Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange

Abstract

Compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown. Furthermore, the application of genomic, transcriptomic, and proteomic techniques to functional questions on sponge host-symbiont interactions is in its infancy. In this study, we generated a transcriptome for the host and a metatranscriptome of its microbial symbionts for the giant barrel sponge, Xestospongia muta, from the Caribbean. In combination with a gene-specific approach, our goals were to (1) characterize genetic evidence for nitrogen cycling in X. muta, an important limiting nutrient on coral reefs (2) identify which prokaryotic symbiont lineages are metabolically active and, (3) characterize the metabolic potential of the prokaryotic community. Xestospongia muta expresses genes from multiple nitrogen transformation pathways that when combined with the abundance of this sponge, and previous data on dissolved inorganic nitrogen fluxes, shows that this sponge is an important contributor to nitrogen cycling biogeochemistry on coral reefs. Additionally, we observed significant differences in gene expression of the archaeal amoA gene, which is involved in ammonia oxidation, between coral reef locations consistent with differences in the fluxes of dissolved inorganic nitrogen previously reported. In regards to symbiont metabolic potential, the genes in the biosynthetic pathways of several amino acids were present in the prokaryotic metatranscriptome dataset but in the host-derived transcripts only the catabolic reactions for these amino acids were present. A similar pattern was observed for the B vitamins (riboflavin, biotin, thiamin, cobalamin). These results expand our understanding of biogeochemical cycling in sponges, and the metabolic interchange highlighted here advances the field of symbiont physiology by elucidating specific metabolic pathways where there is high potential for host-prokaryote interactions.

Keywords: B vitamins; ammonia oxidation; denitrification; metatranscriptome; sponge symbionts.

Figure 1

Relative abundance of 16S ribosomal RNA operational taxonomic units (OTUs) generated by the program EMIRGE from total RNA short reads. 16S rRNA OTUs were generated for one sponge from each location: Florida Keys (FL), Little Cayman (LC), and Lee Stocking Island, Bahamas (LSI). Phyla are listed in the clockwise order of the pie chart.

Figure 2

Relative abundance of prokaryotic and sponge transcripts involved in nitrogen metabolism. MEGAN was used to visualize transcripts on the KEGG map. The map was separated into assimilatory pathways (A) and mostly dissimilatory pathways (B) for visualization. Pie charts near each enzyme number indicate the phyla represented by the transcripts and the number in the pie chart is the number of transcripts. Enzyme names are provided in blue. For clarity not all intermediates are shown.

Figure 3

Relative abundance of prokaryotic and sponge transcripts involved in sulfur metabolism. MEGAN was used to visualize transcripts on the KEGG map. Pie charts near each enzyme number indicate the phyla represented by the transcripts and the number in the pie chart is the number of transcripts. Enzyme names are provided in blue.

Figure 4

Relative abundance of prokaryotic and sponge transcripts involved in methane metabolism. MEGAN was used to visualize transcripts on the KEGG map. The map was separated into pathways centered on carbon monoxide and formate reactions (A) and methane reactions (B) for visualization. Pie charts near each enzyme number indicate the phyla represented by the transcripts and the number in the pie chart is the number of transcripts. Enzyme names are provided in blue. For clarity not all intermediates are shown.

Figure 5

Relative expression of archaeal amoA genes between geographic locations (A) and time points for LSI sponges only (B). Asterisk indicates significant difference [ANOVA, F_{(2, 6)} = 11.67, p = 0.0086; Tukey's HSD, p < 0.05].

Figure 6

Relative abundance of prokaryotic and sponge transcripts involved in lysine metabolism. MEGAN was used to visualize transcripts on the KEGG map. Pie charts near each enzyme number indicate the phyla represented by the transcripts and the number in the pie chart is the number of transcripts. A subset of the map is shown for clarity. Numbers correspond to the following enzymes: (1) aspartate-semialdehyde dehydrogenase (2) homoserine dehydrogenase (3) L-aspartate-4-semialdehyde hydrolyase (4) 4-hydroxy-tetrahydrodipicolinate reductase (5) tetrahydropicolinate succinylase (6) LL-diaminopimelate aminotransferase (7) diaminopimelate epimerase (8) diaminopimelate decarboxylase (9) UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6,-diaminopimelate ligase (10) UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase.

Figure 7

Relative abundance of prokaryotic and sponge transcripts involved in biotin metabolism. MEGAN was used to visualize transcripts on the KEGG map. Pie charts near each enzyme number indicate the phyla represented by the transcripts and the number in the pie chart is the number of transcripts. A subset of the map is shown for clarity. Enzyme names are shown in blue.