Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries
The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifer...
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2024-11-01
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| author | Dimitrios Skliros Maria Kostakou Constantina Kokkari Maria Ioanna Tsertou Christina Pavloudi Haris Zafeiropoulos Pantelis Katharios Emmanouil Flemetakis |
| author_facet | Dimitrios Skliros Maria Kostakou Constantina Kokkari Maria Ioanna Tsertou Christina Pavloudi Haris Zafeiropoulos Pantelis Katharios Emmanouil Flemetakis |
| author_sort | Dimitrios Skliros |
| collection | DOAJ |
| description | The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and <i>Artemia</i>, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of <i>Vibrio</i>, <i>Tenacibaculum</i>, and <i>Photobacterium</i> genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region. |
| format | Article |
| id | doaj-art-32bca74c254c4b82b00f692fca46f500 |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj-art-32bca74c254c4b82b00f692fca46f5002025-08-20T02:48:01ZengMDPI AGMicroorganisms2076-26072024-11-011211228110.3390/microorganisms12112281Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish HatcheriesDimitrios Skliros0Maria Kostakou1Constantina Kokkari2Maria Ioanna Tsertou3Christina Pavloudi4Haris Zafeiropoulos5Pantelis Katharios6Emmanouil Flemetakis7Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, GreeceLaboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, GreeceInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, GreeceInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, GreeceEuropean Marine Biological Resource Centre—European Research Infrastructure Consortium (EMBRC-ERIC), 75252 Paris, FranceLaboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, BelgiumInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, GreeceLaboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, GreeceThe importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and <i>Artemia</i>, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of <i>Vibrio</i>, <i>Tenacibaculum</i>, and <i>Photobacterium</i> genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.https://www.mdpi.com/2076-2607/12/11/2281microbial communitymetagenomicsmicrobial ecologybacteriomeenvironmental microbiology |
| spellingShingle | Dimitrios Skliros Maria Kostakou Constantina Kokkari Maria Ioanna Tsertou Christina Pavloudi Haris Zafeiropoulos Pantelis Katharios Emmanouil Flemetakis Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries Microorganisms microbial community metagenomics microbial ecology bacteriome environmental microbiology |
| title | Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries |
| title_full | Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries |
| title_fullStr | Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries |
| title_full_unstemmed | Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries |
| title_short | Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries |
| title_sort | unveiling emerging opportunistic fish pathogens in aquaculture a comprehensive seasonal study of microbial composition in mediterranean fish hatcheries |
| topic | microbial community metagenomics microbial ecology bacteriome environmental microbiology |
| url | https://www.mdpi.com/2076-2607/12/11/2281 |
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