Microbial Community Structure Changes Following a Change in Vegetative Cover

Nüsslein, K. and J.M. Tiedje

Presented at the All Scientist Meeting (1998-07-21 to 1998-07-22 )

Microbial Community Structure Changes Following a Change in Vegetative CoverMicrobial diversity of soil is extremely high, and most of this diversity cannot be cultured. To compare soil samples for their microbial community composition total genomic DNA of bacteria can be studied. Since the base composition of DNA differs among bacterial genera a community profile based on the guanine and cytosine concentration (%G+C) in the extracted DNA from soil can be made. The resulting profile is based on the relative abundance of DNA of different G+C composition, and creates a fingerprint of the community composition (Holben and Harris, 1991). This is an approximation of the microbial diversity at the genus level.The complex mixture of bacterial genomes is qualitatively and quantitatively characteristic of the microbial community. Therefore, community shifts can be represented in the overall DNA based community profile. The range of bacterial G+C is from 24 (Clostridum and Mycoplasma) to 76% (Oerskoviae). Phylogentically coherent species have not more than 3% difference, and the species of a genus are not expected to differ by more than 10% (Stackebrandt and W. Liesack, 1993).We studied the effect of a change in vegetative cover of a Hawaiian soil from forest to pasture. DNA was extracted from both soils and compared by the abundance of its guanine and cytosine (G+C) composition. A gradient of G+C concentration was then established by equilibrium density gradient ultracentrifugation, and 0.2 ml fractions were collected by a fraction collector. The G+C profile of soil DNA was shifted to significantly higher G+C DNA with the change from forest to pasture (Fig. 1) which indicates significant changes in the composition of the soil bacterial community.The majority of soil DNA was in the 55 to 70% G+C range for both soils but the major peak was 61% G+C for the forest soil DNA and 67% G+C for the pasture soil. The pasture soil community exhibited an additional peak in the 42 to 45% G+C range, and displayed a small peak of 71% G+C. DNA extracted from replicate soil samples showed repeated profiles such that within site variation was much less than differences between the two sites (Fig. 1). The standard deviations of the mean curve differences for the forest and pasture soil communities were small, s = 0.14 and s = 0.27, respectively.Evidence from 3H-labeling experiments and G+C based fractionation of soil community DNA indicates that activity and growth are not confined to a small fraction of the bacterial biomass but are widespread amongst the genera represented in the profile (Harris, 1994).The G+C based fractionation of soil extracted DNA yielded community profiles specific for each soil site and of the entire soil microbial community that can be compared, and allows the selective analysis of soil community subsets. In addition to lowering diversity to a more manageable level, the G+C separation step is also a means to detect less dominant organisms in a community. The reliability of this technique could be shown through statistical comparisons of repetitive experiments. The G+C method provides an analysis at a coarser level of taxon distinction but is comprehensive for all DNA. This method becomes especially powerful when combined with other DNA based techniques such as 16S rRNA clone library analysis.Return to Contents