Distinct seasonal infectious agent profiles in life-history variants of juvenile Fraser River Chinook salmon: An application of high-throughput genomic screening.

Pierre Boudinot,Strahan Tucker,Karia H Kaukinen,David A Patterson,Kristina M Miller,Shaorong Li

doi:10.1371/journal.pone.0195472

Pierre Boudinot, Strahan Tucker + Show 4 more

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https://doi.org/10.1371/journal.pone.0195472

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Abstract

Disease-causing infectious agents are natural components of ecosystems and considered a major selective force driving the evolution of host species. However, knowledge of the presence and abundance of suites of infectious agents in wild populations has been constrained by our ability to easily screen for them. Using salmon as a model, we contrasted seasonal pathogenic infectious agents in life history variants of juvenile Chinook salmon from the Fraser River system (N = 655), British Columbia (BC), through the application of a novel high-throughput quantitative PCR monitoring platform. This included freshwater hatchery origin fish and samples taken at sea between ocean entry in spring and over-winter residence in coastal waters. These variants currently display opposite trends in productivity, with yearling stocks generally in decline and sub-yearling stocks doing comparatively well. We detected the presence of 32 agents, 21 of which were at >1% prevalence. Variants carried a different infectious agent profile in terms of (1) diversity, (2) origin or transmission environment of infectious agents, and (3) prevalence and abundance of individual agents. Differences in profiles tended to reflect differential timing and residence patterns through freshwater, estuarine and marine habitats. Over all seasons, individual salmon carried an average of 3.7 agents. Diversity changed significantly, increasing upon saltwater entrance, increasing through the fall and decreasing slightly in winter. Diversity varied between life history types with yearling individuals carrying 1.3-times more agents on average. Shifts in prevalence and load over time were examined to identify agents with the greatest potential for impact at the stock level; those displaying concurrent decrease in prevalence and load truncation with time. Of those six that had similar patterns in both variants, five reached higher prevalence in yearling fish while only one reached higher prevalence in sub-yearling fish; this pattern was present for an additional five agents in yearling fish only.

Highlights

Infectious disease is known to influence the survival and evolution of wild animals [1, 2], but has been especially difficult to study in the aquatic realm due to logistical constraints inherent in sampling wild populations of fish over time and the tendency for severely infected individuals to disappear [3]
Current knowledge of infectious diseases in salmon is primarily derived from observations of cultured fish, where clinical signs and mortality are observable in freshwater (FW) hatcheries and ocean net pens
Six infectious agents are thought to be transmitted in fresh water, six in salt water, and nine in both environments

Summary

Introduction

Infectious disease is known to influence the survival and evolution of wild animals [1, 2], but has been especially difficult to study in the aquatic realm due to logistical constraints inherent in sampling wild populations of fish over time and the tendency for severely infected individuals to disappear [3]. This is compounded as well by the need for an effective and efficient means of screening for multiple disease agents at once. Despite the knowledge that upwards of 90% of juvenile salmon can die in their first summer and fall in the ocean, setting cohort trajectories and stock abundances [10], because mortality is not observed, few studies have been carried out to assess the potential role that infectious agents and diseases may play in these substantial losses

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