Assessment of nematode biodiversity using DGGE of 18S rDNA following extraction of nematodes from soil

Soil nematodes are both taxonomically and functionally diverse, respond quickly to soil perturbation and have much potential as indicators of soil health. However, because of the perceived difficulty of identifying nematodes to species level morphologically, they are frequently neglected in soil ecological studies. Recently, extraction of soil DNA, amplification of 18S rDNA genes using nematode consensus primers and subsequent separation by denaturing gradient gel electrophoresis (DGGE) has been used to estimate nematode diversity in soil. Here, we investigate an alternative approach whereby nematodes are first extracted from the soil prior the 18S rDNA gene amplification using universal primers. We used this system to estimate nematode species richness in 10 soil samples-five from Scotland and five from the Netherlands. There was no direct correlation between species richness as estimated morphologically and by the PCR-DGGE method. However, inspection of the data suggested that the samples fell into two discrete groups, which was confirmed by canonical and stepwise discriminant function analysis; the values for the Shannon and equitability indices being important discriminators. Further analysis revealed a significant relationship between morphological species richness and DGGE estimates for species that represented greater than 1% of the sample biomass. (C) 2004 Elsevier Ltd. All rights reserved.