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Fig. S1. Quantification of archaeal templates across gradient fractions by (A–C) quantitative reverse transcription-PCR and (D–F) PCR. The gradient fractions, characterized by their buoyant densities, were generated using CsTFA density gradient centrifugation of (left panel) rRNA and using CsCl density gradient centrifugation of (right panel) DNA extracted from anoxic rice field soil after (A) 1 day, (B) 17 days, (C) 21 days, (D) 11 days, (E) 32 days and (F) 67 days of incubation. Fractions from which T-RFLP fingerprints (triangles) or clone libraries (asterisks) were generated are indicated.

Fig. S2. T-RFLP fingerprints of density-resolved bacterial communities retrieved (A–C) from selected rRNA and (D–F) from selected DNA. The T-RFLP assays were performed using gradient fractions from nucleic acids extracted from samples incubated with unlabelled acetate and [U-13C]acetate as indicated in Fig. S1. CsTFA (for rRNA) or CsCl (for DNA) buoyant densities of respective gradient fractions are given in brackets. The fragment lengths (in base pairs) of important T-RFs (as mentioned in the text) are given. Amplicons were generated with Ba27f-FAM/Ba907r primers and digested with MspI.

Fig. S3. Quantification of bacterial templates across gradient fractions by (A–C) quantitative reverse transcription-PCR and (D–F) PCR. The gradient fractions, characterized by their buoyant densities, were generated using CsTFA density gradient centrifugation of (left panel) rRNA and using CsCl density gradient centrifugation of (right panel) DNA extracted from anoxic rice field soil after (A) 1 day, (B) 17 days, (C) 21 days, (D) 11 days, (E) 32 days and (F) 67 days of incubation. Fractions from which T-RFLP fingerprints (triangles) or clone libraries (asterisks) were generated are indicated.

Fig. S4. T-RFLP fingerprints of density-resolved archaeal communities retrieved (A–C) from selected rRNA and (D–F) from selected DNA. The T-RFLP assays were performed using gradient fractions from nucleic acids extracted from samples incubated with unlabelled acetate and [U-13C]acetate as indicated in Fig. S3. CsTFA (for rRNA) or CsCl (for DNA) buoyant densities of respective gradient fractions are given in brackets. The fragment lengths (in base pairs) of important T-RFs (as mentioned in the text) are given. Amplicons were generated with Ar109f/Ar912rt-FAM primers and digested with TaqI.

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