1. Supplementary Fig. 1A

2. WCHB1-57 Uncultured eubacterium (AF050570) 5S4 (3) 5S33 WCHB1-05 Uncultured eubacterium (AF050562) 5C49 (15) WCHB1-43 Uncultured eubacterium (AF050564) 5S49 (15) Uncultured clone TA17 (AF229790) Chloroflexi clone 44aB115 (AY082460) 5S45 (3) 5C62 (2) 9V85 (3) UD6 Uncultured soil clone (DQ297988) 9V76 9S23 Chloroflexi clone AKYG628 (AY922044) Dehalococcoides ethenogenes (AF004928) 9V78 (5) 9S95 5V55 (19) Chloroflexi clone EB1097 (AY395416) Chloroflexus aurantiacus (M34116) 9S61 9S22 Clone JG30KFAS1 Uncultured bacterium (AJ536886) 9S45 WCHB1-15 uncultured eubacterium (AF050596) 5C80 (2) OP11 clone WSA68 (AY193286) Escherichia coli ATCC 11775T (X80725) 0.05 substitutions/site 100 96 92 98 100 99 100 80 100 80 98 96 100 86 99 100 78 99 100 75 100 64 Green nonsulfur Bacteria WS6 OP11 Supplementary Fig. 1B

3. Supplementary Fig. 1C

4. 5F105 (4) 9S80 (6) Bacillus chitinolyticus (AB021183) 9S76 (9) Bacillus sp 19498 (AJ315066) 5F96 Lactococcus lactis (AY675242) 9V80 (7) Anaerovibrio glycerini DSM 5192(T) (AJ010960) 5C94 (10) WCHB1-77 Uncultured eubacterium (AF050590) 5C78 9V73 (3) Desulfosporosinus 44aT3a (AY082482) Desulfitobacterium dehalogenans (L28946) 5C70 (2) Pelotomaculum MGP (AB154390) 5S61 (4) Pelotomaculum schinkii (X91169) 5C90 (3) Clostridium cellobioparum (X71856) 5C3 Clostridium nitrophenolicum (AM261414) 5V45 (3) 9S35 (8) Planctomycetes clone MC98 (X64376) 9V16 (4) Gemmata obscuriglobus (X56305) 5F98 9S4 (3) ISCB46 Uncultured bacterium clone (AY596135) Escherichia coli ATCC 11775T (X80725) 0.01 substitutions/site 96 100 63 100 98 77 70 100 65 91 100 64 85 100 97 100 78 99 Bacilli Clostridia Planctomycetes WS3 Supplementary Fig. 1D

5. Supplementary Fig. 1E