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

Ana Teresa Gonçalves,Rayen Collipal-Matamal,Cristian Gallardo-Escárate,Gustavo Nuñez-Acuña,Valentina Valenzuela-Muñoz,Diego Valenzuela-Miranda

doi:10.1038/s41598-020-59747-0

Ana Teresa Gonçalves, Rayen Collipal-Matamal + Show 4 more

Open Access

https://doi.org/10.1038/s41598-020-59747-0

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Abstract

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.

Highlights

Caligus rogercresseyi is a copepod ectoparasite with a high prevalence in salmon farms in Chile, causing severe welfare and economic concerns to the sector
Et al.[18] used shotgun metagenomics and reported that the majority of microorganisms associated with L. salmonis from the Atlantic and the Pacific Ocean belonged to the phyla Bacteriodetes and Proteobacteria, with a reduced incidence of known fish pathogens
Nanopore sequencing has been applied to understand the interactions of human diseases[31], environmental samples obtained from glacier regions[23], ocean water column[32] and to identify the bacterial community associated with harmful microalgae[30], and these studies demonstrate the potential and applicability of nanopore sequencing for microorganism detection in all environments

Summary

Introduction

Caligus rogercresseyi is a copepod ectoparasite with a high prevalence in salmon farms in Chile, causing severe welfare and economic concerns to the sector. The 16S rRNA gene has nine hypervariable regions with different characteristics, and the V3 and V4 regions have been the most sequenced for taxonomy assignation of the microorganisms associated with aquatic organisms[20], mostly performed on Illumina platforms This sequencing strategy is based on sequencing by synthesis, and despite being frequently used, it is limited to a specific region of the 16S rRNA gene, reducing the estimation capacity of richness[21]. The nanopore technology with the MinIONTM system (Oxford Nanopore Technologies) presents an affordable and portable sequencing strategy that has great potential to evaluate microbiota communities This technology allows the sequencing of the full-16S rRNA gene, increasing the capacity for taxonomical assignation, and it can be performed in real-time with reduced equipment, increasing its potential as a field tool for remote locations[23]. Nanopore sequencing has been applied to understand the interactions of human diseases[31], environmental samples obtained from glacier regions[23], ocean water column[32] and to identify the bacterial community associated with harmful microalgae[30], and these studies demonstrate the potential and applicability of nanopore sequencing for microorganism detection in all environments

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