Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus

Abstract

Background: Spotting disease infects a variety of sea urchin species across many different marine locations. The disease is characterized by discrete lesions on the body surface composed of discolored necrotic tissue that cause the loss of all surface appendages within the lesioned area. A similar, but separate disease of sea urchins called bald sea urchin disease (BSUD) has overlapping symptoms with spotting disease, resulting in confusions in distinguishing the two diseases. Previous studies have focus on identifying the underlying causative agent of spotting disease, which has resulted in the identification of a wide array of pathogenic bacteria that vary based on location and sea urchin species. Our aim was to investigate the spotting disease infection by characterizing the microbiomes of the animal surface and various tissues.

Results: We collected samples of the global body surface, the lesion surface, lesioned and non-lesioned body wall, and coelomic fluid, in addition to samples from healthy sea urchins. 16S rRNA gene was amplified and sequenced from the genomic DNA. Results show that the lesions are composed mainly of Cyclobacteriaceae, Cryomorphaceae, and a few other taxa, and that the microbial composition of lesions is the same for all infected sea urchins. Spotting disease also alters the microbial composition of the non-lesioned body wall and coelomic fluid of infected sea urchins. In our closed aquarium systems, sea urchins contracted spotting disease and BSUD separately and therefore direct comparisons could be made between the microbiomes from diseased and healthy sea urchins.

Conclusion: Results show that spotting disease and BSUD are separate diseases with distinct symptoms and distinct microbial compositions.

Keywords: 16S rRNA; Disease; Infection; Lesion; Microbiome; Pathogenic.

Fig. 1

Sea urchins with spotting disease show discrete lesions at the equatorial to ventral body regions. All sea urchins are positioned with the oral surface facing down. A Diseased sea urchin (D1) has a single large black necrotic lesion. This sea urchin displays unusual orientation of its spines, which point in various directions rather than uniformly perpendicular to the body surface. This is a behavioral indication of disease that has been noted previously [15]. B Diseased sea urchin (D2) has two large black necrotic lesions, labelled “a” and “b”. Parts of the test (white) are exposed around the outer region of lesion a (arrows). This sea urchin has lost all primary spines, including non-lesioned areas of the body surface, which indicates its moribund condition. C Diseased sea urchin (D3) has one large black necrotic lesion. This sea urchin shows typical spine orientation of perpendicular to the body surface, which indicates better health despite the lesion. Exposed test is also evident within the lesion (arrow). D Diseased sea urchin (D4) has a small black necrotic lesion of approximately 1 cm in diameter. The mouth is located on the ventral side (yellow arrow). This sea urchin also shows indications of better health, including primary spines generally pointing perpendicular to the body surface

Fig. 2

The global surface microbiome diversity is not different between diseased and healthy sea urchins. Alpha diversity is analyzed by A Observed Species, B Chao1, and C ACE. The box plots show the mean and quartile values for each group, which are not significantly different (ANOVA, p > 0.05). D Beta diversity is analyzed at the level of ASV sequences using weighted UniFrac and visualized with NMDS. Ellipses around sample groups show 95% confidence intervals assuming a multivariate t-distribution (solid line) or a multivariate normal distribution (dashed line). The beta diversity of the groups is not significantly different (PERMANOVA, p > 0.05), indicating that microbial composition is similar for the global surface microbiomes on diseased and healthy sea urchins housed in the same aquarium

Fig. 3

Global surface microbiomes of diseased vs. healthy sea urchins show taxonomic differences. A All identified phyla for the sea urchin surface samples and the fSW sample (Additional File, Table S1) illustrate the relative abundance of each taxon in each sample. B Genera with an average relative abundance of > 0.1% across all samples (Additional File, Table S2) are illustrated by the relative abundance per sample. fSW is the average of fSW1 and fSW2. Taxa in A and B that could not be assigned at the level of phylum or genus are listed as the most specific known taxonomic level. BD2-3 is in the order Victivallales, the Pir4 lineage is in the family Pirellulaceae, vadinHA49 is in the phylum Planctomycetota, JGI-0000069-P22 is in the class Gracilibacteria, MSBL3 is in the family Kiritimatiellaceae, and HOC36 is in the class Gammaproteobacteria. ASV sequences that could not be assigned to a phylum are grouped as Bacteria. Sample name abbreviations are defined in Table 1

Fig. 4

Many taxa are differentially abundant in the microbiome samples. A heatmap shows all taxa identified by LEfSe that are significantly differentially abundant (p < 0.05) and have an LDA score of > 2 as their abundance per group for A the global surface microbiome samples, B the lesioned body wall (LBW) and lesion surface (LS) microbiome samples, and C the tissue microbiome samples (Additional File, Tables S3, S6, S9). Sample name abbreviations are defined in Table 1

Fig. 5

The microbiome compositions are similar between the lesion surface and the lesioned body wall. Alpha diversity of the microbiomes from the LS and LBW sample groups are evaluated by A Observed Species, B Chao1, and C ACE. The box plots show the mean and quartile values for each group, which are not different (ANOVA, p > 0.05). D Beta diversity is evaluated at the ASV level using weighted UniFrac and visualized with NMDS. Ellipses around sample groups show 95% confidence intervals assuming a multivariate t-distribution (solid line) and a multivariate normal distribution (dashed line). The microbiomes of the LS compared to the LBW sample groups are not significantly different (PERMANOVA, p > 0.05). The sSW sample is shown for comparison. Sample name abbreviations are defined in Table 1

Fig. 6

The microbiomes of the lesion surface and the lesioned body wall are highly similar. A All identified phyla are shown as the relative abundance in each sample (Additional File, Table S4). B Genera with an average relative abundance of > 0.1% across all groups (Additional File, Table S5) are illustrated by the relative abundance per sample. Abundance of taxa from replicated samples are averaged. Both types of seawater control samples are included for comparisons, which are the microbes collected from 500 ml of filtered seawater (fSW) and seawater collected with a swab (sSW). Taxa in A and B that could not be assigned at the level of phylum or genus are listed as the most specific known taxonomic level. Taxa that could not be assigned to a phylum are grouped under Bacteria. Sample name abbreviations are defined in Table 1. BD2-3 is in the order Victivallales, the Pir4 lineage is in the family Pirellulaceae, vadinHA49 is in the phylum Planctomycetota, JGI-0000069-P22 is in the class Gracilibacteria, and HOC36 is in the class Gammaproteobacteria

Fig. 7

The microbiomes of dissected tissues from diseased and healthy sea urchins are different. Alpha diversity is analyzed by A Observed Species, B Chao1, and C ACE. The box plots show the mean and quartile values for each group, which are not significantly different (ANOVA, p > 0.05). D Beta diversity is analyzed at the ASV level using weighted UniFrac. Ellipses around sample groups show 95% confidence intervals assuming a multivariate t-distribution (solid line) and a multivariate normal distribution (dashed line). Groups are not significantly different (PERMANOVA, p > 0.05). Sample name abbreviations are defined in Table 1

Fig. 8

The microbiome of each dissected tissue has a distinct microbial composition. A All phyla that were identified are shown as the relative abundance of each phylum in each sample (Additional File, Table S7). Taxa that could not be assigned to a phylum are grouped under Bacteria. B Genera with an average relative abundance of > 0.1% across all groups are shown as their relative abundance per sample (Additional File, Table S8). Taxa that could not be assigned at the level of genus are listed as the most specific known taxonomic level. Sample name abbreviations are defined in Table 1. BD2-3 is in the order Victivallales, vadinHA49 is in the phylum Planctomycetota, JGI-0000069-P22 is in the class Gracilibacteria, and MSBL3 is in the family Kiritimatiellaceae