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Additional file 12: Fig. S7. Characterisation of the recombinant bacterial CAZymes encoded by the endosymbionts. DNS reducing sugars assays showing activities on a number of substrates for LpsGH5_8, LpsGH11, LpsGH134a and LpsGH134b. CMC = carboxymethyl cellulose, LBG = locust bean gum. The nanomoles of sugars released by the different proteins cannot be compared quantitatively as different amounts were used for the assay. File format .DOCX.

Additional file 8: Table S2. CAZy families. List of the CAZy families mentioned in the results, with the description of the activities that have been recorded for enzymes listed in each family. The information has been gathered from the CAZy database ( http://www.cazy.org ). File format .DOCX.

Additional file 1: Figure S1. Experiment location. Figure S2. Coverage estimates for each 16S rRNA amplicon library for all biological replicates across each time point. Figure S3. CAZyme families identified within the metatranscriptomic databases presented as transcripts per million. Figure S4. CAZyme producing genera and their respective CAZyme contributions. Figure S5. Productivity index for CAZyme producing taxa at family level resolution. Figure S6. Phylogenetic distribution of CAZyme classes at class resolution for week one. Figure S7. Phylogenetic distribution of CAZyme classes at class resolution for week three. Figure S8. Phylogenetic distribution of CAZyme classes at class resolution for week five. Figure S9. Phylogenetic distribution of CAZyme classes at class resolution for week ten. Figure S10. Functional classification of proteins within the metasecretome. Figure S11. Fungal profiles and OTU richness elucidated from internal transcribed spacer region 2 amplicon sequencing across the 16-week time course. Figure S12. Nutrient acquisition strategy of fungi profile across the 16-week time course. Figure S13. Bacteria profiles elucidated from 16S rRNA sequence homology. Figure S14. Bacteria profiles elucidated from 16S rRNA sequence homology. Table S1. Transect position of the five biological replicates in Welwick salt marsh. Table S2. Sequence reads throughout RNA sequence processing and assembly. Table S3. Commands for the replication of the 16S rRNA amplicon database processing pipeline.

Additional file 14: Table S6. Primers used for the cloning of the bacterial proteins LpsGH5_8, LpsGH11, LpsGH134a and LpsGH134b. LpsAA10A could not be amplified from the cDNA and therefore a synthetic version of the gene was codon-optimised for E-coli expression. File format .DOCX.

Additional file 2: Fig. S2. Searching for the opening of the duct of Deshayes in the shipworm digestive system. Left, transverse sections through the shell valve, from the anterior to posterior adductor muscle (A-E). Right, 3D rendered model of the whole shipworm, with the green highlighted region showing the position of the transverse cross section displayed on the left. File format .DOCX.

Additional file 10: Table S4. Details of the proteins for which heterologous recombinant expression from symbionts cDNA was successful. The annotation was performed against the NCBI non-redundant database, the signal peptides were identified with the Signal P4.1 server and the CAZy domains were searched using dbCAN. Dis. bonds = disulfide bonds. File format .DOCX.

Additional file 1: Fig. S1. Scanning electron microscopic images of the gills and food groove of L. pedicellatus. A) Close up of the gills lamellae to show the numerous cilia that capture food and draw it to the food groove. B) Close up of the food groove to show the numerous cilia (most of the mucus is lost during critical point drying). File format .DOCX.

Additional file 6: Fig. S6. Immunogold labelling of LpsGH5_8 in L. pedicellatus using pre-immune serum (negative control). A) SEM image illustrating the anatomical position of the gills, food groove, caecum and mouth in the shipworm body. B-D) Immunogold labelling of the lumen of the food groove (B), lumen of the caecum (C), and the gills (D) performed with pre-immune serum. No gold particles are observed in any of the samples. B = bacteria. File format .DOCX.

Additional file 11: Table S5. The amino acid sequences of the bacterial proteins LpsGH5_8, LpsGH11, LpsGH134a, LpsGH134b and LpsAA10A. Text in red represents the signal peptide. File format .DOCX.

Additional file 7: Table S1. Details of the proteins identified through proteomic analysis of the crystalline style. The annotation was performed against the NCBI non-redundant database, the signal peptides were identified with the Signal P4.1 server and the CAZy domains were searched using dbCAN. Many of the contigs were out of frame or not full length (particularly the bacterial ones) and therefore the identification of the signal peptide was not possible. File format .DOCX.

Additional file 1: Table S1. The functional annotations of proteins identified in the proteome of PfMig188. Table S2. The distribution of upregulated proteins across the different secretomes containing sugarcane bagasse.

Additional file 4: Fig. S4. Bacterial symbionts in L. pedicellatus. A) TEM image of a gill bacteriocyte. Arrows indicate the numerous rod-shaped bacteria in the cell. B) Close-up view of gill bacteria (TEM). C) Detailed TEM showing a cross section of a gill bacterium and some of its features (periplasmic space and membranes). File format .DOCX.

Additional file 5: Fig. S5. SDS-PAGE and nitrocellulose western blot obtained by loading 0.6 ��g of the recombinant purified bacterial LpsGH5_8 (without the appended CBM). A) Coomassie Brilliant Blue stained SDS-PAGE gel of the purified protein. B) Western blot detection performed with the purified pre-immune serum. C) Western blot detection performed with the purified anti-protein serum. File format .DOCX.

Additional file 3: Fig. S3. Scanning electron microscopy of L. pedicellatus. A dissected specimen with the mantle removed, showing the food groove connecting the gills to the mouth. File format .DOCX.

Additional file 13: Fig. S8. MALDI-TOF MS analysis of in vitro activity assays with purified LpsAA10A under the same experimental conditions as in Fig. 5 C. Panels from a to d show spectra of products obtained after incubation of the enzyme with 4 mg mL-1 Avicel (a), 4 mg mL-1 Avicel plus 4 mM gallic acid (b), 4 mg mL-1 Avicel plus 2 ��M LPMO (c) and 4 mg mL-1 Avicel plus 2 ��M LPMO and 4 mM gallic acid (d). In panels a to d, 100% relative intensity represents 1.3 �� 104 arbitrary units (a.u.). The panels from e to g show spectra of products obtained after incubation of 4 mg mL-1 PASC (e), 4 mg mL-1 PASC plus 4 mM gallic acid (f) and 4 mg mL-1 PASC plus 2 ��M LPMO (g). In panels e to g, 100% relative intensity represents 1.0 �� 104 arbitrary units. File format .DOCX.

Additional file 9: Table S3. CAZy families of the caecum. Table showing the relative abundance (calculated from the emPAI score) of eukaryotic and prokaryotic CAZy families identified in the proteomic analysis of the caecum content of L. pedicellatus. File format .DOCX.

Additional file 1. Containing Q-Q plots of GWAS

Additional file 4. Detailed calculation for estimated gains of using a marker in breeding

Additional file 1. The file provides the Additional Tables S1–S14.

Additional file 7. Field trial GPS coordinates

Additional file 9. Containing a report of Genotyping by Sequencing (GBS) – Reference Pipeline

Additional file 7. Field trial GPS coordinates

Additional file 7. Full derivation of the fitness function used for in silico evolution of organic acid production.

Additional file 9. Containing a report of Genotyping by Sequencing (GBS) – Reference Pipeline

Additional file 4. Detailed calculation for estimated gains of using a marker in breeding

Additional file 5: Table S15. Index numbers of mutations and corresponding reactions and mutation effects.