TABLE 4.

Values of nirS and nirK diversity and richness in HID soils, as estimated by Shannon diversity index, Simpson index, and Chao1 richness calculated using DOTUR^a

Gene and site	No. of clones sequenced	No. of OTU	Shannon index	Diversityb	Richnessc	No. of singletons	Coverage (%)
nirK
UND	28	13	2.3 (1.9-2.6)	2.5	20 (13-54)	6	100d
R89	28	12	2.3 (1.8-2.5)	2.2	22 (14-66)	7	69
R97	25	11	2.0 (1.7-2.4)	1.9	21 (13-65)	7	86
R00	30	16	2.4 (1.9-2.8)	2.1	38 (21-102)	12	72
R01	24	12	2.3 (1.9-2.6)	2.4	19 (13-48)	7	45
R03	23	12	2.2 (1.9-2.6)	2.3	26 (15-79)	8	71
All	158
nirS
UND	21	8	1.8 (1.4-2.1)	1.8	11 (8-31)	4	48
R89	17	10	2.2 (1.8-2.5)	2.7	15 (11-39)	6	56
R97	15	16	2.7 (2.4-3.0)	3.7	32 (20-80)	12	67
R00	27	16	2.6 (2.2-2.9)	2.8	82 (38-212)	12	76
R01	15	12	2.4 (2.1-2.7)	3.1	16 (13-34)	7	90
R03	22	18	2.8 (2.5-3.1)	3.8	53 (27-144)	15	45
All	117

^aEstimates of OTU, Shannon index, diversity, and richness are all based on 3% differences in nucleic acid sequence alignments. Values in parentheses are 95% confidence intervals as calculated by DOTUR (28).

^bSample-size-independent estimate of diversity based on negative natural log transformation of Simpson's index values as calculated in DOTUR.

^cChao1 values, a nonparametric estimate of species richness.

^dCoverage values for distance = 0.01, as calculated by ∫-LIBSHUFF (27).