Data from: Microbial dysbiosis precedes signs of sea star wasting disease in wild populations of Pycnopodia helianthoides

Sample collection Samples were collected in the summer of 2016 off the coast of Southeast Alaska (Fig. S1). With the aid of SCUBA, a biopsy from a single ray was collected underwater from each sampled sea star, and isolated until in a wet lab aboard a research vessel (R/V Kestrel, Alaska Department of Fish and Game). Epidermal biopsy samples were collected from sea stars at both impacted and naïve sites at depths ranging from 7 to 18 meters. Seven total sites were sampled (2 Naïve and 5 impacted) with a total of 18 Wasting, 20 Exposed, and 47 Naïve individuals sampled (total N=85). Nonlethal biopsy punches (3.5mm diameter biopsy punch, Robbins Instruments, Chatham, NJ) were taken from the body wall of each individual and preserved in RNAlater (ThermoFisher Scientific, Waltham, MA) in 2ml tubes. Only epidermal body wall tissue was sampled, even when sampling wasting individuals. For individuals displaying SSW symptoms, wasting epidermal tissue at the edge of the lesion was sampled. All biopsy tissue samples were shipped to Vermont on dry ice and stored at −80 °C until processing. RNA extraction and cDNA reverse transcription. RNA was extracted from each biopsy using a modified TRIzol protocol (TRIzol reagent ThermoFisher Scientific, Waltham, MA). After lysing tissue in 250ul TRIzol, it was homogenized for 20 minutes with a plastic pestle with 750ul additional TRIzol using a Vortex Genie2 (Scientific Industries, Bohemia, NY). To extract RNA, 200 ul chloroform (ThermoFisher Scientific, Waltham, MA) was added, inverted 15 times, incubated for 3 minutes at RT, and centrifuged at 4 °C for 15 minutes at 12,000×g. The RNA-containing supernatant was transferred to a new tube and the previous step was repeated. Adding 500 ul isopropanol (ThermoFisher Scientific, Waltham, MA) and 1 ul 5 mg/ml glycogen (Invitrogen, Carlsbad, CA), incubation for 10 minutes at room temperature, and centrifugation for 5minutes at 7500×g at 4 °C precipitated the RNA from the supernatant. After drying for 10 minutes at RT the RNA pellet was dissolved in 50 ul nuclease-free water. A NanoDrop 2000 Spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA) were used to measure the quality and quantity of the RNA extractions. To check for DNA contamination, we performed negative amplification PCR (16S PCR amplification parameters below). Random hexamer primers reverse transcribed cDNA with SuperScript IV (Invitrogen, Carlsbad, CA). 16S PCR amplification and sequencing. To amplify the V3 and V4 region of the 16S bacterial gene, we used the primers: forward 5′TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG and reverse 5′GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC (31). 25 ul PCR reactions (1X MiFi Mix (Bioline, Toronto, Canada), 200nM each primer, and 2ul cDNA) were run with the following conditions: 95 °C for 3 minutes followed by 25 cycles of 95 °C for 30 seconds, 55 °C for 30 seconds, and 72 °C for 30 seconds, with a final extension at 72 °C for 5 minutes. To clean the PCR products, AMPure XP beads (Beckman Coulter, Brea, CA) and MiSeq indexing adapters were added. The indexed PCR products were cleaned again with AMPure XP beads, following Illumina 16S metagenomic sequencing library preparation protocol. To validate band size, the cleaned, indexed PCR products were run on a 2% agarose gel. 16S rRNA Library sequencing was performed at the Cornell Biotechnology Resource Center (Ithaca, NY) using 2 × 300 base pair overlapping paired-end reads on an Illumina MiSeq platform. Sequence data processing, taxonomic assignment, and diversity metrics Sequences were demultiplexed and barcode sequences were removed by the core facility. QIIME2 (v.2-2021.8) was used for data cleaning and analysis (32). Paired end reads were imported into QIIME2 and read quality was assessed using QIIME2’s ‘qiime_demux_summarize’ function. Read quality was determined by Phred score (>30) then subsequently denoised and trimmed using DADA2 (33), which removes errors and noise from data sequenced by Illumina, and creates information about the removed data. DADA2 parameters were set at trimming forward reads at 16bp and truncating at 289bp and reverse reads were trimmed at 0bp and truncated at 257bp. Diversity metrics were run using the ‘qiime_diversity_core-metrics-phylogenetic’ function with an Amplicon Sequence Variant (ASV) sampling depth of 13,547 to ensure maximal sample depth without omitting any samples. ASV richness (alpha diversity) of Naïve, Exposed, and Wasting asteroids was calculated using the Shannon diversity index using the qiime2 plugin and the between-group diversity (beta diversity) was calculated using the weighted_unifrac_distance_matrix to take into account the relative abundance of ASVs shared between samples (34). One sample (HH02_18) was responsible for all identified outliers in our beta-diversity analysis between Naïve samples, and was removed. Variation among Naïve individuals was 22.6% outlier-inclusive, and 19.9% with outliers removed (Fig 1D). Diversity plots were made using Qiime2 outputs visualized in GraphPad Prism version 9.3.0 for windows. Taxonomic Classification Taxonomy was assigned to each ASV by using the q2-feature-classifier (Bokulich et al. 2018) then trained and mapped to known bacterial taxa classified by the Greengenes database (35). Greenegene reference sequences were trimmed to match our data with a minimum length of 100bp and a maximum of 500bp. ASVs mapped to the same taxonomic classification were collapsed into Observable Taxonomic Units (OTUs) at the lowest level of identification provided by Greengenes database using the “qiime_taxa_collapse”. It should be noted that not all taxa were identifiable to the species level. However, ASV’s assigned to the same class, family, or genus could still be identified as distinct OTUs based on phylogenetic mapping, even if Greengenes could not confidently assign a specific species identification. For example, there are two separate classifications assigned to the genus Vibrio with no further classification at the species level, yet retained distinct abundances tracked separately through the analyses. Respiratory profiles (e.g., aerobic, facultative anaerobic, and obligate anaerobic) of microbes of interest were inferred from literature, as cited, describing the genus and/or family. Differential Abundance To test for differential abundance of microbial communities associated with exposure and onset of SSW, we used Analysis of Composition of Microbiomes with Bias Correction (ANCOM-BC) (36) in R version 4.2.1 (37). ANCOM-BC differential abundance analysis uses a series of pairwise comparisons to estimate the average abundance of a given microbial species through linear regression while correcting the bias induced by differences among samples. This method provides false discovery rate (FDR) corrected p-values for each taxon and confidence intervals for differentially abundant taxa. Differentially abundant taxa were defined based on FDR < 0.05 and taxa that were not present in at least 10% of the compared samples were dropped from the analysis. The W score represents the number of times the null-hypothesis (the average abundance of a given species in a group is equal to that in the other group) was rejected for a given species. Beta value represents the effect size as a log-linear (natural log) value relative between compared groups. Fold change was calculated by taking ebeta. Violin plots were constructed using log-10 transformed values from the raw abundance of each taxa using GraphPad Prism version 9.3.0 for windows. Bipartite Clustering Analysis To identify taxonomic communities and other high-level patterns of abundance, we used Bayesian stochastic blockmodeling, a principled approach to network clustering which finds statistically significant partitions in a network. First, a bipartite network was constructed by assigning sea star samples and ASVsOTUs to separate node groups. Samples and taxa were then connected with an edge if the taxa was present, with an edge weight of log(aij )+1, where aij > 0 is the abundance of taxa j in sample i. OTU abundance was aggregated to the species level, and taxa with total abundance less than 100 across all samples were removed. Samples and ASVs were assigned to hierarchical groups following the hierarchical stochastic block model (hSBM), with the maximum a posteriori estimate found using a specialized Markov chain Monte Carlo algorithm (38). We used the ”degree-corrected” variant of the model (39), since it had a smaller minimum description length than the simpler non-corrected model (Fig S4). Analyses were performed using graph-tool version 2.44 (40). Functional profiling Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2 (PICRUSt2) was used to predict the functional content of the microbial communities (Douglas, et al. 2020). PICRUSt2 uses extended ancestral-state reconstruction of unknown microbes and a library of reference genomes to predict which gene families (by KEGG orthology (KO) and EC: enzyme functions) are present. PICRUSt2 also uses these data to infer abundances of metabolic pathways using a map of gene families to pathways from the online metacyc database (https://metacyc.org/). Predicted KO abundance was predicted by Picrust2 from the corresponding metagenomes from the 16s rRNA marker gene and KEGG functional hierarchies at level 2 were mapped using the KEGGREST v1.36 (41) package in R version 4.2.1 (37) to infer biological functional enrichment between the sample groups. Because KO mapping to KEGG orthologs provides predictions for all possible pathways (including eukaryotes), predicted eukaryotic categories were filtered from the analysis. The PICRUSt2 output was visualized with Morpheus (https://software.broadinstitute.org/morpheus). Predicted metacyc pathways (Table S3) and KEGG pathway functional categories differentially abundant between (1) Naïve and Exposed, and (2) Exposed and Wasting individuals were identified by t-test with Benjamini Hochburg False Discovery Rate correction (Padj < 0.01 and Padj < 0.05 respectively).