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Abstract Background Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5) cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. Interestingly, ancestors of extant nematodes most likely acquired these GHF5 cellulases from a prokaryote donor by one or multiple lateral gene transfer events. To obtain insight into the origin of GHF5 cellulases among evolutionary advanced members of the order Tylenchida, cellulase biodiversity data from less distal family members were collected and analyzed. Results Single nematodes were used to obtain (partial) genomic sequences of cellulases from representatives of the genera Meloidogyne, Pratylenchus, Hirschmanniella and Globodera. Combined Bayesian analysis of ≈ 100 cellulase sequences revealed three types of catalytic domains (A, B, and C). Represented by 84 sequences, type B is numerically dominant, and the overall topology of the catalytic domain type shows remarkable resemblance with trees based on neutral (= pathogenicity-unrelated) small subunit ribosomal DNA sequences. Bayesian analysis further suggested a sister relationship between the lesion nematode Pratylenchus thornei and all type B cellulases from root-knot nematodes. Yet, the relationship between the three catalytic domain types remained unclear. Superposition of intron data onto the cellulase tree suggests that types B and C are related, and together distinct from type A that is characterized by two unique introns. Conclusions All Tylenchida members investigated here harbored one or multiple GHF5 cellulases. Three types of catalytic domains are distinguished, and the presence of at least two types is relatively common among plant parasitic Tylenchida. Analysis of coding sequences of cellulases suggests that root-knot and cyst nematodes did not acquire this gene directly by lateral genes transfer. More likely, these genes were passed on by ancestors of a family nowadays known as the Pratylenchidae.

As a result of the scarcity of informative morphological and anatomical characters, nematode systematics have always been volatile. Differences in the appreciation of these characters have resulted in numerous classifications and this greatly confuses scientific communication. An advantage of the use of molecular data is that it allows for an enormous expansion of the number of characters. Here we present a phylogenetic tree based on 1215 small subunit ribosomal DNA sequences (ca 1700 bp each) covering a wide range of nematode taxa. Of the 19 nematode orders mentioned by De Ley et al. (2006) 15 are represented here. Compared with Holterman et al. (2006) the number of taxa analysed has been tripled. This did not result in major changes in the clade subdivision of the phylum, although a decrease in the number of well supported nodes was observed. Especially at the family level and below we observed a considerable congruence between morphology and ribosomal DNA-based nematode systematics and, in case of discrepancies, morphological or anatomical support could be found for the alternative grouping in most instances. The extensiveness of convergent evolution is one of the most striking phenomena observed in the phylogenetic tree presented here - it is hard to find a morphological, ecological or biological characteristic that has not arisen at least twice during nematode evolution. Convergent evolution appears to be an important additional explanation for the seemingly persistent volatility of nematode systematics. [ABSTRACT FROM AUTHOR]

Biological indicators are highly relevant for assessing the condition of a soil as they are integrative; they reflect the overall impact of physical, chemical and biological changes. Indigenous soil organisms are preferable to other test organisms because the diversity and condition of indigenous soil organisms reflect both acute and chronic effects of soil disturbances. Nematodes are ubiquitous, speciose, easily extractable and present in extremely high numbers. Given the ever increasing amount of sequence data, DNA barcode-based community analysis will soon be possible and a next step would be to define objective criteria for the ecological grouping of soil nematodes. Here, we present a framework to ascertain which traits are correlated with a tolerance to stress. For this, a field study on the effects of pH and copper on nematode communities was re-analysed. Changes in abundances of individual genera were correlated with a number of potentially stress tolerance-related characteristics. The generalised least squares (GLS) method was used to account for the phylogenetic dependence of the data. Only the relationship between the ability to enter a survival stage and tolerance to copper at pH 6.1 was found to be significant, but the quantity of missing data probably had a negative impact on the analyses. This study did, however, clearly demonstrate the importance of accounting for the effects of phylogenetic dependence in the data. When the phylogeny was taken into account, we observed an average change in P value of 0.196 (and in some cases as much as 0.6) for the correlations of possible stress-related characteristics and Cu or pH tolerance. This research constitutes a proof-of-principle for a transparent method to relate stress tolerance to (ecological) characteristics. The usefulness of this powerful method should become even clearer when substantially higher numbers of individuals are analysed (as facilitated by using DNA barcodes) and when missing data are filled in. [ABSTRACT FROM AUTHOR]