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Romero J, Díaz O, Miranda CD, Rojas R. Red Cusk-Eel ( Genypterus chilensis) Gut Microbiota Description of Wild and Aquaculture Specimens. Microorganisms 2022; 10:microorganisms10010105. [PMID: 35056554 PMCID: PMC8779451 DOI: 10.3390/microorganisms10010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
Chile has promoted the diversification of aquaculture and red cusk-eel (Genypterus chilensis) is one of the prioritized species. However, many aspects of the biology of the species are unknown or have little information available. These include intestinal microbiota, an element that may play an important role in the nutrition and defense of cultured animals for meat production. This study compares the microbiota composition of the intestinal contents of wild and aquaculture fish to explore the microbial communities present and their potential contribution to the host. DNA was extracted from the intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced using the Ion Torrent platform. After the examination of the sequences, strong differences were found in the composition at the level of phylum, being Firmicutes and Tenericutes the most abundant in aquaculture and wild condition, respectively. At the genus level, the Vagococcus (54%) and Mycoplasma (97%) were the most prevalent in the microbial community of aquaculture and wild condition, respectively. The evaluation of predicted metabolic pathways in these metagenomes showed that in wild condition there is an important presence of lipid metabolism belonging to the unsaturated fatty acid synthesis. In the aquaculture condition, the metabolism of terpenoids and polyketides were relevant. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of red cusk-eel (Genypterus chilensis) of wild and aquaculture origin using high-throughput sequencing.
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Affiliation(s)
- Jaime Romero
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Macul, Santiago 783090, Chile;
- Correspondence: ; Tel.: +56-2-29781524
| | - Osmán Díaz
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Macul, Santiago 783090, Chile;
| | - Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile; (C.D.M.); (R.R.)
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile; (C.D.M.); (R.R.)
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Valderrama B, Ruiz JJ, Gutiérrez MS, Alveal K, Caruffo M, Oliva M, Flores H, Silva A, Toro M, Reyes-Jara A, Navarrete P. Cultivable Yeast Microbiota from the Marine Fish Species Genypterus chilensis and Seriolella violacea. J Fungi (Basel) 2021; 7:515. [PMID: 34203130 DOI: 10.3390/jof7070515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/04/2023] Open
Abstract
Because of its outstanding biological and industrial importance, many efforts have been made to characterize the mycobiota of new environments and their biochemical and biotechnological potentials. Gut mycobiota can be a source of novel yeasts with the potential to be used as probiotics or have industrial applications. In this work, we characterized two as-yet unexplored yeast communities from the intestinal content of the cultured marine Chilean fishes Genypterus chilensis (G. chilensis) and Seriolella violacea (S. violacea). Yeasts were isolated through culture, identified by sequencing their ITS region, and characterized their enzymatic profile with API®ZYM. Rhodotorula mucilaginosa was identified in both fish species. For the first time, Candida palmioleophila, Candida pseudorugosa, Cystobasidium slooffiae, and a member of the Yamadazyma genus were also identified and described as part of the normal fish gut–microbiota. Furthermore, the diverse enzymatic profile exhibited by some of these isolates suggests that it may be possible to develop novel applications for them, such as new probiotics and other biotechnological applications.
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Dettleff P, Zuloaga R, Fuentes M, Estrada JM, Molina A, Valdés JA. Temperature effect on oxidative stress and egg quality-related genes on post-ovulatory eggs and ovary of red cusk-eel ( Genypterus chilensis). J Fish Biol 2021; 98:1475-1480. [PMID: 33423306 DOI: 10.1111/jfb.14672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/26/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Red cusk-eel (Genypterus chilensis) is a native species with potential for Chilean aquaculture diversification. However, no information exists on the effects of temperature on oxidative stress and eggs quality markers in post-ovulatory eggs and ovary of this species. We determine that high and low temperature generate oxidative damage on post-ovulatory eggs, with no effect on ovary. Temperature induces thermal stress markers expression on post-ovulatory eggs, and modulates antioxidant and eggs quality markers on post-ovulatory eggs and ovary, information to consider for quality evaluation in the red cusk-eel management.
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Affiliation(s)
- Phillip Dettleff
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Rodrigo Zuloaga
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - Marcia Fuentes
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - Juan M Estrada
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Alfredo Molina
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Juan A Valdés
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
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Levican A, Fisher JC, McLellan SL, Avendaño-Herrera R. Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing. Animals (Basel) 2020; 10:ani10061055. [PMID: 32570967 PMCID: PMC7341507 DOI: 10.3390/ani10061055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
The red conger eel (Genypterus chilensis, Guichenot) is a native species included in the Chilean Aquaculture Diversification Program due to high commercial demand. In the context of intensified farming, prior reports link two disease outbreaks with emerging pathogens in the Vibrio and Tenacibaculum genera. However, the roles remain unclear for the bacterial community and each specific bacterium is associated with the rearing environment for healthy specimens. The success of red conger eel farming therefore warrants research into the bacterial composition of aquaculture conditions and the antimicrobial susceptibilities thereof. This study used culturing methods and high-throughput sequencing to describe the bacterial community associated with water in which G. chilensis was farmed. With culturing methods, the predominant genera were Vibrio (21.6%), Pseudolteromonas (15.7%), Aliivibrio (13.7%), and Shewanella (7.8%). Only a few bacterial isolates showed amylase, gelatinase, or lipase activity, and almost all showed inhibition zones to commonly-used antibiotics in aquaculture. By contrast, high-throughput sequencing established Paraperlucidibaca, Colwellia, Polaribacter, Saprospiraceae, and Tenacibaculum as the predominant genera, with Vibrio ranking twenty-seventh in abundance. High-throughput sequencing also established a link between previous outbreaks with increased relative abundances of Vibrio and Tenacibaculum. Therefore, monitoring the presence and abundance of these potential pathogens could be useful in providing prophylactic measures to prevent future outbreaks.
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Affiliation(s)
- Arturo Levican
- Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso 2373223, Chile
- Correspondence: or (A.L.); or (R.A.-H.)
| | - Jenny C. Fisher
- Biology Department, Indiana University Northwest, Gary, IN 46408, USA;
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA;
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar 2571015, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4030000, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Casablanca 2480000, Chile
- Correspondence: or (A.L.); or (R.A.-H.)
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Hurtado L, Miranda CD, Rojas R, Godoy FA, Añazco MA, Romero J. Live Feeds Used in the Larval Culture of Red Cusk Eel, Genypterus chilensis, Carry High Levels of Antimicrobial-Resistant Bacteria and Antibiotic-Resistance Genes (ARGs). Animals (Basel) 2020; 10:ani10030505. [PMID: 32197370 PMCID: PMC7142716 DOI: 10.3390/ani10030505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/29/2020] [Accepted: 03/10/2020] [Indexed: 11/27/2022] Open
Abstract
Simple Summary The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibiotics, mainly florfenicol. In this study, the role of live prey (rotifers and the brine shrimp Artemia franciscana) used to feed fish larvae as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis was investigated. Samples of live feeds were collected during the larval growth period and their bacterial contents were determined. High levels of potentially opportunistic pathogens, such as Vibrio spp., as well as florfenicol-resistant bacteria, were detected. Sixty-five florfenicol-resistant isolates were recovered from these cultures and identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%), which exhibited a high incidence of co-resistance to the antibiotics streptomycin, oxytetracycline, co-trimoxazole, and kanamycin. The majority of them carried the florfenicol-resistance encoding genes floR and fexA. The high prevalence of antibiotic-resistant bacteria and the associated genetic elements in live feed administered to reared fish larvae requires the prompt implementation of efficient management strategies to prevent future therapy failures in fish larval cultures and the spread of antibiotic-resistant bacteria to associated aquatic environments. Abstract The culture of red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibacterials. The main aim of this study was to evaluate the role of live feed as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis. Samples of rotifer and Artemia cultures used as live feed were collected during the larval growth period and culturable bacterial counts were performed using a spread plate method. Rotifer and Artemia cultures exhibited high levels of resistant bacteria (8.03 × 104 to 1.79 × 107 CFU/g and 1.47 × 106 to 3.50 × 108 CFU/g, respectively). Sixty-five florfenicol-resistant isolates were identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%) using 16S rRNA gene sequence analysis. A high incidence of resistance to streptomycin (93.8%), oxytetracycline (89.2%), co-trimoxazole (84.6%), and kanamycin (73.8%) was exhibited by resistant isolates. A high proportion of isolates (76.9%) carried the florfenicol-resistance encoding genes floR and fexA, as well as plasmid DNA (75.0%). The high prevalence of multiresistant bacteria in live feed increases the incidence of the resistant microbiota in reared fish larvae, thus proper monitoring and management strategies for live feed cultures appear to be a priority for preventing future therapy failures in fish larval cultures.
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Affiliation(s)
- Luz Hurtado
- Programa Cooperativo de Doctorado en Acuicultura, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile;
| | - Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile;
- Centro AquaPacífico, Universidad Católica del Norte, Coquimbo 1780000, Chile
- Correspondence: ; Tel.: +56-512209762
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile;
- Centro AquaPacífico, Universidad Católica del Norte, Coquimbo 1780000, Chile
| | - Félix A. Godoy
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile; (F.A.G.); (M.A.A.)
| | - Mark A. Añazco
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile; (F.A.G.); (M.A.A.)
| | - Jaime Romero
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Macul, Santiago 7810000, Chile;
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Dettleff P, Hormazabal E, Aedo J, Fuentes M, Meneses C, Molina A, Valdes JA. Identification and Evaluation of Long Noncoding RNAs in Response to Handling Stress in Red Cusk-Eel ( Genypterus chilensis) via RNA-seq. Mar Biotechnol (NY) 2020; 22:94-108. [PMID: 31748906 DOI: 10.1007/s10126-019-09934-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
The red cusk-eel (Genypterus chilensis) is a native species with strong potential to support Chilean aquaculture diversification. Under commercial conditions, fish are exposed to several stressors. To date, little is known about the mechanism involved in the stress response of red cusk-eel, and there is no information related to the regulation mediated by long noncoding RNAs (lncRNAs). The objective of this work was to identify for the first time the lncRNAs in the transcriptome of G. chilensis and to evaluate the differential expression levels of lncRNAs in the liver, head kidney, and skeletal muscle in response to handling stress. We used previously published transcriptome data to identify the lncRNAs by applying a series of filters based on annotation information in several databases to discard coding sequences. We identified a total of 14,614 putative lncRNAs in the transcriptome of red cusk-eel, providing a useful lncRNA reference resource to be used in future studies. We evaluated their differential expression in response to handling stress in the liver, head kidney, and skeletal muscle, identifying 112, 323, and 108 differentially expressed lncRNAs, respectively. The results suggest that handling stress in red cusk-eel generate an altered metabolic status in liver, altered immune response in head kidney, and skeletal muscle atrophy through an important coding and noncoding gene network. This is the first study that identifies lncRNAs in Genypterus genus and that evaluates the relation between handling stress and lncRNAs in teleost fish, thereby providing valuable information regarding noncoding responses to stress in Genypterus species.
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Affiliation(s)
- Phillip Dettleff
- Laboratory of Molecular Biotechnology, Faculty of Life Sciences, Andres Bello University, Republica 440, 8370186, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), 4070386, Concepción, Chile
| | - Elizabeth Hormazabal
- Laboratory of Molecular Biotechnology, Faculty of Life Sciences, Andres Bello University, Republica 440, 8370186, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), 4070386, Concepción, Chile
| | - Jorge Aedo
- Laboratory of Molecular Biotechnology, Faculty of Life Sciences, Andres Bello University, Republica 440, 8370186, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), 4070386, Concepción, Chile
| | - Marcia Fuentes
- Laboratory of Molecular Biotechnology, Faculty of Life Sciences, Andres Bello University, Republica 440, 8370186, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), 4070386, Concepción, Chile
| | - Claudio Meneses
- Plant Biotechnology Center, Andres Bello University, 8370186, Santiago, Chile
- FONDAP Center for Genome Regulation, Andres Bello University, 8370186, Santiago, Chile
| | - Alfredo Molina
- Laboratory of Molecular Biotechnology, Faculty of Life Sciences, Andres Bello University, Republica 440, 8370186, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), 4070386, Concepción, Chile
- CIMARQ, Andres Bello University, Quintay, Chile
| | - Juan Antonio Valdes
- Laboratory of Molecular Biotechnology, Faculty of Life Sciences, Andres Bello University, Republica 440, 8370186, Santiago, Chile.
- Interdisciplinary Center for Aquaculture Research (INCAR), 4070386, Concepción, Chile.
- CIMARQ, Andres Bello University, Quintay, Chile.
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González P, Dettleff P, Valenzuela C, Estrada JM, Valdés JA, Meneses C, Molina A. Evaluating the genetic structure of wild and commercial red cusk-eel ( Genypterus chilensis) populations through the development of novel microsatellite markers from a reference transcriptome. Mol Biol Rep 2019; 46:5875-5882. [PMID: 31598817 DOI: 10.1007/s11033-019-05021-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/03/2019] [Indexed: 11/30/2022]
Abstract
The red cusk-eel (Genypterus chilensis) is a native Chilean species with a high-value market, with the potential to diversify Chilean aquaculture. The objective of this study was to develop a set of microsatellite markers, estimate genetic parameters, determine population differentiation, and identify the population structure of wild and commercial populations of G. chilensis. We discovered 6427 microsatellites markers from RNA-seq data, of which 54.9%, 20.2% and 16.8% were di-, tri-, and tetranucleotides, respectively. We used 12 of these markers to genotype two sets of broodstock, one group from commercial fish, and one group from wild fish from the Coquimbo Region of G. chilensis. We estimate the genetic parameters of the markers, selecting ten polymorphic markers (PIC > 0.5). We observed differences in the inbreeding coefficient among populations, with high values of inbreeding in one broodstock set and lower values in the other groups. The evaluation of population differentiation using Fst showed small (0.0195) to large (0.1888) genetic differentiation between the groups. The structure analysis showed that commercial and wild groups were formed by three clusters, without relevant evidence of admixture process, suggesting that groups evaluated in this study are formed of at least three subpopulations of G. chilensis, which could be explained by the low or lack of migration suggested for this species. This is the first study that identifies a high number of molecular markers in G. chilensis, providing relevant information of the genetic structure of commercial and wild population of this species.
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Affiliation(s)
- Pamela González
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Phillip Dettleff
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Cristián Valenzuela
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Juan Manuel Estrada
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Juan Antonio Valdés
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Alfredo Molina
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile.
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile.
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