Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration
Abstract Background Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to e...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-08-01
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| Series: | Animal Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s42523-021-00116-1 |
| _version_ | 1818904993408745472 |
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| author | Aaron C. Ericsson Susheel B. Busi Daniel J. Davis Henda Nabli David C. Eckhoff Rebecca A. Dorfmeyer Giedre Turner Payton S. Oswalt Marcus J. Crim Elizabeth C. Bryda |
| author_facet | Aaron C. Ericsson Susheel B. Busi Daniel J. Davis Henda Nabli David C. Eckhoff Rebecca A. Dorfmeyer Giedre Turner Payton S. Oswalt Marcus J. Crim Elizabeth C. Bryda |
| author_sort | Aaron C. Ericsson |
| collection | DOAJ |
| description | Abstract Background Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to equilibrate following installation, before fish can be introduced. There is little information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium in RAS in general. Methods A zebrafish housing system was monitored at multiple different system sites including tank water in six different tanks, pre- and post-particulate filter water, the fluidized bed biofilter substrate, post-carbon filter water, and water leaving the ultra-violet (UV) disinfection unit and entering the tanks. All of these samples were collected in quadruplicate, from prior to population of the system with zebrafish through 18 weeks post-population, and analyzed using both 16S rRNA amplicon sequencing and culture using multiple agars and annotation of isolates via matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. Sequencing data were analyzed using traditional methods, network analyses of longitudinal data, and integration of culture and sequence data. Results The water microbiome, dominated by Cutibacterium and Staphylococcus spp., reached a relatively stable richness and composition by approximately three to four weeks post-population, but continued to evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter and water leaving the UV disinfection unit were distinct from water at all other sites. Core taxa detected using molecular methods comprised 36 amplicon sequence variants, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, and showed moderate agreement with sequencing data. Conclusions The microbiome of commercial RAS used for research zebrafish reaches a relatively stable state by four weeks post-population and would be expected to be suitable for experimental use following that time-point. |
| first_indexed | 2024-12-19T21:16:16Z |
| format | Article |
| id | doaj.art-60e65d57f04744128c81c873f1bef564 |
| institution | Directory Open Access Journal |
| issn | 2524-4671 |
| language | English |
| last_indexed | 2024-12-19T21:16:16Z |
| publishDate | 2021-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Animal Microbiome |
| spelling | doaj.art-60e65d57f04744128c81c873f1bef5642022-12-21T20:05:20ZengBMCAnimal Microbiome2524-46712021-08-013111610.1186/s42523-021-00116-1Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibrationAaron C. Ericsson0Susheel B. Busi1Daniel J. Davis2Henda Nabli3David C. Eckhoff4Rebecca A. Dorfmeyer5Giedre Turner6Payton S. Oswalt7Marcus J. Crim8Elizabeth C. Bryda9Department of Veterinary Pathobiology, College of Veterinary Medicine, University of MissouriSystems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of LuxembourgDepartment of Veterinary Pathobiology, College of Veterinary Medicine, University of MissouriDepartment of Veterinary Pathobiology, College of Veterinary Medicine, University of MissouriIDEXX BioAnalyticsDepartment of Veterinary Pathobiology, College of Veterinary Medicine, University of MissouriDepartment of Veterinary Pathobiology, College of Veterinary Medicine, University of MissouriDepartment of Veterinary Pathobiology, College of Veterinary Medicine, University of MissouriIDEXX BioAnalyticsDepartment of Veterinary Pathobiology, College of Veterinary Medicine, University of MissouriAbstract Background Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to equilibrate following installation, before fish can be introduced. There is little information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium in RAS in general. Methods A zebrafish housing system was monitored at multiple different system sites including tank water in six different tanks, pre- and post-particulate filter water, the fluidized bed biofilter substrate, post-carbon filter water, and water leaving the ultra-violet (UV) disinfection unit and entering the tanks. All of these samples were collected in quadruplicate, from prior to population of the system with zebrafish through 18 weeks post-population, and analyzed using both 16S rRNA amplicon sequencing and culture using multiple agars and annotation of isolates via matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. Sequencing data were analyzed using traditional methods, network analyses of longitudinal data, and integration of culture and sequence data. Results The water microbiome, dominated by Cutibacterium and Staphylococcus spp., reached a relatively stable richness and composition by approximately three to four weeks post-population, but continued to evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter and water leaving the UV disinfection unit were distinct from water at all other sites. Core taxa detected using molecular methods comprised 36 amplicon sequence variants, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, and showed moderate agreement with sequencing data. Conclusions The microbiome of commercial RAS used for research zebrafish reaches a relatively stable state by four weeks post-population and would be expected to be suitable for experimental use following that time-point.https://doi.org/10.1186/s42523-021-00116-1ZebrafishDanio rerioAquariumRecirculating aquaculture systemHousingMicrobiota |
| spellingShingle | Aaron C. Ericsson Susheel B. Busi Daniel J. Davis Henda Nabli David C. Eckhoff Rebecca A. Dorfmeyer Giedre Turner Payton S. Oswalt Marcus J. Crim Elizabeth C. Bryda Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration Animal Microbiome Zebrafish Danio rerio Aquarium Recirculating aquaculture system Housing Microbiota |
| title | Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration |
| title_full | Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration |
| title_fullStr | Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration |
| title_full_unstemmed | Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration |
| title_short | Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration |
| title_sort | molecular and culture based assessment of the microbiome in a zebrafish danio rerio housing system during set up and equilibration |
| topic | Zebrafish Danio rerio Aquarium Recirculating aquaculture system Housing Microbiota |
| url | https://doi.org/10.1186/s42523-021-00116-1 |
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