1. 16S rDNA phylotype distribution in libraries obtained from total RNA isolated from Lake Washington sediment and from 13 C-labelled and 12 C-DNA fractions obtained from the microcosm experiments Phylogenetic groupPhylotypes LW RNA Methanol MethylamineFormaldehyde Formate 13 C DNA 12 C DNA 13 C DNA 12 C DNA 13 C DNA 12 C DNA 13 C DNA 12 C DNA Proteobacteria Betaproteobacteria pLW-1, pLW-2, pLW-3, pLW-4 17 331 Comamonadaceae pLW-5, pLW-6 2 12 Oxalobacteraceae pLW-7, pLW-8, pLW-9, pLW- 10 9 Nitrosomonadaceae pLW-11, pLW-12, pLW-13 12210433189 Methylophylaceae pLW-16 1 Gammaproteobacteria Methylobacter/Methylomonas pLW-17, pLW-18, pLW-19, pLW-20, pLW-21, pLW-22 16 Pseudomonas pLW-23, pLW-24 34 11 Achromatium pLW-25 2 Xanthomonadaceae pLW-26, pLW-27 5 Thioploca/Beggiatoa pLW-28, pLW-29 5 Uncl. Gammaproteobacteria pLW-30, pLW-31, pLW-32 2 114 Alphaproteobacteria Caulobacterales pLW-33 1 Rhodobacterales pLW-34 1 Sphingomonadales pLW-35, pLW-36, pLW-37 172 Uncl. Alphaproteobacteria pLW-38, pLW-39, pLW-40 2

2. Deltaproteobacteria Syntrophus pLW-41 1 Polyangiaceae pLW-42 1 Myxococcaceae pLW-43 3 Geobacteraceae pLW-44 1 Uncl. Deltaproteobacteria pLW-45, pLW-46, pLW-47 33 1 Bacteroidetes Flexibacteraceae pLW-48 2 Saprospiraceae pLW-49 2 Sphingobacteriaceae pLW-50, pLW-51 3 Uncl. Bacteroidetes pLW-52, pLW-53, pLW-54, pLW-55, pLW-56, pLW-57 15 311 Acidobacteria Holophaga/Geothrix pLW-58, pLW-59, pLW-60, pLW-61, pLW-62, pLW-63 61131331 Uncl. Acidobacteria pLW-64, pLW-65 2 1 Nitrospirae ncl. Nitrospira pLW-66, pLW-67, pLW-68 214 12 WS3 pLW-69, pLW-70 3 3 Actinobacteria Acidimicrobiaceae pLW-71, pLW-72 31 1 Rubrobacteraceae pLW-73, pLW-74, pLW-75 22 Uncl. Actinobacteria pLW-76, pLW-77 1 11

3. Gemmatimonadetes Gemmatimonadaceae pLW-78, pLW-79, pLW-80, pLW-81, LW-82, pLW-83, pLW-84, pLW-85, pLW-86, pLW-7 3 24184 Verrumicrobia Uncl. Verrumicrobia pLW-88, pLW-89 5 Planctomycetes Uncl. Planctomycetes pLW-90, pLW-91 1 2 Chlorobi Uncl. Chlorobi pLW-92, pLW-93 14 Spirochaetes Leptospiraceae pLW-94 1 Chloroflexi Uncl. Chloflexi pLW-95, pLW-96, pLW-97 1 133 Fibrobacteres Uncl. Fibrobacteres pLW-98 1 Uncl. Bacteria pLW-99 3 pLW-100 31 pLW-101 2 pLW-102 2 pLW-103 1 pLW-104 2 pLW-105 1 pLW-106 1 Total 1074226431467662628

4. a Classification according to the Ribosomal Database Project-II (http://rdp.cme.msu.edu/classifier.jsp); b Phylotypes were defined as sequences less than 97% similar (41). Uncl., phylotypes that could not be assigned with a bootstrap confidence estimate above the default threshold value of the RDP Classifier (80%) are displayed under an artificial ‘unclassified’ taxon