-0.3 -0.2 -0.1 0.0 0.1 -0.25 0.00 0.25 MDS1 M D S 2 Metagenome Belize Orbicella Belize Pseudodiploria Florida Guam Roseofilum enrichment Phyla Bacteroidetes Cyanobacteria Proteobacteria Table S1. Summary of sample characteristics for 54 coral surface microbiomes and 1 Roseofilum culture used to assess bacterial community structure based on the V6 hypervariable region of 16S rRNA genes. Sample Health Location Coral Host Collection Date Sequences A46BB Black Band Belize1 Orbicella annularis Aug-14 374,772 A50BB Black Band Belize Orbicella faveolata Aug-14 197,198 BLZ2 Black Band Belize Orbicella annularis Jul-13 126,593 BLZ4* Black Band Belize Orbicella annularis Jul-13 103,407 BLZ5 Black Band Belize Orbicella annularis Jul-13 85,287 J32BB Black Band Belize Orbicella annularis Jul-13 232,079 MNC Black Band Belize Orbicella annularis Aug-14 264,985 BOF Black Band Belize Orbicella faveolata Aug-14 475,847 DCL Black Band Belize Pseudodiploria clivosa Aug-14 9,498 BPS Black Band Belize Pseudodiploria strigosa Aug-14 222,362 DBB Black Band Belize Pseudodiploria strigosa Aug-14 210,565 A28NC Healthy Coral Belize Orbicella annularis Aug-14 19,215 A33NC Healthy Coral Belize Orbicella annularis Aug-14 86,598 A44NC Healthy Coral Belize Orbicella annularis Aug-14 40,109 F32NC Healthy Coral Belize Orbicella annularis Feb-13 582,387 M40FT Healthy Coral Belize Orbicella annularis Aug-14 76,764 M47FT Healthy Coral Belize Orbicella annularis Aug-14 95,249 M57FT Healthy Coral Belize Orbicella annularis Aug-14 92,464 M61FTA Healthy Coral Belize Orbicella annularis Aug-14 97,566 M61FTB Healthy Coral Belize Orbicella annularis Aug-14 279,181 M70FT Healthy Coral Belize Orbicella annularis Aug-14 438,975 A46NC Healthy Tissue Belize Orbicella annularis Aug-14 27,814 A50NC Healthy Tissue Belize Orbicella faveolata Aug-14 184,473 F28NC Healthy Tissue Belize Orbicella annularis Feb-13 605,049 F29NC Healthy Tissue Belize Orbicella annularis Feb-13 749,884 F33NC Healthy Tissue Belize Orbicella annularis Feb-13 300,367 F44NC Healthy Tissue Belize Orbicella annularis Feb-13 476,809 F50NC Healthy Tissue Belize Orbicella faveolata Feb-13 486,621 J32NC Healthy Tissue Belize Orbicella annularis Jul-13 6,577 J44HE Healthy Tissue Belize Orbicella annularis Jul-13 78,016 J44NC Healthy Tissue Belize Orbicella annularis Jul-13 33,238 MBB Healthy Tissue Belize Orbicella annularis Aug-14 82,393 DNC Healthy Tissue Belize Pseudodiploria strigosa Aug-14 218,292 BLZD* Black Band Belize Pseudodiploria strigosa Feb-13 155,453 FL1 Black Band Florida Montastraea cavernosa May-13 115,256 FL2 Black Band Florida2 Montastraea cavernosa May-13 408,160 FL4 Black Band Florida Montastraea cavernosa May-13 335,680 FL5 Black Band Florida Montastraea cavernosa May-13 57,362 LK1+ Black Band Florida Montastraea cavernosa Jun-13 244,667 LK2+ Black Band Florida Orbicella faveolata Jun-13 158,302 LK4+ Black Band Florida Orbicella faveolata Jun-13 219,775 Cyano* Enrichment culture Florida Montastraea cavernosa Apr-14 524,581 FLA Black Band Florida Montastraea cavernosa Apr-14 229,768 FLB Black Band Florida Montastraea cavernosa Apr-14 152,408 FLC Black Band Florida Montastraea cavernosa Apr-14 342,213 FLA1 Healthy Tissue Florida Montastraea cavernosa Apr-14 159,649 FLA2 Healthy Tissue Florida Montastraea cavernosa Apr-14 133,858 FLB1 Healthy Tissue Florida Montastraea cavernosa Apr-14 70,947 FLB2 Healthy Tissue Florida Montastraea cavernosa Apr-14 185,161 FLB3 Healthy Tissue Florida Montastraea cavernosa Apr-14 356,762 FLC1 Healthy Tissue Florida Montastraea cavernosa Apr-14 136,954 FLC2 Healthy Tissue Florida Montastraea cavernosa Apr-14 357,678 FLC3 Healthy Tissue Florida Montastraea cavernosa Apr-14 127,307 Guam1* Black Band Guam3 Goniopora fruticosa Jun-14 335,373 Guam2 Black Band Guam Goniopora fruticosa Jun-14 280,831 * Metagenomic sequencing also performed on these samples. + Florida samples pooled for metagenomic sequencing. 1 Carrie Bow Cay, Belize: 16.797 N, 88.084 W 2 Looe Key Reef, Florida, USA: 24.548 N, 81.406 W 3 Luminao Reef Flat, Guam: 13.464 N, 144.644 E     1   Table S2. Characteristics of metagenomes from Black Band Disease mats and cultured Roseofilum reptotaenium. Metagenome locus tag Cyano LKpool BLZ4 BLZD Guam IMG Genome ID 3300003272 3300003311 3300003317 3300003641 3300003309 Collection location Looe Key Reef, Florida Looe Key Reef, Florida Carrie Bow Cay, Belize Carrie Bow Cay, Belize Luminao Reef Flat, Guam Collection date April 2014 June 2013 July 2013 Feb 2013 June 2014 Coral host Roseofilum culture, isolated from Montastraea cavernosa pooled: Montastraea cavernosa and Orbicella faveolata Orbicella annularis Pseudodiploria strigosa Goniopora fruticosa Read pairs 34,974,648 32,180,161 34,193,363 16,853,081 44,199,247 SRA Accession SRX1017628 SRX1017632 SRX894068 SRX894049 SRX1017629 Scaffolds 62,162 186,345 524,359 56,139 151,976 Total length of contigs (bp) 117,262,816 124,960,495 279,467,519 34,028,000 113,479,370 Protein coding genes 145,980 238,319 612,757 69,548 207,250 Proportion of reads mapped to assembled scaffolds 92% 61% 72% 41% 71% Estimated sequencing coverage 90% 85% 87% 99% 84% Estimated number of genomes in metagenome 19 - 22 14 - 17 6 -19 2 - 4 7 - 24 Binned genomes 6 5 5 1 9 Domain Phylum Cyano- 3300003272- Gene-Count Cyano- 3300003272- % Guam- 3300003309- Gene-Count Guam- 3300003309- % LKpool- 3300003311- Gene-Count LKpool- 3300003311- % BLZ4- 3300003317- Gene-Count BLZ4- 3300003317- % BLZD- 3300003641- Gene-Count BLZD- 3300003641- % Bacteria Bacteroidetes 20329 13.93 25494 12.3 30784 12.92 17397 2.84 5904 8.49 Bacteria Proteobacteria 18877 12.93 25163 12.14 15006 6.3 29159 4.76 3920 5.64 Bacteria Cyanobacteria 4460 3.06 3679 1.78 4119 1.73 5939 0.97 2778 3.99 Bacteria Firmicutes 3086 2.11 3922 1.89 9370 3.93 11437 1.87 1858 2.67 Bacteria Actinobacteria 2174 1.49 762 0.37 1056 0.44 3356 0.55 408 0.59 Bacteria Cloacimonetes 60 0.04 124 0.06 106 0.04 199 0.03 371 0.53 Bacteria Verrucomicrobia 1927 1.32 277 0.13 390 0.16 1206 0.2 189 0.27 Archaea Euryarchaeota 612 0.42 427 0.21 553 0.23 2254 0.37 166 0.24 Bacteria Spirochaetes 433 0.3 484 0.23 766 0.32 1368 0.22 155 0.22 Bacteria Lentisphaerae 306 0.21 26 0.01 625 0.26 617 0.1 143 0.21 Bacteria Planctomycetes 12015 8.23 255 0.12 418 0.18 862 0.14 140 0.2 Bacteria Fusobacteria 66 0.05 145 0.07 294 0.12 474 0.08 72 0.1 Bacteria Chloroflexi 2136 1.46 141 0.07 160 0.07 474 0.08 68 0.1 Bacteria Chlorobi 148 0.1 180 0.09 187 0.08 233 0.04 53 0.08 Bacteria Acidobacteria 474 0.32 110 0.05 119 0.05 323 0.05 39 0.06 Bacteria Ignavibacteriae 106 0.07 839 0.4 153 0.06 156 0.03 39 0.06 Bacteria Thermotogae 50 0.03 39 0.02 85 0.04 237 0.04 34 0.05 Bacteria Aquificae 70 0.05 54 0.03 79 0.03 308 0.05 26 0.04 Bacteria DeinococcusNThermus 389 0.27 85 0.04 73 0.03 247 0.04 31 0.04 Bacteria Aminicenantes 112 0.08 105 0.05 89 0.04 113 0.02 26 0.04 Archaea Crenarchaeota 69 0.05 48 0.02 57 0.02 564 0.09 19 0.03 Bacteria Chlamydiae 65 0.04 42 0.02 37 0.02 241 0.04 19 0.03 Bacteria Synergistetes 43 0.03 40 0.02 66 0.03 99 0.02 24 0.03 Bacteria Marinimicrobia 56 0.04 57 0.03 85 0.04 125 0.02 18 0.03 Bacteria Caldithrixae 62 0.04 100 0.05 80 0.03 134 0.02 21 0.03 Bacteria Tenericutes 38 0.03 53 0.03 61 0.03 539 0.09 14 0.02 Bacteria Deferribacteres 39 0.03 43 0.02 74 0.03 163 0.03 15 0.02 Bacteria Atribacteria 29 0.02 46 0.02 79 0.03 53 0.01 11 0.02 Bacteria Latescibacteria 88 0.06 47 0.02 78 0.03 79 0.01 16 0.02 Bacteria unclassified 29 0.02 46 0.02 46 0.02 56 0.01 11 0.02 Bacteria Parcubacteria 9 0.01 11 0.01 16 0.01 102 0.02 10 0.01 Bacteria Thermodesulfobacteria 31 0.02 14 0.01 27 0.01 94 0.02 4 0.01 Bacteria Nitrospirae 43 0.03 21 0.01 27 0.01 51 0.01 6 0.01 Bacteria Hydrogenedentes 33 0.02 9 0 21 0.01 36 0.01 4 0.01 Bacteria Fibrobacteres 25 0.02 21 0.01 39 0.02 39 0.01 8 0.01 Bacteria Gemmatimonadetes 93 0.06 19 0.01 20 0.01 64 0.01 8 0.01 Bacteria BRC1 73 0.05 12 0.01 27 0.01 34 0.01 8 0.01 Bacteria Poribacteria 48 0.03 9 0 15 0.01 34 0.01 9 0.01 Bacteria Aerophobetes 33 0.02 17 0.01 18 0.01 22 0 8 0.01 Bacteria Armatimonadetes 69 0.05 10 0 10 0 22 0 4 0.01 Archaea Thaumarchaeota 11 0.01 10 0 10 0 106 0.02 2 0 Bacteria Gracilibacteria 4 0 24 0.01 12 0.01 119 0.02 0 0 Archaea Aigarchaeota 6 0 11 0.01 3 0 40 0.01 0 0 Bacteria Microgenomates 4 0 1 0 2 0 47 0.01 0 0 Bacteria Chrysiogenetes 18 0.01 9 0 9 0 33 0.01 1 0 Bacteria Dictyoglomi 15 0.01 8 0 14 0.01 50 0.01 0 0 Archaea CandidatusTKorarchaeota 7 0 4 0 5 0 58 0.01 2 0 Bacteria Nitrospinae 39 0.03 9 0 25 0.01 39 0.01 3 0 Bacteria Calescamantes 7 0 2 0 4 0 22 0 0 0 Bacteria Fervidibacteria 27 0.02 5 0 6 0 16 0 1 0 Bacteria Omnitrophica 34 0.02 8 0 11 0 24 0 2 0 Archaea Diapherotrites 5 0 4 0 4 0 21 0 0 0 Bacteria Caldiserica 4 0 1 0 5 0 22 0 0 0 Bacteria CandidatusTSaccharibacteria 4 0 0 0 4 0 28 0 0 0 Bacteria Elusimicrobia 3 0 2 0 8 0 5 0 1 0 Bacteria Acetothermia 4 0 4 0 7 0 2 0 1 0 Bacteria EM3 2 0 0 0 0 0 1 0 0 0 Bacteria PER 1 0 4 0 3 0 30 0 2 0 Bacteria WS1 6 0 2 0 1 0 3 0 2 0 Table S3. Genes associated with nitrogen and sulfur cycling in Black Band Disease metagenome-assembled genomes. ! IMG gene_oid IMG Locus Tag Gene Product Name IMG Genome ID Genome Name 2628137143 Ga0079951_10908 cyanophycin synthetase 2627853583 Cyano_bin9_Gammaproteobacteria Ga0079951 2628137144 Ga0079951_10909 cyanophycin synthetase 2627853583 Cyano_bin9_Gammaproteobacteria Ga0079951 2628137703 Ga0079951_11613 cyanophycinase 2627853583 Cyano_bin9_Gammaproteobacteria Ga0079951 2628137704 Ga0079951_11614 cyanophycin synthetase 2627853583 Cyano_bin9_Gammaproteobacteria Ga0079951 2628068922 Ga0079929_112012 cyanophycin synthetase 2627853561 Roseofilum sp. BLZ4_bin2 Ga0079929 2628067756 Ga0079929_10588 cyanophycinase 2627853561 Roseofilum sp. BLZ4_bin2 Ga0079929 2628068923 Ga0079929_112013 cyanophycinase 2627853561 Roseofilum sp. BLZ4_bin2 Ga0079929 2628072855 Ga0079930_105840 cyanophycin synthetase 2627853562 Roseofilum sp. BLZD_bin1 Ga0079930 2628072856 Ga0079930_105841 cyanophycinase 2627853562 Roseofilum sp. BLZD_bin1 Ga0079930 2628072760 Ga0079930_105511 cyanophycinase 2627853562 Roseofilum sp. BLZD_bin1 Ga0079930 2628058810 Ga0079927_105340 cyanophycin synthetase 2627853559 Roseofilum sp. Cyano_bin5 Ga0079927 2628059528 Ga0079927_10888 cyanophycinase 2627853559 Roseofilum sp. Cyano_bin5 Ga0079927 2628058811 Ga0079927_105341 cyanophycinase 2627853559 Roseofilum sp. Cyano_bin5 Ga0079927 2628062588 Ga0079928_102436 cyanophycin synthetase 2627853560 Roseofilum sp. Guam_bin12 Ga0079928 2628062589 Ga0079928_102437 cyanophycinase 2627853560 Roseofilum sp. Guam_bin12 Ga0079928 2628062244 Ga0079928_101985 cyanophycinase 2627853560 Roseofilum sp. Guam_bin12 Ga0079928 2628077039 Ga0079931_13262 cyanophycinase 2627853563 Roseofilum sp. LKpool_bin4 Ga0079931 2628062393 Ga0079928_102162 Mo-nitrogenase MoFe protein subunit NifK 2627853560 Roseofilum sp. Guam_bin12 Ga0079928 2628060320 Ga0079927_117712 Mo-nitrogenase MoFe protein subunit NifK 2627853559 Roseofilum sp. Cyano_bin5 Ga0079927 2628129200 Ga0079949_100635 Mo-nitrogenase iron protein subunit NifH 2627853581 Alteromonadales bin3 BLZ4 Ga0079949 2628075613 Ga0079931_10724 Mo-nitrogenase MoFe protein subunit NifK 2627853563 Roseofilum sp. LKpool_bin4 Ga0079931 2628071631 Ga0079930_102629 Mo-nitrogenase iron protein subunit NifH 2627853562 Roseofilum sp. BLZD_bin1 Ga0079930 2628062394 Ga0079928_102163 nitrogenase molybdenum-iron protein alpha chain 2627853560 Roseofilum sp. Guam_bin12 Ga0079928 2628071635 Ga0079930_102633 Mo-nitrogenase MoFe protein subunit NifK 2627853562 Roseofilum sp. BLZD_bin1 Ga0079930 2628071634 Ga0079930_102632 nitrogenase molybdenum-iron protein alpha chain 2627853562 Roseofilum sp. BLZD_bin1 Ga0079930 2628124723 Ga0079947_14533 Mo-nitrogenase iron protein subunit NifH 2627853579 Rhodospirillales bin7 BLZ4 Ga0079947 2628060321 Ga0079927_117713 nitrogenase molybdenum-iron protein alpha chain 2627853559 Roseofilum sp. Cyano_bin5 Ga0079927 2628060324 Ga0079927_117716 Mo-nitrogenase iron protein subunit NifH 2627853559 Roseofilum sp. Cyano_bin5 Ga0079927 2628124724 Ga0079947_14534 Nitrogenase component 1 type Oxidoreductase 2627853579 Rhodospirillales bin7 BLZ4 Ga0079947 2628131269 Ga0079949_112512 Mo-nitrogenase MoFe protein subunit NifK 2627853581 Alteromonadales bin3 BLZ4 Ga0079949 2628125228 Ga0079947_16012 Mo-nitrogenase MoFe protein subunit NifK 2627853579 Rhodospirillales bin7 BLZ4 Ga0079947 2628131270 Ga0079949_112513 Mo-nitrogenase MoFe protein subunit NifD precursor 2627853581 Alteromonadales bin3 BLZ4 Ga0079949 2628066997 Ga0079929_10325 nitrogenase molybdenum-iron protein alpha chain 2627853561 Roseofilum sp. BLZ4_bin2 Ga0079929 2628075612 Ga0079931_10723 nitrogenase molybdenum-iron protein alpha chain 2627853563 Roseofilum sp. LKpool_bin4 Ga0079931 2628067000 Ga0079929_10328 Mo-nitrogenase iron protein subunit NifH 2627853561 Roseofilum sp. BLZ4_bin2 Ga0079929 2628062390 Ga0079928_102159 nitrogenase molybdenum-iron protein NifN 2627853560 Roseofilum sp. Guam_bin12 Ga0079928 2628125227 Ga0079947_16011 Nitrogenase component 1 type Oxidoreductase 2627853579 Rhodospirillales bin7 BLZ4 Ga0079947 2628066996 Ga0079929_10324 Mo-nitrogenase MoFe protein subunit NifK 2627853561 Roseofilum sp. BLZ4_bin2 Ga0079929 2628083846 Ga0079933_14002 dissimilatory adenylylsulfate reductase beta subunit 2627853565 Desulfovibrio bin6 BLZ4 Ga0079933 2628080331 Ga0079932_12942 dissimilatory adenylylsulfate reductase beta subunit 2627853564 LKpool_bin5_Desulfovibrio Ga0079932 2628083845 Ga0079933_14001 dissimilatory adenylylsulfate reductase alpha subunit precursor 2627853565 Desulfovibrio bin6 BLZ4 Ga0079933 2628080330 Ga0079932_12941 dissimilatory adenylylsulfate reductase alpha subunit precursor 2627853564 LKpool_bin5_Desulfovibrio Ga0079932