Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle

Abstract

Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.

Fig. 1. Overview of experimental approach.

Endozoicomonas 6c was isolated from the tissues of the Red Sea coral Acropora humilis. From the bacterial culture, we generated (i) a high-quality draft genome and (ii) a metabolic reconstruction based on transcriptomic and proteomic responses of Endozoicomonas 6c to tissue extracts of its native coral host in vitro.

Fig. 2. Phylogenetic relationship and genomic characterization of Endozoicomonas genomes.

A Phylogenetic placement of the novel Endozoicomonas marisrubri 6c isolate (highlighted in turquoise) from the Red Sea coral Acropora humilis. The unrooted species tree was generated through the OrthoFinder2 default workflow and visualized in FigTree v1.1.4 [61]. Vertical bars show the two clades of Endozoicomonas and respective genome sizes (purple; asterisks refer to genomes of ≤90% completeness), boxes indicate G+C content (in %; blue hues), and coding density (in %; yellow hues) of the respective genomes. B Distribution of genes and functions proposed to be involved in symbiotic establishment and maintenance across Endozoicomonas clades and genomes according to their associated gene families (ortholog clusters) and Pfam profiles. The color code used for ankyrins, serpins, and ephrins from turquoise to red reflects the number of genes per million base pairs (Mbp) of genome. Black boxes for genes associated with B vitamin biosynthetic gene clusters reflect their presence within the respective genome. C Distribution of protein domains associated with DMSP catabolism across Endozoicomonas genomes based on annotation with Prokka, KEGG, and UniProt. Black boxes reflect the presence of protein domains within the respective genome.

Fig. 3. Direction of regulation in gene expression or protein abundance of significant biological processes (GO terms) associated with the response of Endozoicomonas marisrubri 6c to tissue extracts of its coral host (3 h exposure).

A Transcriptomic response, B Proteomic response. Bubble size reflects the number of features (genes and proteins, respectively) within the respective GO term, color reflects overarching processes (parent terms). Z-scores (x-axis) reflect the overall direction of change of features within GO terms (z < 0: downregulation, z > 0 : upregulation). Threshold represents statistical significance (p < 0.05).

Fig. 4. Reconstructed metabolic pathways and proteins in Endozoicomonas marisrubri 6c based on transcriptomic and proteomic responses of the bacterial cells to ultra-fractionated coral host tissue extract.

A Regulation of differential gene expression within selected significant biological processes (GO terms) and significant transcripts (p < 0.05, |FC| = 2). B Regulation of proteins within selected significant biological processes (GO terms) and differentially abundant proteins (adjusted p < 0.05, |FC| = 0.5) in the E. marisrubri 6c proteome.

Fig. 5

Proposed interactions involved in symbiosis establishment and maintenance in the Acropora-Symbiodiniaceae-Endozoicomonas system based on transcriptomic and proteomic responses of E. marisrubri 6c to coral holobiont cues.