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Questions we would like to address: Curiosity driven Qs:
- what did the mother-of-all-nematodes look like?
Are we able to identify a living representative that is close to the common ancestor of all nematodes?
where do nematodes come from?
Did nematodes arise from marine habitats, if so how often did they invade terrestrial or freshwater habitats? Can we identify groups that returned (regretfully) back to the sea?
how did plant parasitic nematodes arise?
A number of genes have been identified that are needed to exploit plants as a food source. Where did they get these genes from (various donors for distinct lineages?) & how
More practical Qs:
- can we link specific kinds of environmental stress / pollution to defined changes in nematodes communities? DNA barcode-based nematode community analysis will presumably allow us to address this question.
- can we relate nematode community composition to soil suppressiveness? Because of the (trophic) diversity of nematode communities, we will investigate whether we can pinpoint this desirable but badly defined phenomenon on the basis of detailed community analyses.
- would it be possible to analyse – in one go – all known plant parasites in a soil sample of any size, and assess the agro-economical risks?
Small and/or large subunit ribosomal DNA sequences offer excellent resolution till species level for all plant parasites investigated so far including cyst, root knot, lesion and burrowing nematodes. On this basis it would be possible to assess the foreseeable impact of these pathogens during the crop growing season (especially relevant in case (chemical) curative measures are not allowed or scarce, such as in organic farming).
Nematodes constitute one of the largest and most widely distributed groups of animals in marine, freshwater and terrestrial habitats. Their numerical dominance, exceeding often more than one million individuals per square meter and accounting for about 80% of all individual animals on earth, their diversity in lifestyles and their presence at various trophic levels (they may feed on bacteria, fungi, other nematodes, algae etc.) point at an important role in many ecosystems (see figure below).
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Fig 2:Trophic relationships within terrestrial habitats. Because of their trophic diversity
and their abundance, nematodes play a central role in the soil food web.
(Source:USDA Natural Resources Conservation Service) |
Morphology-based nematode systematics.
One of the earliest and most influential classifications of the Nematoda was proposed by Chitwood and Chitwood (1933). They introduced a division of the phylum into the Aphasmidia and Phasmidia, later renamed Adenophorea (‘gland bearers’) and Secernentea (‘secretors’) respectively. This division was based on the fact that the Secernentea share several characteristics including the presence of phasmids, a pair of sensory organs located in the lateral posterior region. This division was adhered to in many later classifications even though it was realized that the Adenophorea were not a uniform group. Within the Adenophorea, Andrassy (1984) distinguished two subclasses, the Torquentia and the Penetrantia. For decades, nematode systematics has been unstable, and articles on nematode systematics invariably started by stating whose classification is used (!).
DNA-based nematode systematics
The scarcity of informative morphological characters made it difficult if not impossible to come up with robust deep phylogenetic relationships within this phylum. Provided true orthologues are used DNA sequence data are very powerful in resolving complex phylogenetic relationships. The first phylum wide framework was proposed about 10 years ago by Blaxter and co-workers (1998). Based on 53 full length SSU rDNA sequences they subdivided the nematodes into 5 major clades (I, II, III, IV and V, see below). More recently, about 350 SSU rDNA sequences were generated by Holterman et al. (2006), and these data suggested fore a subdivision of the phylum Nematode into 12 clades (1, 2, …, 12, see below). In the meantime, the total SSU rDNA alignment includes more than 1,400 sequences and the subdivision of the phylum as proposed by Holterman et al. (2006) still seems to hold. >> Click here for the article.
Identifying (and quantifying) needles in a haystack.
Well-supported phylogenetic resolution will - in most cases – allow for DNA barcode-based species genus and / or family identification. Plant parasites often constitute a small minority within a large pool of bacterivorous, fungivorous, carnivorous and omnivorous nematodes. Because we have characterized a substantial part of the North West European terrestrial and freshwater nematode fauna, it is possible to define DNA sequence signatures characteristic for a given pathogen and absent in all other nematodes (as far as known). By doing, we are able to (quantitatively) analyse large soil samples and detect a single nematode in a pool of 10,000 non targets.
On the basis of the same molecular framework, we are currently working on the full characterisation of terrestrial and freshwater nematode communities at family level. For the proof-of-concept for a particular stress sensitive group see Holterman et al. 2007.
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Example of DNA barcode-based community analysis –
identification and quantification of members of the family Plectidae in a soil sample.
Picture: H. Helder |
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