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emi412042-sup-0001-fS1.tiff382K

Fig. S1. DGGE gel with v3 16S rDNA PCR products for live feed cultures and rearing water at 8, 17, and 32 dph. W Cop, Water from one Cop rearing tank; W RR, Water from one RR rearing tank; W CR, Water from one CR rearing tank; Cop, Copepod culture (diet Cop); Rot RR, Rotifer culture (diet RR); Rot CR, Rotifer culture (diet CR); Art, Artemia live feed culture; M, DGGE marker.

emi412042-sup-0002-fS2.pdf164K

Fig. S2. DGGE gels with v3 16S rDNA PCR products for individual larvae from all replicate rearing tanks at 8 dph for the COP + RR diet (A), the CR + COP diet (B), and the CR + RR diet (C). M: DGGE marker. Lanes labelled ÷ represent PCR products that were amplified from DNA extracts that probably degraded, and they were therefore excluded from analyses.

emi412042-sup-0003-fS3.pdf150K

Fig. S3. DGGE gels with v3 16S rDNA PCR products for individual larvae from all replicate rearing tanks at 17 dph for the COP + RR diet (A), the CR + COP diet (B), and the CR + RR diet (C). M: DGGE marker. Lane labelled * contains a mix of marker and PCR product for a cod larva individual, and marker bands were excluded from the relevant peak area spread sheet.

emi412042-sup-0004-fS4.pdf156K

Fig. S4. DGGE gels with v3 16S rDNA PCR products for individual larvae from all replicate rearing tanks at 32 dph for the COP and RR diet (A), the CR + COP diet (B), and the CR + RR diet (C). M: DGGE marker. Lanes labelled ÷ represent PCR products amplified from DNA extracts of poor quality, and were excluded from analyses.

emi412042-sup-0005-fS5.pdf98K

Fig. S5. DGGE gel with v3 16S rDNA PCR products for cod larvae, rearing water, and live feed cultures for one of the COP (A) and one of the RR (B) rearing tanks. L: larva; W: rearing water; Cop: Copepod culture; Art: Artemia culture; Rot: Rotifers (RR) culture; M: DGGE marker. Lanes labelled ÷ represent live feed samples that were not relevant to the feeding regime in questions, due to a mix-up of samples. These lanes were excluded from analysis. However, the appropriate live feed DGGE profiles were obtained from other DGGE-gels, and were unambiguously incorporated in the relevant peak-area spread sheets. Taxonomic assignments for bands in frames are given in Table S1.

emi412042-sup-0006-fS6.pdf114K

Fig. S6. DGGE gel with v3 16S rDNA PCR products for cod larvae, rearing water, and live feed cultures for two of the COP (A) and two of the RR (B) rearing tanks. L, larva; W, rearing water; Cop, Copepod culture; Art, Artemia culture; Rot, Rotifers (RR) culture; M, DGGE marker. Lanes labelled ÷ represent live feed samples that were not relevant to the feeding regime in questions, due to a mix-up of samples. These lanes were excluded from analysis. However, the appropriate live feed DGGE profiles were obtained from other DGGE-gels, and were unambiguously incorporated in the relevant peak-area spread sheets.

emi412042-sup-0007-tS1.doc38K

Table S1. Taxonomic assignments of DGGE bands for microbiota of cod larvae at 8, 17, and 32 dph.

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