Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis

Link between bacterial communities and contrasted loads in ectoparasitic monogeneans from the external mucus of two wild sparid species (Teleostei)

BACKGROUND

While teleost fishes represent two thirds of marine vertebrates, the role of their external microbiota in relationship with their environment remains poorly studied, especially in wild populations. Hence, the interaction of their microbiota with ectoparasites is largely unknown. Microbiota can act as a protective barrier against pathogens, and/or be involved in host recognition by parasites. Thus, host-parasite associations should now be considered as a tripartite interplay where the microbiota shapes the host phenotype and its relation to parasites. Monogeneans (Platyhelminthes) are direct life cycle ectoparasites commonly found on teleost skin and gills. The role of bacterial communities within skin and gill mucus which either pre-exist monogeneans infestation or follow it remain unclear. This is investigated in this study using the association between Sparidae (Teleostei) and their specific monogenean ectoparasites of the Lamellodiscus genus. We are exploring specificity mechanisms through the characterization of the external mucus microbiota of two wild sparid species using 16s rRNA amplicon sequencing. We investigated how these bacterial communities are related to constrated Lamellodiscus monogeneans parasitic load.

RESULTS

Our results revealed that the increase in Lamellodiscus load is linked to an increase in bacterial diversity in the skin mucus of D. annularis specimens. The date of capture of D. annularis individuals appears to influence the Lamellodiscus load. Correlations between the abundance of bacterial taxa and Lamellodiscus load were found in gill mucus of both species. Abundance of Flavobacteriaceae family was strongly correlated with the Lamellodiscus load in gill mucus of both species, as well as the potentially pathogenic bacterial genus Tenacibaculum in D. annularis gill mucus. Negative correlations were observed between Lamellodiscus load and the abundance in Vibrionaceae in gill mucus of D. annularis, and the abundance in Fusobacteria in gill mucus of P. acarne specimens, suggesting potential applications of these bacteria in mitigating parasitic infections in fish.

CONCLUSIONS

Our findings highlight the dynamic nature of fish microbiota, in particular in relation with monogeneans infestations in two wild sparid species. More generally, this study emphasizes the links between hosts, bacterial communities and parasites, spanning from the dynamics of co-infection to the potential protective role of the host's microbiota.

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

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.

The effect of temperature on ability of Lepeophtheirus salmonis to infect and persist on Atlantic salmon

The salmon louse (Lepeophtheirus salmonis) is an ecologically and economically important parasite of salmonid fish. Temperature is a strong influencer of biological processes in salmon lice, with development rate increased at higher temperatures. The successful attachment of lice onto a host is also predicted to be influenced by temperature; however, the correlation of temperature with parasite survival is unknown. This study describes the effects of temperature on infection success, and survival on the host during development to the adult stage. To accurately describe infection dynamics with varying temperatures, infection success was recorded on Atlantic salmon (Salmo salar) between 2 and 10°C. Infection success ranged from 20% to 50% and was strongly correlated with temperature, with the highest success at 10°C. Parasite loss was monitored during development at eight temperatures with high loss of lice at 3 and 24°C, whilst no loss was recorded in the temperature range from 6 to 21°C. Sea temperatures thus have large effects on the outcome of salmon louse infections and should be taken into account in the management and risk assessment of this parasite. Improving understanding of the infection dynamics of salmon lice will facilitate epidemiological modelling efforts and efficiency of pest management strategies.

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens

Caligus rogercresseyi is a copepod ectoparasite with a high prevalence in salmon farms in Chile, causing severe welfare and economic concerns to the sector. Information on the parasite's underpinning mechanisms to support its life strategy is recently being investigated. Due to the critical role of microbiota, this study aimed to characterize the microbiota community associated with C. rogercresseyi from different regions with salmon aquaculture in Chile. Using third-generation sequencing with Nanopore technology (MinION) the full 16S rRNA gene from sea lice obtained from 8 areas distributed over the three main aquaculture regions were sequenced. Microbiota of the parasite is mainly comprised of members of phyla Proteobacteria and Bacteroidetes, and a core microbiota community with 147 taxonomical features was identified, and it was present in sea lice from the three regions. This community accounted for 19% of total identified taxa but more than 70% of the total taxonomical abundance, indicating a strong presence in the parasite. Several taxa with bioactive compound secretory capacity were identified, such as members of genus Pseudoalteromonas and Dokdonia, suggesting a possible role of the lice microbiota during the host infestation processes. Furthermore, the microbiota community was differentially associated with the salmon production, where several potential pathogens such as Vibrio, Tenacibaculum, and Aeromonas in Los Lagos, Aysén, and Magallanes region were identified. Notably, the Chilean salmon industry was initially established in the Los Lagos region but it's currently moving to the south, where different oceanographic conditions coexist with lice populations. The results originated by this study will serve as foundation to investigate putative role of sea lice as vectors for fish pathogens and also as reservoirs for antibiotic-resistant genes.