B a Figure S1. (A) Location of Well MC252, and (B) Sampling

a Louisiana b 29.0 29.2 30 35

MC252 28.74

28.8 0 km

Gulf of Mexico 28.72 28.6 Latitude −88.37 −88.36

59.5 km 28.2 28.4 15 20 25 −100 −95 −90 −85 −80 −75 −70 −89.4 −89.2 −89.0 −88.8 −88.6 −88.4 −88.2 −88.0 Longitude Figure S1. (a) Location of well MC252, and (b) sampling locations. Samples >3 km from MC252 are shown in blue, while near-well samples are shown in red (inset). a

Key 20 GSC 46 34 52 b 01 Gammaproteobacteria 50 23 02 43 03 3 52 42 04 05 1 7 06 49 07 52 32 1-2 4 08 5-6 47 09 10 44 31 45 26 52 c 11 24 19 21 12 40 13

25 Alphaproteobacteria Gammaproteobacteria 28 16 8 10 14 35-36 18 15 48 52 16 17 33 24 17 18 38 39 52 30 15 37 19 52 20 41 51 22 12 21 27 22 14 37 11 29 23 35 9 24 25 26 d 27 b c 28 29 20 20 46 46 34 52 34 52 30 50 23 50 23 43 43 31 3 3 52 42 52 42 32 1 7 1 7 49 49 52 33 52 32 4 32 1-2 4 1-2 5-6 5-6 47 47 34 Deltaproteobacteria 44 31 44 52 31 45 26 52 45 26 35 24 19 21 24 19 21 e 40 40 36 25 25 16 10 28 16 8 10 28 8 35-36 18 35-36 18 37 48 52 48 52 17 33 24 17 33 24 38 38 39 52 30 38 39 52 30 15 37 15 37 39 52 52 41 51 22 41 51 22 12 40 27 12 27 14 37 11 14 37 11 29 29 41 35 9 35 9 d 42

43 Bacteroidetes d e 44 45 20 20 46 46 34 52 34 52 46 50 23 50 23 43 43 47 3 3 52 42 52 42 48 1 7 1 7 49 49 52 52 32 4 32 49 1-2 4 1-2 5-6 47 5-6 47 50

44 31 44 52 31 b-e 45 26 52 45 26 51 24 19 21 24 19 21 40 40 52 25 25 28 16 8 10 28 16 8 10 35-36 18 35-36 18 48 52 48 52 17 33 24 17 33 24 38 39 52 30 38 39 52 30 15 37 15 37 52 52 41 51 22 41 51 22 12 27 12 27 14 37 11 14 37 11 29 29 35 9 35 9

Figure S2. (a) ESOM of co-assembly constructed using tetranucleotide frequencies of 5 kbp long genomic fragments and differential coverage. Bin (GSC) numbers are shown in red. Dark lines demark cluster edges. Collections of small clusters are contigs containing virus-associated genes. (b-e) ESOM with data points representing 2 kbp long genomic fragments and colored by bin (see key). GSC01 GSC02 GSC03 GSC04 GSC05 * GSC06 GSC07 GSC08 GSC09 GSC10

GSC11 GSC12 GSC13 GSC14 GSC15

* * GSC16 GSC17 GSC18 GSC19 GSC20

GSC21 GSC22 GSC23 GSC24 GSC25

GSC26 GSC27 GSC28 GSC29 GSC30

GSC31 GSC32 GSC33 GSC34 GSC35

* GSC36 GSC37 GSC38 GSC39 GSC40

* GSC41 GSC42 GSC43 GSC44 GSC45

GSC50 GSC51

GSC46 GSC47 GSC48 GSC49

Figure S3. Coverage and GC content of contigs within each bin. Y-axes have different scales (LHS of each plot). *Compositionally similar co-binned genomes with imprecise coverage separation. a 100% Eukaryota b Bac.-Proteobacteria Gammaproteobacteria Bac.-WS3_genera_incertae_sedis 90% Bac.-Planctomycetacia 3000 Vibrionaceae Thioprofundum Bac.-Phycisphaerae Sedimenticola Bac.-Spirochaetes Reinekea 80% Bac.-Erysipelotrichia Psychrosphaera Bac.-Planctomycetes 2500 Psychromonas Bac.-Bacteroidetes_incertae_sedis Pseudoalteromonadaceae 70% Bac.-Bacteroidetes Piscirickettsiaceae Bac.-Sphingobacteria Oleiphilus Bac.-Firmicutes Oceaniserpentilla 60% Bac.-Bacteria 2000 Neptunomonas Bac.-Alphaproteobacteria Moritella Bac.-Flavobacteria Methylobacter 50% Bac.-Deltaproteobacteria Haliea Eionea Bac.-Gammaproteobacteria 1500 Ectothiorhodospiraceae Bac.-Opitutae Dasania 40% Bac.-Nitrospira Colwelliaceae Relative abundance Bac.-Ignavibacteria Alteromonadales Bac.-Holophagae 1000 Alteromonadaceae 30% Bac.-Epsilonproteobacteria Spongiispira Gammaproteobacteria Bac.-Clostridia Porticoccus Bac.-Chloroplast gene sequence coverage rRNA Methylococcaceae 20% Bac.-Betaproteobacteria Oleispira Bac.-Anaerolineae 500 Gammaproteobacteria_incertae_sedis Bac.-Actinobacteria Oceanospirillales 10% Bac.-Acidobacteria_Gp3 Marinicella Bac.-Acidobacteria_Gp22 Oceanospirillaceae Bac.-Acidobacteria_Gp21 Cycloclasticus 0% 0 Glaciecola Bac.-Acidobacteria_Gp10 Colwellia 0.3 0.5 0.6 0.7 0.9 1.1 2.7 0.3 0.5 0.6 0.7 0.9 1.1 2.7 Bac.-Acidobacteria 10.1 15.1 24.8 33.9 48.8 59.5 Gammaproteobacteria 10.1 15.1 24.8 33.9 48.8 59.5 Archaea-Thermoprotei Distance (km) Distance (km) Archaea-Archaea c Chromatiales Methylococcales Thioalkalivibrio/ Pseudomonadales Methylococcus Thioprofundum /Alteromonadales Spongiibacter/Cellvibrio/Melitea

Thiotrichales Methylococcales Thiomicrospira/ Methylomonas Beggiatoa

Thiotrichales Cycloclasticus

Oceanospirillales/ Altermonadales Colwellia Kangiella/ Teredinibacter

Thalassomonas Oceanospirillales Neptunomonas/ Marinobacterium

Glaciecola Pseudomonadales Alteromonadales Azobacter/Pseudomonas

Marinobacter Oceanospirillales Endozoicomonas Porticoccus/Microbulbifer Figure S4. Phylogeny based on rRNA genes reconstructed from rarefied data, (a) Phylogeny per site. Eukaryota are relatively abundant in distal sites (23-52% versus 6-34% near-well). Bacteria, particularly Gammaproteobacteria increase in abundance relative to both Eukaryota and Archaea. (b) Stacked bar chart of Gammaproteobacteria rRNA gene sequence coverage per site based on RDP genus level designation or higher. The average number of unique designations is 13 ± 2 (1 standard deviation) for near-well sites, twice that for distal sites (7 ± 3). (c) Neighbor-joining tree depicting phylogenetic 16S rRNA gene diversity among the Gammaproteobacteria for near-well (red) and distal samples (blue), compared with reference sequences (black). Genus (italics) and order (bold) names are given for reference sequence clusters. Gammaproteobacterial richness at near-well sites was 317 (15,000x total 16S rRNA gene coverage), and the richness at distal sites was 152 (6,000x total 16S rRNA gene coverage). where totalalkanes= materials online in boxplots arefromMasonetal.(2014bsupplementary data presented geochemical underlying hydrocarbons, (T)PHC; higher near-well. weight, wt;nitrogen(DIN).*Concentrations dissolved inorganic The trations inall64samplesreportedbyMasonetal.(2014b) at0-265kmdistance. (total) petroleum Abbreviations: ofammonium+nitrate.(d) DIN valuescomprised (distal) fromtheMC252wellhead. yellow.and in black given (c) of binnumbers abundance bers arelistedinboxescentraltoeachplot.Pointsyellowrepresentthecombined possessing genesassociatedwithhydrocarbondegradation. Pointsarefittedcurves. with exponentialBinnum- km (near-well) and10-60km (distal) from the MC252 wellhead.(b) Summed persiteof abundance genome bins Figure andcarbonconcentrationsinthe13metagenomesamples0-3 S5. (a)Boxplotsofpetroleumhydrocarbon a c N and S concentrations in WGS sample subset Petroleum hydrocarbons in WGS sample subset (μg/kg) 0 1000 2000 3000 4000 5000 6000 0 10000 20000 30000 40000 50000 ** * * * DIN 0-3 TPHC * * * 0-3 (μg/kg) 10-60 0 30000 40000 50000 n-Alkanes 0-3 10-60 10-60 0 1000 2000 3000 4000 5000 0 10000 20000 30000 40000 50000 (μg/kg) Ammonium Branched Alkanes 0-3 0-3 wellDistance from head(km) 10-60 0 3000 4000 5000 6000 Alkanes Cyclic Distance from wellDistance from head(km) 0-3 10-60 n-alkanes). 0 500 1000 1500 2000 10-60 0 40 60 80 100 (μg/kg) Nitrate Aromatic Boxplots of N and S concentrations in samples 0-3 km (near-well) and 10-60 km 10-60 and 0-3 km(near-well) in samples S concentrations of Nand Boxplots

0-3 OtherPHC PAH PHC 0-3 10-60 0 2000 3000 4000 5000 6000

10-60 0-3 0.00 0.05 0.10 0.15 0.20 0.25 0.30 10-60 (% drywt) Total N 0 3000 4000 5000 6000

0-3 0-3 10-60 0 6 8 (dry wt%) Carbon 10-60 0-3 0.0 0.2 0.4 0.6 0.8 1.0 1.2 10-60 (% drywt) Total Sulfur *

0-3 b Summed genome coverages 0 50 100 150 200 250 300 Alkanes (AlkBG) 10-60 0 Alkanes (AlkB) 10 R 2 .320.8211 0.8362 0.6129 20 38 36 35 30 26 22 20 16 15 24 30 9 7 6 5 d 40 0 1000 2000 3000 4000 5000 6000 50 0 50 100 150 200 250 300 DIN

* * 0 + accessory R

0-3 10 CYP153 CYP153 2 0.7944

20 19 16 22 14 30 5 0-265 40 50 0 1000 2000 3000 4000 5000 wellDistance from head(km)

Ammonium 0 50 100 150 200 250 300

0 /MmoXYZCB) (partic. ABC R 10 Methane Distance from wellDistance from head(km) 0-3 2 0.8297

20 21 18 14 30 8 Boxplots ofNandSconcen- 0-265 40 0 500 1000 1500 2000 50 0 50 100 150 200 250 300 Xylene (XylMA) Nitrate 0 Xylene (XylM)

0-3 10 R 0.7911 2 0.7686 20 22 24 16 30 9 0-265 40 0.0 0.1 0.2 0.3 0.4 50 0 50 100 150 200 250 300 Total N

0 dio

10 R xygenase

0-3 2 PAH 0.8934 AB

20 22 15 30 9 0-265 40 0.0 0.2 0.4 0.6 0.8 1.0 1.2 50 0 50 100 150 200 250 300 (DmpKLMNOP /DmpMNOPR) Total Sulfur 0

10 R Phenol 0-3 2 0.8933

20 22 30 9 0-265 40 50 60 unknown Bacteria(grey). (CFB, pink), and group Cytophaga-Flavobacterium-Bacteroides (blue), Deltaproteobacteria ria (yellow), shown inyellow. Gammaproteobacteria(green), Plotsare organizedbyphylogeneticgroup: Alphaproteobacte- points and are bolded points) (white to theco-assembly contributing Samples deviation. bars =1standard Figure S6. Average genomebincoveragespersite determinedbymappingreadsto the co-assembly. Error Coverage 0 5 15 0 10 20 0 20 40 600 5 10 200 40 80 0 5 15 25 0 100 200 0 40 80 0 100 200 Co 0.3 0.5 0.6 0.7 0.9 GSC49 GSC43 GSC37 GSC31 GSC25 GSC19 GSC13 GSC7 1.1 GSC1 2.7 10.1 15.1 24.8 33.9 48.8 0 10 20 0 20 40 0 10 30 0 10 20 0 5 10 15 0 10 20 0 20 40 0 20 60 0 40 80 59.5 Co Co-assembly (Co)andDistancefromwellhead (km) 0.3 0.5 0.6 0.7 0.9 GSC50 GSC44 GSC38 GSC32 GSC26 GSC20 GSC14 GSC8 1.1 GSC2 2.7 10.1 15.1 24.8 33.9 48.8 0 10 15 10 20 0 40 80 0 5 15 0 5 15 0 10 20 0 10 20 30 0 10 20 30 0 10 20 59.5 Co 0.3 0.5 0.6 0.7 0.9 GSC51 GSC45 GSC39 GSC33 GSC27 GSC21 GSC15 GSC9 1.1 GSC3 2.7 10.1 15.1 24.8 33.9 48.8−50 0 50 0 10 20 0 10 20 0 5 15 0 5 10 15 0 10 20 30 0 20 40 60 0 20 40 0 40 80 59.5 Co 0.3 0.5 0.6 0.7 0.9 GSC46 GSC40 GSC34 GSC28 GSC22 GSC16 GSC10 1.1 GSC4 2.7 10.1 15.1 24.8 33.9 48.8 59.5 0 5 10 15 0 5 10 200 20 40 0 5 15 0 10 20 30 0 20 40 0 200 500 0 20 40 60 Co 0.3 0.5 0.6 0.7 0.9 GSC47 GSC41 GSC35 GSC29 GSC23 −17 GSC11 1.1 GSC5 2.7 10.1 15.1 24.8 33.9 48.8 0 5 10 15 0 20 40 60 0 10 30 0 10 20 30 0 40 80 0 20 40 0 200 400 0 10 30 59.5 Co 0.3 0.5 0.6 0.7 0.9 GSC48 GSC42 GSC36 GSC30 GSC24 GSC18 GSC12 1.1 GSC6 2.7 10.1 15.1 24.8 33.9 48.8 59.5 unknown Bacteria(grey). (CFB, pink),and group Cytophaga-Flavobacterium-Bacteroides (blue), Deltaproteobacteria (yellow), group: by taxonomic are colored red). Bins(RHS) (dark color same the assigned are ≥10 bolded. Abundances are co-assembly the to contributing Samples per siteorCo-assembly(Co). Figure clusteringofgenomebinabundance S7. Heatmapandhierarchical Coverage 10tomax 6 2 max =347

59.5 24.8 48.8 33.9 Distance fromwellhead(km) 1.1 10.1 15.1

Gammaproteobacteria (green), Alphaproteobacteria Gammaproteobacteria 0.6 2.7 0.3 0.7 0.9 0.5 Co GSC34 GSC28 GSC46 GSC45 GSC44 GSC33 GSC51 GSC48 GSC49 GSC31 GSC29 GSC30 GSC32 GSC27 GSC43 GSC42 GSC47 GSC50 GSC7 GSC12 GSC17 GSC16 GSC9 GSC19 GSC22 GSC15 GSC14 GSC11 GSC13 GSC41 GSC40 GSC6 GSC20 GSC35 GSC3 GSC36 GSC37 GSC24 GSC18 GSC21 GSC23 GSC26 GSC10 GSC8 GSC1 GSC25 GSC5 GSC4 GSC38 GSC2 GSC39 97 (gi.519054709) Gilvimarinus chinensis 39 (gi.753218343) Gilvimarinus agarilyticus 62 (gi.655501699) Teredinibacter turnerae 40 (gi.753795811) Cellvibrio japonicus 42 (gi.504862052) Simiduia agarivorans 0.05 (gi.738977472) Porticoccus hydrocarbonoclasticus 50 GSC15 40 GSC11 76 81 GSC14 21 (gi.496312383) Luminiphilus syltensis 97 (gi.497262065) gamma proteobacterium IMCC3088 99 (gi.750266999) Reinekea blandensis (gi.88779067) Reinekea sp. MED297 7 (gi.494080046) Neptuniibacter caesariensis 33 (gi.166220655) Marinobacter hydrocarbonoclasticus VT8 87 14 85 (gi.490716180) Marinobacter nanhaiticus (gi.330720883) gamma proteobacterium IMCC2047 3 56 GSC18 (gi.498232775) gamma proteobacterium HIMB30 (gi.488797617) Thiothrix nivea 0 45 (gi.655039096) Thiothrix lacustris 92 (gi.291579832) Nitrosococcus halophilus Nc 4 30 (gi.502984873) Nitrosococcus watsonii (gi.655035814) Thioalkalivibrio sp. ALE17 0 98 (gi.759373304) Xanthomonadaceae bacterium 3.5X 14 (gi.738184440) Luteibacter sp. 9135 3 (gi.644767274) Thioalkalivibrio thiocyanoxidans (gi.740247493) Thiobacillus prosperus 21 GSC22 GSC19 3 GSC8 0 35 (gi.407256456) Cycloclasticus sp. P1 99 (gi.511532667) Cycloclasticus sp. PY97M 93 (gi.528328776) Cycloclasticus zancles 7-ME 100 (gi.503600980) Thioalkalimicrobium cyclicum 66 (gi.493506144) Thioalkalimicrobium aerophilum (gi.78485933) Thiomicrospira crunogena XCL-2 73 (gi.655037427) Thiomicrospira chilensis 55 (gi.380881453) Thiorhodovibrio sp. 970 5 56 (gi.759394170) Solemya velum gill symbiont (gi.494100533) Thiorhodococcus drewsii GSC23 8 GSC25 14 99 GSC26 99 (gi.517453997) Kangiella aquimarina (gi.502478763) Kangiella koreensis (gi.654656087) Ferrimonas senticii 6 (gi.410169496) Glaciecola psychrophila 170 29 (gi.517858287) Colwellia piezophila 100 (gi.696551298) Colwellia psychrerythraea 62 44 GSC5 (gi.494245881) Methylophaga aminisulfidivorans (gi.697076962) Methylomonas sp. LW13 39 (gi.344260662)) Methylobacter tundripaludum SV96 8 47 (gi.652902782) Methylobacter luteus 6 (gi.635650374) Methylosarcina lacus 61 (gi.496497828) Sulfuricella denitrificans 8 3 (gi.347446582) Calyptogena fossajaponica symbiont GSC21 (gi.386429745) Beggiatoa alba B18LD 17 (gi.723287915) Candidatus Thiomargarita nelsonii 99 GSC1 98 90 GSC3 Figure S8. Maximum-Likelihood tree showing the phylogenetic relatedness of genome bins based on recovered predicted protein sequences of the highly conserved housekeeping gene recombinase A (recA). Sequences from our seafloor genome bins are shown in green, while those from reference organisms are in black. Reference sequence GenBank accession numbers are in parentheses. Tree construction employed 190 amino acid positions and 500 bootstrap replicates. Cycloclasticus sp. P1 MCCC 1A01040 Colwellia sp. NF1-20 a Cycloclasticus spirillensus c Colwellia sp. SW2-3E Cycloclasticus pugetii 15BN12U-14 15 Colwellia sp. BSi20435 99 Cycloclasticus sp. E Colwellia psychrerythraea 34H Cycloclasticus* sp. BG-2 0.3 km (hemg5 81) NP 0.84% Cycloclasticus sp. A5 0.01 Colwellia psychroerythrus IC064 99 Cycloclasticus oligotrophus 15.1 km (hemg13 310) NP 3.5% Cycloclasticus sp. G 30 0.6 km (hemg3 165) NP 0.88% 68 Cycloclasticus sp. W 2.7 km (hemg7 866) NP 1.7% * 1.1 km (hemg2 208) NP 1.8% 12 * 15.1 km (hemg13 7192) NP 0.79% 100 0.6 km (hemg3 53) NP 2.0% 9 46 0.9 km (hemg4 174) NP 0.82% 46 10.1 km (hemg14 510) NP 1.5% 59 2215 10.1 km (hemg14 767) NP 2.6% 0.3 km (hemg5 73) NP 3.3% 9 43 0.7 km (hemg6 299) NP 1.1% 2.7 km (hemg7 337) NP 0.24% 67 99 54 0.5 km (hemg8 75) NP 2.8% 0.7 km (hemg6 1045) NP 2.4% 2.7 km (hemg7 23) NP 1.4% 1.1 km (hemg2 273) NP 3.2% 54 30 1.1 km (hemg2 359) NP 0.70% 24.8 km (hemg11 387) NP 5.3% 10.1 km (hemg14 496) NP 0.83% 33.9 km (hemg10 221) NP 7.0% 0.6 km (hemg3 85) NP 1.3% 4 0.5 km (hemg8 102) NP 3.4% 0.3 km (hemg5 112) NP 1.5% 0.6 km (hemg3 5) NP 1.9% 67 0.9 km (hemg4 231) NP 0.70% 0.3 km (hemg5 171) NP 1.4% 62 0.7 km (hemg6 208) NP 0.61% 47 2.7 km (hemg7 66) NP 2.1% 0.9 km (hemg4 87) NP 5.4% 79 2.7 km (hemg7 626) NP 1.1% 0.5 km (hemg8 78) NP 2.6% 36 100 Methylomonas scandinavica SR5 58 DWH plume Colwellia HUGN SAG 96 Methylomonas rubra 3 **0.9 km (hemg4 12) NP 3.6% Methylobacter psychrophilus Z-0021 Colwellia rossensis ANT9247 Methylococcus capsulatus Bath 0.5 km (hemg8 29) NP 3.5% Marinobacterium stanieri MARIS-02 23 0.7 km (hemg6 29) NP 1.1% 98 Marinomonas mediterranea MMB-1 100 0 78 0.3 km (hemg5 33) NP 1.6% 100 Marinomonas sp. Y5 2.7 km (hemg7 49) NP 3.1% Colwellia piezophila Y223G 6 0.9 km (hemg4 594) NP 0.49% 0.7 km (hemg6 132) NP 1.8% 0 b 96 Pseudomonas fluorescens strain PGPR1 0.6 km (hemg3 1099) NP 0.72% 0.02 95 Pseudomonas synxantha Thalassomonas agarivorans M23b 100 33 Pseudomonas libanensis strain CIP 105460 100 Thalassomonas loyana M33a 46 Pseudomonas putida strain 75 59.5 km (hemg9 5948) NP 1.5% Endosymbiont of Ridgeia piscesae Thalassomonas sp. CAU1252 Endosymbiont of Vestimentiferan tubeworm from Riftia 2 10.1 km (hemg14 695) NP 0.88% 52 100 30 59 Endosymbiont of Oasisia alvinae 3 33.9 km (hemg10 1007) NP 0.89% 98 Microbulbifer gwangyangensis strain M9 5 0.9 km (hemg4 227) NP 1.0% Microbulbifer elongatus strain DSM 6810 1.1 km (hemg2 8595) NP 0.50% 6 44 0.9 km (hemg4 25) NP 0.59% 100 Microbulbifer chitinilyticus strain ABABA 212 0 Microbulbifer marinus strain Y215 24 0.5 km (hemg8 283) NP 1.3% 69 Microbulbifer taiwanensis strain CC-LN1-12 2.7 km (hemg7 291) NP 0.78% 96 3 56 1.3 km (15.1 km (hemg13 789) NP 2.0% 30 Pelagiobacter variabilis strain A4 100 Gamma proteobacterium HTCC231 11 10.1 km (hemg14 317) NP 1.6% 100 Gamma proteobacterium HTCC230 1.1 km (hemg2 673) NP 1.4% 31 0.6 km (hemg3 378) NP 0.94% Marine gamma proteobacterium HTCC2121 2 21 Colwellia aestuarii SMK-10 100 Marine gamma proteobacterium HTCC2120 98 0.3 km (hemg5 270) NP 1.5% Porticoccus hydrocarbonoclasticus strain MCTG13d 12 10.1 km (hemg14 1495) NP 1.8% Porticoccus litoralis strain NBRC 102686 2 0.9 km (hemg4 792) NP 0.48% 71 0.3 km (hemg5 747) NP 0.31% 34 0.7 km (hemg6 2415) NP 0.56% 95 0.5 km (hemg8 362) NP 0.21% 99 92 1 0.6 km (hemg3 1002) NP 0.72% 0.6 km (hemg3 1485) NP 0.57% 15.1 km (hemg13 97) NP 2.9% 93 0.5 km (hemg8 1432) NP 0.28% 13 33.9 km (hemg10 611) NP 1.2% 0.9 km (hemg4 851) NP 0.39% 15.1 km (hemg13 7190) NP 0.75% 63 17 83 0.7 km (hemg6 919) NP 0.25% 2.7 km (hemg7 368) NP 0.86% 16 0.5 km (hemg8 701) NP 0.56% 0.6 km (hemg3 1298) NP 0.43% 0.7 km (hemg6 373) NP 0.81% 39 33.9 km (hemg10 319) NP 0.68% 7 0.5 km (hemg8 1021) NP 0.22% 59.5 km (hemg9 5952) NP 1.4% 0.9 km (hemg4 1998) NP 0.75% 2 0.6 km (hemg3 1012) NP 0.66% 76 Glaciecola chathamensis S18K5 75 57 Glaciecola mesophila KMM 241 42 Glaciecola polaris LMG 21857 36 Glaciecola nitratireducens FR1064 23 98 1.1 km (hemg2 8594) NP 0.49% 63 15.1 km (hemg13 7191) NP 0.572% 10.1 km (hemg14 21) NP 0.93% 69 0.6 km (hemg3 116) NP 0.77% 0.02 72 2.7 km (hemg7 1216) NP 0.36% 99 0.5 km (hemg8 405) NP 0.29% 0.7 km (hemg6 425) NP 0.78% 0.9 km (hemg4 83) NP 0.68% 34 1.1 km (hemg2 129) NP 1.3% 83 15.1 km (hemg13 142) NP 1.7% 0.3 km (hemg5 182) NP 0.90% Figure S9. Maximum-Likelihood trees showing the phylogenetic relatedness of 16S rRNA genes sequences from near-well (red) and distal (blue) sites that are most closely related to (a) Cycloclasticus, (b) Porti- coccus, and (c) Colwellia species. Sequence identifiers are in parentheses. Norm Priors (NP) denote abundances per sample. Tree construction employed near full-length 16S rRNA genes and 500 bootstrap replicates.16S sequences related to these hydrocarbonoclastic genera were recovered from rarified sequence data up to ~10 km from MC252 for Cycloclasticus and Porticoccus, or 33.9 km in the case of Colwellia. *Northern Gulf of Mexico Cycloclasticus strains (Geiselbrecht et al., 1998). **16S from a DWH plume Colwellia single amplified genome (SAG) sequence (Mason et al., 2014a). a Xylene Oxidation b Toluene Oxidation * PRESENT * p-/o-/m-Xylene Toluene CH XylMA 9 15 22 IN BINS XylMA 9 15 22 3 4-/2-/3-Methylbenzyl-alcohol Benzyl alcohol EC1.1.1.90 9 15 22 EC1.1.1.90 9 15 22 4-/2-/3-Methylbenzaldehyde Benzaldehyde EC1.2.1.7/28 9 15 22 MISSING EC1.2.1.7/28 9 15 22 p-/o-/m-Methylbenzoate IN BINS Benzoate EC1.14.12.-/10 9 15 22 EC1.14.12.10 9 15 22 cis-1,2-Dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate cis-1,2-Dihydroxycyclohexa-3,5-diene-1-carboxylate EC1.3.1.67(p-)/68(o-)/25(m-) 9 15 22 EC1.3.1.25 9 15 22 4-/3-/3-Methylcatechol Catechol EC1.13.11.-/12 9 15 22 EC1.13.11.2 9 15 22 cis,cis-2-Hydroxy-6-oxohept-2,4-dienate 2-Hydroxymuconate-semialdehyde EC3.7.1.9(p-)/-(o-)/-(m-) 9 15 22 EC3.7.1.9 9 15 22 cis-2-Hydroxypenta-2,4-dienoate 2-Oxopent-4-enoate 4.2.1.80 9 15 22 EC4.2.1.80 9 15 22 4-Hydroxy-2-oxopentanoate 3-Hydroxy-2-oxopentanoate 4.1.3.39 9 15 22 EC4.1.3.39 9 15 22 Pyruvate + Acetaldehyde Pyruvate + Acetaldehyde

c Aerobic Octane Oxidation d Aerobic Butane Oxidation n-Octane Butane EC1.14.15.3 5 7 8 9 14 15 16 18 19 20 21 22 24 26 Mmo/ EC1.14.15.- 9 14 18 21 1-Octanol 1-Butanol EC1.1.1.1 5 7 8 9 14 15 16 18 19 20 21 22 24 26 EC1.1.1.- 9 14 18 21 1-Octanal Butanal EC1.2.1.3 5 7 8 9 14 15 16 18 19 20 21 22 24 26 EC1.2.1.10 9 14 18 21 Octanoate Butanoyl-CoA EC6.2.1.3 5 7 8 9 14 15 16 18 19 20 21 22 24 26 EC1.3.8.1 9 14 18 21 Octanoyl-CoA Crotonoyl-CoA 5 7 8 9 14 15 16 18 19 20 21 22 24 26 EC4.2.1.17 9 14 18 21 β-oxidation (S)-3-Hydroxybutanoyl-CoA EC1.1.1.35/157 9 14 18 21 Acetyl-CoA Acetoacetyl-CoA (β-oxidation) EC2.3.1.9 9 14 18 21 Acetyl-CoA

e C1 Metabolism f Aerobic Ammonia Oxidation Methane (CH4) Ammonia (NH3) EC1.14.13.25 (sMmo)/1.14.18.3 (pMmo) 7 8 9 14 18 21 EC1.14.99.39 (AMO≈Mmo) 7 8 9 14 18 21 Methanol (CH3OH) Hydroxylamine(NH2OH) EC1.1.2.7/1.1.3.13/1.1.1.244 7 8 9 14 18 21 EC1.7.2.6 (HAO) 7 8 9 14 18 21 Formaldehyde (CH2O) Nitrite (NO2-) (multistep/path) 7 8 9 14 18 21 Formate (CH2O2) EC1.2.1.2 7 8 9 14 18 21 CO2

Figure S10. (a-b) Aromatic hydrocarbon oxidation pathways indicated by a yellow * in genome bin Group 4 (Fig. 4). (c-d) Alkane oxidation pathways using (c) alkane 1-monoxygenase and targeting C5-C10 alkanes, or (d) methane monooxygenase, Mmo, and targeting C1-C5 alkanes. (e-f) Incomplete methane and ammonium oxidation pathways using Mmo. (a-f) Genome bin numbers are shown to the right of pathway arrows. Genes present are shown in grey. Bins with some of the pathway genes present are shown in black. Genes missing and bins with genes unidentified for particular steps are shown in red. 90

80 Ca. Colwellia GSC5-7

R = 0.49638 70 CFB GSC42-43,46

gammaproteobacteria GSC5-6,15,22,24 50

30 Average amino acid identity of genome bins Average

20 20 30 40 50 60 70 80 90 Amino acid identity of alkB genes

Figure S11. Comparisons of alkB gene and genome bin relatedness based on pairwise amino acid identities determined during reciprocal searches. 100 (gi511530880)_PAH_dioxygenase_large_subunit_Cycloclasticus_sp._PY97M (gi407257818)_PAH_dioxygenase_large_subunit_Cycloclasticus_sp._P1 100 (gi504819926)_MULTISPECIES:_naphthalene_1,2-dioxygenase_Cycloclasticus 51 unbinned--contig-75_23470_2 99 unbinned--contig-75_30038_2 94 (gi669023944)_naphthalene_1,2-dioxygenase_Sphingobium_yanoikuyae 93 100 (gi126030183)_PAH-Hydroxylating_Dioxygenase_From_Sphingomonas_Sp_Chy-1 GSC15--contig-75_1297_12 Na ph thalene 53 GSC22--contig-75_12133_1 100 GSC22--contig-75_19117_1 GSC15--contig-75_3264_2 100 GSC22--contig-75_30621_2 56 GSC9--contig-75_2703_2 71 81 GSC22--contig-75_2864_3 (gi659836894)_naphthalene_1,2-dioxygenase_Polycyclovorans_algicola (gi680269001)_naphthalene_1,2-dioxygenase_Burkholderia_sp._K24 93 97 (gi567430947)_naphthalene_1,2-dioxygenase_Marinomonas_profundimaris 100 93 (gi589144769)_naphthalene_1,2-dioxygenase_Pseudomonas_fluorescens_HK44 94 (gi692379038)_naphthalene_1,2-dioxygenase_Comamonas_testosteroni 100 (gi582952965)_naphthalene_1,2-dioxygenase_Pseudomonas_stutzeri_KOS6 75 (gi612178105)_naphthalene_1,2-dioxygenase_Pseudomonas_bauzanensis 66 GSC22--contig-75_23019_2 GSC15--contig-75_1297_5 100 97 unbinned--contig-75_21450_1 GSC15--contig-75_24031_2

GSC15--contig-75_15019_2 B

96 iph e 68 GSC9--contig-75_13604_2 100 GSC9--contig-75_19777_2

100 (gi504819486)_MULTISPECIES:_benzene_1,2-dioxygenase_Cycloclasticus ny l + Be n 99 100 (gi511531526)_biphenyl_dioxygenase_subunit_alpha_Cycloclasticus_sp._PY97M 100 (gi501996347)_benzene_1,2-dioxygenase_Rhodococcus_opacus 98 (gi672606826)_benzene_1,2-dioxygenase_Comamonas_testosteroni_TK102 100 (gi3023401)_Biphenyl_dioxygenase_subunit_alpha_Pseudomonas sp. KKS102 69 ze ne (gi3023413)_Biphenyl_dioxygenase_subunit_alpha_Comamonas testosteroni 98 (gi518582711)_benzene_1,2-dioxygenase_Pseudomonas_putida (gi3023415)_Biphenyl_dioxygenase_subunit_alpha_Pseudomonas pseudoalcaligenes 100

99 (gi584852)_Biphenyl_dioxygenase_subunit_alpha_Burkholderia xenovorans LB400 Py (gi393662546)_pyrene_dioxygenase_alpha_subunit_Pseudomonas_sp._Jpyr-1 unbinned--contig-75_8948_3 re ne 99 100 GSC15--contig-75_12302_2 100 (gi430793396)_benzoate_dioxygenase_subunit_alpha_Pseudomonas_putida_HB3267 100 (gi395808436)_benzoate_dioxygenase_subunit_alpha_Pseudomonas_stutzeri_DSM_10701 (Ortho-halo)benzoate + Anthranilate 64 (gi31407697)_benzoate_1,2_dioxygenase_alpha_subunit_Acinetobacter_calcoaceticus_PHEA-2 70 (gi490338311)_benzoate_1,2-dioxygenase_hydroxylase_subunit_alpha_Ralstonia_sp._GA3-3 100 (gi3511232)_anthranilate_dioxygenase_large_subunit_Acinetobacter_sp._ADP1 47 (gi528329170)_benzoate_dioxygenase_Cycloclasticus_zancles_7-ME 100 (gi511533039)_ring_hydroxylating_dioxygenase_subunit_alpha_Cycloclasticus_sp._PY97M (gi504819893)_aromatic_ring-hydroxylating dioxygenase_Cycloclasticus_sp._P1 100 (gi4406507)_ortho-halobenzoate_1,2-dioxygenase_alpHA_Pseudomonas_aeruginosa (gi91688639)_ortho-halobenzoate_1,2-dioxygenase_alpha_subunit_Burkholderia_xenovorans_LB400 52 (gi58616669)_ortho-halobenzoate_1,2-dioxygenase_alpha_Achromobacter_xylosoxidans_A8 (gi91693790)_anthranilate_dioxygenase_large_subunit_Burkholderia_xenovorans_LB400 100 (gi75445985)_anthranilate_1,2-dioxygenase_large_subunit_Burkholderia cepacia 100 (gi256858052)_biphenyl_dioxygenase_large_subunit_Sphingomonas_sp._DN1 GSC15--contig-75_1297_11 98 (gi407257819)_Aromatic_dioxygenase_large_subunit_Cycloclasticus_sp._P1 97 (gi703406609)_Rieske_(2Fe-2S)_protein_Cycloclasticus_pugetii 0.2 100 (gi33456989)_aromatic_dioxygenase_large_subunit_Cycloclasticus_sp._A5 95 (gi511530879)_Aromatic_dioxygenase_large_subunit_Cycloclasticus_sp._PY97M (gi737884652)_MULTISPECIES:_Rieske_(2Fe-2S)_protein_Cycloclasticus

Figure S12. Maximum-Likelihood tree depicting the phylogenetic relatedness among predicted protein sequences of (near) full length candidate PAH dioxygenases alpha subunits from our genome bins (green) compared with reference naphthalene, biphenyl, pyrene and anthranilate PAH dioxygenases and benzene and (ortho-halo-)benzoate aromatic dioxygenases. GenBank accession numbers for reference sequences are in parentheses. Tree construction employed 340 amino acid positions and 500 bootstrap replicates. Table S1. Sequence data input (trimmed), and IDBA-UD assembly summary. WGS PE WGS Assembled WTS PE Reads Reads rRNA Sample Distance Max Contig RNA types RNA reads length length N50 reads mapped mapped (% of ID (km) 1 2 contig count* 1 analyzed amplified (millions) (Gbp) (Mbp) (millions) to rRNA to CDS reads) BP_331 0.3 166 17 28 3,417 73,930 8,010 48 6,161,432 714,996 89.6 rRNA+mRNA Yes BP_315 0.5 275 28 63 4,052 101,350 15,864 58 3,956,483 330,029 92.3 rRNA+mRNA - BP_350 0.6 153 15 26 3,672 74,260 7,077 52 3,243,259 185,051 94.6 rRNA+mRNA - BP_139 0.7 187 19 79 3,981 76,457 19,965 50 3,018,430 306,824 90.8 rRNA+mRNA - BP_143 0.9 204 21 58 4,101 51,853 14,517 58 3,854,101 353,822 91.6 rRNA+mRNA - BP_366 1.1 266 27 34 3,760 131,389 8,923 37 3,390,160 377,874 90.0 rRNA+mRNA Yes BP_120 1.3 ------37 1,808,118 244,029 88.1 rRNA Yes BP_278 2.7 144 15 28 3,384 73,930 7,896 53 3,293,179 291,043 91.9 rRNA+mRNA - Average 1.0 199 20 45 3,767 80,746 11,750 49 3,590,645 350,459 91.1 - - BP_101 10.1 285 29 18 3,648 78,608 4,640 32 3,326,370 522,218 86.4 rRNA+mRNA Yes BP_155 15.1 344 35 12 3,464 58,165 3,517 21 1,990,232 225,102 89.8 rRNA+mRNA Yes BP_444 24.8 369 37 2 3,182 26,366 557 ------BP_463 33.9 291 29 6 3,139 42,788 1,732 36 1,337,250 202,961 86.8 rRNA+mRNA Yes BP_501 48.8 355 36 10 4,238 26,854 2,481 ------BP_186 59.5 295 30 1 2,646 23,506 481 ------Average 27.6 305 31 8 3,386 42,715 2,235 30 2,217,951 316,760 87.7 - - Co- 0.5+0.7+0.9 666 68 181 4,748 134,227 41,000 ------assembly Note: Co-assembly and co-assembled samples are shown in blue. 1Trimmed read counts 2Contigs >2kbp long.

Table S2. Genomic bin characteristics. Bin AAI1 (%) RecA Average Average %CGs %Surplus Genomes Phylog. AAI2 CDS Bin length Contig Nearest related genome (reference) Nearest RecA GSC to reference %ID G+C coverage /107 CGs /107 per bin cluster (%) to bin count (bp) count 1 Candidatus Thiomargarita nelsonii 66 Ca. Thiomargarita nelsonii 84 32 156 83 4 1 1 86 GSC3 4,088 4,888,626 787 2 Candidatus Thiomargarita nelsonii 65 - - 32 46 10 0 1 1 80 GSC1 264 276,972 41 3 Candidatus Thiomargarita nelsonii 66 Ca. Thiomargarita nelsonii 86 32 23 76 1 1 1 86 GSC1 2,709 2,996,330 465 4 Colwellia psychrerythraea 34H 73 - - 36 90 41 2 1 2 82 GSC6 1,929 1,928,427 406 5 Colwellia psychrerythraea 34H 73 C. psychrerythraea 92 36 38 53 3 1 2 81 GSC4 2,020 2,113,321 218 6 Colwellia psychrerythraea 34H 68 - - 36 18 7 0 1 2 82 GSC4 643 575,276 175 7 Colwellia psychrerythraea 34H 90 - - 38 90,22 57 2 2* 2 74 GSC4 4,925 5,186,372 909 8 Cycloclasticus zancles 73 Cycloclasticus sp. P1, C.zancles 94 42 42 50 0 1 3 86 GSC10 1,691 1,571,359 288 9 Cycloclasticus sp. P1 79 Cycloclasticus sp. P1, C.zancles 94 44 26 48 21 2** 3 73 GSC8 2,643 2,296,057 617 10 Cycloclasticus sp. P1 72 - - 42 22 17 0 1 3 86 GSC8 1,070 889,100 249 11 Porticoccus hydrocarbonoclasticus MCTG13d 59 P. hydrocarbonoclasticus MCTG13d 86 49 347 30 0 1 4 83 GSC13 563 547,319 149 12 Porticoccus hydrocarbonoclasticus MCTG13d 58 - - 51 150 13 0 1 4 82 GSC11 776 758,082 213 13 Porticoccus hydrocarbonoclasticus MCTG13d 56 - - 50 29 14 1 1 4 82 GSC11 1,516 1,432,455 384 14 Porticoccus hydrocarbonoclasticus MCTG13d 61 P. hydrocarbonoclasticus MCTG13d 84 48 47 82 1 1 4 73 GSC11 1,541 1,513,903 287 15 Porticoccus hydrocarbonoclasticus MCTG13d 60 P. hydrocarbonoclasticus MCTG13d 88 50 27 80 0 1 4 64 GSC14 1,824 1,791,859 350 16 gammaproteobacterium HdN1 54 - - 43 71,21 38 0 2* - 54 GSC18 2,657 2,489,254 673 17 Teredinibacter turnerae T7901 58 - - 46 17 31 2 1 - 55 GSC14 1,630 1,513,391 426 18 gammaproteobacterium IMCC2047 61 gammaproteobacterium IMCC2047 85 49 33,15 79 11 2* - 55 GSC14 2,537 2,473,031 476 19 gammaproteobacterium IMCC2047 54 gammaproteobacterium HIMB30 76 47 21 48 0 1 - 55 GSC18 1,722 1,606,611 336 20 Cycloclasticus sp. P1 50 - - 41 19 69 2 1 - 50 GSC23 2,790 2,689,849 549 21 Candidatus Thiomargarita nelsonii 53 Thiothrix nivea 79 49 24 80 1 1 - 53 GSC8 1,979 1,865,361 371 22 Nitrosococcus watsonii 51 Ca. Tenderia electrophaga 79 51 29 42 15 2** - 50 GSC21 2,713 2,555,975 636 23 Kangiella koreensis SW-125 54 Oleiagrimonas soli, K. aquimarina 80 37 26 64 20 2** - 51 GSC5 5,478 5,384,675 1,125 24 Hahella chejuensis KCTC 2396 57 - - 41 72 76 0 1 - 55 GSC18 4,534 4,514,783 667 25 Cycloclasticus sp. P1 50 Thiorhodovibrio sp. 970 87 37 100 49 2 1 5 73 GSC26 1,633 1,525,989 378 26 Kangiella koreensis SW-125 48 Solemya velum gill symbiont, Methylophaga frappieri 81 35 18 34 2 1 5 72 GSC25 2,765 2,737,699 608 27 Micavibrio aeruginosavorus 57 M. aeruginosavorus EPB 79 42 23 87 22 2** - 54 GSC29 1,757 1,606,244 268 28 Micavibrio aeruginosavorus 54 O. indicum, O. pacidicum 77 41 16 41 2 1 - 53 GSC27 1,259 1,046,950 296 29 Micavibrio aeruginosavorus 56 - - 44 20 38 7 1 - 54 GSC27 2,107 1,839,492 441 30 Rhodobacterales bacterium HTCC2255 63 Rhodobacterales bacterium HTCC2255 83 47 34 97 2 1 6 60 GSC31 3,424 3,436,081 110 31 Rhodobacterales bacterium HTCC2255 59 Sulfitobacter mediterraneus 86 52 18 42 0 1 6 60 GSC30 1,756 1,405,749 386 32 Oceanibaculum indicum P24 53 Sneathiella glossodoripedis 90 46 26 89 3 1 - 51 GSC28 3,365 3,184,965 458 33 Oceanibaculum indicum P24 51 endosymbiont of Acanthamoeba sp. UWC36 76 39 20 66 1 1 - 51 GSC32 1,095 976,746 159 34 Rickettsia bellii 54 - - 33 21 76 1 1 - 48 GSC33 1,078 999,820 178 35 Polaribacter sp. MED152 61 Lutibacter sp. LP1 94-96 30 64,22 67 74 3* ** 11 66 GSC44 7,657 7,284,376 1,605 36 Polaribacter sp. MED152 74 Polaribacter atrinae 96 30 20 88 65 3** 11 63 GSC42 3,939 4,125,614 523 37 Polaribacter sp. MED152 60 Tenacibaculum dicentrarchi 93 33 26 13 0 1 11 65 GSC42 1,327 1,218,909 372 38 Aequorivita sublithincola 9-3 66 Ulvibacter sp. LPB0005 90 32 19 52 6 1 11 64 GSC46 2,770 2,718,766 495 39 Formosa sp. AK20 68 Algibacter lectus 92 34 18 54 2 1 11 64 GSC45 2,765 2,643,860 527 40 Marinilabilia salmonicolor JCM 21150 50 - - 33 16 34 0 1 - 53 GSC49 1,288 1,278,012 314 41 Anaerophaga sp. HS1 52 Marinifilum fragile 84 30 18 46 2 1 - 53 GSC47 2,107 2,098,621 475 42 Marinilabilia salmonicolor JCM 21150 49 Spingobacterium sp. PM2-P1-29 82 33 19 32 0 1 - 54 GSC47 2,075 2,112,534 522 43 Desulfobacterium autotrophicum HRM2 53 Desulfatirhabdium butyrativorans 80 40 45 69 3 1 12 70 GSC37 5,893 6,773,533 593 44 Desultotalea psychrophila LSv54 47 - - 39 24 0 22 2** 12 64 GSC35 421 475,316 65 45 Desulfobacterium autotrophicum HRM2 54 D. autotrophicum HRM2 88 39 76,38,16 93 7 3* 12 70 GSC35 5,659 6,042,683 861 46 Desulfobacula toluolica Tol2 65 - - 47 21 27 3 1 - 52 GSC37 2,528 2,270,163 722 47 Desulfobulbus propionicus 1pr3 59 Desulfobulbus japonicus 83 48 72 68 1 1 - 57 GSC41 2,397 2,382,941 491 48 Desulfotalea psychrophila LSv54 60 - - 43 21 59 1 1 - 58 GSC41 2,229 2,096,970 552 49 Desulfocapsa sulfexigens SB164P1 74 - - 45 16 53 3 1 - 59 GSC40 1,775 1,684,524 476 50 uncultured bacterium (gcode 4) 46 - - 23 21 10 0 1 - 47 GSC2 539 484,216 145 51 Ignavibacterium album Mat9-16 43 - - 55 15 12 - 1 - 43 GSC33 1,125 1,037,969 322 52 (Virus-associated) - - - 40 44 - - - - - 11,444 7,892,159 1,225 - (Unbinned) ------59,689 53,523,903 16,518 Abbreviations: Phylogenetic (phylog.); average amino acid identity (AAI); ID (identity); core genes (CGs); coding DNA sequence (CDS). Bacteria bins are: Gammaproteobacteria (green), Alphaproteobacteria (yellow), Deltaproteobacteria (blue), Bacteroidetes (pink), and unclassified Bacteria (grey). AAI are given for comparisons between genome bins and: 1the nearest related reference genome, or 2the nearest related genome bin. Phylogenetically clustered genomes share AAIs of ≥60%, while un-clustered bins share <60% AAI with any other bin. Genome completion estimates are based on the percentage of 107 unique CGs present, without correction for co-binning. Bins estimated to be ≥50% complete are highlighted in purple. Co-binned genomes are clearly indicated by: *the detection of ≥2 compositionally similar genomes using ESOM with imprecise separation of contigs based on coverage; and are suggested by **the presence of surplus CG copies in a bin, which are typically present in a genome as single copy genes. Table S3. Pearson's correlations between distance and (hydro)carbon concentrations or genome coverage. Distance Distance Correlation coefficient (linear) P-value Correlation coeff. (exponential*) P-value Total_petroleum_hydrocarbons -0.17 1.00 0.03 1.00 Aromatics -0.40 1.00 NaN NaN Alkanes -0.39 1.00 -0.15 1.00 PAHs -0.26 1.00 -0.10 1.00 Branched_alkanes 0.15 1.00 0.08 1.00 Cyclic_alkanes 0.07 1.00 0.16 1.00 Other_petroleum_hydrocarbons 0.22 1.00 NaN NaN Carbon -0.61 0.17 -0.73 0.02 GSC1 -0.33 1.00 -0.82 0.01 GSC2 -0.41 1.00 -0.80 0.02 GSC3 -0.51 1.00 -0.82 0.01 GSC4 -0.37 1.00 -0.82 0.01 GSC5 -0.37 1.00 -0.80 0.02 GSC6 -0.44 1.00 -0.82 0.01 GSC7 -0.51 1.00 -0.52 0.14 GSC8 -0.40 1.00 -0.86 0.01 GSC9 -0.78 0.08 -0.95 0.00 GSC10 -0.52 1.00 -0.91 0.00 GSC11 -0.49 1.00 -0.87 0.00 GSC12 -0.65 0.62 -0.85 0.01 GSC13 -0.69 0.36 -0.89 0.00 GSC14 -0.68 0.44 -0.85 0.01 GSC15 -0.77 0.11 -0.84 0.01 GSC16 -0.73 0.22 -0.91 0.00 GSC17 -0.38 1.00 -0.51 0.14 GSC18 -0.44 1.00 -0.76 0.02 GSC19 -0.72 0.26 -0.77 0.02 GSC20 -0.49 1.00 -0.82 0.01 GSC21 -0.58 1.00 -0.84 0.01 GSC22 -0.74 0.18 -0.81 0.02 GSC3 -0.69 0.39 -0.88 0.00 GSC24 -0.32 1.00 -0.76 0.02 GSC25 -0.59 0.99 -0.94 0.00 GSC26 -0.63 0.74 -0.89 0.00 GSC27 -0.75 0.15 -0.89 0.00 GSC28 -0.87 0.01 -0.80 0.02 GSC29 -0.62 0.76 -0.91 0.00 GSC30 -0.59 1.00 -0.90 0.00 GSC31 -0.50 1.00 -0.82 0.01 GSC32 -0.65 0.62 -0.85 0.01 GSC33 -0.27 1.00 -0.63 0.07 GSC34 -0.85 0.01 -0.82 0.01 GSC35 -0.40 1.00 -0.82 0.01 GSC36 -0.46 1.00 -0.81 0.02 GSC37 -0.45 1.00 -0.84 0.01 GSC38 -0.51 1.00 -0.82 0.01 GSC39 -0.38 1.00 -0.81 0.02 GSC40 -0.44 1.00 -0.78 0.02 GSC41 -0.41 1.00 -0.75 0.02 GSC42 -0.51 1.00 -0.87 0.00 GSC43 -0.65 0.62 -0.89 0.00 GSC44 -0.66 0.56 -0.77 0.02 GSC45 -0.64 0.65 -0.70 0.03 GSC46 -0.81 0.04 -0.88 0.00 GSC47 -0.65 0.61 -0.90 0.00 GSC48 -0.48 1.00 -0.75 0.02 GSC49 -0.42 1.00 -0.82 0.01 GSC50 -0.58 1.00 -0.72 0.03 GSC51 -0.52 1.00 -0.88 0.00 Values with significant p-values (≤0.05) are highlighted in yellow. Correlations were determined using the R psych package, and p-values were adjusted for multiple tests using the "hommel" method. *Linear correlation following log transformation of data. Table S4. Percentage of contigs with mapped reads at each site. GSC Co 0.3 0.5 0.6 0.7 0.9 1.1 2.7 10.1 15.1 24.8 33.9 48.8 59.5 Min* Min* Min* 1 100 100 100 100 100 100 100 100 93 92 90 91 92 90 90 100 90 2 100 100 100 100 100 100 100 100 93 93 83 88 83 90 83 100 83 3 100 100 100 100 100 100 99 100 96 94 93 91 93 89 89 99 89 4 100 100 100 100 100 100 100 100 100 99 98 100 99 93 93 100 93 5 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 6 100 100 100 100 100 100 98 100 98 95 95 96 97 87 87 98 87 7 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 8 100 100 100 100 100 100 100 100 99 99 97 98 94 98 94 100 94 9 100 100 100 100 100 100 100 100 100 100 100 100 99 99 99 100 99 10 100 100 100 100 100 100 100 100 100 100 98 100 91 98 91 100 91 11 100 100 100 100 100 100 100 100 100 100 99 100 98 95 95 100 95 12 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 13 100 100 100 100 100 100 100 100 99 99 98 99 98 94 94 100 94 14 100 100 100 100 100 100 100 100 100 100 100 100 100 96 96 100 96 15 100 100 100 100 100 100 100 100 100 100 100 100 100 97 97 100 97 16 100 100 100 100 100 100 100 100 100 100 97 100 97 85 85 100 85 17 100 100 100 100 100 100 100 100 100 100 100 99 100 90 90 100 90 18 100 98 100 100 99 100 100 100 93 92 87 90 89 83 83 98 83 19 100 100 100 100 100 100 100 100 100 100 100 100 100 96 96 100 96 20 100 100 100 100 100 100 96 100 98 100 75 81 73 65 65 96 65 21 100 100 100 100 100 100 100 100 100 100 97 94 90 85 85 100 85 22 100 100 100 100 100 100 100 100 100 100 100 100 100 97 97 100 97 23 100 100 100 100 100 100 100 100 100 100 95 98 89 77 77 100 77 24 100 100 100 100 100 100 100 100 99 99 98 100 100 86 86 100 86 25 100 100 100 100 100 100 100 100 100 100 98 100 98 77 77 100 77 26 100 100 100 100 100 100 100 100 100 100 97 96 92 76 76 100 76 27 100 100 100 100 100 100 100 100 100 100 100 99 99 84 84 100 84 28 100 100 100 100 100 100 100 100 100 100 100 100 100 92 92 100 92 29 100 100 100 100 100 100 100 100 100 100 100 95 88 82 82 100 82 30 100 100 100 100 100 100 100 100 100 100 100 100 100 99 99 100 99 31 100 100 100 100 100 100 100 100 100 100 96 100 96 86 86 100 86 32 100 100 100 100 100 100 100 100 100 100 100 100 100 98 98 100 98 33 100 100 98 98 100 97 96 96 94 94 89 89 86 84 84 96 84 34 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 35 100 100 100 100 100 100 100 100 89 89 88 91 89 88 88 100 88 36 100 100 100 100 100 100 100 100 89 94 92 92 89 89 89 100 89 37 100 100 100 100 100 100 99 100 79 83 73 82 76 68 68 99 68 38 100 100 100 100 100 100 99 100 72 81 65 80 82 63 63 99 63 39 100 100 100 100 100 100 99 100 85 89 84 85 86 83 83 99 83 40 100 100 100 100 100 100 100 100 87 93 75 79 99 54 54 100 54 41 100 100 100 100 94 100 92 100 74 79 61 78 66 59 59 92 59 42 100 100 100 100 100 100 100 100 99 99 98 99 98 95 95 100 95 43 100 100 100 100 100 100 100 100 99 100 98 100 98 96 96 100 96 44 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 45 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 46 100 100 100 100 100 100 100 100 100 100 100 100 100 99 99 100 99 47 100 100 100 100 100 100 100 100 94 95 90 94 88 81 81 100 81 48 100 100 100 100 100 100 100 100 96 95 95 96 93 89 89 100 89 49 100 100 100 100 100 100 95 100 94 91 86 86 86 72 72 95 72 50 100 100 100 99 100 100 98 100 99 100 98 97 98 93 93 98 93 51 100 100 100 100 100 100 97 100 85 82 73 94 82 72 72 97 72 *Minimum % of contigs detected across all, proximal or distal sites. Abbreviation: Co-assembly, Co. Table S5. Average mapped-read genome bin coverages per site.

GSC Co 0.3 0.5 0.6 0.7 0.9 1.1 2.7 10.1 15.1 24.8 33.9 48.8 59.5 Cnt* Cnt* Cnt* 1 156.34 11.91 20.29 9.42 175.76 10.64 1.19 41.16 0.53 0.53 0.30 0.46 0.37 0.28 7 7 0 2 46.28 9.04 16.73 4.62 69.15 17.44 0.79 18.54 0.38 0.48 0.30 0.52 0.57 0.41 6 6 0 3 22.97 6.02 11.13 1.60 6.96 17.91 0.67 4.74 0.49 0.61 0.37 0.50 0.41 0.31 6 6 0 4 89.61 14.24 100.23 7.16 16.64 14.11 2.32 20.47 2.60 2.74 0.90 2.11 1.50 0.53 11 7 4 5 37.88 10.30 50.57 4.94 7.61 7.23 2.30 8.99 2.78 2.89 1.16 2.24 1.45 1.04 13 7 6 6 17.92 6.09 26.97 3.21 6.44 4.97 1.34 8.40 1.42 1.51 0.60 1.12 0.98 0.34 10 7 3 7 78.19 15.45 46.32 18.25 27.30 44.37 13.77 16.34 19.61 27.18 9.99 30.35 10.87 1.76 13 7 6 8 41.80 17.88 64.39 7.34 7.37 8.13 3.44 15.43 2.20 2.02 0.86 1.46 0.69 1.37 11 7 4 9 26.37 29.16 23.48 27.07 13.70 13.20 26.02 13.85 7.08 5.24 1.94 2.30 0.89 0.87 11 7 4 10 22.00 42.91 34.75 12.97 6.34 7.54 3.88 17.77 1.94 1.62 0.57 1.63 0.46 0.72 10 7 3 11 348.42 101.31 418.61 57.84 112.94 143.09 30.56 95.28 25.54 21.87 4.37 15.02 7.35 1.48 13 7 6 12 150.44 81.35 216.21 82.18 71.33 120.43 57.47 53.86 51.28 47.49 12.92 27.63 16.36 4.29 13 7 6 13 28.87 56.78 123.45 47.00 48.42 68.10 34.11 42.93 27.57 20.71 5.68 14.44 6.40 2.21 13 7 6 14 47.07 22.66 29.28 15.42 25.43 44.62 7.62 13.94 9.60 10.78 2.58 5.39 2.19 0.83 12 7 5 15 26.60 18.67 22.29 31.28 16.14 20.67 34.17 8.02 22.77 10.13 2.11 4.32 1.86 0.98 12 7 5 16 52.94 16.59 25.04 17.13 32.89 25.22 9.01 13.94 4.08 5.45 0.96 3.27 1.10 0.40 11 7 4 17 16.66 8.74 8.51 12.72 8.15 7.25 28.79 1.96 43.91 25.97 5.01 1.13 1.09 0.52 12 7 5 18 30.11 2.78 35.94 5.07 3.87 11.24 5.45 29.97 1.10 1.24 0.64 1.03 0.77 0.58 10 7 3 19 21.06 10.81 11.06 8.15 11.77 17.84 6.80 8.05 5.90 6.58 2.23 6.49 4.36 1.07 13 7 6 20 19.34 2.60 5.62 1.74 14.10 9.28 0.75 2.58 0.77 1.34 0.27 0.48 0.28 0.21 7 6 1 21 24.20 6.97 20.74 5.56 5.18 16.14 3.24 17.67 1.94 3.15 0.75 1.17 0.80 0.66 10 7 3 22 29.30 18.05 20.42 13.26 11.45 28.64 12.74 9.30 9.46 11.73 2.36 7.82 2.89 0.95 12 7 5 23 25.50 9.92 15.45 7.68 18.31 9.89 3.48 4.74 3.76 5.20 0.61 1.41 0.47 0.28 10 7 3 24 71.72 5.24 12.02 7.82 89.89 3.05 8.40 11.78 1.40 1.65 0.71 2.54 1.71 0.39 11 7 4 25 99.93 28.70 66.12 29.01 40.05 30.34 4.15 10.52 2.58 2.69 0.60 1.68 0.75 0.33 10 7 3 26 18.46 7.06 11.36 5.20 15.40 6.41 1.71 4.01 1.66 3.14 0.53 0.71 0.39 0.22 9 7 2 27 23.41 7.49 12.56 6.67 13.54 9.50 3.83 4.95 5.02 3.67 0.93 1.24 0.79 0.41 10 7 3 28 16.21 9.65 10.49 8.64 12.17 8.90 6.84 5.44 6.86 7.36 2.00 3.76 1.92 0.43 12 7 5 29 20.22 4.82 18.78 7.10 10.75 4.96 6.54 2.75 3.67 2.59 0.72 0.56 0.37 0.30 9 7 2 30 33.65 8.19 20.39 7.60 15.73 7.18 4.40 4.84 1.34 1.62 0.66 1.94 1.72 0.44 11 7 4 31 17.84 3.84 16.05 2.72 7.35 6.09 1.41 3.94 1.34 2.11 0.59 1.26 0.74 0.61 10 7 3 32 25.97 5.40 11.63 5.42 14.74 9.79 3.00 4.75 3.46 3.22 0.96 2.07 1.43 0.53 11 7 4 33 19.60 3.94 1.15 0.60 22.51 0.73 0.50 0.54 0.45 0.53 0.33 0.46 0.36 0.32 3 3 0 34 20.86 12.59 9.76 11.21 9.98 7.80 10.36 4.05 8.94 7.97 3.96 3.49 1.84 0.97 12 7 5 35 45.36 4.20 21.86 1.61 47.07 12.78 0.65 3.84 0.22 0.27 0.19 0.30 0.23 0.22 6 6 0 36 24.40 5.76 11.69 1.15 26.99 8.37 0.46 7.21 0.19 0.24 0.22 0.25 0.25 0.21 6 6 0 37 39.09 5.56 37.45 2.10 15.81 14.15 0.65 7.09 0.27 0.34 0.20 0.34 0.25 0.20 6 6 0 38 21.17 7.06 33.58 3.53 16.89 13.55 0.81 16.96 0.32 0.45 0.31 0.45 0.47 0.31 6 6 0 39 71.88 15.51 89.69 3.60 9.83 22.23 0.85 17.91 0.44 0.53 0.39 0.56 0.56 0.53 6 6 0 40 20.67 3.55 26.31 1.92 7.80 6.51 0.72 14.04 0.32 0.48 0.23 0.35 0.80 0.17 6 6 0 41 15.91 1.75 9.16 2.46 0.88 15.79 0.43 3.48 0.29 0.39 0.21 0.39 0.27 0.22 5 5 0 42 33.78 11.72 38.18 7.34 19.38 9.20 2.55 10.61 1.33 1.58 0.63 2.67 0.85 0.42 10 7 3 43 20.40 10.86 14.42 5.25 15.20 10.34 1.89 7.59 1.64 1.69 0.84 1.84 0.98 0.53 10 7 3 44 25.95 17.90 35.23 15.57 25.75 22.91 7.58 17.37 9.16 8.97 2.90 12.76 6.13 1.60 13 7 6 45 19.00 11.55 15.66 8.97 15.46 9.94 5.75 10.92 6.88 6.68 3.12 11.62 4.86 1.68 13 7 6 46 17.69 14.33 13.49 13.24 13.44 9.26 6.90 4.63 7.54 6.96 1.91 3.05 1.48 0.72 12 7 5 47 15.96 10.15 12.26 5.89 5.73 10.53 0.88 7.91 0.47 0.58 0.30 0.63 0.32 0.23 6 6 0 48 18.18 1.28 14.12 1.88 3.95 8.21 0.64 8.15 0.41 0.46 0.28 0.55 0.32 0.25 6 6 0 49 18.70 3.81 19.24 1.42 4.99 4.64 0.34 3.54 0.38 0.37 0.20 0.39 0.26 0.15 6 6 0 50 20.66 11.41 18.08 2.44 11.12 15.13 0.64 14.61 1.76 1.64 0.92 1.00 1.36 0.66 10 6 4 51 15.24 7.37 6.46 3.28 12.88 3.20 0.70 2.08 0.43 0.44 0.21 0.79 0.36 0.29 6 6 0 Average 43 15 38 11 24 19 7 13 6 6 2 4 2 1 Standard Deviation 53 19 65 15 31 26 11 16 11 9 2 6 3 1 % present out of 51 100 100 100 98 98 98 69 98 69 71 31 65 41 18 *Genome counts (Cnt) across all, proximal or distal sites based on an average coverage of >=1. Abbreivation: Co-assembly, Co. Table S6. Pairwise average amino acid identities (AAI) shared between genome bins. GSC 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 1 100 80 86 49 49 45 49 53 51 51 49 49 49 52 52 50 49 52 51 50 52 49 49 52 49 47 45 45 44 44 44 45 44 43 43 40 43 42 44 44 44 41 42 41 42 41 41 41 41 41 40 2 79 100 67 48 49 43 48 51 50 47 50 48 50 53 51 45 50 52 53 49 52 49 48 53 48 44 42 44 46 44 45 45 46 42 44 32 44 40 46 41 44 41 41 39 38 38 40 39 39 47 39 3 86 68 100 49 49 46 49 53 52 52 50 49 49 52 52 51 49 52 52 50 52 50 49 51 49 48 44 44 43 44 44 45 44 43 42 41 44 43 44 44 45 41 42 42 41 41 42 41 41 40 40 4 49 48 49 100 81 82 74 50 49 49 48 49 48 50 49 50 50 50 50 48 50 46 51 51 46 46 43 42 43 43 43 44 44 42 42 41 42 41 42 42 42 41 41 41 41 41 40 39 41 38 39 5 49 49 49 80 100 74 73 50 48 50 49 48 48 50 49 50 49 50 50 48 50 46 51 51 46 47 43 43 42 43 43 44 44 42 42 44 42 41 42 43 42 41 41 41 41 40 40 40 41 39 39 6 45 43 46 82 74 100 67 48 49 47 47 47 46 47 46 48 48 48 46 46 47 43 47 47 43 44 38 39 39 41 39 41 42 40 40 41 41 40 40 41 41 39 39 38 38 38 39 39 38 40 35 7 49 49 49 74 73 67 100 50 49 50 49 48 48 50 50 49 50 50 50 48 50 46 51 51 46 46 43 43 42 43 43 44 43 42 42 40 42 41 41 43 41 41 41 40 41 42 40 39 40 39 39 8 53 51 53 50 50 48 50 100 73 86 50 49 49 52 52 51 50 52 51 50 53 50 49 52 49 48 44 45 43 44 43 44 44 42 43 41 43 42 43 43 43 41 41 42 41 41 42 41 40 39 39 9 51 50 52 49 48 48 48 73 100 73 50 48 49 50 51 49 49 50 50 49 51 50 48 50 48 46 43 43 42 43 42 43 43 41 42 40 42 41 43 42 42 40 41 41 41 40 40 40 39 39 39 10 51 48 52 49 49 47 50 86 73 100 49 47 47 50 50 49 49 51 50 49 52 49 49 50 47 47 42 43 43 42 42 43 43 41 42 47 42 40 42 42 42 40 40 40 40 40 41 40 41 39 39 11 50 50 50 48 49 47 49 50 50 49 100 82 82 73 64 50 53 53 53 48 51 49 49 53 47 45 43 43 43 44 43 44 44 41 41 39 41 41 41 43 41 40 41 41 40 40 39 39 40 38 39 12 49 48 49 49 48 47 48 49 48 48 82 100 77 70 60 47 52 52 51 47 50 46 47 51 45 45 40 40 40 40 40 42 41 38 40 37 40 40 42 42 42 39 39 38 39 39 37 38 39 36 38 13 49 50 49 48 48 46 48 49 48 47 83 77 100 68 60 47 50 51 49 45 48 46 47 49 44 44 42 43 40 43 42 43 42 42 40 38 41 40 41 41 40 40 39 40 40 39 39 40 38 36 38 14 51 53 52 50 50 47 50 52 50 50 73 70 68 100 64 52 55 55 54 50 53 49 50 54 48 47 45 44 44 44 44 45 44 42 43 40 43 43 45 45 44 41 42 40 41 41 41 41 40 39 40 15 51 52 52 49 49 46 49 52 51 50 63 60 60 64 100 53 54 55 54 50 52 49 51 54 48 47 45 44 43 44 44 45 43 42 42 37 43 42 45 44 44 41 42 40 42 42 41 42 40 41 40 16 50 45 50 50 50 47 49 50 49 49 50 47 48 52 52 100 50 54 52 49 50 47 48 53 48 46 44 43 43 44 44 44 45 44 41 37 42 41 45 43 43 41 42 40 40 40 40 41 40 39 41 17 49 50 49 50 49 47 50 50 49 49 53 51 50 55 54 49 100 53 52 48 50 47 49 53 47 46 43 43 42 43 44 43 42 41 42 37 42 39 42 41 42 41 41 40 41 41 42 39 41 42 39 18 52 52 52 51 50 47 50 52 51 51 53 52 51 56 55 54 53 100 55 49 52 50 50 55 48 47 44 45 44 44 44 45 45 43 42 38 42 42 44 44 43 41 42 42 41 42 41 41 40 40 40 19 51 52 52 50 49 46 50 51 50 50 53 51 50 54 54 52 53 55 100 49 52 50 51 54 49 47 44 44 44 44 44 45 45 42 43 41 43 41 44 44 43 41 41 40 41 41 41 41 40 40 40 20 50 48 50 48 48 45 48 50 49 49 48 47 45 50 50 49 47 49 49 100 50 47 51 50 50 50 44 44 43 44 44 44 44 42 42 41 43 42 43 44 43 41 41 41 42 41 42 41 41 38 40 21 52 53 53 50 50 47 49 54 52 52 51 50 48 53 52 50 50 53 52 50 100 50 49 52 49 48 44 44 44 44 44 45 45 43 43 42 43 43 45 45 43 41 42 42 42 41 40 41 40 40 40 22 49 49 49 46 46 43 46 50 50 49 49 46 46 49 50 47 47 49 50 47 50 100 47 48 47 45 43 43 43 43 43 44 44 42 42 39 42 41 43 42 42 40 41 40 40 40 41 41 40 39 39 23 49 48 49 51 51 47 50 50 49 49 49 48 47 50 50 48 49 50 51 50 49 47 100 50 49 49 44 44 43 43 44 45 44 42 42 40 42 41 43 43 42 42 41 41 42 42 41 41 41 40 40 24 51 52 51 52 51 47 51 52 50 50 53 52 49 54 54 53 53 54 54 50 52 48 51 100 48 47 45 44 44 44 44 45 45 42 43 39 43 42 44 43 43 41 41 40 41 41 40 41 40 39 40 25 48 48 49 46 46 44 47 49 48 47 46 44 44 48 48 48 48 48 49 50 49 47 49 48 100 72 45 45 44 44 44 45 44 43 42 35 43 41 42 43 41 41 41 42 41 41 41 42 40 37 40 26 47 44 48 46 47 44 46 48 46 47 46 45 44 47 47 46 46 47 47 50 48 45 49 47 73 100 43 42 43 42 43 43 43 41 41 42 41 41 42 41 42 41 41 42 41 42 40 41 40 42 40 27 45 42 44 43 43 38 43 44 43 42 43 40 42 45 45 44 43 44 44 44 44 43 43 44 45 43 100 53 54 48 49 50 49 46 42 37 42 41 44 44 43 41 42 40 41 41 41 41 40 39 41 28 45 44 44 42 43 39 43 44 43 43 43 40 42 44 45 44 42 45 44 44 44 43 44 44 45 42 53 100 53 49 49 51 50 48 42 37 42 40 43 42 41 42 42 41 42 41 42 41 40 38 40 29 44 46 43 43 43 39 42 43 42 43 43 40 41 44 43 44 42 44 44 43 44 43 43 44 44 42 54 53 100 48 48 50 49 45 41 36 42 40 42 43 42 41 41 41 40 41 40 40 40 39 40 30 44 44 44 43 43 41 43 44 43 42 44 41 43 44 44 44 43 44 44 44 45 43 44 44 43 42 49 49 48 100 60 50 48 46 41 38 42 41 43 43 43 40 41 41 41 41 40 40 40 39 40 31 44 46 44 43 43 40 43 43 42 43 43 40 42 44 44 44 44 44 44 44 44 43 44 44 44 43 49 49 48 60 100 51 48 46 41 36 42 40 44 42 43 40 41 39 40 40 40 40 39 43 39 32 45 45 45 44 44 41 44 44 44 43 44 42 43 45 45 44 43 45 45 44 45 44 45 45 45 43 50 51 50 50 51 100 51 48 42 38 42 41 43 43 43 41 42 41 42 42 41 41 40 39 39 33 44 46 44 44 44 42 43 45 44 43 44 41 42 44 44 45 42 45 45 44 45 44 44 45 45 43 49 50 49 48 48 51 100 48 42 42 43 42 43 43 43 41 42 41 42 40 41 41 41 38 43 34 43 42 43 42 42 40 42 41 41 41 41 39 42 42 42 44 41 43 42 42 43 42 42 42 43 41 46 47 46 46 46 48 48 100 40 39 42 40 43 42 42 40 42 41 41 41 39 42 40 38 39 35 43 45 42 42 42 40 42 43 42 42 41 40 40 43 43 42 41 42 43 42 43 42 42 43 42 41 42 42 41 41 41 42 42 40 100 64 70 52 46 47 47 41 41 41 41 41 41 41 41 41 41 36 40 32 42 41 43 41 40 41 40 47 39 37 37 40 37 37 37 38 41 41 41 39 41 39 34 41 38 38 36 38 35 38 40 39 64 100 59 44 46 42 46 39 41 40 42 38 38 36 41 47 37 37 43 44 44 42 42 42 42 43 42 42 42 40 41 43 43 42 42 43 43 43 43 42 42 43 43 41 42 42 42 42 42 42 43 42 70 59 100 52 47 49 47 41 42 41 41 41 41 42 41 41 40 38 42 40 42 41 41 40 41 42 41 40 41 40 40 43 42 41 39 42 41 42 42 41 42 42 42 41 41 40 40 41 40 41 42 40 51 44 52 100 46 47 45 40 40 40 41 41 41 41 40 37 39 39 44 46 44 42 43 41 42 43 43 42 41 43 41 46 45 45 42 45 44 43 44 44 43 44 43 42 44 43 42 43 44 43 43 43 46 46 47 46 100 56 57 42 43 40 42 42 41 42 42 40 40 40 44 41 44 42 43 41 43 43 42 42 43 42 41 45 44 43 42 44 44 44 45 42 43 44 43 41 44 42 43 43 42 43 43 42 47 43 49 47 56 100 59 42 43 40 42 43 41 42 41 39 42 41 44 44 45 42 42 40 42 43 42 42 41 42 40 44 44 43 42 43 44 43 43 42 42 43 41 42 43 41 42 43 42 43 43 42 47 49 47 45 57 58 100 42 42 43 41 42 41 41 40 38 41 42 41 41 41 40 41 39 41 41 40 40 40 39 40 41 41 41 41 41 41 41 41 40 41 41 41 41 41 42 40 40 40 41 41 40 41 39 41 40 41 42 41 100 63 65 60 61 51 50 50 40 40 43 42 40 42 41 41 39 41 42 41 40 41 39 39 42 42 42 41 41 42 41 42 41 41 42 41 42 42 42 41 41 41 42 42 42 41 41 42 40 43 43 42 63 100 62 59 61 49 50 50 41 40 44 41 39 41 41 41 38 41 41 41 39 41 38 40 41 40 40 40 42 40 41 42 39 41 40 42 42 41 41 41 41 39 41 41 41 41 39 41 40 40 41 43 66 62 100 59 60 49 49 49 41 40 45 41 39 42 41 41 37 41 41 41 40 40 39 40 42 42 40 41 41 41 42 42 40 42 41 41 41 41 41 40 41 40 42 41 41 41 41 41 40 42 42 41 60 59 59 100 64 48 49 50 39 40 46 41 38 41 41 40 38 42 41 40 40 40 39 39 42 42 40 41 42 41 41 42 40 42 41 42 42 41 41 41 41 40 42 40 41 40 37 41 41 42 43 42 61 61 60 64 100 49 49 50 40 41 47 41 40 41 40 40 38 41 42 41 41 40 38 39 41 41 40 42 41 41 42 40 41 41 40 41 40 41 41 40 40 40 41 41 40 41 37 41 41 42 41 41 51 49 49 49 49 100 53 54 36 40 48 41 39 41 39 40 39 39 41 40 40 40 37 39 41 42 41 39 41 41 41 41 41 41 41 42 41 42 42 40 40 40 41 41 42 41 36 42 41 42 42 41 50 50 49 49 48 53 100 52 39 40 49 41 39 41 41 41 38 40 40 39 41 40 39 38 40 40 40 41 40 40 41 40 40 41 40 40 40 40 40 40 40 39 40 41 40 41 42 41 40 42 41 40 50 50 48 50 49 53 52 100 38 40 50 41 48 40 38 40 40 39 39 39 41 38 36 36 39 41 39 43 40 40 38 40 39 40 39 38 40 39 38 39 39 41 39 39 38 41 47 41 37 40 39 38 40 41 40 39 40 35 39 38 100 36 51 40 38 41 39 39 36 39 40 39 39 38 38 38 40 41 40 38 39 40 40 40 39 40 40 41 40 41 40 40 40 39 39 42 39 41 37 40 39 40 42 40 41 41 40 40 41 40 40 40 35 100 Gammaproteobacteria: GSC1-26; Alphaproteobacteria: GSC27-34; Deltaproteobacteria: GSC35-41; Bacteroidetes: GSC42-49; Other: 50-51. Table S7. Average amino acid identities (AAI) shared between genome bins (left) and reference genomes (top).

GSC Beggiatoa_alba_B18LDBeggiatoa_sp._PSCandidatus_Thiomargarita_nelsoniiThiothrix_nivea_DSM_5205Colwellia_piezophilaColwellia_psychrerythraea_34HGlaciecola_arctica_BSs20135Cycloclasticus_pugetiiCycloclasticus_sp._strain_P1Cycloclasticus_zanclesMethylomicrobium_alcaliphilum_20Zmarine_gamma_proteobacterium_HTCC2143Porticoccus_hydrocarbonoclasticus_MCTG13dgamma_proteobacterium_HTCC2207Simiduia_agarivorans_SA1Teredinibacter_turnerae_T7901Saccharophagus_degradans_2-40gamma_proteobacterium_IMCC2047gamma_proteobacterium_HdN1Nitrosococcus_halophilus_Nc4Nitrosococcus_watsoniiThioalkalivibrio_sp._HL-EbGR7Neptuniibacter_caesariensisKangiella_koreensis_SW-125Hahella_chejuensis_strain_KCTC_2396Micavibrio_aeruginosavorusOceanibaculum_indicum_P24Rhodobacteraceae_bacterium_HTCC2150Rhodobacterales_bacterium_HTCC2255Dinoroseobacter_shibae_DFL_12Thalassospira_profundimaris_WP0211Rickettsia_belliiDesulfobacterium_autotrophicum_strain_HRM2Desulfatibacillum_alkenivorans_strain_AK-01Desulfobacula_toluolica_strain_Tol2Desulfococcus_oleovorans_Hxd3Desulfobulbus_propionicus_1pr3Desulfotalea_psychrophila_LSv54Desulfocapsa_sulfexigens_SB164P1Polaribacter_sp._MED152Formosa_sp._AK20Aequorivita_sublithincola_strain_9-3Flavobacteriales_bacterium_ALC-1Anaerophaga_sp._HS1Marinilabilia_salmonicolor_JCM_21150uncultured_bacterium_gcode_4Caldithrix_abyssi_DSM_13497Ignavibacterium_album_Mat9-16 GSC01 59 64 66 53 49 49 42 50 53 53 53 51 52 51 50 50 50 52 51 52 55 54 51 52 51 46 45 43 44 43 41 41 43 43 43 44 44 44 44 40 40 41 40 40 40 40 43 43 GSC02 58 64 65 53 50 49 42 50 53 53 54 52 54 51 50 51 51 52 52 52 54 55 52 50 50 45 45 43 44 42 40 40 44 44 44 46 45 45 44 40 39 40 39 40 39 40 43 44 GSC03 59 63 66 52 50 49 42 50 53 53 52 51 52 52 51 50 50 52 51 52 55 54 51 51 51 45 45 43 44 43 40 41 44 44 43 44 44 44 44 40 40 41 40 40 40 40 43 43 GSC04 49 49 50 50 73 73 48 48 50 50 49 50 50 50 50 49 50 50 49 47 49 49 51 51 50 43 43 43 43 42 40 40 42 41 42 42 42 42 42 39 40 40 40 39 39 39 41 41 GSC05 49 49 50 49 73 73 48 47 50 50 49 50 50 50 50 49 49 51 50 48 49 49 51 52 50 44 43 43 43 42 40 40 42 42 41 42 42 42 43 40 40 40 40 39 39 39 41 41 GSC06 47 47 45 47 66 68 46 45 48 48 46 46 47 46 47 46 46 48 46 46 47 47 48 47 46 39 40 39 42 40 40 39 41 41 41 41 42 42 43 38 39 39 39 39 39 37 39 39 GSC07 49 49 50 49 81 90 49 47 50 50 48 50 50 50 49 49 49 51 49 47 49 49 51 51 49 44 43 43 43 43 41 40 42 41 41 41 42 42 42 40 40 41 40 39 40 39 41 41 Scale (% identity): GSC08 53 52 54 52 50 50 43 68 73 73 55 50 51 51 51 51 51 51 51 51 53 53 51 51 51 44 44 43 44 43 41 41 43 43 43 43 43 43 43 40 40 41 40 40 40 39 42 42 34 90 GSC09 52 51 52 51 49 48 43 75 79 79 54 49 50 50 49 50 50 51 49 51 52 52 50 50 50 44 43 42 42 42 40 40 42 41 41 42 42 43 43 39 39 40 39 39 39 38 40 41 GSC10 52 50 52 51 49 49 44 67 72 72 54 49 50 50 49 49 50 50 49 50 52 52 50 49 50 42 43 41 43 42 40 40 42 41 41 42 42 42 42 39 39 40 39 40 40 37 41 41 GSC11 50 49 50 50 50 49 44 46 51 50 50 53 59 57 55 54 54 54 52 50 51 50 53 51 52 45 44 43 44 43 41 41 42 43 41 42 43 43 42 39 39 40 40 39 39 39 42 41 GSC12 50 50 49 49 48 48 43 46 50 50 48 52 58 55 53 52 52 52 50 47 49 50 51 48 50 41 42 41 41 41 40 37 41 40 40 40 42 42 42 38 39 39 38 38 38 38 39 39 GSC13 49 48 49 48 47 47 42 46 49 50 48 52 56 54 52 51 52 52 49 47 49 49 50 50 50 44 43 43 43 42 40 39 41 41 39 41 42 42 42 38 38 40 38 38 39 38 40 40 GSC14 52 52 52 52 51 50 43 48 52 52 51 55 61 58 56 55 56 55 53 50 52 52 54 51 54 45 44 43 44 43 41 40 43 43 43 43 44 44 44 40 40 41 40 39 39 41 42 43 GSC15 52 52 52 52 51 50 43 50 53 53 51 54 60 58 56 55 55 55 53 50 52 52 53 52 54 45 45 43 44 43 40 40 44 43 42 43 44 44 44 40 40 41 40 40 40 40 42 42 Gammaproteobacteria GSC16 51 50 50 50 49 50 42 48 51 51 50 52 53 52 52 51 51 52 54 48 51 50 52 51 51 44 44 42 44 43 41 40 43 42 42 44 43 44 44 40 39 40 39 40 40 41 41 42 GSC17 50 50 50 50 49 49 43 47 51 51 50 53 55 54 55 58 58 53 52 48 50 50 52 50 52 43 44 42 43 43 40 39 42 42 41 42 43 42 43 40 39 40 40 39 40 40 40 41 GSC18 52 52 53 52 50 50 44 48 52 52 51 54 55 54 54 53 54 61 54 51 53 53 54 52 54 45 45 43 44 44 41 40 43 43 43 43 44 44 44 40 40 40 40 40 40 40 42 42 GSC19 52 52 52 52 50 50 44 48 52 52 51 54 54 53 53 52 53 54 52 50 52 52 53 51 53 45 45 43 44 43 41 40 43 43 42 43 43 44 44 40 40 41 40 39 39 40 42 42 GSC20 50 50 50 50 48 48 44 47 50 50 49 49 50 49 48 48 49 49 49 48 50 50 48 50 49 45 44 43 43 42 41 40 43 42 42 42 43 44 43 40 40 41 40 40 40 39 42 42 GSC21 53 53 53 52 50 50 43 49 53 53 53 50 52 51 50 50 51 52 51 51 53 52 51 52 51 45 45 43 44 43 41 40 44 43 43 43 44 45 44 40 40 41 40 40 40 40 42 42 GSC22 50 49 50 49 46 46 42 48 50 50 49 48 49 49 48 48 48 49 48 49 51 50 48 48 48 43 44 43 43 42 40 39 42 42 42 43 43 43 43 39 39 40 39 39 39 39 41 41 GSC23 49 49 49 49 51 51 46 47 50 50 49 49 50 50 49 48 49 50 49 47 50 49 49 54 49 44 44 43 43 42 41 40 42 42 42 42 42 43 43 41 41 41 41 39 40 39 41 42 GSC24 52 51 52 51 51 51 44 49 52 52 51 54 54 53 53 52 53 55 52 49 52 51 55 52 57 45 45 43 44 43 42 41 43 42 42 43 43 44 43 40 40 41 40 39 40 39 42 42 GSC25 49 49 49 49 47 46 42 47 50 50 47 47 47 48 47 47 47 47 48 46 49 49 48 49 48 45 44 43 43 42 40 39 43 43 42 42 43 44 43 40 40 41 40 40 40 40 41 42 GSC26 47 47 48 47 47 46 43 44 48 48 46 46 46 46 46 46 46 47 46 46 47 47 46 48 47 43 42 42 42 41 40 39 42 41 41 41 42 42 41 41 40 41 40 39 39 38 40 41 GSC27 45 44 46 44 44 43 39 42 44 44 44 44 44 44 44 43 43 44 44 42 44 44 44 45 44 57 52 48 48 47 45 44 43 43 42 43 43 43 43 39 39 41 40 39 39 40 42 43 GSC28 45 44 45 45 43 42 38 42 45 44 44 43 44 44 43 43 43 44 44 42 44 44 44 44 44 54 53 48 50 47 45 44 42 42 42 42 43 42 42 40 39 41 39 40 40 40 42 42 GSC29 44 44 45 44 42 42 39 42 44 44 43 43 44 43 43 43 43 43 43 42 43 44 44 44 43 56 51 47 48 46 45 43 41 42 41 41 42 41 42 39 39 41 39 39 39 39 41 41 GSC30 44 44 47 44 43 43 40 43 45 45 43 44 44 44 44 43 43 44 44 42 44 44 44 44 44 50 50 60 63 58 45 43 42 42 41 42 43 42 42 40 39 40 39 39 39 39 41 42 GSC31 45 44 46 45 43 44 40 43 44 44 44 44 44 45 44 43 43 44 44 42 44 45 44 45 44 50 50 58 59 58 46 43 42 41 41 42 42 42 42 39 38 39 39 38 38 40 42 41 Alphaproteobacteria GSC32 46 44 46 45 44 44 41 44 46 46 44 45 45 45 45 44 44 44 45 43 45 45 45 45 45 51 53 50 50 49 47 44 42 43 42 43 43 43 43 40 40 41 40 40 40 40 42 42 GSC33 45 44 46 45 43 43 39 42 45 45 44 44 45 44 44 44 44 44 44 43 44 45 45 45 45 50 51 48 48 47 45 46 43 43 42 43 43 43 43 39 40 41 39 40 40 39 42 43 GSC34 44 43 43 43 42 42 37 40 43 43 43 42 43 42 42 41 41 43 43 41 43 43 42 44 43 47 48 44 45 44 41 54 41 42 41 42 42 42 42 39 38 41 39 39 39 40 43 43 GSC35 42 42 43 43 42 42 39 41 43 43 42 42 42 42 42 42 42 42 42 41 42 42 42 42 42 42 41 41 41 40 39 39 53 51 53 52 47 47 46 40 40 41 40 41 41 40 43 42 GSC36 40 41 43 42 40 41 40 41 39 42 44 36 39 41 38 40 38 38 38 42 41 38 39 39 38 36 40 36 38 39 39 37 45 44 46 44 44 47 46 40 41 42 42 39 40 41 40 38 GSC37 43 43 43 44 43 42 39 42 43 43 43 43 43 43 42 42 42 42 43 41 43 42 43 43 43 42 42 41 42 41 40 40 54 51 54 53 47 48 47 41 40 42 40 41 41 40 43 43 GSC38 42 41 41 42 41 41 38 42 42 42 41 41 42 42 42 41 41 42 41 41 42 42 42 42 42 41 41 40 40 40 38 39 57 50 65 51 47 46 46 40 40 41 40 40 40 38 42 42 Deltaproteobacteria GSC39 44 44 45 44 43 42 41 43 44 45 44 44 44 44 43 43 44 44 44 43 44 43 43 44 43 44 44 42 43 41 41 40 47 47 47 47 59 54 56 40 40 41 41 41 40 40 44 44 GSC40 44 44 43 44 43 43 40 42 44 44 43 43 44 43 43 43 43 43 43 42 44 44 44 44 44 43 43 42 42 42 40 39 49 48 48 48 56 60 59 40 40 41 40 41 41 40 43 43 GSC41 43 44 44 44 42 42 39 43 44 44 43 43 43 43 43 42 43 43 43 42 45 44 43 43 43 42 43 42 41 41 39 39 47 48 47 48 57 58 74 40 40 41 41 40 40 40 43 43 GSC42 41 41 41 41 41 41 40 40 41 42 41 41 41 41 41 41 41 42 41 40 41 41 41 41 41 42 40 40 40 40 38 39 41 41 41 41 42 42 42 61 59 58 58 48 48 39 44 44 GSC43 42 42 42 42 42 42 40 41 42 42 42 42 42 42 42 41 41 41 42 41 42 41 41 43 42 42 41 41 41 41 38 39 42 42 41 42 42 42 42 74 59 58 59 48 47 41 44 45 GSC44 40 39 41 41 41 41 40 40 41 42 41 41 41 41 41 41 41 41 41 39 41 41 41 41 40 42 40 41 40 40 39 39 41 41 41 40 41 42 42 60 58 58 58 47 47 40 43 44 GSC45 41 41 42 41 42 41 39 40 42 42 41 41 42 41 41 41 41 41 41 40 41 41 41 42 41 42 40 40 40 40 38 39 42 41 41 41 42 41 42 57 60 66 60 47 47 40 43 44 GSC46 41 41 41 41 42 42 39 41 42 42 41 41 42 42 42 41 41 41 41 40 41 41 41 42 41 42 40 41 41 40 38 39 41 42 41 41 41 42 42 59 68 62 67 47 47 39 43 44 Bacteroidetes GSC47 41 41 41 41 40 40 39 40 41 41 41 41 41 40 40 40 41 40 40 40 41 41 40 41 41 42 40 40 40 40 38 38 42 42 42 42 42 41 42 48 47 49 47 50 50 38 45 46 GSC48 41 41 41 41 40 40 39 39 41 41 41 40 41 41 41 40 40 40 41 40 41 40 40 41 41 42 41 40 40 39 38 39 42 42 42 42 41 42 42 48 48 49 48 52 51 40 44 45 GSC49 40 40 40 41 41 41 39 39 41 41 41 41 40 40 40 40 40 40 40 39 40 40 40 41 41 40 39 39 39 39 37 39 41 41 40 41 42 41 42 47 48 49 47 49 49 40 44 44 GSC50 40 39 40 39 40 39 38 38 39 39 39 39 39 40 40 39 40 40 39 37 38 38 38 40 41 40 39 38 40 39 37 39 40 41 39 41 39 40 40 40 40 40 40 39 38 46 40 39 GSC51 40 40 40 40 39 39 38 38 40 40 39 40 40 40 40 39 39 40 40 39 40 40 40 40 41 39 40 38 40 39 37 38 43 42 40 41 41 41 42 39 39 41 39 40 40 37 43 43 Bacteria Bacteria Gammaproteobacteria Alphaproteobacteria Deltaproteobacteria Bacteroidetes Ignavibacteriae Table S8. Summary of candidate hydrocarbon degradation genes distributed among 25 bacterial genome bins, GSC52 and the unbinned fraction.

Predicted protein Substrate GSC4 GSC5 GSC6 GSC7 GSC8 GSC9 GSC10 GSC14 GSC15 GSC16 GSC18 GSC19 GSC20 GSC21 GSC22 GSC24 GSC26 GSC30 GSC35 GSC37 GSC42 GSC43 GSC46 GSC48 GSC49 GSC52 unbinned Sum Transmembrane alkane 1-monooxygenase AlkB n-alkanes 0 1 1 1 0 4 0 0 2 2 0 0 1 0 2 2 1 2 0 0 1 1 1 0 0 0 6 Alkane-1 monooxygenase accessory--Rubredoxin-2 AlkG n-alkanes 0 1 1 1 00000000000 1 0 0 0 0 0 0 0 0 0 0 2 Alkane-1 monooxygenase accessory--Rubredoxin-2 RubB/RubA2 n-alkanes 0 0 0 1 0000000000000000000000 1 Alkane-1 monooxygenase accessory--Rubredoxin-NAD(+) reductase AlkT n-alkanes 000000000000000 1 0 0 0 0 0 0 0 0 0 0 1 38 Cytochrome P450 accessory:2Fe-2S ferredoxin n-alkanes 00000000000000 1 000000000000 Cytochrome P450 accessory:Ferredoxin reductase--Rubredoxin-NAD(+) reductase n-alkanes 0 0 0 0 0 0 0 1 0000000000000000000 Cytochrome P450--CYPX_CD_Family--CYP153_gene n-alkanes 1 3 0 0 0 0 0 1 0 3 0 9 0 0 1 000000000000 20 Soluble methane monooxygenase hydroxylase component A alpha-subunit MmoX methane, ammoniumn, n-alkanes 0000000000000 1 0000000000000 Soluble methane monooxygenase hydroxylase component A beta-subunit MmoY methane, ammoniumn, n-alkanes 0000000000000 1 0000000000000 Soluble methane monooxygenase hydroxylase component A gamma-subunit MmoZ methane, ammoniumn, n-alkanes 0000000000000 1 0000000000000 Soluble methane monooxygenase reductase component C MmoC methane, ammoniumn, n-alkanes 0000000000000 2 0000000000000 Soluble methane monooxygenase regulatory protein B MmoB methane, ammoniumn, n-alkanes 0000000000000 1 0000000000000 6 Particulate methane monooxygenase subunit A methane, ammoniumn, n-alkanes 0 0 0 0 1 0 0 1 0 0 2 0 0 1 000000000000 3 Particulate methane monooxygenase subunit B methane, ammoniumn, n-alkanes 0 0 0 0 1 1 0 1 0 0 1 0 0 1 000000000000 6 Particulate methane monooxygenase subunit C methane, ammoniumn, n-alkanes 0 0 0 3 2 2 0 1 0 0 2 0 0 2 00000000000 2 2 35 Aromatic dioxygenase L PAHs 00000000000000 1 000000000000 PAH dioxygenase L--Benzene/Biphenyl* PAHs 0 0 0 0 0 2 0 0 2 000000000000000000 PAH dioxygenase L--Benzene/Biphenyl/Pyrene/Naphthalene* PAHs 00000000000000 1 000000000000 PAH dioxygenase L--Naphthalene* PAHs 0 0 0 0 0 4 0 0 8 0 0 0 0 0 6 00000000000 5 PAH dioxygenase L--Ortho-halobenzoate/Benzoate/Anthranilate* PAHs 0 0 0 0 0 3 0 0 1 0 0 0 0 0 4 00000000000 2 PAH dioxygenase L--Pyrene* PAHs 0 0 0 0 0 0 0 0 1 0 0 0 0 0 3 00000000000 1 Aromatic dioxygenase S PAHs 0 0 0 0 0 1 000000000000000000000 PAH dioxygenase S--Benzene/Biphenyl* PAHs 0 0 0 0 0 2 0 0 1 0 0 0 0 0 1 000000000000 PAH dioxygenase S--Naphthalene* PAHs 0 0 0 0 0 3 0 0 5 0 0 0 0 0 5 00000000000 4 PAH dioxygenase S--Ortho-halobenzoate/Benzoate/Anthranilate* PAHs 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 000000000000 PAH dioxygenase S--Pyrene* PAHs 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 00000000000 1 PAH dioxygenase electron transfer component--Ferredoxin--NAD(+) reductase PAHs 00000000000000000000000000 1 PAH dioxygenase electron transfer component--Rieske (2Fe-2S) ferredoxin PAHs 0 0 0 0 0 0 1 00000000000000000000 74 Phenol 2-monooxygenase--CD=FAD-dependent Phenol hydoxylase (PHOX) family phenol, benzene, toluene 0 0 0 1 00000000000000000000000 Phenol hydroxylase, P0 assembly protein DmpK/LapK phenol, benzene, toluene 0 0 0 0 0 1 00000000000000000000 2 Phenol hydroxylase, P1 oxygenase component DmpL phenol, benzene, toluene 0 0 0 0 0 3 00000000000000000000 2 Phenol hydroxylase, P2 regulatory component DmpM phenol, benzene, toluene 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 00000000000 1 Phenol hydroxylase, P3 oxygenase component DmpN phenol, benzene, toluene 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 00000000000 1 Phenol hydroxylase, P4 oxygenase component DmpO phenol, benzene, toluene 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 000000000000 Phenol hydroxylase, FAD- and [2Fe-2S]-containing reductase P5 component DmpP phenol, benzene, toluene 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 000000000000 Positive regulator of phenol hydroxylase, DmpR phenol, benzene, toluene 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 000000000000 23 Membrane protein involved in aromatic hydrocarbon degradation--CD=Toluene_X toluene 0 1 0 0 2 1 0 0 0 6 0 0 0 0 1 1 0 0 6 3 3 1 0 1 1 0 4 Toluene-4-monooxygenase protein_A TmoA toluene 0 0 0 0 0 1 00000000000000000000 1 Toluene-4-monooxygenase protein_B TmoB toluene 00000000000000000000000000 1 Toluene-4-monooxygenase protein_C TmoC toluene 00000000000000000000000000 1 Toluene-4-monooxygenase protein_D TmoD toluene 00000000000000000000000000 1 Toluene-4-monooxygenase protein_E TmoE toluene 00000000000000000000000000 1 Toluene-4-monoxygenase electron transfer component TmoF toluene 0 0 0 0 0 0 1 0000000000000000000 1 39 Xylene monooxygenase electron transfer component XylA xylenes, toluene 0 0 0 0 0 2 0 0 0 3 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 2 Xylene monooxygenase hydroxylase subunit XylM xylenes, toluene 0 0 0 0 0 2 0 0 0 2 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 5 20 Ethylbenzene dehydrogenase alpha subunit EbdA toluene (anaerobic) 00000000000000000000000000 2 Ethylbenzene dehydrogenase beta subunit EbdB toluene (anaerobic) 00000000000000000000000000 1 Ethylbenzene dehydrogenase gamma subunit EbdC toluene (anaerobic) 00000000000000000000000000 1 4 Benzylsuccinate synthase alpha subunit BssA toluene (anaerobic) 00000000000000000000000000 2 Benzylsuccinate synthase beta subunit BssB toluene (anaerobic) 00000000000000000000000000 1 Benzylsuccinate synthase gamma subunit BssC toluene (anaerobic) 00000000000000000000000000 2 5 Sum 1 6 2 7 6 41 2 5 21 16 5 9 1 10 35 81263421112 67 264 Genes present (1) or absent (0) Alkanes 111111011111111111001110011 22 Genes present (1) or absent (0) PAHs 000001101000001000000000001 5 Genes present (1) or absent (0) Aromatic hydrocarbons 010111100100001100111101101 15 Bacteria bins are: Gammaproteobacteria (green), Alphaproteobacteria (yellow), Deltaproteobacteria (blue), Bacteroidetes (pink), and virus/unbinned (grey). Abbreviations: PAH dioxygenase L (large subunit); PAH dioxygenase S (small subunit). *PAH and aromatic dioxygenases with highest sequence identities.