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. 2011 Oct;77(19):6908–6917. doi: 10.1128/AEM.05891-11

Table 2.

Samples processed during the studya

Date received Description Sample code Amplicon code MID n Groupb No. of OTUs SHIN SIM No. of taxac
10/28/2009 Pipe-associated solids PAS-821LPd 941 TACGCTGTCT 6,251 a 174 2.16 0.29 80
PAS-821LPd 940 TACAGATCGT 5,908 a 252 2.34 0.26 62
PAS-821LPd 929 ATATCGCGAG 4,850 a 313 2.35 0.28 53
PAS-821LPd 930 CGTGTCTCTA 5,522 a 268 2.59 0.2 70
10/28/2009 Pipe-associated water PAW-821LP 939 TACACGTGAT 5,318 b 212 2.8 0.15 91
PAW-821LP 928 ATCAGACACG 4,653 b 294 3.19 0.11 96
8/13/2009 Pipe-associated solids PAS-616Pe 516 AGACGCACTC 2,329 c 136 2.19 0.23 58
PAS-616Pe 1351 TAGTATCAGC 9,785 c 325 1.91 0.38 79
1/21/2010 Pipe-associated solids PAS-821TPf 1718 ATACGACGTA 8,678 d 152 1.51 0.32 65
9/24/2009 McMurray water E2-2 938 TACACACACT 3,796 e 47 0.34 0.9 26
E2-2 926 ACGCTCGACA 4,829 e 94 0.65 0.8 34
9/24/2009 Comingled water E3-2 927 AGACGCACTC 4,372 e 122 0.7 0.82 60
1/27/2010 Grand Rapids water E1-3 1714 TGATACGTCT 11,755 e 136 0.88 0.66 69
9/24/2009 Grand Rapids water E1-2 937 CGACGTGACT 5,456 e 156 1.69 0.42 91
E1-2 925 ACGAGTGCGT 4,200 e 194 1.62 0.52 79
1/21/2010 Pipe-associated water PAW-821TP 1717 CGAGAGATAC 9,488 f 354 2.82 0.16 169
1/27/2010 Comingled water E3-3 1716 CATAGTAGTG 10,450 f 267 2.45 0.22 104
1/27/2010 McMurray water E2-3 1715 TACTGAGCTA 9,396 f 187 1.61 0.29 99
8/13/2009 Pipe-associated water PAW-616P 515 ACGCTCGACA 2,352 g 210 3.62 0.06 133
PAW-616P 514 ACGAGTGCGT 2,065 g 352 4.16 0.05 151
9/7/2009 Comingled water E3-1 365 TGATACGTCT 3,211 h 250 3.57 0.06 99
9/7/2009 McMurray water E2-1 364 TCTCTATGCG 6,055 i 522 4.15 0.04 179
a

Multiple table entries for a given sample were for amplicons obtained through different DNA isolation and/or PCR procedures as explained in the text. The multiplex identification sequence (MID) and the number of good 16S pyrotags obtained for each amplicon library (n) are indicated. The number of OTUs observed, the Shannon index (SHIN) and the Simpson index (SIM), and the number of derived taxa, describing microbial community diversity, are also indicated. The data are ordered according to the dendrogram in Fig. 3. Dates are given as month/day/year.

b

Dendrogram subgroup (see Fig. 3).

c

Data represent numbers of entries with at least one good read (see Table S1 in the supplemental material).

d

Pipe section 821LP had an inner diameter (ID) of 20 cm, a length (L) of 14.5 cm (Fig. 2C), an internal surface area (A) of 910 cm2, and an internal volume (V) of 4,553 cm3.

e

Pipe section 616P had an ID of 6 to 8 cm, an L of 21.5 cm (Fig. 2A), an A of 473 cm2, and a V of 827 cm3.

f

Pipe section 821TP had an ID of 17.2 cm, an L of 38.7 cm (Fig. 2E), an A of 810 cm2, and a V of 23763.