chondroitin sulfate (Td max. ~42 h) laminarin (Td max. ~47 h) mannose (Td max. ~34 h) time [h]

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1 .4 chondroitin sulfate (Td max. ~42 h) laminarin (Td max. ~47 h) mannose (Td max. ~34 h) optical density (6 nm) time [h] Supplementary Figure S1 Growth curves of Polaribacter sp. Hel1_33_49. The strain was grown at 12 C in modified HaHa_1 medium with.1 g L -1 peptone,.1 g L -1 casamino acids, 2 µm NH 4 Cl, and 16 µm KH 2 PO 4. Laminarin (L9634, Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany) or chondroitin 4-sulfate (2742, Sigma-Aldrich) were used as carbon source, and D-mannose served as control (concentrations: 2. g L -1 ). Experiments with laminarin and chondroitin sulfate were carried out in triplicates. Maximum doubling times (Td) were estimated from semi-logarithmic plots of the data.

2 6 5 4 Counts/Mbp GH1 GH2 GH3 GH5 GH1 GH13 GH15 GH16 GH17 GH18 GH19 GH2 GH23 GH25 GH26 GH27 GH28 GH29 GH3 GH31 GH32 GH33 GH35 GH36 GH37 GH39 GH42 GH43 GH51 GH63 GH65 GH67 GH73 GH74 GH76 GH78 GH81 GH82 GH86 GH88 GH89 GH92 GH95 GH97 GH1 GH15 GH16 GH19 GH11 GH113 GH115 GH117 GH12 GH125 GH127 GH128 GH129 GH13 GH families Supplementary Figure S2 Variation of abundant GH families in 27 marine Flavobacteriaceae genomes (Supplementary Table S3). Data are shown as box and whisker plots with boxes representing inner quartiles Q2 and Q3 and whiskers extending to 5% and 95% percentiles. Circles represent data outside these boundaries. Only those 58 GH families are shown that are represented by at least three copies in the entire dataset. Only families GH3, GH13 and GH23 were universally present in all analyzed genomes (red triangles).

3 Counts/Mbp Po.CBM RF.CBM Po.CE RF.CE Po.GH RF.GH Po.GT RF.GT Po.PL RF.PL Supplementary Figure S3 Comparison of CAZyme categories (CBM, CE, GH, GT, PL) between Polaribacter species (Po) and other marine reference Flavobacteriaceae (RF) with sequenced genomes (Supplementary Table S3). Data are shown as notched box and whisker plots with boxes representing quartiles Q2 and Q3 and whiskers and extending to 5% and 95% percentiles. Circles represent data outside these boundaries. CBM = carbohydrate-binding module; CE = carbohydrate esterase; GH = glycoside hydrolase; GT = glycosyltransferase; PL = polysaccharide lyase.

4 A 385,564 bp SusE SusE ,2 bp B 767,561 bp , 6 788,453 bp C 1,426,382 bp 51 * nc 51 nc ,57,274 bp D 2,277,629 bp nc , 8 nc 2,316,374 bp TBDR glycoside hydrolase sulfatase SusD-like protein carbohydrate esterase transporter transcriptional regulator carbohydrate-binding module other Supplementary Figure S4 PULs of the Polaribacter sp. Hel1_33_49 genome (all located on the larger of the two contigs). Numbers in genes indicate family affiliations of glycoside hydrolases, carbohydrate esterases, sulfatases and carbohydrate-binding modules. The asterisk indicates a likely sequencing error in an A-homopolymer stretch that results into two seemingly fused genes.

5 181,275 bp 164,17 bp 648,798 bp 795,953 bp 1,332,345 bp 481,882 bp 636,575 bp TBDR carbohydrate esterase sulfatase SusD-like protein polysaccharide lyase transporter transcriptional regulator glycoside hydrolase carbohydrate-binding module other Supplementary Figure S5 PULs and a PUL-like gene cluster (E) of the Polaribacter sp. Hel1_85 genome. Superscript characters indicate contigs (a-c = from the largest down to smaller contigs). Numbers in genes indicate family affiliations of glycoside hydrolases, carbohydrate esterases, sulfatases and carbohydrate-binding modules.

6 Counts/Mbp A8 C1 C14 C25 C26 C39 C4 C44 C45 C51 C56 C82 M1 M3 M4 M12 M13 M14 M15 M16 M19 M2 M22 M23 M24 M28 M29 M36 M38 M41 M42 M43 M48 M49 M5 M56 M57 M61 M75 M79 M82 M9 P1 S1 S8 S9 S1 S11 S12 S13 S14 S15 S16 S24 S26 S33 S41 S45 S46 S49 S51 S54 S66 T2 T3 U32 U62 U69 MEROPS Category Supplementary Figure S6 Abundant peptidase families in 27 marine Flavobacteriaceae with sequenced genomes (Supplementary Table S3). Data are shown as box and whisker plots with boxes representing quartiles Q2 and Q3 and whiskers extending to 5% and 95% percentiles. Circles represent data outside these boundaries. Ninety different MEROPS families were found, but only families with at least three peptidases in the entire dataset are shown. Red triangles indicate the total of 27 families that were universally present in all Flavobacteriaceae.

7 Counts/Mbp Po.C RF.C Po.M RF.M Po.S RF.S 2. Counts/Mbp Po.A RF.A Po.T RF.T Po.U RF.U Supplementary Figure S7 Comparison of MEROPS categories (C-, M- S-, A-, T-, U-type peptidases) between Polaribacter species (Po) and other marine reference Flavobacteriaceae (RF) with sequenced genomes (Supplementary Table S3). Data are shown as notched box and whisker plots with boxes representing quartiles Q2 and Q3 and whiskers extending to 5% and 95% percentiles. Circles represent data outside these boundaries. The abundant cysteine- (C), metallo- (M), and serine- (S) peptidases are shown in the upper panel, and the less abundant aspartic- (A), threonine- (T), and unknown (U) type peptidases in the lower panel.

8 Polaribacter sp. MED152 (ZP_518337)* * Supplementary Figure S8 Phylogenetic tree of proteorhodopsin (PR) genes sequences of Polaribacter sp. Hel1_33_49 and related Flavobacteriaceae. PR gene sequences were retrieved from Genbank and aligned using MAFFT. Full-length PR sequences were used to construct phylogenetic trees in Arb using a 4% base conservation filter with the neighbor-joining with Jukes-Cantor correction and the RAxML maximum likelihood methods. A consensus tree was built and partial PR sequences were subsequently added by parsimony. Strains were PR activity was shown are indicated by a hash; strains for which genomes are available are indicated by an asterisk. Bar:.1 substitutions per nucleotide position.

9 DNA photolyase, class I tspo glutathione peroxidase short chain dehydrogenase GTP cyclohydrolase I (EC ) type 1 DNA photolyase/cryptochrome, cryptochrome and (6-4) photolyase subfamily photolyase- related protein cryptochrome, DASH family A B C 1, bp A: Polaribacter irgensii 23- P B: Polaribacter sp. Hel1_33_49 C: Polaribacter sp. MED 152 Supplementary Figure S9 Synteny of the DNA photolyase/cryptochrome (red) gene clusters among the three rhodopsin-containing Polaribacter strains 23-P T (A), Hel1_33_49 (B), and MED152 (C). Genes in white are conserved hypotheticals or genes that belong to generic superfamilies, but for which the exact functions are unknown. Genes that are not present in all three strains are depicted in bold.

10 4 Mannitol_dh Bac_rhodopsin 4 Mannitol_dh Polaribacter sp. Hel1_33_49 Polaribacter sp. Hel1_ Bac_rhodopsin CAZy families Sulfatase Sulfatase Polaribacter sp. Hel1_33_49 Polaribacter sp. Hel1_ CAZy families Supplementary Figure S1 Comparative genomics of 27 Flavobacteriaceae genomes (Supplementary Table S3): Relationship between mannitol dehydrogenase, bacteriorhodopsin and sulfatase gene copy numbers (based on matches to the Pfam profiles Mannitol_dh, Bac_rhodopsin with E-5 and sulfatase with E-13) and the number of CAZyme families (trend lines: 2nd order polynominal regressions).

11 A Polaribacter sp. Hel1_85 C D G E A B Methylomicrobium alcaliphilum 2Z T B A E G D C Halorhodospira halophila SL1 T A E G D C B pyruvate-flavodoxin oxidoreductase ferredoxin-nadp+ reductase rnf B Supplementary Figure S11 (A) Structure of the rnf operon of Polaribacter sp. Hel1_85 and the two most similar rnf operons in terms of best BLAST hits from Methylomicrobium alcaliphilum 2Z T and Halorhodospira halophila SL1 T. Numbers above genes refer to locus tags of strain Hel1_85. (B) Distribution of phylum-level best BLAST hits for the Polaribacter sp. Hel1_85 rnf operon indicating lateral acquisition from a gammaproteobacterial species.

12 Polaribacter sp. Hel1_33_49 Polaribacter sp. Hel1_85 Flavobacterium johnsoniae UW11 T Desulfurococcus fermentans Z-1312 T Cytophaga hutchinsonii Cyh1 T Chitinophaga pinensis DSM 2588 T Locus P. sp. Hel1_33_49 P. sp. Hel1_85 PHEL49_ PHEL85_ Annotation Supplementary Figure S12 Clustered assimilatory nitrate reduction genes in the Polaribacter sp. Hel1_33_49 and sp. Hel1_85 genomes as well as in other Flavobacteriaceae.