Influence of soil sample sizes on the assessment of bacterial community structure

Abstract

When assessing bacterial community structure in soil it is important to establish a satisfactory procedure for sampling. The influence of sample sizes of a forest soil on the assessment of bacterial community structure was investigated. Four sample sizes (0.01, 0.1, 1.0, and 10.0 g) were evaluated. Time of colony appearance on a nutrient-limited soil extract agar was used to characterise the culturable heterotrophic and Pseudomonas communities. Genetic community structure was assessed with denaturing gradient gel electrophoresis (DGGE) of 16S rDNA using a bacterial primer set. The largest variation in the heterotrophic community structure for bacteria was seen when comparing the 0.01 g replicates. Variation was also seen for the 0.1 and 1.0 g replicates. However, there was no significant difference between the 10.0 g replicates. The 0.01 and 0.1 g replicates showed variation in genetic community structure within the sample sizes, whereas variation between the replicates within the larger sample sizes (1.0, 10.0 g) was negligible. Variation in the heterotrophic community structure for Pseudomonas was seen between replicates of all sample sizes. Hence, the size of soil samples influenced the bacterial community structure observed for bacteria, whereas chance seemed to play an important role when looking at a more narrow community structure.