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Franke A, Beemelmanns A, Miest JJ. Are fish immunocompetent enough to face climate change? Biol Lett 2024; 20:20230346. [PMID: 38378140 PMCID: PMC10878809 DOI: 10.1098/rsbl.2023.0346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024] Open
Abstract
Ongoing climate change has already been associated with increased disease outbreaks in wild and farmed fish. Here, we evaluate the current knowledge of climate change-related ecoimmunology in teleosts with a focus on temperature, hypoxia, salinity and acidification before exploring interactive effects of multiple stressors. Our literature review reveals that acute and chronic changes in temperature and dissolved oxygen can compromise fish immunity which can lead to increased disease susceptibility. Moreover, temperature and hypoxia have already been shown to enhance the infectivity of certain pathogens/parasites and to accelerate disease progression. Too few studies exist that have focussed on acidification, but direct immune effects seem to be limited while salinity studies have led to contrasting results. Likewise, multi-stressor experiments essential for unravelling the interactions of simultaneously changing environmental factors are still scarce. This ultimately impedes our ability to estimate to what extent climate change will hamper fish immunity. Our review about epigenetic regulation mechanisms highlights the acclimation potential of the fish immune response to changing environments. However, due to the limited number of epigenetic studies, overarching conclusions cannot be drawn. Finally, we provide an outlook on how to better estimate the effects of realistic climate change scenarios in future immune studies in fish.
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Affiliation(s)
- Andrea Franke
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129 Oldenburg, Germany
- Alfred-Wegener-Institute, Helmholtz-Centre for Polar and Marine Research (AWI), 27570 Bremerhaven, Germany
| | - Anne Beemelmanns
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V0A6 Québec, Canada
| | - Joanna J. Miest
- School of Psychology and Life Sciences, Canterbury, Kent CT1 1QU, UK
- School of Science, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK
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2
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Lokesh J, Siriyappagouder P, Fernandes JMO. Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon. Sci Rep 2024; 14:981. [PMID: 38200059 PMCID: PMC10781754 DOI: 10.1038/s41598-023-50883-x] [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: 07/14/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.
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Affiliation(s)
- Jep Lokesh
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France.
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3
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Vargas-González A, Barajas M, Pérez-Sánchez T. Isolation of Lactic Acid Bacteria (LAB) from Salmonids for Potential Use as Probiotics: In Vitro Assays and Toxicity Assessment of Salmo trutta Embryonated Eggs. Animals (Basel) 2024; 14:200. [PMID: 38254369 PMCID: PMC10812622 DOI: 10.3390/ani14020200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/26/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
This research investigates the potential of lactic acid bacteria (LAB) from freshwater salmonids as prospective probiotics for application in aquaculture. LAB and pathogenic bacteria were obtained from mucus and tissues of Oncorhynchus mykiss and Salmo trutta from fish farms in northeast Spain that had not used antibiotics for the six months preceding the study. Isolates were identified using Gram staining and sequencing of 16S rRNA and ITS-1. To assess the safety of the LAB, antibiotic susceptibility tests (ASTs) against 23 antimicrobials were performed. In vitro antagonism assays were conducted to evaluate the inhibitory effects of living LAB using the agar diffusion test method and their metabolites using the agar well diffusion method. The assays targeted six specific pathogens: Aeromonas salmonicida subsp. salmonicida, Carnobacterium maltaromaticum, Vagococcus salmoninarum, Yersinia ruckeri, Lactococcus garvieae, and the marine pathogen Vibrio jasicida. Additionally, a toxicity assay was conducted on embryonic eggs of S. trutta. The ASTs on probiotic LAB candidates revealed varied responses to antimicrobials, but no resistance to oxytetracycline or florfenicol, which are two antibiotics commonly used in aquaculture, was detected. The in vitro assays indicate that LAB exhibit antagonistic effects against pathogens, primarily when directly stimulated by their presence. In applications involving embryonic eggs or larvae, certain live strains of LAB were found to have adverse effects, with some isolates resulting in higher mortality rates compared to the control group or other isolates. Furthermore, the potential pathogenicity of certain LAB strains, typically considered safe in salmonids, warrants deeper investigation.
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Affiliation(s)
- Augusto Vargas-González
- Biochemistry Area, Health Science Department, Faculty of Health Sciences, Public University of Navarra, 31008 Pamplona, Spain;
| | - Miguel Barajas
- Biochemistry Area, Health Science Department, Faculty of Health Sciences, Public University of Navarra, 31008 Pamplona, Spain;
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The Development of the Bacterial Community of Brown Trout ( Salmo trutta) during Ontogeny. Microorganisms 2023; 11:microorganisms11010211. [PMID: 36677503 PMCID: PMC9863972 DOI: 10.3390/microorganisms11010211] [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: 12/22/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish's bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.
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Duval C, Marie B, Foucault P, Duperron S. Establishment of the Bacterial Microbiota in a Lab-Reared Model Teleost Fish, the Medaka Oryzias latipes. Microorganisms 2022; 10:2280. [PMID: 36422350 PMCID: PMC9696534 DOI: 10.3390/microorganisms10112280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2023] Open
Abstract
Oryzias latipes is an important model organism for physiology, genetics, and developmental studies, and has also emerged as a relevant vertebrate model for aquatic ecotoxicology. Knowledge regarding its associated microbiota on the other hand is still scarce and limited to adults, despite the relevance of the associated microbiome to the host's biology. This study provides the first insights into the establishment of bacterial microbiota during early developmental stages of laboratory-reared medaka using a 16S-rRNA-sequencing-based approach. Major shifts in community compositions are observed, from a Proteobacteria-dominated community in larvae and juveniles to a more phylum-diverse community towards adulthood, with no obvious difference between female and male specimens. Major bacterial taxa found in adults, including genera Cetobacterium and ZOR0006, establish progressively and are rare during early stages. Dominance shifts are comparable to those documented in another major model teleost, the zebrafish. Results from this study provide a basis for future work investigating the influence of medaka-associated bacteria during host development.
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Affiliation(s)
| | | | | | - Sébastien Duperron
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, CNRS, 75005 Paris, France
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6
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Najafpour B, Pinto PIS, Moutou KA, Canario AVM, Power DM. Factors Driving Bacterial Microbiota of Eggs from Commercial Hatcheries of European Seabass and Gilthead Seabream. Microorganisms 2021; 9:2275. [PMID: 34835401 PMCID: PMC8619918 DOI: 10.3390/microorganisms9112275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023] Open
Abstract
A comprehensive understanding of how bacterial community abundance changes in fishes during their lifecycle and the role of the microbiota on health and production is still lacking. From this perspective, the egg bacterial communities of two commercially farmed species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), from different aquaculture sites were compared, and the potential effect of broodstock water microbiota and disinfectants on the egg microbiota was evaluated. Moreover, 16S ribosomal RNA gene sequencing was used to profile the bacterial communities of the eggs and broodstock water from three commercial hatcheries. Proteobacteria were the most common and dominant phyla across the samples (49.7% on average). Vibrio sp. was the most highly represented genus (7.1%), followed by Glaciecola (4.8%), Pseudoalteromonas (4.4%), and Colwellia (4.2%), in eggs and water across the sites. Routinely used iodine-based disinfectants slightly reduced the eggs' bacterial load but did not significantly change their composition. Site, species, and type of sample (eggs or water) drove the microbial community structure and influenced microbiome functional profiles. The egg and seawater microbiome composition differed in abundance but shared similar functional profiles. The strong impact of site and species on egg bacterial communities indicates that disease management needs to be site-specific and highlights the need for species- and site-specific optimization of disinfection protocols.
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Affiliation(s)
- Babak Najafpour
- Centro de Ciências do Mar (CCMAR/CIIMAR), Universidade do Algarve, 8005-139 Faro, Portugal; (B.N.); (P.I.S.P.); (A.V.M.C.)
| | - Patricia I. S. Pinto
- Centro de Ciências do Mar (CCMAR/CIIMAR), Universidade do Algarve, 8005-139 Faro, Portugal; (B.N.); (P.I.S.P.); (A.V.M.C.)
| | - Katerina A. Moutou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41221 Larissa, Greece;
| | - Adelino V. M. Canario
- Centro de Ciências do Mar (CCMAR/CIIMAR), Universidade do Algarve, 8005-139 Faro, Portugal; (B.N.); (P.I.S.P.); (A.V.M.C.)
| | - Deborah M. Power
- Centro de Ciências do Mar (CCMAR/CIIMAR), Universidade do Algarve, 8005-139 Faro, Portugal; (B.N.); (P.I.S.P.); (A.V.M.C.)
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7
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Bishop C, Jurga E, Graham L. Patterns of bacterial diversity in embryonic capsules of the spotted salamander Ambystoma maculatum: an expanding view of a symbiosis. FEMS Microbiol Ecol 2021; 97:6364358. [PMID: 34482407 DOI: 10.1093/femsec/fiab128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 09/02/2021] [Indexed: 11/14/2022] Open
Abstract
The unicellular green alga, Oophila amblystomatis, populates egg capsules of the spotted salamander Ambystoma maculatum. This nutrient-exchange mutualism is widely perceived as a bipartite interaction, but the presence and contributing effects of bacteria to this symbiosis are unknown. We used standard cultivation techniques and amplicon sequencing of the V4/V5 region of 16S rRNA gene to identify and compare diversity of bacterial taxa in embryonic capsules with that in the aquatic breeding habitat. Our sampling regime allowed us to investigate diversity among individual capsules of an egg mass and between two ponds and sampling years. Capsules contain much lower diversity of bacteria than pond water, and spatial and temporal variation in intracapsular and pond bacterial diversity was observed. Despite this variation, sequences corresponding to species in the orders Burkholderiales and Oligoflexales were either prevalent or abundant, or both. Isolates most commonly recovered from capsules were closely related to species in the genus Herbaspirillum (Burkholderiaceae); other isolates were pseudomonads, but in all cases are closely related to known vascular plant-associated species. We conclude that, despite observed variation, there are bacterial taxa whose presence is held in common spatially and temporally among capsules and that the symbiosis between O. amblystomatis and A. maculatum may involve these taxa.
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Affiliation(s)
- Cory Bishop
- Department of Biology, St Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Emil Jurga
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle Toronto, ON M5S 1A8, Canada
| | - Lori Graham
- Department of Biology, St Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
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Bone A, Bekaert M, Papadopoulou A, McMillan S, Adams A, Davie A, Desbois AP. Bacterial Communities of Ballan Wrasse (Labrus bergylta) Eggs at a Commercial Marine Hatchery. Curr Microbiol 2020; 78:114-124. [PMID: 33230621 PMCID: PMC7815581 DOI: 10.1007/s00284-020-02286-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
Ballan wrasse (Labrus bergylta, Ascanius 1767) are cleaner fish cultured in northern Europe to remove sea lice from farmed Atlantic salmon (Salmo salar, Linnaeus 1758). Despite increasing appreciation for the importance of the microbiota on the phenotypes of vertebrates including teleosts, the microbiota of wrasse eggs has yet to be described. Therefore, the aim of this present study was to describe the bacterial component of the microbiota of ballan wrasse eggs shortly after spawning and at 5 days, once the eggs had undergone a routine incubation protocol that included surface disinfection steps in a common holding tank. Triplicate egg samples were collected from each of three spawning tanks and analysis of 16S rRNA gene sequences revealed that 88.6% of reads could be identified to 186 taxonomic families. At Day 0, reads corresponding to members of the Vibrionaceae, Colwelliaceae and Rubritaleaceae families were detected at greatest relative abundances. Bacterial communities of eggs varied more greatly between tanks than between samples deriving from the same tank. At Day 5, there was a consistent reduction in 16S rRNA gene sequence richness across the tanks. Even though the eggs from the different tanks were incubated in a common holding tank, the bacterial communities of the eggs from the different tanks had diverged to become increasingly dissimilar. This suggests that the disinfection and incubation exerted differential effects of the microbiota of the eggs from each tank and that the influence of the tank water on the composition of the egg microbiota was lower than expected. This first comprehensive description of the ballan wrasse egg bacterial community is an initial step to understand the role and function of the microbiota on the phenotype of this fish. In future, mass DNA sequencing methods may be applied in hatcheries to screen for pathogens and as a tool to assess the health status of eggs.
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Affiliation(s)
- Aileen Bone
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Athina Papadopoulou
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Stuart McMillan
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Andrew Davie
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Andrew P Desbois
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
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9
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Nyholm SV. In the beginning: egg-microbe interactions and consequences for animal hosts. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190593. [PMID: 32772674 PMCID: PMC7435154 DOI: 10.1098/rstb.2019.0593] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2020] [Indexed: 12/19/2022] Open
Abstract
Microorganisms are associated with the eggs of many animals. For some hosts, the egg serves as the ideal environment for the vertical transmission of beneficial symbionts between generations, while some bacteria use the egg to parasitize their hosts. In a number of animal groups, egg microbiomes often perform other essential functions. The eggs of aquatic and some terrestrial animals are especially susceptible to fouling and disease since they are exposed to high densities of microorganisms. To overcome this challenge, some hosts form beneficial associations with microorganisms, directly incorporating microbes and/or microbial products on or in their eggs to inhibit pathogens and biofouling. Other functional roles for egg-associated microbiomes are hypothesized to involve oxygen and nutrient acquisition. Although some egg-associated microbiomes are correlated with increased host fitness and are essential for successful development, the mechanisms that lead to such outcomes are often not well understood. This review article will discuss different functions of egg microbiomes and how these associations have influenced the biology and evolution of animal hosts. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269USA
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10
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Geffroy B, Wedekind C. Effects of global warming on sex ratios in fishes. JOURNAL OF FISH BIOLOGY 2020; 97:596-606. [PMID: 32524610 DOI: 10.1111/jfb.14429] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/18/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
In fishes, sex is determined by genetics, the environment or an interaction of both. Temperature is among the most important environmental factors that can affect sex determination. As a consequence, changes in temperature at critical developmental stages can induce biases in primary sex ratios in some species. However, early sex ratios can also be biased by sex-specific tolerances to environmental stresses that may, in some cases, be amplified by changes in water temperature. Sex-specific reactions to environmental stress have been observed at early larval stages before gonad formation starts. It is therefore necessary to distinguish between temperature effects on sex determination, generally acting through the stress axis or epigenetic mechanisms, and temperature effects on sex-specific mortality. Both are likely to affect sex ratios and hence population dynamics. Moreover, in cases where temperature effects on sex determination lead to genotype-phenotype mismatches, long-term effects on population dynamics are possible, for example temperature-induced masculinization potentially leading to the loss of Y chromosomes or feminization to male-biased operational sex ratios in future generations. To date, most studies under controlled conditions conclude that if temperature affects sex ratios, elevated temperatures mostly lead to a male bias. The few studies that have been performed on wild populations seem to confirm this general trend. Recent findings suggest that transgenerational plasticity could mitigate the effects of warming on sex ratios in some populations.
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Affiliation(s)
- Benjamin Geffroy
- MARBEC, University of Montpellier, Ifremer, IRD, CNRS, Palavas-les-Flots, France
| | - Claus Wedekind
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
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Zanuzzo FS, Beemelmanns A, Hall JR, Rise ML, Gamperl AK. The Innate Immune Response of Atlantic Salmon ( Salmo salar) Is Not Negatively Affected by High Temperature and Moderate Hypoxia. Front Immunol 2020; 11:1009. [PMID: 32536921 PMCID: PMC7268921 DOI: 10.3389/fimmu.2020.01009] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
Climate change is predicted to increase water temperatures and decrease oxygen levels in freshwater and marine environments, however, there is conflicting information regarding the extent to which these conditions may impact the immune defenses of fish. In this study, Atlantic salmon were exposed to: (1) normoxia (100–110% air saturation) at 12°C; (2) an incremental temperature increase (1°C per week from 12 to 20°C), and then held at 20°C for an additional 4 weeks; and (3) “2” with the addition of moderate hypoxia (~65–75% air saturation). These conditions realistically reflect what farmed salmon in some locations are currently facing, and future conditions in Atlantic Canada and Europe, during the summer months. The salmon were sampled for the measurement of head kidney constitutive anti-bacterial and anti-viral transcript expression levels, and blood parameters of humoral immune function. Thereafter, they were injected with either the multi-valent vaccine Forte V II (contains both bacterial and viral antigens) or PBS (phosphate-buffer-saline), and the head kidney and blood of these fish were sampled at 6, 12, 24, and 48 h post-injection (HPI). Our results showed that: (1) neither high temperature, nor high temperature + moderate hypoxia, adversely affected respiratory burst, complement activity or lysozyme concentration; (2) the constitutive transcript expression levels of the anti-bacterial genes il1β, il8-a, cox2, hamp-a, stlr5-a, and irf7-b were up-regulated by high temperature; (3) while high temperature hastened the peak in transcript expression levels of most anti-bacterial genes by 6–12 h following V II injection, it did not affect the magnitude of changes in transcript expression; (4) anti-viral (viperin-b, mx-b, and isg15-a) transcript expression levels were either unaffected, or downregulated, by acclimation temperature or V II injection over the 48 HPI; and (5) hypoxia, in addition to high temperature, did not impact immune transcript expression. In conclusion, temperatures up to 20°C, and moderate hypoxia, do not impair the capacity of the Atlantic salmon's innate immune system to respond to bacterial antigens. These findings are surprising, and highlight the salmon's capacity to mount robust innate immune responses (i.e., similar to control fish under optimal conditions) under conditions approaching their upper thermal limit.
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Affiliation(s)
- Fábio S Zanuzzo
- Department of Ocean Sciences, Memorial University, St. John's, NL, Canada
| | - Anne Beemelmanns
- Department of Ocean Sciences, Memorial University, St. John's, NL, Canada
| | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Ocean Sciences Centre, Memorial University, St. John's, NL, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University, St. John's, NL, Canada
| | - Anthony K Gamperl
- Department of Ocean Sciences, Memorial University, St. John's, NL, Canada
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12
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Zolfaghari Emameh R, Kuuslahti M, Nosrati H, Lohi H, Parkkila S. Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates. BMC Genomics 2020; 21:352. [PMID: 32393172 PMCID: PMC7216627 DOI: 10.1186/s12864-020-6762-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/30/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The inaccuracy of DNA sequence data is becoming a serious problem, as the amount of molecular data is multiplying rapidly and expectations are high for big data to revolutionize life sciences and health care. In this study, we investigated the accuracy of DNA sequence data from commonly used databases using carbonic anhydrase (CA) gene sequences as generic targets. CAs are ancient metalloenzymes that are present in all unicellular and multicellular living organisms. Among the eight distinct families of CAs, including α, β, γ, δ, ζ, η, θ, and ι, only α-CAs have been reported in vertebrates. RESULTS By an in silico analysis performed on the NCBI and Ensembl databases, we identified several β- and γ-CA sequences in vertebrates, including Homo sapiens, Mus musculus, Felis catus, Lipotes vexillifer, Pantholops hodgsonii, Hippocampus comes, Hucho hucho, Oncorhynchus tshawytscha, Xenopus tropicalis, and Rhinolophus sinicus. Polymerase chain reaction (PCR) analysis of genomic DNA persistently failed to amplify positive β- or γ-CA gene sequences when Mus musculus and Felis catus DNA samples were used as templates. Further BLAST homology searches of the database-derived "vertebrate" β- and γ-CA sequences revealed that the identified sequences were presumably derived from gut microbiota, environmental microbiomes, or grassland ecosystems. CONCLUSIONS Our results highlight the need for more accurate and fast curation systems for DNA databases. The mined data must be carefully reconciled with our best knowledge of sequences to improve the accuracy of DNA data for publication.
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Affiliation(s)
- Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, 14965/161 Iran
| | - Marianne Kuuslahti
- Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland
| | - Hassan Nosrati
- Department of Materials Engineering, Tarbiat Modares University, Tehran, Iran
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland
- Fimlab Laboratories Ltd. and Tampere University Hospital, FI-33520 Tampere, Finland
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Campbell LJ, Garner TWJ, Hopkins K, Griffiths AGF, Harrison XA. Outbreaks of an Emerging Viral Disease Covary With Differences in the Composition of the Skin Microbiome of a Wild United Kingdom Amphibian. Front Microbiol 2019; 10:1245. [PMID: 31281291 PMCID: PMC6597677 DOI: 10.3389/fmicb.2019.01245] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/20/2019] [Indexed: 12/19/2022] Open
Abstract
There is growing appreciation of the important role of commensal microbes in ensuring the normal function and health of their hosts, including determining how hosts respond to pathogens. A range of infectious diseases are threatening amphibians worldwide, and evidence is accumulating that the host-associated bacteria that comprise the microbiome may be key in mediating interactions between amphibian hosts and infectious pathogens. We used 16S rRNA amplicon sequencing to quantify the skin microbial community structure of over 200 individual wild adult European common frogs (Rana temporaria), from ten populations with contrasting history of the lethal disease ranavirosis, caused by emerging viral pathogens belonging to the genus Ranavirus. All populations had similar species richness irrespective of disease history, but populations that have experienced historical outbreaks of ranavirosis have a distinct skin microbiome structure (beta diversity) when compared to sites where no outbreaks of the disease have occurred. At the individual level, neither age, body length, nor sex of the frog could predict the structure of the skin microbiota. Our data potentially support the hypothesis that variation among individuals in skin microbiome structure drive differences in susceptibility to infection and lethal outbreaks of disease. More generally, our results suggest that population-level processes are more important for driving differences in microbiome structure than variation among individuals within populations in key life history traits such as age and body size.
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Affiliation(s)
- Lewis J Campbell
- Environment and Sustainability Institute, University of Exeter, Penryn, United Kingdom.,Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | | | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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14
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Marques da Cunha L, Uppal A, Seddon E, Nusbaumer D, Vermeirssen EL, Wedekind C. No additive genetic variance for tolerance to ethynylestradiol exposure in natural populations of brown trout ( Salmo trutta). Evol Appl 2019; 12:940-950. [PMID: 31080506 PMCID: PMC6503824 DOI: 10.1111/eva.12767] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
One of the most common and potent pollutants of freshwater habitats is 17-alpha-ethynylestradiol (EE2), a synthetic component of oral contraceptives that is not completely eliminated during sewage treatment and that threatens natural populations of fish. Previous studies found additive genetic variance for the tolerance against EE2 in different salmonid fishes and concluded that rapid evolution to this type of pollution seems possible. However, these previous studies were done with fishes that are lake-dwelling and hence typically less exposed to EE2 than river-dwelling species. Here, we test whether there is additive genetic variance for the tolerance against EE2 also in river-dwelling salmonid populations that have been exposed to various concentrations of EE2 over the last decades. We sampled 287 adult brown trout (Salmo trutta) from seven populations that show much genetic diversity within populations, are genetically differentiated, and that vary in their exposure to sewage-treated effluent. In order to estimate their potential to evolve tolerance to EE2, we collected their gametes to produce 730 experimental families in blockwise full-factorial in vitro fertilizations. We then raised 7,302 embryos singly in 2-ml containers each and either exposed them to 1 ng/L EE2 (an ecologically relevant concentration, i.e., 2 pg per embryo added in a single spike to the water) or sham-treated them. Exposure to EE2 increased embryo mortality, delayed hatching time, and decreased hatchling length. We found no population differences and no additive genetic variance for tolerance to EE2. We conclude that EE2 has detrimental effects that may adversely affect population even at a very low concentration, but that our study populations lack the potential for rapid genetic adaptation to this type of pollution. One possible explanation for the latter is that continuous selection over the last decades has depleted genetic variance for tolerance to this synthetic stressor.
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Affiliation(s)
| | - Anshu Uppal
- Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - Emily Seddon
- Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - David Nusbaumer
- Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | | | - Claus Wedekind
- Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
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15
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Sullam KE, Pichon S, Schaer TMM, Ebert D. The Combined Effect of Temperature and Host Clonal Line on the Microbiota of a Planktonic Crustacean. MICROBIAL ECOLOGY 2018; 76:506-517. [PMID: 29274070 DOI: 10.1007/s00248-017-1126-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 12/08/2017] [Indexed: 05/09/2023]
Abstract
Host-associated microbiota vary across host individuals and environmental conditions, but the relative importance of their genetic background versus their environment is difficult to disentangle. We sought to experimentally determine the factors shaping the microbiota of the planktonic Crustacean, Daphnia magna. We used clonal lines from a wide geographic distribution, which had been kept under standardized conditions for over 75 generations. Replicate populations were kept for three generations at 20 and 28 °C. The interaction of the host clonal line and environment (i.e., temperature) influenced microbiota community characteristics, including structure, the relative abundance of common microbial species, and the microbial richness and phylogenetic diversity. We did not find any correlation between host-associated microbiota and the geographic origin of the clones or their temperature tolerance. Our results highlight the prominent effects that host clonal lineage and its interaction with the environment has on host-associated microbiota composition.
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Affiliation(s)
- Karen E Sullam
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Samuel Pichon
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, bâtiment I étage 1 bureau 1340, Université François Rabelais de Tours, Parc Grandmont, 37200, Tours, France
| | - Tobias M M Schaer
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Dieter Ebert
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
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16
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Consumption of carotenoids not increased by bacterial infection in brown trout embryos (Salmo trutta). PLoS One 2018; 13:e0198834. [PMID: 29897970 PMCID: PMC5999266 DOI: 10.1371/journal.pone.0198834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/25/2018] [Indexed: 02/02/2023] Open
Abstract
Carotenoids are organic pigment molecules that play important roles in signalling, control of oxidative stress, and immunity. Fish allocate carotenoids to their eggs, which gives them the typical yellow to red colouration and supports their resistance against microbial infections. However, it is still unclear whether carotenoids act mainly as a shield against infection or are used up during the embryos' immune defence. We investigated this question with experimental families produced from wild-caught brown trout (Salmo trutta). Singly raised embryos were either exposed to the bacterial pathogen Pseudomonas fluorescens or sham-treated at one of two stages during their development. A previous study on these experimental families reported positive effects of egg carotenoids on embryo growth and resistance against the infection. Here, we quantified carotenoid consumption, i.e. the active metabolization of carotenoids into compounds that are not other carotenoid types, in these infected and sham-infected maternal sib groups. We found that carotenoid contents mostly decreased during embryogenesis. However, these decreases were neither linked to the virulence induced by the pathogen nor dependent on the time point of infection. We conclude that egg carotenoids are not significantly used up by the embryos' immune defence.
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17
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Zhang Z, Li D, Refaey MM, Xu W, Tang R, Li L. Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water. Front Microbiol 2018; 9:495. [PMID: 29616008 PMCID: PMC5869207 DOI: 10.3389/fmicb.2018.00495] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/02/2018] [Indexed: 12/21/2022] Open
Abstract
Host development influences gut microbial assemblies that may be confounded partly by dietary shifts and the changing environmental microbiota during ontogenesis. However, little is known about microbial colonization by excluding dietary effects and compositional differences in microbiota between the gut and environment at different ontogenetic stages. Herein, a developmental gut microbial experiment under controlled laboratory conditions was conducted with carnivorous southern catfish Silurus meridionalis fed on an identical prey with commensal and abundant microbiota. In this study, we provided a long-term analysis of gut microbiota associated with host age at 8, 18, 35, 65, and 125 day post-fertilization (dpf) and explored microbial relationships among host, food and water environment at 8, 35, and 125 dpf. The results showed that gut microbial diversity in southern catfish tended to increase linearly as host aged. Gut microbiota underwent significant temporal shifts despite similar microbial communities in food and rearing water during the host development and dramatically differed from the environmental microbiota. At the compositional abundance, Tenericutes and Fusobacteria were enriched in the gut and markedly varied with host age, whereas Spirochaetes and Bacteroidetes detected were persistently the most abundant phyla in food and water, respectively. In addition to alterations in individual microbial taxa, the individual differences in gut microbiota were at a lower level at the early stages than at the late stages and in which gut microbiota reached a stable status, suggesting the course of microbial successions. These results indicate that host development fundamentally shapes a key transition in microbial community structure, which is independent of dietary effects. In addition, the dominant taxa residing in the gut do not share their niche habitats with the abundant microbiota in the surrounding environment. It's inferred that complex gut microbiota could not be simple reflections of environmental microbiota. The knowledge enhances the understanding of gut microbial establishment in the developing fish and provides a useful resource for such studies of fish- or egg-associated microbiota in aquaculture.
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Affiliation(s)
- Zhimin Zhang
- Department of Fishery Resources and Environment, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, China
| | - Dapeng Li
- Department of Fishery Resources and Environment, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, China
| | - Mohamed M Refaey
- Department of Fishery Resources and Environment, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, China.,Department of Animal Production, Faculty of Agriculture, Mansoura University, Al-Mansoura, Egypt
| | - Weitong Xu
- Department of Fishery Resources and Environment, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, China
| | - Rong Tang
- Department of Fishery Resources and Environment, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, China
| | - Li Li
- Department of Fishery Resources and Environment, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, China
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18
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de Bruijn I, Liu Y, Wiegertjes GF, Raaijmakers JM. Exploring fish microbial communities to mitigate emerging diseases in aquaculture. FEMS Microbiol Ecol 2017; 94:4675208. [DOI: 10.1093/femsec/fix161] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Irene de Bruijn
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
| | - Yiying Liu
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
| | - Geert F Wiegertjes
- Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, Wageningen 6708WD, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, Leiden 2333 BE, Leiden, The Netherlands
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19
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Wilkins LGE, Marques da Cunha L, Menin L, Ortiz D, Vocat-Mottier V, Hobil M, Nusbaumer D, Wedekind C. Maternal allocation of carotenoids increases tolerance to bacterial infection in brown trout. Oecologia 2017; 185:351-363. [PMID: 28894954 DOI: 10.1007/s00442-017-3952-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 09/03/2017] [Indexed: 11/27/2022]
Abstract
Life-history theory predicts that iteroparous females allocate their resources differently among different breeding seasons depending on their residual reproductive value. In iteroparous salmonids there is typically much variation in egg size, egg number, and in the compounds that females allocate to their clutch. These compounds include various carotenoids whose functions are not sufficiently understood yet. We sampled 37 female and 35 male brown trout from natural streams, collected their gametes for in vitro fertilizations, experimentally produced 185 families in 7 full-factorial breeding blocks, raised the developing embryos singly (n = 2960), and either sham-treated or infected them with Pseudomonas fluorescens. We used female redness (as a measure of carotenoids stored in the skin) and their allocation of carotenoids to clutches to infer maternal strategies. Astaxanthin contents largely determined egg colour. Neither egg weight nor female size was correlated with the content of this carotenoid. However, astaxanthin content was positively correlated with larval growth and with tolerance against P. fluorescens. There was a negative correlation between female skin redness and the carotenoid content of their eggs. Although higher astaxanthin contents in the eggs were associated with an improvement of early fitness-related traits, some females appeared not to maximally support their current offspring as revealed by the negative correlation between female red skin colouration and egg carotenoid content. This correlation was not explained by female size and supports the prediction of a maternal trade-off between current and future reproduction.
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Affiliation(s)
- Laetitia G E Wilkins
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Department of Environmental Sciences, Policy and Management, 130 Mulford Hall #3114, University of California, Berkeley, CA, 94720, USA
| | - Lucas Marques da Cunha
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Laure Menin
- Institute of Chemical Sciences and Engineering ISIC, Batochime, EPFL, 1015, Lausanne, Switzerland
| | - Daniel Ortiz
- Institute of Chemical Sciences and Engineering ISIC, Batochime, EPFL, 1015, Lausanne, Switzerland
| | - Véronique Vocat-Mottier
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Matay Hobil
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - David Nusbaumer
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Claus Wedekind
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
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20
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Wilkins LGE, Fumagalli L, Wedekind C. Effects of host genetics and environment on egg-associated microbiotas in brown trout (Salmo trutta). Mol Ecol 2016; 25:4930-45. [PMID: 27507800 DOI: 10.1111/mec.13798] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/25/2016] [Accepted: 08/05/2016] [Indexed: 12/22/2022]
Abstract
Recent studies found fish egg-specific bacterial communities that changed over the course of embryogenesis, suggesting an interaction between the developing host and its microbiota. Indeed, single-strain infections demonstrated that the virulence of opportunistic bacteria is influenced by environmental factors and host immune genes. However, the interplay between a fish embryo host and its microbiota has not been studied yet at the community level. To test whether host genetics affects the assemblage of egg-associated bacteria, adult brown trout (Salmo trutta) were sampled from a natural population. Their gametes were used for full-factorial in vitro fertilizations to separate sire from dam effects. In total, 2520 embryos were singly raised under experimental conditions that differently support microbial growth. High-throughput 16S rRNA amplicon sequencing was applied to characterize bacterial communities on milt and fertilized eggs across treatments. Dam and sire identity influenced embryo mortality, time until hatching and composition of egg-associated microbiotas, but no link between bacterial communities on milt and on fertilized eggs could be found. Elevated resources increased embryo mortality and modified bacterial communities with a shift in their putative functional potential. Resource availability did not significantly affect any parental effects on embryo performance. Sire identity affected bacterial diversity that turned out to be a significant predictor of hatching time: embryos associated with high bacterial diversity hatched later. We conclude that both host genetics and the availability of resources define diversity and composition of egg-associated bacterial communities that then affect the life history of their hosts.
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Affiliation(s)
- Laetitia G E Wilkins
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Lausanne, Switzerland.
| | - Luca Fumagalli
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Lausanne, Switzerland
| | - Claus Wedekind
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Lausanne, Switzerland
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