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SUPPLEMENTAL MATERIAL Physiology of Genotypes of Coral-Associated Endosymbionts

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SUPPLEMENTAL MATERIAL Physiology of Genotypes of Coral-Associated Endosymbionts SUPPLEMENTAL MATERIAL Physiology of Genotypes of Coral-Associated Endosymbionts (Breviolum antillogorgium) in Response to Bacterial Communities By Chelsea Aline Brisson Master of Science in Biology SUPPLEMENTARY TABLES Table T1) Pairwise post hoc contrasts of H’ alpha diversity metrics using emmeans in both experiments. Significant differences within and between experiments are bold. Experiment 4x4 Experiment Temp-Env Bacterial Community 16-0583 16-0584 16-0630 16-0732 16-0583 16-0630 16-0723 16-0584 0.9994 - - - - - - 16-0630 0.5113 0.78 - - - - - 4x4 Experiment 16-0732 0.2253 0.1119 0.0121 - - - - 16-0583 1 0.9911 0.377 0.3214 - - - 16-0630 0.9912 1 0.8178 0.0515 0.9498 - - Env - 16-0723 1 1 0.5853 0.0983 0.9974 0.9994 - Temp Experiment Environmental 0.9757 0.8271 0.1595 0.6479 0.9967 0.6408 0.8617 Table T2) Taxa in Experiment 1 that significantly differ in relative abundance between genotypes – results from ANCOM analysis (Qiime2). Taxa shown are only those that are significantly different enough to reject the null hypothesis that the relative abundance is the same among all genotypes (W statistic). Phylogenetic Taxa W Level Class Bacteria – Spirochaetes – Leptospirae 16 Order Bacteria – Bacteroidetes – Bacteroidia – unknown 72 Family Bacteria – Bacteroidetes – Bacteroidia – Cytophagales – 102 Amoebophilaceae Genus Bacteria – Bacteroidetes – Bacteroidia – Cytophagales – 137 Amoebophilaceae – Uncultured Table T3) Taxa in initial/inoculum communities from Experiment 2 that significantly differ in relative abundance between genotypes – results from ANCOM analysis (Qiime2). Taxa shown are only those that are significantly different enough to reject the null hypothesis that the relative abundance is the same among all genotypes (W statistic). Phylogenetic Taxa W Level Class Bacteroidetes – Rhodothermia 20 Class Planctomycetes – Phycisphaerae 17 Order Proteobacteria – Alphaproteobacteria – Sphingomonadales 80 Order Proteobacteria – Alphaproteobacteria – Thalassobaculales 77 Family Proteobacteria – Alphaproteobacteria – Sphingomonadales – 126 Sphingomonadaceae Family Proteobacteria – Alphaproteobacteria – Thalassobaculales – 122 Thalassobaculaceae Family Proteobacteria – Alphaproteobacteria – Rhizobiales – Stappiaceae 116 Family Proteobacteria – Alphaproteobacteria – Rhodospirillales – 115 Terasakiellaceae Genus Proteobacteria – Alphaproteobacteria – Sphingomonadales – 191 Sphingomonadaceae – Altererythrobacter Genus Proteobacteria – Alphaproteobacteria – Thalassobaculales – 186 Thalassobaculaceae – Thalassobaculum Table T4) Pairwise PERMANOVA tests of all final bacterial communities in Experiment Temp- Env. Communities were tested at the genus level using the (a) Bray-Curtis metric and (b) binary- Jaccard metric. Communities were grouped by which bacterial community they were inoculated with and tested against all other communities. Bold denotes a significant p-value. Values below the diagonal are p-values; above the diagonal have a Bonferroni correction. Values on the diagonal are the initial bacterial community composition tested against any final samples inoculated with that community. (a) Initial Community 16-0583 16-0630 16-0723 Environmental y 16-0583 0.252 0.028 1 0.028 16-0630 0.001 0.42 0.028 0.028 Final Final 16-0723 0.126 0.001 0.28 0.028 Communit Environmental 0.001 0.001 0.001 1 (b) Initial Community 16-0583 16-0630 16-0723 Environmental 16-0583 0.196 0.028 1 0.028 ty 16-0630 0.001 0.056 0.028 0.026 Final Final 16-0723 0.094 0.001 0.168 0.028 Communi Environmental 0.001 0.001 0.001 0.812 Table T5) Summary table of ANOVA results of the effects of microbiome, host genotype, and temperature on taxa that changed the most from initial to final community. These are separated by (a) phyla, (b) families within the class Alphaproteobacteria, (c) families within the class Gammaproteobacteria, and (d) families within the phyla Bacteroidetes. (a) Phyla: Bacteroidetes Proteobacteria Planctomycetes Factor F value P value F value P value F value P value Algal Genotype 1.521 0.23596 0.247 0.7828 0.659 0.5253 Bacterial Community 5.590 0.00391 1.380 0.2694 0.286 0.8354 Temperature 4.829 0.03643 0.472 0.4976 4.474 0.0434 Genotype : Bacteria 2.498 0.04614 0.964 0.4671 1.066 0.4060 Genotype : Temperature 0.653 0.52843 0.045 0.9558 1.301 0.2882 Bacteria : Temperature 8.008 0.00178 2.544 0.0866 0.524 0.5976 3-way Interaction 0.213 0.80985 2.017 0.1519 3.014 0.0652 (b) Family: Rhizobiales Rhodobacterales Sphingomonadales Caulobacterales Factor F value P value F value P value F value P value F value P value Algal Genotype 0.199 0.8209 2.579 0.09376 1.652 0.20981 1.823 0.1802 Bacterial Community 2.074 0.1262 10.607 7.88*10-5 33.713 1.96*10-9 14.77 5.9*10-6 Temperature 0.652 0.4261 0.543 0.46716 9.000 0.00562 0.2407 0.2407 Genotype : Bacteria 0.104 0.9953 2.264 0.06604 1.818 0.13164 3.129 0.0179 Genotype : Temperature 0.213 0.8091 0.298 0.74471 0.507 0.60796 0.014 0.9866 Bacteria : Temperature 2.683 0.0859 0.934 0.40481 11.878 0.00018 0.706 0.5023 3-way Interaction 0.368 0.6952 9.479 0.00072 0.517 0.60209 0.004 0.9959 (c) Family: Alteromonadales Cellvibrionales Oceanospirillales Salinisphaerales Factor F value P value F value P value F value P value F value P value Algal Genotype 2.804 0.0776 6.777 0.00398 1.248 0.3027 1.634 0.21328 Bacterial Community 74.836 1.74*10-13 15.238 4.53*10-6 1.510 0.2335 5.506 0.00422 Temperature 5.018 0.0332 5.940 0.02141 0.060 0.8077 0.026 0.87347 Genotype : Bacteria 3.260 0.0147 7.449 7.80*10-5 0.833 0.5545 2.708 0.03351 Genotype : Temperature 5.846 0.0076 7.744 0.00210 0.153 0.8593 0.591 0.56058 Bacteria : Temperature 9.378 0.0008 4.636 0.01823 4.999 0.0139 0.149 0.86187 3-way Interaction 2.588 0.0931 9.215 8.41*10-4 1.628 0.2144 0.772 0.47145 (d) Family: Balneolales Cytophagales Flavobacteriales OPB56 Factor F value P value F value P value F value P value F value P value Algal Genotype 4.899 0.015 0.402 0.67272 0.857 0.4353 0.444 0.646 Bacterial Community 0.461 0.711 0.983 0.41495 4.155 0.0148 1.10532 <2.0*10-16 Temperature 0.566 0.458 0.219 0.64324 3.157 0.0865 0.024 0.878 Genotype : Bacteria 1.101 0.386 2.232 0.06941 0.713 0.6425 0.640 0.697 Genotype : Temperature 1.353 0.275 1.713 0.00229 0.030 0.9702 0 1.0 Bacteria : Temperature 0.179 0.837 7.614 0.19869 2.276 0.1214 0 1.0 3-way Interaction 0.149 0.862 0.746 0.48325 0.015 0.9847 0 1.0 Table T6) P-values from Spearman’s Rank Correlation tests of the most abundant bacteria at each phylogenetic level vs each physiological trait at ambient (26C) temperature. Bold signifies a significant p-value. Taxa are listed in order of average relative abundance (greatest to least) for each phylogenetic level. GROWTH RATE Class Order Family Genus Alphaproteobacteria 0.693 Rhizobiales 0.3998 Rhodobacteraceae 0.5022 Pseudohongiella 0.0927 Gammaproteobacteria 0.2665 Rhodobacterales 0.5022 Hyphomonadaceae 0.0544 Labrenzia 0.4268 Bacteroidia 0.8438 Oceanospirillales 0.8915 Pseudohongiellaceae 0.0927 Algimonas 0.0220 Rhodothermia 0.6158 Caulobacterales 0.0544 Stappiaceae 0.4268 Roseivivax 0.9821 Phycisphaerae 0.1889 Cytophagales 0.0721 Halomonadaceae 0.4814 Marinobacter 0.7043 PHOTOSYNTHETIC EFFICIENCY Class Order Family Genus Alphaproteobacteria 0.1076 Rhizobiales 0.159 Rhodobacteraceae 0.1136 Pseudohongiella 0.982 Gammaproteobacteria 0.0595 Rhodobacterales 0.1136 Hyphomonadaceae 0.6734 Labrenzia 0.3652 Bacteroidia 0.6623 Oceanospirillales 0.3554 Pseudohongiellaceae 0.982 Algimonas 0.6067 Rhodothermia 0.8867 Caulobacterales 0.6734 Stappiaceae 0.3652 Roseivivax 0.2903 Phycisphaerae 0.8035 Cytophagales 0.6623 Halomonadaceae 0.7918 Marinobacter 0.124 CHLOROPHYLL A Class Order Family Genus Alphaproteobacteria 0.1081 Rhizobiales 0.917 Rhodobacteraceae 0.0522 Pseudohongiella 0.4133 Gammaproteobacteria 0.1458 Rhodobacterales 0.0522 Hyphomonadaceae 0.7043 Labrenzia 0.3215 Bacteroidia 0.7156 Oceanospirillales 0.1702 Pseudohongiellaceae 0.4133 Algimonas 0.493 Rhodothermia 0.5322 Caulobacterales 0.7043 Stappiaceae 0.3215 Roseivivax 0.2171 Phycisphaerae 0.5408 Cytophagales 0.253 Halomonadaceae 0.3396 Marinobacter 0.0667 PHOTOSYNTHESIS RATE Class Order Family Genus Alphaproteobacteria 0.1119 Rhizobiales 0.4265 Rhodobacteraceae 0.2334 Pseudohongiella 0.5781 Gammaproteobacteria 0.0439 Rhodobacterales 0.2334 Hyphomonadaceae 0.8676 Labrenzia 0.6097 Bacteroidia 0.253 Oceanospirillales 0.0069 Pseudohongiellaceae 0.5781 Algimonas 0.2717 Rhodothermia 0.5733 Caulobacterales 0.8676 Stappiaceae 0.6097 Roseivivax 0.2913 Phycisphaerae 0.5008 Cytophagales 0.8676 Halomonadaceae 0.3007 Marinobacter 0.0459 RESPIRATION RATE Class Order Family Genus Alphaproteobacteria 0.208 Rhizobiales 0.4591 Rhodobacteraceae 0.0164 Pseudohongiella 0.0599 Gammaproteobacteria 0.8343 Rhodobacterales 0.0164 Hyphomonadaceae 0.2732 Labrenzia 0.5699 Bacteroidia 0.5886 Oceanospirillales 0.7936 Pseudohongiellaceae 0.0599 Algimonas 0.8889 Rhodothermia 0.1195 Caulobacterales 0.2732 Stappiaceae 0.5699 Roseivivax 0.0880 Phycisphaerae 0.1156 Cytophagales 0.3254 Halomonadaceae 0.0455 Marinobacter 0.4268 Table T7) P-values from Spearman’s Rank Correlation tests of the most abundant bacteria at each phylogenetic level vs each physiological trait at elevated (30C) temperature. Bold signifies a significant p-value. Taxa are listed in order of average relative abundance (greatest to least) for each phylogenetic level. GROWTH RATE Class Order Family Genus Alphaproteobacteria 0.6584 Rhizobiales 0.5264 Rhodobacteraceae 0.9663 Pseudohongiella 0.0186 Gammaproteobacteria 0.3446 Rhodobacterales 0.9663 Hyphomonadaceae 0.5451 Labrenzia 0.3876
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