Diversity Indices

The number of RFLP types (richness) and the frequency distribution of the RFLP types (evenness) in each of the clone libraries were evaluated by using a variety of standard diversity indices and results were summarized in Table 7.2.

Table 7.2. Diversity indices based on Cfol RFLP patterns in 16S rDNA clone libraries from young, mature, and old granules

Parameter

Young

Mature

Old

RFLP type richness E(S)a

19.7

22.8

21.2

Shannon-Weaver diversity (H )b

2.742395

3.034237

2.927977

Evenness (E )c

0.900764

0.920627

0.933817

Simpson's dominance (c)d

0.09037

0.06213

0.067451

Equitability (J )e

0.72042

0.767919

0.760484

aE(S) (Cho and Kim, 2000) was calculated by rarefaction for a standardized sample size of 40 clones for each clone library.

bH was calculated as follows: H = — (pi)(lnpi), where pi is the proportion for each RFLP pattern. cEvenness (E) was calculated from H as follows: E = H/ln S, where S is the total number of RFLP patterns in each clone library. dc was calculated as follows: c = (pi)2.

eJ was calculated as follows: J = H/Hmax, where Hmax = Log2 X, where X is the total number of clones in each library.

aE(S) (Cho and Kim, 2000) was calculated by rarefaction for a standardized sample size of 40 clones for each clone library.

bH was calculated as follows: H = — (pi)(lnpi), where pi is the proportion for each RFLP pattern. cEvenness (E) was calculated from H as follows: E = H/ln S, where S is the total number of RFLP patterns in each clone library. dc was calculated as follows: c = (pi)2.

eJ was calculated as follows: J = H/Hmax, where Hmax = Log2 X, where X is the total number of clones in each library.

Since the libraries differed in size, estimated RFLP type richness [E(S)] was calculated by rarefaction for smaller sample sizes (40 clones) to allow standardized comparisons. The estimated value of richness in the mature clone library was much higher than that in the young and old libraries. With the exception of Simpson's dominance index as shown in Table 7.2, the mature and old clone libraries had higher values on diversity indices such as richness, the Shannon-Weaver diversity index, evenness, and equitabil-ity than the young clone libraries. The young clone library contained a few RFLP types. Overall, the calculated diversity index values showed that the bacterial communities of mature and old granules were more diverse than that of the young granules. The values of coverage (Table 7.2) were also used to approximate the probability that all species present in a given sample were represented at least once in the library (Dang and Lovell, 2000). These three libraries had percent coverage values ranging from 68.6 to 77.1, which indicated that the microbial communities present in this study contained substantial diversity.

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