Table 4.

Relative abundance (percentage of total sequences) of different phylogenetic taxa obtained conventional cloning and sequencing (Clone lib) and by pyrosequencing of 16S rRNA genes from site 2 (microbial mat) using different sequencing platforms and primer sets.

Taxa	Percent of sequences
	Clone lib	V4–454	V6–454	V1-Illumina	V4-Illumina
Bacteria/Firmicutes	0	29	28	29	8
Bacilli	0	29	28	29	7
Bacillales	0	29	28	29	7
Sporolactobacillaceae	0	0	28	0	0
Tuberibacillus	0	0	28	0	0
Bacillaceae	0	29	0	29	7
Bacillus	0	24	0	29	0
Bacteria/Firmicutes	6	0	0	0	0
Bacteria/Proteobacteria	94	71	72	70	92
Betaproteobacteria	94	70	69	70	86
Burkholderiales	38	67	63	62	76
Comamonadaceae	8	67	62	61	75
Acidovorax	0	59	2	<1	0
Pseudorhodoferax	0	0	59	0	0
Rhodoferax	9	0	0	0	0
Unclassified Comamonadaceae	0	5	2	60	75
Unclassified Burkholderiales	30	0	0	0	0
Aquabacterium	30	0	0	0	0
Rhodocyclales	0	<1	1	5	6
Rhodocyclaceae	0	<1	1	5	6
Propionivibrio	0	0	0	5	0
Unclassified Rhodocyclaceae	0	<1	1	0	6
Nitrosomonadales	56	<1	5	0	0
Gallionellaceae	56	<1	5	0	0
Gallionella	38	0	0	0	0
Candidatus Nitrotoga	11	0	0	0	0
Sideroxydans	7	0	5	0	0
Unclassified Betaproteobacteria	0	<1	<1	0	5
Gammaproteobacteria	0	1	3	<1	5
Total no. of sequences	57	3076	15,689	19,747	119,631

V1, V4, and V6 refer to different variable regions of the 16S rRNA gene; 454 refers to the Roche 454 GS20 (V6) or GS FLX (V4) platform; Illumina refers to the Illumina GAIIx platform. Black, red, blue, green, and magenta text refer to Domain/Phylum, Class, Order, Family, and Genus level assignments, respectively. Taxa present at >20% abundance are shown in bold; relative abundances of <1% ranged from 0.1 to 0.99%; values of 0 correspond to <0.1%.