Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns

Bacterial diversity in unimproved and improved grassland soils was assessed by PCR amplification of bacterial 16S ribosomal DNA (rDNA) from directly e xtracted soil DNA, followed by sequencing of similar to 45 16S rDNA clones from each of three unimproved and three improved grassland samples (A. E. M cCaig, L. A. Glover, and J. I. Prosser, Appl. Environ. Microbiol. 65:1721-1 730, 1999) or by denaturing gradient gel electrophoresis (DGGE) of total am plification products. Semi-improved grassland soils were analyzed only by D GGE. No differences between communities were detected by calculation of div ersity indices and similarity coefficients for clone data (possibly due to poor coverage). Differences were not observed between the diversities of in dividual unimproved and improved grassland DGGE profiles, although consider able spatial variation was observed among triplicate samples. Semi-improved grassland samples, however, were less diverse than the other grassland sam ples and had much lower within-group variation. DGGE banding profiles obtai ned from triplicate samples pooled prior to analysis indicated that there w as less evenness in improved soils, suggesting that selection for specific bacterial groups occurred. Analysis of DGGE profiles by canonical variate a nalysis but not by principal-coordinate analysis, using unweighted data (co nsidering only the presence and absence of bands) and weighted data (consid ering the relative intensity of each band), demonstrated that there were cl ear differences between grasslands, and the results were not affected by we ighting of data. This study demonstrated that quantitative analysis of data obtained by community profiling methods, such as DGGE, can reveal differen ces between complex microbial communities.