Exploring the microbial ecology and energetics of wild and domesticated Atlantic salmon (Salmo salar)

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dc.contributor.advisorMcGinnity, Philip
dc.contributor.advisorReed, Thomas
dc.contributor.advisorexternalLlewellyn, Martinen
dc.contributor.authorSchaal, Patrick Danielen
dc.contributor.funderBiotechnology and Biological Sciences Research Council
dc.contributor.funderScience Foundation Ireland
dc.contributor.funderHigher Education Authority
dc.date.accessioned2024-09-16T15:19:03Z
dc.date.available2024-09-16T15:19:03Z
dc.date.issued2023en
dc.date.submitted2023
dc.description.abstractSince the inception of Atlantic salmon (Salmo salar) aquaculture in the 1970s, millions of domesticated fish have escaped from aquaculture facilities into the wild. This phenomenon raises concerns about the ecological and genetic consequences of farmed fish interbreeding with their wild counterparts. The fitness of hybrid offspring from such interactions has long been recognised as diminished compared to pure wild salmon populations, thereby posing a substantial threat to the overall health and robustness of Atlantic salmon populations. This study takes a comprehensive approach to investigate the impact of domestication on two vital aspects of Atlantic salmon biology: gut microbial communities and metabolism. Both traits have been identified as critical determinants of fish health and well-being. To disentangle the genetic effects from confounding environmental factors, this study employed common garden experiments. These experiments involved rearing fish with diverse genetic backgrounds, including wild, domesticated and reciprocal hybrids, together from the eyed-egg stage through both freshwater and marine phases. This design allowed us to simulate farmed escape and hybridisation events that naturally occur in the wild. The first data chapter examines the drivers and sources that shape gut microbial assembly over time in juvenile Atlantic salmon in a natural river system. The study shows that the major contributors to the salmon intestine's microbial taxa come from macroinvertebrates, a potential food source, rather than the water column. Moreover, results suggest a possible role of host genetics in driving inter-individual differences in gut microbial community composition, leading to distinct microbiota assemblages between farmed, wild and hybrid fish. Neutral modelling further revealed that the majority of gut taxa are transient, underscoring the dynamic nature of these microbial communities and emphasizing the need to distinguish between transient and resident taxa within the gut environment. The second data chapter examines the seasonal dynamics of gut microbial communities and energetics in juvenile Atlantic salmon, considering potential variations among farmed, wild and hybrid fish. The study unveils genetic factors as significant influencers of metabolic flexibility in Atlantic salmon. Wild fish exhibit lower metabolic rates in winter and higher rates in summer compared to farmed salmon, indicating their adaptability to seasonal environmental changes. This metabolic flexibility potentially enhances their chances of survival in variable wild environments compared to their farmed counterparts, which might exhibit less adaptability due to artificial selection for commercially favoured traits. Furthermore, our research unveils shifts in gut microbial communities during the winter months, particularly among the offspring of wild fish, possibly attributable to reduced feeding activity. This reduced activity, in turn, might be associated with their generally lower metabolic demands in winter. The third data chapter assesses whether survivability, gut microbial structure and metabolic rate of Atlantic salmon reared in marine sea pens are affected by amoebic gill disease (AGD), a parasitic infection that poses a significant challenge to Atlantic salmon reared in aquaculture facilities, and if those effects vary between fish from farmed, wild and hybrid origins. Wild fish exhibited substantially higher mortality rates compared to their farmed counterparts, while hybrids fell in between. All fish, regardless of genetic origin, showed significantly lower metabolic rates with increased AGD infection rates. In addition, gut microbial diversity significantly declined in AGD-infected fish. In summary, our study significantly contributes to our understanding of the complex interactions between host genetics, environmental factors and gut microbiota in Atlantic salmon. It offers indications that the domestication process in Atlantic salmon has influenced both host-associated microbiota and metabolism. As aquaculture continues to expand, these findings underscore the need for comprehensive conservation strategies to safeguard the ecological integrity of wild Atlantic salmon populations in the face of evolving aquaculture practices and the potential consequences of farmed fish escape events.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationSchaal, P. D. 2023. Exploring the microbial ecology and energetics of wild and domesticated Atlantic salmon (Salmo salar). PhD Thesis, University College Cork.
dc.identifier.endpage335
dc.identifier.urihttps://hdl.handle.net/10468/16371
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectBB/T016280/1
dc.relation.projectBB/P001203/1
dc.relation.projectBB/N024028/1
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/BBSRC-SFI Joint Funding Programme::Responsive Mode/16/BBSRC/3316/IE/A microbial basis for Atlantic salmon energetics/
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Investigator Programme/15/IA/3028/IE/Wild farmed interactions in a changing world: formulation of a predictive methodology to inform environmental best practice to secure long-term sustainability of global wild and farm fish populations/
dc.relation.projectHigher Education Authority (Covid-19 Cost extension (Call Three))
dc.rights© 2023, Patrick Daniel Schaal.
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectAtlantic salmon
dc.subjectGut microbiota
dc.subjectMetabolism
dc.subjectAmoebic gill disease
dc.subjectHybridisation
dc.subjectFarmed escapes
dc.subjectAquaculture
dc.subjectDomestication
dc.subjectCommon garden experiments
dc.subjectSalmon population fitness
dc.titleExploring the microbial ecology and energetics of wild and domesticated Atlantic salmon (Salmo salar)
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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