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Zamparo S, Orioles M, Brocca G, Marroni F, Castellano C, Radovic S, Mandrioli L, Galeotti M, Verin R. Novel insights on microbiome dynamics during a gill disease outbreak in farmed rainbow trout (Oncorhynchus mykiss). Sci Rep 2024; 14:17791. [PMID: 39090156 PMCID: PMC11294328 DOI: 10.1038/s41598-024-68287-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
The generic term "Gill disease" refers to a wide range of disorders that affect the gills and severely impact salmonid aquaculture systems worldwide. In rainbow trout freshwater aquaculture, various etiological agents causing gill diseases have been described, particularly Flavobacterium and Amoeba species, but research studies suggest a more complex and multifactorial aetiology. Here, a cohort of rainbow trout affected by gill disease is monitored both through standard laboratory techniques and 16S rRNA Next-Generation Sequencing (NGS) analysis during a natural disease outbreak and subsequent antibiotic treatment with Oxytetracycline. NGS results show a clear clustering of the samples between pre- and post-treatment based on the microbial community of the gills. Interestingly, the three main pathogenic bacteria species in rainbow trout (Yersinia ruckeri, Flavobacterium psychrophilum, and Flavobacterium branchiophilum) appear to be weak descriptors of the diversity between pre-treatment and post-treatment groups. In this study, the dynamics of the gill microbiome during the outbreak and subsequent treatment are far more complex than previously reported in the literature, and environmental factors seem of the utmost importance in determining gill disease. These findings present a potential novel perspective on the diagnosis and management of gill diseases, showing the limitations of conventional laboratory methodologies in elucidating the complexity of this disease in rainbow trout. To the authors' knowledge, this work is the first to describe the microbiome of rainbow trout gills during a natural outbreak and subsequent antibiotic treatment. The results of this study suggest that NGS can play a critical role in the analysis and comprehension of gill pathology. Using NGS in future research is highly recommended to gain deeper insights into such diseases correlating gill's microbiome with other possible cofactors and establish strong prevention guidelines.
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Affiliation(s)
- Samuele Zamparo
- Azienda Agricola Erede Rossi Silvio di Rossi Niccola, 62025, Sefro, MC, Italy
| | - Massimo Orioles
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Ginevra Brocca
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, PD, Italy.
- Aquatic Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, C1A 4P3, Charlottetown, Prince Edward Island, Canada.
| | - Fabio Marroni
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Ciro Castellano
- Azienda Agricola Erede Rossi Silvio di Rossi Niccola, 62025, Sefro, MC, Italy
| | | | - Luciana Mandrioli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064, Ozzano dell'Emilia, BO, Italy
| | - Marco Galeotti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Ranieri Verin
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, PD, Italy
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Clinton M, Wyness AJ, Martin SAM, Brierley AS, Ferrier DEK. Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study. BMC Vet Res 2024; 20:340. [PMID: 39090695 PMCID: PMC11293161 DOI: 10.1186/s12917-024-04125-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Understanding the relationship between resident microbiota and disease in cultured fish represents an important and emerging area of study. Marine gill disorders in particular are considered an important challenge to Atlantic salmon (Salmo salar) aquaculture, however relatively little is known regarding the role resident gill microbiota might play in providing protection from or potentiating different gill diseases. Here, 16S rRNA sequencing was used to examine the gill microbiome alongside fish health screening in farmed Atlantic salmon. Results were used to explore the relationship between microbial communities and gill disease. RESULTS Microbial community restructuring was observed throughout the sampling period and linked to varied drivers of change, including environmental conditions and severity of gill pathology. Taxa with significantly greater relative abundance on healthier gills included isolates within genus Shewanella, and taxa within family Procabacteriaceae. In contrast, altered abundance of Candidatus Branchiomonas and Rubritalea spp. were associated with damaged gills. Interestingly, more general changes in community richness and diversity were not associated with altered gill health, and thus not apparently deleterious to fish. Gross and histological gill scoring demonstrated seasonal shifts in gill pathology, with increased severity of gill damage in autumn. Specific infectious causes that contributed to observed pathology within the population included the gill disorder amoebic gill disease (AGD), however due to the uncontrolled nature of this study and likely mixed contribution of various causes of gill disease to observed pathology results do not strongly support an association between the microbial community and specific infectious or non-infectious drivers of gill pathology. CONCLUSIONS Results suggest that the microbial community of farmed Atlantic salmon gills undergo continual restructuring in the marine environment, with mixed influences upon this change including environmental, host, and pathogenic factors. A significant association of specific taxa with different gill health states suggests these taxa might make meaningful indicators of gill health. Further research with more frequent sampling and deliberate manipulation of gills would provide important advancement of knowledge in this area. Overall, although much is still to be learnt regarding what constitutes a healthy or maladapted gill microbial community, the results of this study provide clear advancement of the field, providing new insight into the microbial community structure of gills during an annual production cycle of marine-stage farmed Atlantic salmon.
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Affiliation(s)
- Morag Clinton
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK.
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Sitka Sound Science Center, Alaska, Sitka, USA.
| | - Adam J Wyness
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK
- Scottish Association for Marine Science, Oban, UK
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, University of Aberdeen, Aberdeen, UK
| | | | - David E K Ferrier
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK.
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Kelly LA, Yost CK, Cooke SJ. Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research. JOURNAL OF FISH BIOLOGY 2024; 104:912-919. [PMID: 38226503 DOI: 10.1111/jfb.15650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024]
Abstract
The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.
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Affiliation(s)
- Lisa A Kelly
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | - Christopher K Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
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Ruiz A, Torrecillas S, Kashinskaya E, Andree KB, Solovyev M, Gisbert E. Comparative study of the gut microbial communities collected by scraping and swabbing in a fish model: a comprehensive guide to promote non-lethal procedures for gut microbial studies. Front Vet Sci 2024; 11:1374803. [PMID: 38585300 PMCID: PMC10997143 DOI: 10.3389/fvets.2024.1374803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
In the present study, we propose the use of swabs in non-lethal sampling procedures to collect the mucosa-adhered gut microbiota from the posterior intestine of fish, and therefore, we compare the bacterial communities collected by conventional scraping and by swabbing methods. For this purpose, samples of the posterior intestine of rainbow trout (Oncorhynchus mykiss) were collected first using the swabbing approach, and after fish euthanasia, by mucosa scraping. Finally, bacterial communities were compared by 16S rRNA gene Illumina sequencing. Results from the current study revealed that similar values of bacterial richness and diversity were found for both sampling procedures. Similarly, there were no differences between procedures when using qualitative metrics (Jaccard and unweighted UniFrac) for estimating inter-individual diversity, but the quantitative metrics (Bray-Curtis and weighted UniFrac) showed a higher dispersion when samples were obtained by swabbing compared to scraping. In terms of bacterial composition, there were differences in abundance for the phyla Firmicutes and Proteobacteria. The cause of these differential abundances may be the inability of the swab to access to certain areas, such as the basal region of the intestinal villi. Moreover, swabbing allowed a higher representation of low abundant taxa, which may also have an important role in host microbiome regardless of their low abundance. Overall, our results demonstrate that the sampling method is a factor to be considered in experimental design when studying gut bacterial communities to avoid potential biases in the interpretation or comparison of results from different studies. In addition, the advantages and disadvantages of each procedure (swabbing vs scraping) are discussed in detail, concluding that swabbing can be implemented as a reliable and non-lethal procedure for posterior gut microbiota studies, which is of particular interest for animal welfare and the 3Rs principle, and may offer a wide range of novel applications.
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Affiliation(s)
- Alberto Ruiz
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Silvia Torrecillas
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Elena Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Karl B. Andree
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Mikhail Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- Biological Institute, Tomsk State University, Tomsk, Russia
| | - Enric Gisbert
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
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Derikvand P, Sauter B, Keddie A, Stein LY. Inoculum and pH effects on ammonium removal and microbial community dynamics in aquaponics systems. iScience 2024; 27:109073. [PMID: 38361614 PMCID: PMC10867649 DOI: 10.1016/j.isci.2024.109073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/11/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
Understanding the ecology of microorganisms is essential for optimizing aquaponics systems. Effects of pH and inoculum on ammonium removal and dynamics of microbial community composition from all compartments of lab-scale aquaponics systems were examined. Initial ammonium accumulation in systems with comammox-enriched inocula were 47% and 69% that of systems enriched with ammonia-oxidizing bacteria (AOB), with higher rates of ammonium removal and transient nitrite accumulation measured in the latter systems. By the end of operation, Nitrosomonas and Nitrosospira AOB were dominant nitrifiers in systems at pH 7.6-7.8, whereas comammox (Nitrospira) nitrifiers and plant growth-promoting microbes were abundant in systems operating at pH 5.8-6.0. Lower pH systems supported more robust plant growth with no significant effects on fish health. This study demonstrated functional redundancy of aquaponics microbiota, with selectivity of nitrifying taxa as a function of pH. The results suggest that inoculum and pH are important considerations for aquaponics system initiation and optimization.
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Affiliation(s)
- Peyman Derikvand
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Brittany Sauter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Andrew Keddie
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Lisa Y. Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Meriggi N, Russo A, Renzi S, Cerasuolo B, Nerini M, Ugolini A, Marvasi M, Cavalieri D. Enhancing seafood traceability: tracking the origin of seabass and seabream from the tuscan coast area by the analysis of the gill bacterial communities. Anim Microbiome 2024; 6:13. [PMID: 38486253 PMCID: PMC10938666 DOI: 10.1186/s42523-024-00300-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/04/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND The seafood consumption and trade have increased over the years, and along its expected expansion pose major challenges to the seafood industry and government institutions. In particular, the global trade in fish products and the consequent consumption are linked to reliable authentication, necessary to guarantee lawful trade and healthy consumption. Alterations or errors in this process can lead to commercial fraud and/or health threats. Consequently, the development of new investigative tools became crucial in ensuring unwanted scenarios. Here we used NGS techniques through targeted metagenomics approach on the V3-V4 region of the 16S rRNA genes to characterize the gill bacterial communities in wild-caught seabream (Sparus aurata) and seabass (Dicentrarchus labrax) within different fisheries areas of the "Costa degli Etruschi'' area in the Tuscan coast. Our challenge involved the possibility of discriminating between the microbiota of both fish species collected from three different fishing sites very close to each other (all within 100 km) in important areas from a commercial and tourist point of view. RESULTS Our results showed a significant difference in the assembly of gill bacterial communities in terms of diversity (alpha and beta diversity) of both seabass and seabream in accordance with the three fishing areas. These differences were represented by a unique site -related bacterial signature, more evident in seabream compared to the seabass. Accordingly, the core membership of seabream specimens within the three different sites was minimal compared to the seabass which showed a greater number of sequence variants shared among the different fishing sites. Therefore, the LRT analysis highlighted the possibility of obtaining specific fish bacterial signatures associated with each site; it is noteworthy that specific taxa showed a unique association with the fishing site regardless of the fish species. This study demonstrates the effectiveness of target-metagenomic sequencing of gills in discriminating bacterial signatures of specimens collected from fishing areas located at a limited distance to each other. CONCLUSIONS This study provides new information relating the structure of the gill microbiota of seabass and seabream in a fishing area with a crucial commercial and tourist interest, namely "Costa degli Etruschi". This study demonstrated that microbiome-based approaches can represent an important tool for validating the seafood origins with a central applicative perspective in the seafood traceability system.
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Affiliation(s)
- Niccolò Meriggi
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Pisa, IT56124, Italia
| | - Alessandro Russo
- Department of Biology, University of Florence, Sesto Fiorentino, IT50019, Italy
| | - Sonia Renzi
- Department of Biology, University of Florence, Sesto Fiorentino, IT50019, Italy
| | - Benedetta Cerasuolo
- Department of Biology, University of Florence, Sesto Fiorentino, IT50019, Italy
| | - Marta Nerini
- Department of Biology, University of Florence, Sesto Fiorentino, IT50019, Italy
| | - Alberto Ugolini
- Department of Biology, University of Florence, Florence, IT50125, Italia
| | | | - Duccio Cavalieri
- Department of Biology, University of Florence, Sesto Fiorentino, IT50019, Italy.
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Amill F, Gauthier J, Rautio M, Derome N. Characterization of gill bacterial microbiota in wild Arctic char ( Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems. Microbiol Spectr 2024; 12:e0294323. [PMID: 38329329 PMCID: PMC10923216 DOI: 10.1128/spectrum.02943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.
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Affiliation(s)
- Flora Amill
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Jeff Gauthier
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Milla Rautio
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Nicolas Derome
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
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Maeda K, Hotta D, Matsui T, Iwai S, Okanao S. Effect of water temperature on the anesthetic effects of alfaxalone in carp (Cyprinus carpio). J Adv Vet Anim Res 2024; 11:27-32. [PMID: 38680807 PMCID: PMC11055594 DOI: 10.5455/javar.2024.k743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/08/2023] [Accepted: 01/03/2024] [Indexed: 05/01/2024] Open
Abstract
Objective To evaluate the effect of water temperature on intramuscular injected alfaxalone anesthesia in carp (Cyprinus carpio). Materials and Methods Six healthy adult carp (C. carpio) were intramuscularly injected with alfaxalone (2.5, 5.0, or 7.5 mg/kg) at normal water temperature (25°C) and at low water temperature (2.5 mg/kg, 15°C). The respiratory rate, heart rate (HR), and anesthesia depth (AD) were evaluated every 5 min for 30 min after administration and every 1 h after 60 min after injection. Results The respiratory and HRs did not change significantly upon alfaxalone injection, regardless of dose. However, a dose-dependent increase in AD scores was observed. Furthermore, 2.5 mg/kg alfaxalone injected in 15°C water showed an almost equal anesthetic effect to that of 5.0 mg/kg alfaxalone in 25°C water. Conclusion Alfaxalone is readily available, and its anesthetic effect in carp was enhanced by lowering water temperature, illustrating the possibility of intramuscular injection of alfaxalone in fish.
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Affiliation(s)
- Kenichi Maeda
- Kitasato University School of Veterinary Medicine, Towada, Japan
| | - Daiki Hotta
- Kitasato University School of Veterinary Medicine, Towada, Japan
| | - Takuma Matsui
- Kitasato University School of Veterinary Medicine, Towada, Japan
| | - Satomi Iwai
- Kitasato University School of Veterinary Medicine, Towada, Japan
| | - Shozo Okanao
- Kitasato University School of Veterinary Medicine, Towada, Japan
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François-Étienne S, Nicolas L, Eric N, Jaqueline C, Pierre-Luc M, Sidki B, Aleicia H, Danilo B, Luis VA, Nicolas D. Important role of endogenous microbial symbionts of fish gills in the challenging but highly biodiverse Amazonian blackwaters. Nat Commun 2023; 14:3903. [PMID: 37414754 PMCID: PMC10326040 DOI: 10.1038/s41467-023-39461-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/09/2023] [Indexed: 07/08/2023] Open
Abstract
Amazonian blackwaters are extremely biodiverse systems containing some of Earth's most naturally acidic, dissolved organic carbon -rich and ion-poor waters. Physiological adaptations of fish facing these ionoregulatory challenges are unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response of 964 fish-microbe systems from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq and 16 S rRNA of gill samples. We find that host transcriptional responses to blackwaters are species-specific, but occasionally include the overexpression of Toll-receptors and integrins associated to interkingdom communication. Blackwater gill microbiomes are characterized by a transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. We explore further blackwater fish-microbe interactions by analyzing transcriptomes of axenic zebrafish larvae exposed to sterile, non-sterile and inverted (non-native bacterioplankton) blackwater. We find that axenic zebrafish survive poorly when exposed to sterile/inverted blackwater. Overall, our results suggest a critical role for endogenous symbionts in blackwater fish physiology.
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Affiliation(s)
- Sylvain François-Étienne
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada.
- Fisheries and Oceans, Gulf Fisheries Center, 343 University Ave, Moncton, NB, E1C 5K4, Canada.
| | - Leroux Nicolas
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| | - Normandeau Eric
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| | - Custodio Jaqueline
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, AM, 69067-375, Brazil
| | - Mercier Pierre-Luc
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| | - Bouslama Sidki
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| | - Holland Aleicia
- La Trobe University, School of Agriculture, Biomedicine and Environment, Department of Environment and Genetics, Centre for Freshwater Ecosystems, Albury/Wodonga Campus, Vic, Australia
| | - Barroso Danilo
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, AM, 69067-375, Brazil
| | - Val Adalberto Luis
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, AM, 69067-375, Brazil
| | - Derome Nicolas
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
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Sylvain FÉ, Leroux N, Normandeau É, Holland A, Bouslama S, Mercier PL, Luis Val A, Derome N. Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont. Microbiol Spectr 2022; 10:e0206422. [PMID: 36445161 PMCID: PMC9769777 DOI: 10.1128/spectrum.02064-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.
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Affiliation(s)
| | - Nicolas Leroux
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Aleicia Holland
- La Trobe University, School of Life Science, Department of Ecology, Environment and Evolution, Centre for Freshwater Ecosystems, Wodonga, Victoria, Australia
| | - Sidki Bouslama
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Adalberto Luis Val
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Amazonas, Brazil
| | - Nicolas Derome
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Amazonas, Brazil
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Birlanga VB, McCormack G, Ijaz UZ, MacCarthy E, Smith C, Collins G. Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon. Sci Rep 2022; 12:16719. [PMID: 36202859 PMCID: PMC9537138 DOI: 10.1038/s41598-022-17008-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 04/11/2022] [Indexed: 12/18/2022] Open
Abstract
Amoebic gill disease (AGD) and complex gill disease (CGD) are recurrent gill disorders in Atlantic salmon, resulting in significant aquaculture losses. The role of gill microbiomes in gill disease development is unclear. We undertook a longitudinal study to characterise the gill tissue and gill mucus microbiomes of farmed Atlantic salmon before, and during, a gill disease episode. Using a newly optimised DNA extraction protocol, we sequenced rRNA genes from microbiomes of gill samples taken from 105 individual salmon on a farm, over a summer season. The AGD aetiological agent, Neoparamoeba perurans, was PCR-quantified targeting 18S rRNA genes. Similar analyses were carried out on mucus samples. Mucus scrapings were suitable, non-lethal substitutes for characterisation of the gill prokaryotic community in this study. Gill tissue and gill mucus microbiomes changed during the campaign, correlating with N. perurans concentrations. Time explained 35% of the gill tissue and gill mucus microbiome variance, while N. perurans concentrations explained 5%. Genera including Dyadobacter, Shewanella and Pedobacter were maximally abundant in gill and mucus samples at the timepoint prior to the the detection of gill disorder signs, at T3. Shewanella was significantly more abundant before than during the gill disease episode, and we suggest this genus could be considered in future studies addressing relationships between gill disease and the gill microbiome.
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Affiliation(s)
- Victor B Birlanga
- Microbiology, School of Natural Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
| | - Grace McCormack
- School of Natural Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.,Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Umer Z Ijaz
- Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT, UK
| | - Eugene MacCarthy
- Institute of Science, Technology and Medicine, Galway-Mayo Institute of Technology, Galway, H91 T8NW, Ireland
| | - Cindy Smith
- Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT, UK
| | - Gavin Collins
- Microbiology, School of Natural Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.,Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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