Comparative transcriptomics reveal conserved impacts of rearing density on immune response of two important aquaculture species

Abstract

Background: Infectious diseases represent an important barrier to sustainable aquaculture development. Rearing density can substantially impact fish productivity, health and welfare in aquaculture, including growth rates, behaviour and, crucially, immune activity. Given the current emphasis on aquaculture diversification, stress-related indicators broadly applicable across species are needed. Results: Utilising an interspecific comparative transcriptomic (RNAseq) approach, we compared gill gene expression responses of Atlantic salmon (Salmo salar) and Nile tilapia (Oreochromis niloticus) to rearing density and Saprolegnia parasitica infection. Salmon reared at high-density showed increased expression of stress-related markers (e.g. c-fos and hsp70), and downregulation of innate immune genes. Upon pathogen challenge, only salmon reared at low density exhibited increased expression of inflammatory interleukins and lymphocyte-related genes. Tilapia immunity, in contrast, was impaired at low-density. Using overlapping gene ontology enrichment and gene ortholog analyses, we found that density-related stress similarly impacted salmon and tilapia in key immune pathways, altering the expression of genes vital to inflammatory and Th17 responses to pathogen challenge. Conclusions: Given the challenges posed by ectoparasites and gill diseases in fish farms, this study underscores the importance of optimal rearing densities for immunocompetence, particularly for mucosal immunity. Our comparative transcriptomics analyses identified density stress impacted immune markers common across different fish taxa, providing key molecular targets with potential for monitoring and enhancing aquaculture resilience in a wide range of farmed species.

Shining a light on parasite behaviour: daily patterns ofArgulusfish lice

“…The subsequent impact of these altered light regimes on both fish behaviour and health is now being considered. Recent studies have also found parasitic infection can alter host circadian gene expression, further complicating the relationship between parasites, hosts and the rhythms they both follow (Ellison et al, 2018(Ellison et al, , 2020. Considering the positive phototactic response of fish lice, aquaculture lights could attract lice to cages and facilitate infection (Trippel, 2010, Stewart et al, 2013.…”

Moving towards improved surveillance and earlier diagnosis of aquatic pathogens: From traditional methods to emerging technologies

“…Many fish, especially those in the ornamental trade, are transferred long distances to reach the end user and this movement also increases susceptibility and disease risk through mechanical disturbances 15 and reduced water quality from increased CO 2 and build‐up of other toxic compounds 16 . Within intensive aquaculture systems, water quality including dissolved oxygen levels are controlled, but stocking density is often pushed to its limit, which can also affect disease susceptibility 17,18 . For many species, high densities increase stress, as is the case with Atlantic salmon ( Salmo salar ) resulting in increased disease susceptibility 18 .…”

“…16 Within intensive aquaculture systems, water quality including dissolved oxygen levels are controlled, but stocking density is often pushed to its limit, which can also affect disease susceptibility. 17,18 For many species, high densities increase stress, as is the case with Atlantic salmon (Salmo salar) resulting in increased disease susceptibility. 18 For territorial species, such as Nile tilapia (Oreochromis niloticus), high densities can lower stress, as social aggression is reduced 19 and consequently so too is disease susceptibility.…”

“…17,18 For many species, high densities increase stress, as is the case with Atlantic salmon (Salmo salar) resulting in increased disease susceptibility. 18 For territorial species, such as Nile tilapia (Oreochromis niloticus), high densities can lower stress, as social aggression is reduced 19 and consequently so too is disease susceptibility. 20 So, disease mitigation is critically dependent on the system and species.…”

Circadian dynamics of the teleost skin immune-microbiome interface

“…Therefore, extreme lighting regimes may have profound implications for fish health and response to infection. Moreover, there are indications that infection and/or stress may impact expression of fish circadian clocks 34,35 .…”