The following supplement accompanies the article

Fine-scale transition to lower bacterial diversity and altered community composition precedes shell disease in laboratory-reared juvenile American lobster

Sarah G. Feinman, Andrea Unzueta Martínez, Jennifer L. Bowen, Michael F. Tlusty*

*Corresponding author: [email protected]

Diseases of Aquatic Organisms 124: 41–54 (2017)

Figure S1. Principal coordinates analysis of bacterial communities on lobster shell samples taken on different days. Principal coordinates analysis of the weighted UniFrac metric comparing bacterial community composition of diseased lobster shell on different days of sampling. Diseased lobster shell includes samples collected from the site of disease (square), as well as 0.5 cm (circle), 1 cm (triangle), and 1.5 cm (diamond) away from the site of the disease, while colors depict different days of sampling. Note that by day four, two of the lobsters had molted, hence there are fewer red symbols

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Figure S2. Rank relative abundance curve for the 200+ most abundant OTUs for each shell condition. The number of OTUs, their abundance, and their order varies for each bar graph based on the relative abundance of each OTU in that shell condition. Please note the difference in scale along the y-axis for each bar graph. Bars appear in color if the OTU is a part of the core microbiome of that shell condition or appear in black if the OTU is not a part of the core microbiome of that shell condition. Dotted lines indicate OTUs that are part of the “abundant microbiome,” i.e. those whose cumulative total is ~50%, as well as OTUs that are a part of the “rare microbiome,” i.e. those whose cumulative total is 75% or less. The cutoff for the “rare microbiome” varies based on the shape of the rank abundance curve for each shell condition.

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Table S1. Taxonomy for the 20 most abundant OTUs from each shell condition. Closest cultured representative for the 20 most abundant OTUs from each shell condition in A) affected shell, B) transitionary shell, and C) unaffected shell. OTUs appear in order of their abundance in a particular shell condition (see Fig. S2 for rank abundance curves). OTUs that are also a part of the core microbiome for that shell condition appear in bold. Abundance is relative abundance in that shell condition.

A) Affected Shell OTU Order Family Genus Identity Abundance 0 - - Thioglobus* 91% 15.0% 18 Flavobacteriales Flavobacteriaceae Aquimarina 100% 11.8% 4 Rhodobacterales Rhodobacteraceae Octadecabacter 100% 6.5% 19 Flavobacteriales Flavobacteriaceae Lutimonas 96% 5.2% 28 Alteromonadales Colwelliaceae Colwellia 100% 4.6% 47 Alteromonadales Colwelliaceae Colwellia 100% 3.9% 113 Vibrionales Vibrionaceae Vibrio 100% 2.3% 29 Alteromonadales Colwelliaceae Colwellia 100% 2.3% 117 Rhizobiales Hyphomicrobiaceae Devosia 94% 2.3% 118 Arenicellales Arenicellaceae Arenicella 99% 1.9% 44 Alteromonadales Alteromonadaceae Marinobacter 100% 1.3% 186 Cytophagales Flammeovirgaceae Roseivirga 98% 1.2% 21 Flavobacteriales Flavobacteriaceae Maritimimonas 96% 1.1% 237 Rhizobiales Phyllobacteriaceae Lentilitoribacter 98% 1.0% 188 Alteromonadales Alteromonadaceae Unclassified 98% 0.9% 1 Arenicellales Arenicellaceae Perspicuibacter 99% 0.9% 71 Flavobacteriales Flavobacteriaceae Maribacter 99% 0.9% 241 Rhodobacterales Rhodobacteraceae Loktanella 100% 0.9% 78 Rhodobacterales Rhodobacteraceae Loktanella 100% 0.8% 227 Kordiimonadales Kordiimonadaceae Emcibacter 92% 0.8%

B) Transitionary Shell OTU Order Family Genus Identity Abundance 0 - - Thioglobus* 91% 8.7% 1 Arenicellales Arenicellaceae Perspicuibacter 99% 7.0% 38 Arenicellales Arenicellaceae Arenicella 99% 4.0% 47 Alteromonadales Colwelliaceae Colwellia 99% 2.7% 19 Flavobacteriales Flavobacteriaceae Lutimonas 96% 2.2% 18 Flavobacteriales Flavobacteriaceae Aquimarina 100% 2.1% 112 Flavobacteriales Flavobacteriaceae Maribacter 98% 2.0% 106 Cellvibrionales Cellvibrionaceae Endobugula* 97% 1.9% 121 Rhodobacterales Hyphomonadaceae Robiginitomaculum 96% 1.7% 44 Alteromonadales Alteromonadaceae Marinobacter 100% 1.5% 135 Rhizobiales Methylobacteriaceae Methylobacterium 100% 1.5%

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22 Thiotrichales Thiotrichaceae Cocleimonas 97% 1.5% 118 Arenicellales Arenicellaceae Arenicella 99% 1.5% 74 Verrucomicrobiales Rubritaleaceae Rubritalea 97% 1.2% 125 Planctomycetales Planctomycetaceae Blastopirellula 91% 1.0% 160 Cellvibrionales Cellvibrionaceae Endobugula* 99% 1.0% 71 Flavobacteriales Flavobacteriaceae Maribacter 99% 0.9% 98 Rhodobacterales Hyphomonadaceae Litorimonas 97% 0.9% 81 Thiotrichales Thiotrichaceae Leucothrix 98% 0.9% 192 Rhizobiales Methylobacteriaceae Methylobacterium 100% 0.7%

C) Unaffected Shell OTU Order Family Genus Identity Abundance 1 Arenicellales Arenicellaceae Perspicuibacter 99% 5.4% 38 Arenicellales Arenicellaceae Arenicella 99% 4.1% 74 Verrucomicrobiales Rubritaleaceae Rubritalea 97% 2.2% 106 Cellvibrionales Cellvibrionaceae Endobugula* 97% 1.8% 20 Flavobacteriales Flavobacteriaceae Lutimonas 97% 1.6% 125 Planctomycetales Planctomycetaceae Blastopirellula 91% 1.5% 19 Flavobacteriales Flavobacteriaceae Lutimonas 96% 1.5% 45 Oceanospirillales Oceanospirillaceae Marinospirillum 94% 1.4% 98 Rhodobacterales Hyphomonadaceae Litorimonas 97% 1.2% 82 Acidimicrobiales Microthrixaceae Microthrix* 91% 1.1% 44 Alteromonadales Alteromonadaceae Marinobacter 100% 1.0% 22 Thiotrichales Thiotrichaceae Cocleimonas 97% 1.0% 71 Flavobacteriales Flavobacteriaceae Maribacter 99% 0.9% 75 Rhodobacterales Rhodobacteraceae Loktanella 99% 0.9% 131 Arenicellales Arenicellaceae Perspicuibacter 93% 0.9% 135 Rhizobiales Methylobacteriaceae Methylobacterium 100% 0.8% 2 Arenicellales Arenicellaceae Perspicuibacter 99% 0.8% 136 Acidimicrobiales Acidimicrobiaceae Acidithiomicrobium 91% 0.8% 124 Arenicellales Arenicellaceae Arenicella 97% 0.8% 147 Rhizobiales Hyphomicrobiaceae Filomicrobium 96% 0.8%

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