The shift in vegetative cover from forest to pasture caused some changes in soil properties, including a decrease in soil acidity and organic carbon and an increase in bulk density (Table ). The higher cation-exchange capacity in the forest soil than in the pasture soil is likely due to its higher soil organic matter content.
TABLE 1 Differences in soil properties between the Kohala forest soil and pasturesoil
The G+C content profile of soil DNA was shifted to significantly higher G+C content of DNA with the change to pasture (Fig. ). These profiles are highly habitat specific since both small- and large-scale replicate samples showed the same shift. Furthermore, three additional samples from other, similar Big Island forest soils gave the same forest profile, and one additional pasture sample gave the pasture profile (data not shown). The standard deviations (SDs) of the mean curve differences for the small-scale replicates of forest and pasture soil communities were small (SDs were 0.14 and 0.27, respectively) (Fig. ).
FIG. 1 Comparison of G+C content profiles of DNA extracted from three forest soils and three pasture soils in the Kohala area. One soil supports a rain forest, and the adjacent soil was converted to pasture 80 years ago. Samples collected in the same (more ...)
The majority of soil DNA had G+C content in the 55 to 70% range for both soils, but the major peaks were 61% G+C content for the forest soil DNA and 67% G+C content for the pasture soil DNA. The pasture soil community exhibited an additional peak in the 42 to 45% G+C content range, which was especially prominent for the samples collected in 1994, and displayed a shoulder peak of 71% G+C content.
The same phylotypes were observed for replicate soil samples for the three dominant phylotypes in eight of the nine cases for the forest and the pasture soils (Fig. ). Examples of ARDRA data documenting the presence of the same phylotypes in replicates of the pasture soil are shown in Fig. . The dominant phylotypes, however, were different between forest and pasture samples, suggesting that the populations were different at the two sites. Nondominant phylotypes were very different, even between replicates of the same vegetation type, as would be expected if the clone library were generated from a random process. Twenty-two percent of the phylotypes of rare clones (n = 1) were found in replicates of the pasture community with 63% G+C content, while 12% of the rare clones were found in replicates of the forest community. Only seven of the rare phylotypes were found under both vegetation types. The two most dominant phylotypes of the fraction of the forest soil with 35% G+C content had frequencies ± SDs of only 6.5% ± 2.5% and 4.5% ± 0.5%, but were found in both replicates.
FIG. 2 Frequency distribution of the total number of SSU rDNA gene phylotypes from the 63% G+C content fractions (A) and the 35% G+C content fractions (B) from the rain forest and pasture soils. Each graph shows the median and (more ...)
FIG. 3 An ARDRA profile following double digestion with HaeIII and HhaI of clones from the 63% fraction of the pasture soil. Similar patterns can be seen for three groups of clones, each found in both replicates, lanes, 2, 5, 15; 6, 7, 8, 10, 14, 17 (more ...)
The phylotype abundance curves (Fig. ) of both the forest soil and pasture soil replicated well with very low SDs. The two profiles of the 63% fraction of the forest soil were similar, i.e., 94% of all data fell within a single SD range (SD, ± 1.17) of the mean curve difference. The corresponding number for the profiles of the 63% fraction of the pasture profile was 93% (SD, ± 0.77).
Microbial rDNA diversity in the 63% G+C content fraction of the pasture soil differed from that of the forest soil. The rank abundance profiles of the 63% G+C content fractions are separated by the stronger trend for dominance in the forest soil but the much greater phylotype richness in the pasture soil (Fig. A). The four most dominant members contributed 77% ±6% (mean ± SD) of the forest soil community clones while they represented about half, i.e., 47% ± 3%, of the pasture soil community clones. With 62 ± 4 phylotypes among ca. 120 clones selected, the pasture had a phylotype richness which was almost 2.2 ± 0.4 times greater than that for the forest soil. The difference in abundance within the four most dominant phylotypes was more prominent in the forest soil community. Clones of the first phylotype were almost three times as abundant as those of the next group, while the corresponding difference in the pasture clones was under 60% (Fig. A).
The pasture soil displayed a prominent rRNA dominance structure of the first three phylotypes from the 35% G+C content fraction (Fig. B), while both replicates of the forest soil showed no significant dominance pattern or phylotype frequency over 10%. The three most dominant members represent 47% of the pasture clone community but only about one third of that in the forest soil community, where they constitute only 15% ± 3% (mean ± SD) of the clone community. The phylotype richness of the 35% G+C content fraction was about 43% ± 4% greater than that for the forest soil.
One clone of each of the three dominant phylotypes was sequenced. Most clones sequenced were moderately to distantly related to sequences of known taxa (Table ). The dominant clones from the two vegetation types were very different; they represented two very different phyla, Fibrobacter and Proteobacteria. Many of the clones within the Fibrobacter group were dissimilar to each other (Table ), while those within the Proteobacteria were affiliated with Burkholderia and more similar to each other (Tables and ).
TABLE 2 Phylogenetic affiliations based on SSU rDNA genes of the three most dominant phylotypes of the two replicates from the 63% G+C content fractions of the rainforest soil and the pasturesoil
TABLE 3 Sequence similarities among SSU rDNA clones from dominant members of the 63% G+C content fractions of the rain forest community and pasture soilcommunity