Additional file 1 of Bacterial aerobic methane cycling by the marine sponge-associated microbiome
Creators: name: Ramírez, Gustavo A.
name: Bar-Shalom, Rinat
name: Furlan, Andrea
name: Romeo, Roberto
name: Gavagnin, Michelle
name: Calabrese, Gianluca
name: Garber, Arkadiy I.
name: Steindler, Laura
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Amplicon Sequence Variants (ASVs) community composition and activity based on 16S rRNA genes amplified using as template either genomic DNA (gDNA, panel A) or complementary DNA (cDNA; synthesized from RNA; panel B) from the same four sponge specimens used in the metatranscriptomics libraries. Color codes represent the relative (A) community composition and (B) a proxy for the transcriptional activity of prokaryotic lineages classified at the Class-level of taxonomy. Each sponge specimen was sampled 24h apart at noon. Figure S2. Abundance normalized activity survey for 37 dominant lineages, based on metatranscriptomic read mapping against MAGs, shown for all four sponge replicates sampled at noon 24h apart. Data is arranged based on phylogenomic relatedness and color-coded at the Phylum-level of taxonomy, in the A. aerophoba-associated microbiome. Relative activity is represented by circle size and also color-coded based onthe Phylum-level association of each depicted lineage. Figure S3. Complete KEGG-decoder pathway estimates heatmaps for all metatranscriptomic samples. Additional functional categories shown here and not in Figure 1 include: O2 cytochromes, hydrogen cycle, vitamins and transporters, secretion systems, and amino acid synthesis. Figure S4. mttB gene transcript homologue alignment localized to a window between residues 303-440. The red column highlights residue 333, an expected non-conical pyrrolysine “O” residue found in all functional trimethylamine-corrinoid protein co-methyltransferases and absent in the sponge bacterial homologues. Figure S5. Delta-BLAST analysis for conserved functional motifs in proteins predicted from transcribed aat gene homologues. Figure S6. Annotated version of phylogenetic tree of aat genes and transcripts presented in Fig. 3. Figure S7. Relative percent abundance of 16S rRNA sequences with &gt;98% sequence ID and 99% of query length to the A. aerophoba bin18 (Binatota) 16S rRNA gene sequence, summarized in quartile boxplots. Quartile box plots are arranged in descending median values of all observations from top to bottom. Aplysina aerophoba and Petrosia ficiformis, both sponges analyzed in this study, are highlighted in red and purple, respectively. Single and double asterisks depict sponge species with significantly (student t-test, Pval &lt; 0.05) higher abundance of bin18-related sequences than in marine pelagic and marine sediment 16S rRNA datasets, respectively. Figure S8. Meta-analysis of methane-cycling genes using public MAGs (arranged based on phylogenomic relatedness, (Burgsdorf et al. 2022) and metatranscriptomes from Mediterranean P. ficiformis sponges (Britstein et al. 2020). (A) Detected methane-related genes (black circles) and associated transcripts (red circles) for a collection of sponge symbiont MAGs. (B) Alignment metrics of metatranscriptome predicted (Transcript_ID) and MAG retrieved (Protein_ID) protein sequences identified as aat homologues including query (Tlen) and sequence length (Plen), %ID, Eval, and presence or absence of conserved domains. (C) Delta-BLASTp summaries of conserved domain position along a representative transcribed aat homologue sequence (all transcribed aat homologues shown in panel A contained identical conserved domain positions). TableS1. Metatranscriptomic read retention percentages following adapter trimming, interleaving, and rRNA library alignments for in silico rRNA depletion, prior to de novo assembly using rnaSPAdes.