Table 3. List of the relative abundances in percent for pyrosequence reads identified to taxonomic classes >1% (organized by phylum for nonproteobacterial classes) for Edwards Aquifer wells and Comal Springs, including unclassified bacteria.

Comal Springs (%)	Girl Scout Deep (%)	Girl Scout Shallow (%)	LCRA Deep (%)	LCRA Shallow (%)	Paradise Alley Deep (%)	Paradise Alley Shallow (%)	Aquarena (%)
Firmicutes (43; Bacilli, 42.5)	Betaproteobacteria (36.8)	Betaproteobacteria (58.2)	Firmicutes (34.0; Bacilli, 33.6)	Firmicutes (21.6; Bacilli, 20.9)	Alphaproteobacteria (43.5)	Deltaproteobacteria (15.7)	Gammaproteobacteria (59.4)
Betaproteobacteria (21.2)	Gammaproteobacteria (7.7)	Deltaproteobacteria (7.5)	Betaproteobacteria (33.0)	Betaproteobacteria (18.7)	Deltaproteobacteria (16.1)	Alphaproteobacteria (15.2)	Deltaproteobacteria (13.1)
Gammaproteobacteria (9.9)	Deltaproteobacteria (5.2)	Gammaproteobacteria (3.7)	Deltaproteobacteria (4.4)	Deltaproteobacteria (7.6)	Betaproteobacteria (9.1)	Chloroflexi (15.0; Anaerolineae, 14.8)	Epsilonproteobacteria (6.3)
Bacteroidetes (5.5; Flavobacteria, 2.4; Sphringobacteria, 2.2)	Firmicutes (1.5; Bacilli, 1.4)	Firmicutes (2.8; Bacilli, 2.3)	Gammaproteobacteria (3.2)	Alphaproteobacteria (5.4)	Chloroflexi (9.1; Anaerolineae, 9.1)	Betaproteobacteria (8.9)	Chloroflexi (4.3; Anaerolineae, 4.2)
Deltaproteobacteria (1.3)	Chloroflexi (1.3; Anaerolineae, 1.3)	Alphaproteobacteria (1.0)		Gammaproteobacteria (5.2)	Bacteroidetes (1.6; unclassified 1.6)	Firmicutes (1.6; Bacilli, 1.2)	Bacteroidetes (3.6; Bacteroidia, 3.2)
	Alphaproteobacteria (1.2)			Chloroflexi (1.8, Anaerolineae, 1.2; Dehalococcoides, 0.6)	Firmicutes (1.1; Bacilli, 1.1)		Betaproteobacteria (1.4)
							Firmicutes (1.3; Bacilli, 1.2)
Unclassified bacteria (5.8)	Unclassified bacteria (45.3)	Unclassified bacteria (22.4)	Unclassified bacteria (21.0)	Unclassified bacteria (37.1)	Unclassified bacteria (17.7)	Unclassified bacteria (36.0)	Unclassified bacteria (7.1)