexpectedly we could develop quantitative (Q-PCR-based) assays at species level for notorious plant parasites such as root knot (Meloidogyne sp.), cyst (Heterodera and Globodera sp.), lesion (Pratylenchus sp.), and burrowing (Radopholus sp.) on the basis of the SSU and LSU rDNA. For this we cooperate intensively with Prof. dr. Gerrit Karssen (Plant Protection Service of The Netherlands) and a number of commercial partners.