Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(3)

Published: Feb. 14, 2024

Abstract The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. composition microbiomes varies across species in response to variety stressors, however, there been no systematic analysis these studies evaluate how factors shape microbiomes. Here, we examined 1922 from 36 included 98 nine rearing conditions investigate associations between microbiome, species, water physiochemical factors. Proteobacteria, particularly class Gammaproteobacteria, were present all marine freshwater Acinetobacter, Aeromonas, Ralstonia, Sphingomonas Flavobacterium most abundant genera within microbiomes, Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter Vibrio saltwater fish. Our results show different culturing (rearing) environments have small but significant effect on bacterial community compositions. Water temperature, pH, dissolved oxygen concentration, salinity significantly correlated differences beta-diversity not necessarily alpha-diversity. To improve study comparability provide recommendations for approaches analyses sequencing data reproducibility.

Language: Английский

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Comparison of the gill and gut microbiomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio) and their RAS environment

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 896, P. 165212 - 165212

Published: June 28, 2023

Recirculating aquaculture systems (RAS) are increasingly being used to grow fish, as intensive water reuse reduces consumption and environmental impact. RAS use biofilters containing nitrogen-cycling microorganisms that remove ammonia from the water. Knowledge of how microbial communities relate fish-associated microbiome is limited, knowledge microbiota in general. Recently, bacteria have been discovered zebrafish carp gills shown detoxify a manner similar biofilter. Here, we compared biofilter microbiomes with gut gill laboratory housing either (Danio rerio) or common (Cyprinus carpio) using 16S rRNA gene amplicon sequencing. The phylogeny ammonia-oxidizing environment was investigated more detail by phylogenetic analysis monooxygenase subunit A (amoA). location which sampled (RAS compartments gut) had stronger effect on community composition than fish species, but species-specific differences were also observed. We found carp- zebrafish-associated highly distinct their respective microbiomes, characterized lower overall diversity small core consisting taxa specifically adapted organ. defined high proportion unique taxa. Finally, amoA sequences those Our results showed share microbially-rich environment.

Language: Английский

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Microbial and histopathological insights into gill health of Atlantic salmon (Salmo salar) across Scottish aquaculture sites

Aquaculture, Journal Year: 2025, Volume and Issue: unknown, P. 742166 - 742166

Published: Jan. 1, 2025

Language: Английский

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Growth, sexual maturation, cataracts, and blood biochemistry in diploid and triploid Atlantic salmon post-smolts reared at one of eight constant temperatures from 3.0 to 20.5 °C for 140 days

Aquaculture, Journal Year: 2025, Volume and Issue: unknown, P. 742323 - 742323

Published: Feb. 1, 2025

Language: Английский

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The Future of Pathogen Detection in Aquaculture: Miniature Labs, Field‐Compatible Assays, environmental DNA and RNA, CRISPR and Metatranscriptomics

Aquaculture Fish and Fisheries, Journal Year: 2025, Volume and Issue: 5(3)

Published: May 5, 2025

ABSTRACT Inland recirculating aquaculture is a thriving food industry providing sustainable and locally sourced high‐quality protein. However, its expansion accompanied by emerging challenges regarding the spread of pathogens diseases. Detection management in remain underdeveloped compared to other animal farming sectors due vast diversity species involved, non‐domesticated limited knowledge pathogens, host responses disease mechanisms. Furthermore, systems are heavily dependent on beneficial bacterial communities for waste product removal water quality maintenance, with opportunistic constituting an inherent component these microbial communities. To enhance potential inland as source protein, it imperative adopt advanced tools pathogen detection monitoring assessing overall health ecosystem. This paper presents overview promising current molecular technological advancements that offer solutions system aquaculture. We focus recently developed point‐of‐care on‐site methods using miniaturized laboratory equipment robust workflows operate independently cold chain logistics. explore methodologies environment rather than through fish assessments. Lastly, we discuss techniques from scientific disciplines aquaculture, including CRISPR‐Cas protocols implementation ‘omics’ approaches comprehensive characterization states. These demonstrate considerable surveillance and, subsequently, early dynamic field. Through better understanding available options, managers scientists can collaborate optimize systems. aims facilitate communication between managers, equipping their facilities.

Language: Английский

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Acute Effect of Short-Term Benzocaine Anesthesia on the Skin Mucus Microbiome of Atlantic salmon (Salmo salar)

Animals, Journal Year: 2025, Volume and Issue: 15(11), P. 1566 - 1566

Published: May 27, 2025

Routine aquaculture practices such as capture, transportation, and handling can disrupt the relationship between commensal opportunistic bacteria in fish skin microbiome. Anesthetic baths are a common welfare practice to reduce stress during handling. However, date, no studies assessed effect of anesthetics on bacterial communities mucus. This study is first evaluate influence benzocaine, widely used anesthetic, mucus microbiome Atlantic salmon reared recirculating system (RAS). Using Illumina high-throughput 16S rRNA gene sequencing, we found that richness diversity were significantly reduced samples from with anesthesia (ANE) when compared those without (CTR). The predominant classes both groups Gammaproteobacteria (54.1–62.6%) Betaproteobacteria (22.6–22.9%). significant dissimilarities beta observed community structure ANE CTR. These findings demonstrate benzocaine exposure alters potentially leading dysbiosis. also provides baseline information an RAS. As temporal resampling was performed, duration persistence these changes remain unknown warrant further investigation.

Language: Английский

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Assessment of gill microbiome of two strains of Atlantic salmon reared in flowthrough and recirculation hatcheries and following seawater transfer

Aquaculture, Journal Year: 2023, Volume and Issue: 580, P. 740322 - 740322

Published: Nov. 7, 2023

The gill mucosal microbiome of Atlantic salmon has a significant impact on health and physiology under homeostatic conditions, but the microbial community may itself be influenced by host genetics, culture system seawater transfer. In this study, two commercial strains salmon, reared in parallel hatchery systems (flow-through -FT recirculation -RAS) was investigated. Samples microbiome, tank biofilm water were collected from fish cohorts at hatcheries following Though commercially equivalent FT RAS had similar beta alpha diversity, diversity indicators bacterial communities gills significantly increased after input. Ultimately, no effect genetic strain detected. Our results showed that or with common source, comparable microbiomes.

Language: Английский

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Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study

BMC Veterinary Research, Journal Year: 2024, Volume and Issue: 20(1)

Published: Aug. 1, 2024

Abstract Background Understanding the relationship between resident microbiota and disease in cultured fish represents an important emerging area of study. Marine gill disorders particular are considered challenge to Atlantic salmon ( Salmo salar ) aquaculture, however relatively little is known regarding role might play providing protection from or potentiating different diseases. Here, 16S rRNA sequencing was used examine microbiome alongside health screening farmed salmon. Results were explore microbial communities disease. Microbial community restructuring observed throughout sampling period linked varied drivers change, including environmental conditions severity pathology. Taxa with significantly greater relative abundance on healthier gills included isolates within genus Shewanella, taxa family Procabacteriaceae . In contrast, altered Candidatus Branchiomonas Rubritalea spp. associated damaged gills. Interestingly, more general changes richness diversity not health, thus apparently deleterious fish. Gross histological scoring demonstrated seasonal shifts pathology, increased damage autumn. Specific infectious causes that contributed pathology population disorder amoebic (AGD), due uncontrolled nature this study likely mixed contribution various results do strongly support association specific non-infectious Conclusions suggest undergo continual marine environment, influences upon change environmental, host, pathogenic factors. A significant states suggests these make meaningful indicators health. Further research frequent deliberate manipulation would provide advancement knowledge area. Overall, although much still be learnt what constitutes a healthy maladapted community, clear field, new insight into structure during annual production cycle marine-stage

Language: Английский

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Assessing the Benefits and Challenges of Recirculating Aquaculture Systems (RAS) for Atlantic Salmon Production

Reviews in Fisheries Science & Aquaculture, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 22

Published: Dec. 17, 2024

Language: Английский

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Time is a stronger predictor of microbiome community composition than tissue in external mucosal surfaces of Atlantic salmon (Salmo salar) reared in a semi-natural freshwater environment

Aquaculture, Journal Year: 2022, Volume and Issue: 566, P. 739211 - 739211

Published: Dec. 28, 2022

The mucosal surfaces provide the first line of defence to opportunistic pathogens in external environment as well other physiological functions including osmoregulation, gas exchange or nutrient absorption gut. Atlantic salmon is most valuable salmonid species cultured worldwide and its anadromous life cycle dictates periods growth both fresh seawater. transition fish between these two habitats often accompanied by high levels mortality. Communities commensal microbes inhabiting are vital health also subjected an abrupt change salinity temperature during seawater transfer salmon. In this study we followed a cohort through parr-smolt transformation open freshwater loch exposed natural decline water month post-transfer sea. Mucus swabs were taken from gill skin, hindgut collected n = 6 triplicate pens at four sampling points (FW) first- fourth-weeks post sea (n 18 total per sampling). Distinct temporal dynamics communities identified three surfaces. microbiome diversity was stable characterized inter-individual variability terms community composition. Microbiome decreased skin throughout FW rearing immediately but recovered pre-transfer after one Gill declined continued further due single dominant taxon Candidatus Clavichlamydia salmonicola, member phylum Chlamydiae. Mucosal all largely distinct surrounding water. This highlights importance considering impact time, conjunction with salinity, when determining composition urges caution inferring general functionality time point.

Language: Английский

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