Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi

Abstract

The sea louse Caligus rogercresseyi has become one of the main constraints for the sustainable development of salmon aquaculture in Chile. Although this parasite's negative impacts are well recognized by the industry, some novel potential threats remain unnoticed. The recent sequencing of the C. rogercresseyi genome revealed a large bacterial community associated with the sea louse, however, it is unknown if these microorganisms should become a new focus of sanitary concern. Herein, chromosome proximity ligation (Hi-C) coupled with long-read sequencing were used for the genomic reconstruction of the C. rogercresseyi microbiota. Through deconvolution analysis, we were able to assemble and characterize 413 bacterial genome clusters, including six bacterial genomes with more than 80% of completeness. The most represented bacterial genome belonged to the fish pathogen Tenacibacullum ovolyticum (97.87% completeness), followed by Dokdonia sp. (96.71% completeness). This completeness allowed identifying 21 virulence factors (VF) within the T. ovolyticum genome and four antibiotic resistance genes (ARG). Notably, genomic pathway reconstruction analysis suggests putative metabolic complementation mechanisms between C. rogercresseyi and its associated microbiota. Taken together, our data highlight the relevance of Hi-C techniques to discover pathogenic bacteria, VF, and ARGs and also suggest novel host-microbiota mutualism in sea lice biology.

Figure 1

Summary of the genomic reconstruction of bacterial clusters associated with Caligus rogercresseyi. (A) Genome cluster classification according with their completeness in near complete (> 95%), substantial (> 80%), and moderate (< 80%). (B) Genome completeness and contamination among the 50 most represented bacterial clusters. (C) Main genomic features of the top 5 represented genomes clusters in sea lice microbiota.

Figure 2

General overview of Tenacibaculum and Dokdonia sp. genomes. (A) Circos plot representing different Tenacibaculum genomes including the genome size (a), GC content (b), CDS density (c), ncRNA density (d) and synteny blocks (ribons). (B) Genome characterization of Dokdonia sp. cluster. Circos plot representing Dokdonia sp. genome including the genome size (a), GC content (b), CDS density (c), ncRNA density (d) and synteny blocks (ribons). (C) Functional annotation of the CDS characterize in Dokdonia sp. genome provided by RAST annotation. (D) Functional annotation of the CDS within amino acids metabolism found in Dokdonia sp. genome.

Figure 3

(A) Graphical representation of the metabolic pathways reconstructed for Caligus rogercresseyi (blue) and its associated microbiome (green). The amino acid metabolism is highlighted in red. (B) Percentage of genes annotated for the different metabolic pathways encoded in the sea lice genome (blue) and that were exclusively encoded in the microbiome (green). All pathways were constructed using KEGG pathways as reference.

Figure 4

Metabolic reconstruction of the leucine, valine and isoleucine metabolism. Each box represents a gene coding for a protein in the pathway, where the blue boxes represent genes found in C. rogercresseyi genome and the red boxes genes found just in Dokdonia sp. Genome.