Comparison of nematode community similarities assessed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) and by morphological identification

Abstract

AbstractMolecular biology techniques for nematode community analysis that are high throughput and operable by non-experts are in high demand for soil biological assessments. In the development of such techniques, the closeness of the analytical results to those obtained by conventional methods is of key importance. In this context, we compared similarity relationships of nematode community structures between polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) and individual-based morphological identification (CONV) using 12 nematode samples recovered from crop field soils in four localities in Japan. First, we determined whether the primer set chosen to amplify the 18s rRNA genes of nematode taxa was suitable for DGGE by comparing community structures of four selected samples between clone libraries (CLs) and those revealed by CONV. We considered the primer set to be suitable because we found significant correlations in the structures between CLs and CONV in three of the four samples examined. Then we determined the community structure of 12 samples by both DGGE and CONV, and calculated distance matrices to examine if analytical results were similar between the two methods. The correlations in matrices were 0.400-0.603, depending on the types of distance measures, and were always significant between the two methods. In comparing dendrograms drawn based on the matrices, DGGE and CONV were actually similar to some extent in that samples from a single locality tended to group together, although some localities were split in DGGE. We also conducted DGGE with four additional selected samples to confirm that the band pattern (i.e., number, position and relative intensity) was consistent in each sample across subsamples and gels. Given these results, we expect DGGE to become a useful and efficient tool for nematode community analysis, especially for non-experts, but our method of evaluation has limitations and more tests are needed.