Supplementary Information

A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes

Sheila Podell, Jessica M. Blanton, Aaron Oliver, Michelle A. Schorn, Vinayak Agarwal, Jason S. Biggs, Bradley S. Moore, Eric E. Allen

Contents

Supplementary Figures S1-S13 ...... 2

Supplementary Tables S1-S8 ...... 16

References ...... 26

Supplementary Figure 1. MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree [1], with Crinalium epipsammum as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives. Guidelines for assigning species, genus, family, and order-level taxonomic granularity were based on [2, 3] for AAI and [4] for 16S rRNA gene percent nucleotide identity.

A B Pleurocapsa_PCC_7327

1 Stanieria_cyanosphaera

1 SP5CPC1

1 0.993 Prochloron_didemni_P3 1 Prochloron_didemni_P4

Gloeobacter_violaceus Stanieria_cyanosphaera SP5CPC Prochloron_didemni_P3 Prochloron_didemni_P4 Gloeobacter_violaceus Crinalium_epipsammum Desertifilum_IPPASB1220 GM7CHS1 GM202CHS1 GM102CHS1 SP12CHS1 SP5CHS1 Nostoc_punctiforme 92/65 89/61 89/61 89/61 88/51 90/63 91/62 90/60 90/60 -/60 89/60 90/60 88/63 Pleurocapsa_PCC_7327 Crinalium_epipsammum 92/59 93/60 92/61 88/49 90/60 91/60 91/58 90/58 -/59 90/58 91/58 89/60 Stanieria_cyanosphaera 95/69 94/69 88/47 89/57 90/58 92/58 91/58 -/57 92/58 92/57 90/57 SP5CPC Desertifilum_IPPASB1220 100/97 89/48 90/58 90/58 92/58 91/58 -/58 92/58 92/58 89/59 Prochloron_didemni_P3 88/48 89/59 90/58 91/59 90/59 -/59 91/59 91/59 89/59 Prochloron_didemni_P4 1 GM7CHS1 88/50 88/51 89/49 88/49 -/49 88/50 88/49 87/52 Gloeobacter_violaceus 91/63 90/61 89/61 -/61 89/61 89/61 90/66 Crinalium_epipsammum 1GM202CHS1 Species 92/64 90/64 -/64 90/64 90/64 90/63 Desertifilum_IPPASB1220 16S >98.8, AAI 95-100 98/93 -/92 99/92 99/92 90/61 GM7CHS1 0.83 -/92 98/93 98/92 90/61 GM202CHS1 GM102CHS1 Genus -/97 -/97 -/62 GM102CHS1 0.977 1 16S 95-98.6, AAI 65-95 SP5CHS1 100/99 90/62 SP12CHS1 1 Family 90/61 SP5CHS1 16S 92-95, AAI 45-65 SP12CHS1 Ambiguous Nostoc_punctiforme Family/Order

0.5

Supplementary Figure 2. Bacteroidetes MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree [1], with SP5OBV1 as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives.

A B

Marinoscillum_furvescens

Ekhidna_lutea

1 SP12BCY1

1 GM202BCY1 SP12BCY1 SP5BCY1 Marinoscillum_furvescens GM202BCY1 95/67 95/67 95/67 92/57 Ekhidna_lutea 0.639 100/98 100/98 91/57 GM202BCY1 SP5BCY1 100/99 91/57 SP12BCY1 91/57 SP5BCY1 Species SP5OBV1 16S >98.8, AAI 95-100 Genus 0.8 16S 95-98.6, AAI 65-95 Family 16S 92-95, AAI 45-65

Ambiguous Family/Order

3 Supplementary Figure 3. Alphaproteobacteria MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree [1], with SP5OBV1 as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives.

A B Magnetococcus

GM7ARS4 1 s u S 1 1 2 S R S 1 2 cc 4 1 AMS 2 A 2 3 1 R R o P GM202ARS2 B S B B c P S B A A i H R R R R H R R a A A a 202 A A A un ll A A A t e 102 7 202 7 7 M ll 5 12 GM202ARS1 5 5 12 oe e U M M M M M i ep H G SP SP SP G G G SP SP N G N G SP5ARS3 0.833 -/87 -/49 86/50 -/41 84/41 86/41 86/42 88/42 89/45 88/45 86/47 86/46 86/46 89/45 Azospirillum 1 0.995 -/51 -/52 -/44 -/44 -/45 -/45 -/45 -/47 -/48 -/48 -/48 -/48 -/48 SP5ARS3 GM102ARS1 ARS -/51 -/44 -/44 -/45 -/45 -/45 -/46 -/47 -/48 -/48 -/48 -/48 GM102ARS1 0.986 -/44 88/44 86/45 86/45 87/44 84/46 89/45 88/47 87/48 87/47 86/46 GUM202ARS1 Azospirillum -/55 -/41 -/41 -/41 -/41 -/41 -/42 -/42 -/42 -/41 GM7ARS4 0.989 86/41 86/41 87/41 86/41 88/41 88/41 86/42 84/41 88/41 GM202ARS2 Oceanibaculum 100/99 95/61 85/44 84/44 88/45 89/45 88/45 87/45 SP5AHP2 95/61 85/44 84/44 88/45 89/46 88/45 87/45 SP12AHP1 SP5ARB1 0.995 85/44 84/43 88/45 88/45 88/45 88/45 Hallea 98/59 87/59 85/59 85/56 83/56 SP5ARB1 SP12ARB2 1 88/59 83/60 88/56 82/57 SP12ARB2 GM7ARB2 Species 95/66 93/60 89/58 Nioella 0.999 1 ARB 16S >98.8, AAI 95-100 92/58 87/60 GM7ARB1 Neptunicoccus 88/65 Neptunicoccus 1 Genus 1 GM7ARB1 16S 95-98.6, AAI 65-95 0.959 Family Nioella 16S 92-95, AAI 45-65

Hellea Ambiguous 1 Family/Order SP5AHP2 AHP 1 SP12AHP1

SP5OBV1

2 0

4 Supplementary Figure 4. Gammaproteobacteria MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree [1], with SP5OBV1 as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives.

A B SP5GCR1

Thioglobus_MAG68

1 2 -

Gammaproteobacteria_TMED119 16 -

Methyloumidiphilus_alinensis 0.914 GM7GCV1 Halieaceae_LZ Halioglobus_HI00S01 Marinimicrobium_SW121 Marinobacter_R17 SP5GCR1 TMED119 Thioglobus_MAG68 Spiribacter_E85 1 Marinobacter_R17 1 -/50 87/50 88/50 88/48 85/43 -/45 -/45 86/47 GM7GCV1 -/65 -/52 -/50 -/44 -/46 -/46 -/48 Halieaceae_LZ-16-2 Halioglobus_U0301 0.992 91/51 88/50 86/43 -/46 -/47 -/47 Halioglobus_HI00S01 1 91/51 87/43 -/46 -/46 48 Marinimicrobium_SW121 Halieaceae_bacterium_LZ-16-2 88/44 -/46 -/47 49 Marinobacter_R17 0.972 0.924 -/48 -/49 87/45 SP5GCR1 Teredinibacter_turnerae Species 16S >98.8, AAI 95-100 -/97 -/48 TMED119 1 -/48 Thioglobus_MAG68 Marinimicrobium_SW121 Genus 16S 95-98.6, AAI 65-95

Spiribacter_E85_protein Family 16S 92-95, AAI 45-65

SP5OBV1 Ambiguous Family/Order

2.0

5 Supplementary Figure 5. Oligoflexia MAG classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree [1], with Oceanobaculum indicum as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives.

A B

Oligoflexus_tunisiensis 1 Silvanigrella_aquatica

1 Bdellovibrionales_RIFOXYA1_FULL_38_20_2713163136

1 Halobacteriovorax_marinus_SJ 0.821 Bacteriovorax_stolpii_UKi2 Silvanigrella_aquatica Bdellovibrionales_RIFOXYA1 Halobacteriovorax_marinus_SJ Bacteriovorax_stolpii_UKi2 SP5OBV1 Bdellovibrio_CG10 Bdellovibrio_bacteriovorus_Tiberius Bdellovibrio_bacteriovorus_HD100 84/37 -/35 86/36 88/37 85/36 86/38 88/38 88/38 Oligoflexus_tunisiensis SP5OBV1 -/35 88/36 86/36 85/36 86/37 86/37 86/37 Silvanigrella_aquatica -/46 -/45 -/36 -/36 -/36 -/36 Bdellovibrionales_RIFOXYA1 1 Bdellovibrio_CG10_8_21_14_0_10_47_8 89/50 85/37 85/38 85/38 86/38 Halobacteriovorax_marinus_SJ 86/36 87/39 88/40 88/40 Bacteriovorax_stolpii_UKi2 1 88/40 85/40 83/40 SP5OBV1 Bdellovibrio_bacteriovorus_Tiberius Species 90/54 90/54 Bdellovibrio_CG10 0.927 16S >98.8, AAI 95-100 99/94 Bdellovibrio_bacteriovorus_Tiberius Bdellovibrio_bacteriovorus_HD100 Genus 16S 95-98.6, AAI 65-95 Oceanibaculum_indicum_P24 Family 16S 92-95, AAI 45-65

2.0 Ambiguous Family/Order

6 Supplementary Figure 6. Relative abundance of metagenomically assembled sequences in 16S rRNA gene amplicon data sets. Amplified 16S rRNA gene sequences were recruited by blastn search at 97% identity to metagenomically assembled 16S rRNA genes and pooled into taxonomic groups as shown in Figure 3. Relative abundances in this chart are normalized to compensate for differences in total number of 16S rRNA reads obtained for each sponge sample (see Supplementary table 2 for total numbers of cleaned, merged amplicon reads). Metagenomically assembled genomes GM102CHS1, GM7ARS4, SP5ARS3, and GM102ARS1 could not be included in this table because they did not contain any sequences overlapping the amplified region of the 16S rRNA gene.

group SP12 SP5 SP1 SP8 GUM038 GUM040 GUM058 GUM096 GUM204 GUM020 GUM102 GUM203 GUM201 GUM202 GUM069 GUM007 seawater CHS 28% 46% 36% 20% 38% 26% 24% 36% 67% 47% 41% 24% 51% 57% 47% 46% 0.1% CPC 40% 5% 7% 1% 7% 0% 21% 10% 0% 0% 0% 32% 0% 0% 0% 0% 0.0% ARB 2% 4% 7% 2% 7% 2% 7% 4% 1% 2% 8% 9% 1% 0% 10% 11% 0.0% GCR 3% 1% 5% 2% 3% 5% 3% 4% 8% 22% 14% 5% 0% 0% 0% 0% 0.0% AHP 4% 9% 1% 6% 9% 13% 5% 8% 0% 0% 0% 5% 0% 0% 0% 0% 0.0% ARS 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 28% 21% 0% 0% 0.0% BCY 4% 1% 6% 7% 2% 2% 2% 3% 0% 0% 0% 1% 7% 4% 0% 0% 0.0% GCV 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 12% 12% 0.0% AMS 1% 1% 2% 0% 1% 1% 2% 1% 0% 0% 0% 1% 1% 1% 0% 0% 0.0% OBV 0% 0% 0% 0% 0% 0% 0% 0% 0% 1% 0% 0% 0% 0% 0% 0% 0.0%

Total 82% 68% 62% 39% 67% 48% 62% 65% 76% 72% 63% 76% 88% 82% 70% 69% 0.1%

7 Supplementary Figure 7. Relative abundance of raw metagenomic reads mapping to assembled MAGS. Percentages are based on Bowtie read recruitment at 100% identity. MAGs were pooled into taxonomic groups as shown in Figure 3. A) Relative abundances for all classified reads; B) read recruitment percentages, including unclassified reads. All percentages have normalized for number of reads per sample, but not adjusted for potential differences in genome size.

A B Ia Ia Ib II III 100%

90% SP12 SP5 GUM102 GUM202 GUM7 OBV CHS 7.1% 3.6% 6.2% 12.9% 37.6% 80% CPC ARB 0.9% 10.8% 2.4% 70% GCV s BCY 1.1% 1.6% 0.6%

ead GCR

r 60% AHP 1.0% 1.9% ed l AMS b 50% ARS 1.6% 0.2% 4.5% m e ARS GCV 3.4%

ss 40% AHP GCR 1.6% una

t 30% c AMS 0.2% 0.1% P BCY 20% OBV 0.5% ARB 10% CPC 1.4% CHS 0% other 89.9% 76.9% 93.7% 81.8% 56.4% 5 7 2 2 2 1 P M 10 20 P S U S M M G U U

G G

8 Supplementary Figure 8. Host associations of Type III secretion protein YscR homologs. A) Highlighted YscR homologs from MAGs of this study are shown in the context of a phylogenetic tree annotated with host types as described in [5]. B) Position of YscR homolog in Yersinia Type III secretion structure, adapted from [6].

Chlamydia_trachomatis_644746261 1 A Chlamydophila_pneumoniae_637024342 B Pseudomonas_fluorescens_2511827602 Dickeya_chrysanthemi_2552730626 0.829 1 0.998 Erwinia_amylovora_646705291 0.363 Pseudomonas_savastanoi_2728468992 0.974 Pseudomonas_syringae_2508867384 0.842 Yersinia_enterocolitica_2637528842 1 Pseudomonas_fluorescens_2511823774 0.95 Shigella_flexneri_640051816 0.857 Escherichia_coli_2586093862 Salmonella_typhimurium_637212157 0.817 0.094 Yersinia_pestis_2651002459 0.983 Yersinia_pseudotuberculosis_2631632861 Edwardsiella_tarda_646414907 0.124 Candidatus_Glomeribacter_2537342170 Animal associated 0.958 0.706 Chromobacterium_violaceum_637453415 Azoarcus_sp_WP_136386469.1 0.979 Ottowia_thiooxydans_WP_028605255.1 0.957 Achromobacter_xylosoxidans_WP_006383889.1 Plant associated 0.966 0.771 Bordetella_pertussis_637113416 GM202ARS2__2809152217 1 0.813 GM7ARS4__2809160796 Fungus associated Thalassospira_sp_MBC05410.1 Stigmatella_aurantiaca_639864093 0.999 Stigmatella_aurantiaca_639862896 Xanthomonas_campestris_637756104 Insect associated 0.891 1 0.924 Burkholderia_pseudomallei_637570841 0.889 0.681 Collimonas_fungivorans_651048881 0.938 0.971 Ralstonia_solanacearum_2562607160 Free-living Variovorax_paradoxus_649888208 0.069 0.976 Burkholderia_multivorans_2598440961 0.992 Burkholderia_vietnamiensis_640185619 Agrobacterium_radiobacter_643643257 1 Rhizobium_etli_640427156 0.909 0.764 0.913 Pseudomonas_savastanoi_2728463951 0.554 Mesorhizobium_loti_637078336 0.998 Bradyrhizobium_japonicum_637369381 YscR position Burkholderia_xenovorans_2598512078 1 Burkholderia_phytofirmans_642616298 Algicola_sagamiensis_WP_018692215.1 0.837 Thalassomonas_viridans_WP_044839857.1 Hahella_ganghwensis_WP_020408621.1 SP5GCR1__2809171518 0.861 Candidatus_Competibacteraceae_RUQ37199.1 0.864 Desulfovibrio_vulgaris_639813904 0.891 Candidatus_Competibacter_WP_048674153.1 Vibrio_parahaemolyticus_637398651 0.997Photorhabdus_luminescens_637465519 0.982Yersinia_pestis_2650998465 0.946 1Yersinia_pseudotuberculosis_2631633359 Yersinia_enterocolitica_2637532614 Thalassomonas_viridans_WP_044840622.1

0.2

9 Supplementary Figure 9. VirSorter candidate scaffolds in holobiont assemblies. Virus taxonomic groups were obtained by DarkHorse assignment based on blastx matches to a custom database containing all viral sequences in the GenBank nr database as of Jaunuary 2, 2019.

A B

45 Ia Ia Ib II III

40

35 Unclassified Total Virsorter Non-

Herpesvirales assembled scf candidate prophage Prophage 30 sample > 3K scf > 3K candidates candidates Baculoviridae SP12 9,939 7 7 0 25 Microviridae SP5 5,437 17 14 3 20 Bicaudaviridae GUM102 16,484 20 17 3 GUM202 34,352 36 31 5 Num Scaffolds 15 Caudovirales - Podoviridae GUM7D2 30,973 42 36 6 Caudovirales - Myoviridae 10

Caudovirales - Siphoviridae 5

0

SP5 SP12 GUM102 GUM202 GUM7D2

10 Supplementary Figure 10. Flavin-dependent aromatic halogenases from SP12AHP1 and SP5AHP2. A) Operon structure map from IMG-MER [7] showing relative positions of tandem repeats in red. B) Phylogenetic tree of protein sequences, showing positions of putative halogenase sequences from this study relative to experimentally characterized database examples described in [8]. The tree is rooted with the bmp5 gene of Pseudoalteromonas putida [9]. PDBE pathway halogenases from Hormoscilla strains SP5, SP12, GUM102, and GUM202 clade with the bmp5 outgroup.

FDH_Mpy11 1 FDH_PrnC 0.926 A B FDH_Mpy10 SP5CPC1_2830828043 0.996 GUM202CHS1_2747876046 1 GM7CHS!_Ga0115830_14160 1 FDH_CndH 0.024 Variant B Single genes 0.814 FDH_SgcC3 0.946 FDH_ComH carrier-bound 0.983FDH_BhaA chlorinated substrates 1 0.881 FDH_VhaA FDH_PltA FDH_Clz5 0.9991 0.826 FDH_HrmQ 0.763 0.709FDH_Pyr29 FDH_Mpy16 FDH_AltN FDH_MibH 1 FDH_AmmC Tandem repeats SP5CPC1_2830827449 Variant A FDH_PrnA 0.974 1 Free soluble 0.594 FDH_ThaI 0.943FDH_RebH clorinated substrates 0.748 0 FDH_KtzQ FDH_KtzR 0.999 0.922 FDH_PyrH SP12ARB1_2809162401 1 SP5ARB1_2809178732 SP5AHP2_2809180060 1 SP12AHP1_2809166809 0.3820.762 SP5AHP2_2809180675 1 SP12AHP1_2809166550 0.779 SP5AHP2_2809180674 0.995 SP12AHP1_2809166551 BrvH_12 Prefer bromine SP5AHP2_2809180061 1 vs chlorine? 0.916 SP12AHP1_2809166810 SP12AHP1_2809166808 0.9680.95 SP5AHP2_2809180062 1SP5AHP2_2809180063 0.952 0.231 SP12AHP1_2809166811 SP5AHP2_2809179335 1 SP12AHP1_2809166002 0.883 SP5AHP2_2809179334 1 SP12AHP1_2809166003 11 Supplementary Figure 11. Comparison of candidate haloaromatic degradation gene neighborhoods. A) Gene neighborhood maps with halocatechol dioxygenase genes indicated in red. Maps and tables of predicted genes for B) SP12AHP1, C) SP5AHP2 and D) Altererythrobacter marensis were obtained using the automated IMG-ER annotation pipeline [7]

A

12 aa locus_tag start end str aa len product B locus_tag start end str len product D Ga0081733_11974 990774 990863 - - tRNA Ga0325877_10273 827 1456 - 210 3-oxoacid CoA-transferase subunit B Ga0081733_11973 989592 990704 + 371 ribonuclease Z Ga0325877_10274 1456 2166 - 237 3-oxoacid CoA-transferase subunit A Ga0081733_11972 989065 989595 + 177 AhpC/TSA family protein Ga0325877_10275 2163 2432 - 90 hypothetical protein Ga0081733_11971 988430 989065 + 212 3-oxoadipate CoA-transferase, beta subunit Ga0325877_10276 2426 3637 - 404 acetyl-CoA acyltransferase Ga0081733_11970 987729 988433 + 235 3-oxoacid CoA-transferase, alpha subunit Ga0081733_11969 987475 987732 + 86 hypothetical protein Ga0325877_10277 3637 4698 - 354 maleylacetate reductase (EC:1.3.1.32) Ga0081733_11968 986258 987475 + 406 acetyl-CoA C-acetyltransferase Ga0325877_10278 4695 5396 - 234 carboxymethylenebutenolidase (EC:3.1.1.45) Ga0081733_11967 985194 986261 + 356 Alcohol dehydrogenase, class IV Ga0325877_10279 5422 6201 - 260 chlorocatechol 1,2-dioxygenase (EC:1.13.11) Ga0081733_11966 984499 985197 + 233 carboxymethylenebutenolidase Ga0325877_102710 6347 7234 + 296 AraC-like DNA-binding protein Ga0081733_11965 983647 984429 + 261 chlorocatechol 1,2-dioxygenase Ga0325877_102711 7231 8196 - 322 vanillate O-demethylase ferredoxin subunit (EC:1.14.13) Ga0081733_11964 982628 983536 - 303 AraC-type DNA-binding protein Ga0325877_102712 8287 10815 - 843 iron complex outermembrane receptor protein Ga0081733_11963 981635 982597 + 321 vanillate O-demethylase ferredoxin subunit Ga0325877_102713 10945 11847 - 301 DNA-binding transcriptional LysR family regulator Ga0081733_11962 979176 981575 + 800 iron complex outermembrane recepter protein Ga0325877_102714 11989 13176 + 396 muconate cycloisomerase (EC:5.5.1.11) Ga0081733_11961 978159 979067 + 303 DNA-binding transcriptional LysR family regulator Ga0325877_102715 13280 14659 + 460 Rieske-like 2Fe-2S protein Ga0081733_11960 976848 978008 - 387 muconate cycloisomerase Ga0081733_11959 975362 976741 - 460 Phenylpropionate dioxygenase Ga0325877_102716 15002 15586 + 195 Cu-Zn family superoxide dismutase Ga0081733_11958 972321 975227 + 969 outer membrane autotransporter Ga0081733_11957 971208 972179 + 324 Helix-turn-helix domain-containing protein locus_tag start end str aa len product Ga0081733_11956 968082 970967 + 962 zinc protease C Ga0325883_104610 9624 10412 - 263 AAA domain-containing protein Ga0081733_11955 964450 967980 + 1177 TonB-dependent receptor Ga0325883_104611 10750 10974 + 75 hypothetical protein Ga0081733_11954 963170 964294 + 375 transmembrane sensor Ga0081733_11953 962644 963183 + 180 RNA polymerase sigma-70 factor Ga0325883_104612 10988 11617 - 210 3-oxoacid CoA-transferase subunit B Ga0081733_11952 962311 962469 + 53 hypothetical protein Ga0325883_104613 11617 12072 - 152 3-oxoacid CoA-transferase A subunit Ga0081733_11951 960329 962191 + 621 monovalent cation:H+ antiporter Ga0325883_104614 12084 12245 - 54 coenzyme A transferase Ga0081733_11950 958779 960191 + 471 dihydrolipoamide dehydrogenase Ga0325883_104615 12084 12360 - 92 hypothetical protein Ga0081733_11949 958294 958683 + 130 acyl-CoA thioesterase YciA Ga0325883_104616 12084 12626 - 181 hypothetical protein Ga0081733_11948 957889 958290 + 134 hypothetical protein Ga0325883_104617 12084 13831 - 582 acetyl-CoA acyltransferase Ga0081733_11947 956595 957887 + 431 pyruvate dehydrogenase Ga0325883_104618 12084 14892 - 936 maleylacetate reductase (EC:1.3.1.32) Ga0325883_104619 12084 15590 - 1169 carboxymethylenebutenolidase (EC:3.1.1.45) Ga0325883_104620 12084 16395 - 1437 chlorocatechol 1,2-dioxygenase (EC:1.13.11) Ga0325883_104621 12084 17428 + 1781 AraC-like DNA-binding protein Ga0325883_104622 12084 18144 - 2020 vanillate O-demethylase ferredoxin subunit

Ga0325883_103332 28948 29029 + 27 tRNA Ga0325883_103333 29544 30128 - 195 Cu-Zn family superoxide dismutase Ga0325883_103334 30471 31850 - 460 Rieske-like 2Fe-2S protein Ga0325883_103335 31954 33141 - 396 muconate cycloisomerase Ga0325883_103336 33283 34185 + 301 DNA-binding transcriptional LysR family regulator Ga0325883_103337 34315 36207 + 631 iron complex outermembrane receptor protein

13 Supplementary Figure 12. Phylogenetic tree of halocatechol 1,2 dioxygenases. Tree shows SP12AHP1 and SP5AHP1 halocatechol 1,2- dioxygenases, highlighted in red, compared to closest GenBank nr database protein relatives. Chemically characterized chlorocatechol 1,2- dioxygenases are highlighted in blue. WP_119166128.1_Rhodospirillaceae 1 WP_085793379.1_Roseivivax TDJ63453.1_Proteobacteria 0.53 1 TDJ68190.1_Proteobacteria WP_072598894.1_Sphingomonas 0.725 1 ADQ90213.1_Pseudomonas 0.431 0.909 AAT99373.1_Sphingomonas WP_037467144.1_Sphingobium 0.999CAF32818.1_Sphingobium 0.795 WP_020997466.1_Sphingomonas WP_121938853.1_Eilatimonas

0.952 WP_084394776.1_Henriciella SP5AHP2_2809179740 0.976 1 SP12AHP1_2809166342 0.97 WP_074204617.1_Sphingorhabdus 0.391 WP_047806098.1_Altererythrobacter KEY98321.1_Sphingomonas 1 WP_013040396.1_Sphingobium 0.988 KER36759.1_Sphingobium WP_031358749.1_Caballeronia 0.267 WP_063495246.1_Burkholderia 0.576 0.325 WP_061164391.1_Caballeronia 1 1 BAB56009.1_Burkholderia AAR88247.1_Pseudomonas WP_015061606.1_Ralstonia 0.974 0.999 AEV57110.1_uncultured 0.937 BAA88069.1_Variovorax 0.773 AAK81678.1_Burkholderia 0.87 AYE88699.1_Diaphorobacter 1WP_012250645.1_Bordetella 0.757 ABM87945.1_Pseudomonas 0.198 WP_063599759.1_Pandoraea 1WP_012248463.1_Bordetella 0.768 WP_088138667.1_Achromobacter 0.786 WP_020206961.1_Cupriavidus

0.08

14 Supplementary Figure 13. MySQL schema for extracting sample metadata and abundance statistics from the Sponge Microbiome Database. Tables were populated using data in Supplementary tables 3,4, and 5 from [10].

samples hosts sample_id varchar(50) host_name varchar(50) host_name varchar(50) matches (index table) host_genus varchar(50) site_name varchar(255) match_id int(11) auto_increment host_abrev varchar(10) longitude decimal(3,6) P otu_id varchar(50) P host_taxid int(11) latitude decimal(3,6) sample_id varchar(50) host_lineage varchar(255) depth decimal(3,6) num_hits int(11) reads int(11) num_otus int(11) collect_date date

otus otu_id varchar(50) rep_seq_name varchar(50) rep_seq_ungap_seq varchar(100) silva128_match_id varchar(50) silva128_match_lineage varchar(255)

15 Supplementary Table 1. Lamellodysidea sponge sampling metadata.

16S Host amplicon Illumina PacBio clade Sample Collect NCBI merged metagenomic metagenomic (ITS) name Location date Description Biosample ID seqs reads reads Ia SP12 Anae Island June 2014 lime green, purple patches, flat SAMN04939363 227,847 45,810,804 - Piti Bomb lime green, purple base, lettuce leaf Ia SP5 Holes June 2014 SAMN04939377 126,418 46,496,996 - Piti Bomb lime green, purple base, lettuce leaf Ia SP1 Holes June 2014 SAMN04939374 97,761 - - Piti Bomb lime green, purple base, lettuce leaf Ia SP8 Holes June 2014 SAMN04939378 112,399 - - Ia GUM038 Anae Island July 2015 white/gray, flat SAMN04939360 114,867 - - Ia GUM040 Anae Island July 2015 white/gray, flat SAMN04939361 213,095 - - Piti Bomb Ia GUM058 Holes July 2015 lime green, lettuce leaf SAMN04939368 84,608 - - Piti Bomb Ia GUM096 Holes July 2015 lime green, lettuce leaf SAMN04939369 114,282 - - Piti Bomb Ia GUM203 Dec. 2016 lime green, purple base, lettuce leaf SAMN12982864 3,280 Holes - - Piti Bomb Ib GUM020 Holes July 2015 green with white ridged fingers SAMN04939367 123,293 - - Piti Bomb Ib GUM102 Holes July 2015 green with white ridged fingers SAMN04939373 195,184 148,726,466 - Ib GUM204 Tumon Bay Dec. 2016 green with white ridged fingers SAMN12982865 6,503 - - II GUM201 Anae Island Dec. 2016 green flat with delicate fingers SAMN12982858 5,096 - - II GUM202 Anae Island Dec. 2016 white/gray flat with delicate fingers SAMN10266269 4,237 100,368,352 31,034 III GUM069 Pago Bay July 2015 dark green ridged, fleshy fingers SAMN04939366 128,996 - - III GUM7D2 Pago Bay July 2015 dark green ridged, fleshy fingers SAMN04939364 79,191 178,947,320 - trichome enrichment of sample III GUM007 Pago Bay July 2015 GUM7D2 SAMN04939365 - 82,554,626 180,838 na GUM61 Anae Island July 2015 seawater SAMN12983225 1,405,063 - -

16 Supplementary Table 2. Sponge holobiont and trichome metagenomic assembly statistics.

Avg Sample pct reads Read read Assembled scf Max scf name Sample type assembled type length reads >3K len SP12 holobiont tissue 32% Illumina 90 14,534,232 9,939 75,936 SP5 holobiont tissue 37% Illumina 90 17,349,474 5,437 235,084 GUM102 holobiont tissue 46% Illumina 135 68,102,612 16,294 75,068 GUM202 holobiont tissue 75% Illumina 150 75,290,051 34,352 442,614 GUM7D2 holobiont tissue 33% Illumina 150 27,376,842 30,974 325,242 trichome GUM202 enrichment nd PacBio 3852 31,034 67* 304,029* trichome GUM007 enrichment 40% PacBio 4445 71,965 6 3,147,220

*GUM202 trichome enrichment reads were assembled in combination with Illumina GUM202 holobiont sequences, as previously described in [11].

17 Supplementary Table 3. MIMAG parameters for assembled genomes.

Comp Conta Compl analysis letene minati eteness Host Assembly project assemb. MIMAG ss on softwar clade Name Organism name type software Multi-marker qual score score e Hyphomonadaceae bacterium idba-ud Alphaproteobacteria;Rhodobacterales; Check Ia SP12AHP1 MAG high 91.4 0.0 SP12AHP1 v. 1.1.1 Hyphomonadaceae M Rhodobacteraceae bacterium idba-ud Alphaproteobacteria;Rhodobacterales; Check Ia SP12ARB1 MAG med 69.1 0.0 SP12ARB1 v. 1.1.1 Rhodobacteraceae M idba-ud Bacteroidetes;Cytophagia;Cytophagales; Check Ia SP12BCY1 Ekhidna sp. SP12BCY1 MAG high 100.0 0.0 v. 1.1.1 Cytophagaceae;Ekhidna M idba-ud Cyanobacteria;Oscillatoriophycideae; Check Ia SP12CHS1 Hormopscilla sp. SP12CHS1 MAG high 96.6 0.2 v. 1.1.1 Oscillatoriales;Gomontiellaceae;Hormoscilla M

Celera Hyphomonadaceae bacterium Alphaproteobacteria;Rhodobacterales; Check Ia SP5AHP2 MAG Assem. med 87.8 0.0 SP5AHP1 Hyphomonadaceae M v.8.3 Rhodobacteraceae bacterium idba-ud Alphaproteobacteria;Rhodobacterales; Check Ia SP5ARB1 MAG med 82.4 3.4 SP5ARB1 v. 1.1.1 Rhodobacteraceae M Rhodospirllales bacterium idba-ud Check Ia SP5ARS3 MAG Alphaproteobacteria:Rhodospirillales med 94.8 0.0 SP5ARS3 v. 1.1.1 M idba-ud Bacteroidetes;Cytophagia;Cytophagales; Check Ia SP5BCY1 Ekhidna sp. SP5BCY1 MAG high 96.4 0.5 v. 1.1.1 Cytophagaceae;Ekhidna M idba-ud Cyanobacteria;Oscillatoriophycideae; Check Ia SP5CHS1 Hormopscilla sp. SP5CHS1 MAG high 96.6 0.2 v. 1.1.1 Oscillatoriales;Gomontiellaceae;Hormoscilla M idba-ud Cyanobacteria;;Prochloraceae; Check Ia SP5CPC1 Pochlorn sp SP5CPC1 MAG med 77.4 0.0 v. 1.1.1 Prochloron M Chromatiales bacterium idba-ud Check Ia SP5GCR1 MAG Gammaproteobacteria;Chromatiales high 98.3 0.0 SP5GCR1 v. 1.1.1 M Bdellovibrionales bacterium idba-ud Check Ia SP5OBV1 MAG Oligoflexia;Bdellovibrionales high 91.2 0.0 SP5)BV1 v. 1.1.1 M

Rhodospirillales bacterium idba-ud Check Ib GM102ARS1 MAG Alphaproteobacteria:Rhodospirillales low 41.2 0.8 GM102ARS1 v. 1.1.1 M idba-ud Cyanobacteria;Oscillatoriophycideae; Check Ib GM102HS1 Hormopscilla sp. GM102CHS1 MAG med 95.7 1.8 v. 1.1.1 Oscillatoriales;Gomontiellaceae;Hormoscilla M

Rhodospirillales bacterium Celera Check II GM202ARS1 MAG Alphaproteobacteria:Rhodospirillales high 100.0 0.0 GM202ARS1 Assem. M 18 Comp Conta Compl analysis letene minati eteness Host Assembly project assemb. MIMAG ss on softwar clade Name Organism name type software Multi-marker taxonomy qual score score e v.8.3 Candidatus Methylospongiales idba-ud Alphaproteobacteria:Candidatus Check II GM202ARS2 MAG med 85.3 0.8 bacterium GM202ARS2 v. 1.1.1 Methylospongiales M Celera Bacteroidetes;Cytophagia;Cytophagales; Check II GM202BCY1 Ekhidna sp. GM202BCY1 MAG Assem. high 94.9 0.5 Cytophagaceae;Ekhidna M v.8.3 SPAdes Cyanobacteria;Oscillatoriophycideae; Check II GM202CHS1 Hormoscilla sp. GM202CHS1 MAG high 97.4 2.0 v. 3.10.1 Oscillatoriales;Gomontiellaceae;Hormoscilla M

Celera Rhodobacteraceae bacterium Alphaproteobacteria;Rhodobacterales; Check III GM7ARB1 MAG Assem. high 96.6 0.0 GM7ARB1 Rhodobacteraceae M v.8.3 Celera Rhodobacteraceae bacterium Alphaproteobacteria;Rhodobacterales; Check III GM7ARB2 MAG Assem. high 93.7 0.9 GM7ARB2 Rhodobacteraceae M v.8.3 Candidatus Methylospongiales idba-ud Alphaproteobacteria:Candidatus Check III GM7ARS4 MAG med 91.0 0.8 bacterium GM7ARS2 v. 1.1.1 Methylospongiales M CANU Cyanobacteria;Oscillatoriophycideae; Check III GM7CHS1pb Hormopscilla sp. GM7CHS1 MAG high 100.0 1.8 v. 1.8 Oscillatoriales;Gomontiellaceae;Hormoscilla M Celera Cellvibrionales bacterium Check III GM7GCV1 MAG Assem. Gammaproteobacteria;Cellvibrionales med 89.1 0.0 GM7GCV1 M v.8.3

19 Supplementary Table 4. Closest environmental matches from the GenBank nr database to 16S rRNA genes obtained from MAGs. GM102CHS1, GM7ARS4, SP5ARS3, GM102ARS1 are not included in this table because they did not include any 16S rRNA genes of 300 nt or longer.

Env. 16S Tax Environ 16S pct Aln group MAG tophit ident len Environ tophit habitat Ref. Lineage Cyanobacteria;Oscillatoriophycideae;Oscillatoriales; CHS GM202CHS1 AY615507.1 99% 1410 Sponge - Lamellodysidea [12] Gomontiellaceae;Hormoscilla Cyanobacteria;Oscillatoriophycideae;Oscillatoriales; CHS GM7CHS1 AY615501.1 100% 1410 Sponge - Lamellodysidea [12] Gomontiellaceae;Hormoscilla Cyanobacteria;Oscillatoriophycideae;Oscillatoriales; CHS SP12CHS1 AY615505.1 99% 1410 Sponge - Lamellodysidea [12] Gomontiellaceae;Hormoscilla Cyanobacteria;Oscillatoriophycideae;Oscillatoriales; CHS SP5CHS1 AY615505.1 100% 1410 Sponge - Lamellodysidea [12] Gomontiellaceae;Hormoscillaa CPC SP5CPC1 DQ357958.1 99% 1443 - Lissoclinum [13] Cyanobacteria;Synechococcales;Prochloraceae;Prochloron AMS GM202ARS2 AY845234.1 99% 1425 Sponge - Lamellodysidea [12] Alphaproteobacteria:Candidatus Methylospongiales AMS GM202ARS1 AY845233.1 100% 1468 Sponge - Lamellodysidea [12] Alphaproteobacteria:Rhodospirillales ARB SP5ARB1 AY845235.1 99% 1384 Sponge - Lamellodysidea [12] Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae ARB SP12ARB2 AY845235.1 98% 1379 Sponge - Lamellodysidea [12] Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae ARB GM7ARB1 KM051808.1 97% 1448 Basaltic Crust Borehole biofilm Un-published Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae ARB GM7ARB2 CP016093.1 88% 1474 Biocathode biofilm Un-published Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae AHP SP12AHP1 JF769570.1 96% 1467 seawater near algae (sea lettuce) Un-published Alphaproteobacteria;Rhodobacterales;Hyphomonadaceae AHP SP5AHP2 JF769570.1 96% 1467 seawater near algae (sea lettuce) Un-published Alphaproteobacteria;Rhodobacterales;Hyphomonadaceae BCY GM202BCY1 AM259890.1 96% 1460 sponge - Tethya [14] Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae BCY SP5BCY1 AM259890.1 96% 1460 sponge - Tethya [14] Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae BCY SP12BCY1 AM259890.1 96% 1460 sponge - Tethya [14] Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae GCR SP5GCR1 JX391667.1 91% 1514 PBDE contam marine sediment Un-published Gammaproteobacteria;Chromatiales GCV GM7GCV1 JQ062844.1 90% 1500 sponge- Stylissa [15] Gammaproteobacteria;Cellvibrionales;Cellvibrionaceae OVB SP5OBV1 EF092260 96% 1442 sponge - Axinella Un-published Oligoflexia;Bdellovibrionales

20 Supplementary Table 5. Assembled MAG 16S rRNA gene matches to Sponge Microbiome Database samples at 97% nucleotide identity. Database sequences were 99 bp segments amplified from the V4 region of the 16S rRNA gene [10]. Sponge Microbiome Database samples with the maximum number of matches to each MAG-associated 16S rRNA gene from this study were selected to determine the number and percent of matched sequences, and reported here along with host genus and geographical collection site. GM102CHS1, GM7ARS4, SP5ARS3, GM102ARS1 are not included in this table because they did not include any sequences overlapping the V4 region of the 16S rRNA gene.

total max OTU num max pct Tax 16S in OTU OTU group MAGs len All host genera Host with max pct sample matches matches site name sample_id

SP12CHS1, SP5CHS1, CHS 1486 Xestospongia, Cliona Xestospongia bocatorensis 647 57 16.7% Panama P10X53.1020516 GM202CHS1, GM7CHS1 Carteriospongia, GUM202BCY1, Cymbastela, Dysidea, Davies BCY SP5BCY1, 1524 Cymbastela coralliophila 304 4 1.3% Webster.1.E1.49.1019860 Ectyoplasia, Mycale, Reef SP12BCY1 marine sediment Limski ARB GM7ARB2 1243 Dysidea Dysidea avara 336 15 4.5% GC.4.2.1019709 Canal Chondrilla, Cinachyrella, Cliona, Dysidea, ARB GM7ARB1 1470 Ectyoplasia, Lissodendoryx colombiensis 237 1 0.4% Panama P12x59.1019532 Lissodendoryx, Mycale, seawater, marine sediment SP5ARB1, ARB 1497 Dysidea, Xestospongia Xestospongia bocatorensis 678 1 0.1% Panama SI06.11.1019752 SP12ARB1 Limski ARS GM202ARS2 1504 Dysidea Dysidea avara 336 2 0.6% GC.4.2.1019709 Canal Davies ARS GUM202ARS1 1507 Cymbastela. Xestospongia Cymbastela coralliophila 1341 3 0.2% Reef SS.9.2.1019758 SP12AHP1 Banco AHP 1479 Ircinia Ircinia strobilina 2940 1 0.04% 17.1020038 SP5AHP2 Chinchorros Cymbastela, Ircinia, Sponge DBV SP5DBV1 1517 Cymbastela 1085 3 0.3% ZA.44.1020227 Mycale Farm Carteriospongia, Kimberley, GCR SP5GCR1 1548 Cymbastela, Cliona, Carteriospongia foliascens 953 4 0.4% Western Webster.3.H4.276.1019944 Xestospongia Australia 21 total max OTU num max pct Tax 16S in OTU OTU group MAGs len All host genera Host with max pct sample matches matches site name sample_id GCV GM7GCV1 1517 no matches above threshold nd nd nd nd nd nd CPC SP5CPC1 1442 no matches above threshold nd nd nd nd nd nd

22 Supplementary Table 6. Tally of membrane-associated gene products in MAGs. Values for adhesive genes, signal sequences, and transporter types were tallied based on keyword searches of MAG annotations at IMG-MER [7].

pct chemo- Type num pct num CDS as taxis cadherin ankyrin IV signal signal tax num trans- trans- proteins motility domain domain pili peptide peptide signal signal group Genome name CDS porters porter (Che/Mot) type proteins proteins genes genes genes proteases glycosidases CHS SP12CHS1 5961 195 3.3% 6 twitching 2 12 74 1.2 5 0 CHS SP5CHS1 5738 176 3.1% 4 twitching 2 11 80 1.4 7 0 CHS GM102CHS1 6390 172 2.7% 2 twitching 1 2 16 78 1.2 6 0 CHS GM7CHS1 7441 196 2.6% 5 twitching 2 3 13 111 1.4 6 1 CHS GM202CHS1 6160 247 4.0% 6 twitching 5 15 113 1.5 7 0 CPC SP5CPC1 3413 122 3.6% 24 twitching 5 8 83 2.4 4 1 AMS GM7ARS4 1377 76 5.5% 0 none 3 8 57 4.0 4 0 AMS GM202ARS2 1836 91 5.0% 0 none 18 11 88 4.7 6 0 ARS GM202ARS1 2858 251 8.8% 1 none 14 2 136 4.7 5 2 ARS SP5ARS3 2570 312 12.1% 0 none 22 146 5.6 2 2 ARS GM102ARS1 1161 102 8.8% 1 none 8 47 4.0 2 1 ARB GM7ARB1 2449 247 10.1% 2 none 14 124 5.0 4 0 ARB GM7ARB2 2505 234 9.3% 1 none 8 1 129 5.1 5 3 ARB SP12ARB1 3273 263 8.0% 1 none 1 6 2 121 3.7 5 1 ARB SP5ARB1 2628 237 9.0% 1 none 6 2 130 4.9 1 1 AHP SP12AHP1 2275 113 5.0% 0 none 30 152 6.5 7 7 AHP SP5AHP2 2292 107 4.7% 0 none 32 135 5.8 6 6 BCY SP12BCY1 2828 128 4.5% 12 gliding 29 10 1 147 5.1 12 4 BCY SP5BCY1 2774 126 4.5% 12 gliding 31 8 1 142 5.1 9 4 BCY GM202BCY1 2879 125 4.3% 12 gliding 30 11 1 134 4.6 9 3 GCR SP5GCR1 1474 91 6.2% 0 none 13 8 70 4.6 4 2 GCV GM7GCV1 1744 109 6.3% 1 twitching 2 10 123 6.9 5 3 OVB SP5OBV1 1744 66 3.8% 0 twitching 31 13 60 3.9 1 0 23 Supplementary Table 7. Viral defense genes in assembled MAGs. Values were tallied based on keyword searches of MAG annotations at IMG- MER [7].

integrated IMG DNA- CRISPR loci prophage IMG IMG restriction modiification toxin/anti-toxin tax group MAG (Minced) recovered trans-posases endo-nuclease methylase genes CHS SP12CHS1 5 0 60 7 6 81 CHS SP5CHS1 14 0 50 51 16 78 CHS GM102CHS1 8 2 117 67 20 67 CHS GM202CHS1 4 1 318 51 11 93 CHS GM7CHS1 5 2 226 113 6 91 CPC SP5CPC1 0 0 73 12 8 29 AMS GM202ARS2 5 3 38 6 7 10 AMS GM7ARS4 6 0 1 4 5 1 ARS GM202ARS1 11 0 4 6 3 3 ARS SP5ARS3 14 0 1 7 3 2 ARS GM102ARS1 10 1 0 1 1 1 ARB SP5ARB1 6 0 15 9 0 0 ARB SP12ARB1 12 0 11 4 15 3 ARB GM7ARB1 16 0 0 5 21 7 ARB GM7ARB2 27 0 7 5 23 4 AHP SP12AHP1 15 0 34 7 7 6 AHP SP5AHP2 13 0 66 117 8 7 BCY GM202BCY1 8 0 33 9 24 14 BCY SP5BCY1 5 0 20 9 27 16 BCY SP12BCY1 9 0 19 7 30 16 GCR SP5GCR1 11 0 9 3 7 2 GCV GM7GCV1 14 1 6 6 21 6 OVB SP5OBV1 24 0 28 4 14 1

24 Supplementary Table 8. Biosynthetic gene clusters predicted by AntiSmash [16], supplemented with aromatic halogenases predicted by Pfam database model PF04820 [17].

Type Type bacter- Aromatic cyano- Lasso- tax I III terpene- terpene terpene iocin beta- halogenases bactin Lanthi- peptide group genome PKS NRPS PKS phosphonate carotenoid other (RiPP) lactone PDBE (PF04820) (RiPP) peptide (RiPP)

CHS SP12CHS1 1 1 1 1 1 1 CHS SP5CHS1 2 1 1 1 CHS GM102CHS1 1 1 1 1 CHS GM7CHS1pb 3 5 2 1 1 1 1 CHS GM202CHS1 4 7 2 1 1 1 1 CPC SP5CPC1 2 4 2 1 1 AMS GM202ARS2 1 1 AMS GM7ARS4 1 ARS SP5ARS3 1 1 ARS GM202ARS1 1 ARS GM102ARS1 1 1 ARB GM7ARB1 1 1 1 ARB GM7ARB2 1 1 ARB SP12ARB1 1 1 1 1 ARB SP5ARB1 1 1 1 1 AHP SP5AHP2 1 1 11 AHP SP12AHP 1 1 8 BCY SP12BCY1 1 1 1 BCY GM202BCY1 1 1 1 BCY SP5BCY1 1 1 1 GCR SP5GCR1 2 GCV GM7GCV1 1 1 OVB SP5OVB1

25 References

1. Segata, N., et al., PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun, 2013. 4: p. 2304. 2. Rodriguez-R, L. and K. Konstantinidis, The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints, 2016. 4: p. e1900v1. 3. Rodriguez-R, L.M., and Konstantinos T. Konstantinidis, Bypassing Cultivation To Identify Bacterial Species. Microbe, 2014. 9(3): p. 111-8. 4. Yarza, P., et al., Uniting the classification of cultured and uncultured and archaea using 16S rRNA gene sequences. Nat Rev Microbiol, 2014. 12(9): p. 635-45. 5. Nazir, R., et al., The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent. Front Microbiol, 2017. 8: p. 38. 6. Dewoody, R.S., P.M. Merritt, and M.M. Marketon, Regulation of the Yersinia type III secretion system: traffic control. Front Cell Infect Microbiol, 2013. 3: p. 4. 7. Chen, I.A., et al., IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res, 2017. 45(D1): p. D507-D516. 8. Neubauer, P.R., et al., A flavin-dependent halogenase from metagenomic analysis prefers bromination over chlorination. PLoS One, 2018. 13(5): p. e0196797. 9. Agarwal, V., et al., Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. Nat Chem Biol, 2014. 10(8): p. 640-7. 10. Thomas, T., et al., Diversity, structure and convergent evolution of the global sponge microbiome. Nat Commun, 2016. 7: p. 11870. 11. Schorn, M.A., et al., Comparative of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges. MBio, 2019. 10(3): p. e00821-19. 12. Ridley, C.P., D. John Faulkner, and M.G. Haygood, Investigation of Oscillatoria spongeliae-dominated bacterial communities in four dictyoceratid sponges. Appl Environ Microbiol, 2005. 71(11): p. 7366-75. 13. Donia, M.S., et al., Complex microbiome underlying secondary and primary metabolism in the -Prochloron symbiosis. Proc Natl Acad Sci U S A, 2011. 108(51): p. E1423-32. 14. Thiel, V., et al., Spatial distribution of sponge-associated bacteria in the Mediterranean sponge Tethya aurantium. FEMS Microbiol Ecol, 2007. 59(1): p. 47-63. 15. Giles, E.C., et al., Bacterial community profiles in low microbial abundance sponges. FEMS Microbiol Ecol, 2013. 83(1): p. 232-41. 16. Blin, K., et al., antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res, 2019. 47(W1): p. W81-W87. 17. Finn, R.D., et al., The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res, 2016. 44(D1): p. D279-85.

26