Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

ABSTRACT Flowthrough and pond aquaculture system microbiome management practices aim to mitigate fish disease and stress. However, the operational success of recirculating aquaculture systems (RAS) depends directly on system microbial community activities. In RAS, each component environment is engin...

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Autores principales:	Ryan P. Bartelme, Matthew C. Smith, Osvaldo J. Sepulveda-Villet, Ryan J. Newton
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Flavobacterium Nitrospira ammonia-oxidizing Archaea aquaponics biofilter comammox Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/8ea6c4d9ef714e1b8bf481ba1d7c90d4
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spelling	oai:doaj.org-article:8ea6c4d9ef714e1b8bf481ba1d7c90d42021-11-15T15:22:27ZComponent Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems10.1128/mSphere.00143-192379-5042https://doaj.org/article/8ea6c4d9ef714e1b8bf481ba1d7c90d42019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00143-19https://doaj.org/toc/2379-5042ABSTRACT Flowthrough and pond aquaculture system microbiome management practices aim to mitigate fish disease and stress. However, the operational success of recirculating aquaculture systems (RAS) depends directly on system microbial community activities. In RAS, each component environment is engineered for a specific microbial niche for waste management, as the water continuously flowing through the system must be processed before returning to the rearing tank. In this study, we compared waste management component microbiomes (rearing tank water, pH correction tank, solid-waste clarifier, biofilter, and degassing tower) within a commercial-scale freshwater RAS by high-throughput 16S rRNA gene sequencing. To assess consistency among freshwater RAS microbiomes, we also compared the microbial community compositions of six aquaculture and aquaponic farms. Community assemblages reflected site and source water relationships, and the presence of a hydroponic subsystem was a major community determinant. In contrast to the facility-specific community composition, some sequence variants, mainly classified into Flavobacterium, Cetobacterium, the family Sphingomonadaceae, and nitrifying guilds of ammonia-oxidizing archaea and Nitrospira, were common across all facilities. The findings of this study suggest that, independently of system design, core taxa exist across RAS rearing similar fish species but that system design informs the individual aquatic microbiome assemblages. Future RAS design would benefit from understanding the roles of these core taxa and then capitalizing on their activities to further reduce system waste/added operational controls. IMPORTANCE Recirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and AP rely on microbial consortia for maintaining water quality and promoting fish/plant health, but little is known about the microorganisms actually present. This lack of knowledge prevents optimization of designs and operational controls to target the growth of beneficial microbial species or consortia. The significance of our research is in identifying the common microorganisms that inhabit production RAS and AP and the operational factors that influence which microorganisms colonize and become abundant. Identifying these organisms is a first step toward advanced control of microbial activities that improve reproducibility and reduce costs.Ryan P. BartelmeMatthew C. SmithOsvaldo J. Sepulveda-VilletRyan J. NewtonAmerican Society for MicrobiologyarticleFlavobacteriumNitrospiraammonia-oxidizing ArchaeaaquaponicsbiofiltercomammoxMicrobiologyQR1-502ENmSphere, Vol 4, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Flavobacterium Nitrospira ammonia-oxidizing Archaea aquaponics biofilter comammox Microbiology QR1-502
spellingShingle	Flavobacterium Nitrospira ammonia-oxidizing Archaea aquaponics biofilter comammox Microbiology QR1-502 Ryan P. Bartelme Matthew C. Smith Osvaldo J. Sepulveda-Villet Ryan J. Newton Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems
description	ABSTRACT Flowthrough and pond aquaculture system microbiome management practices aim to mitigate fish disease and stress. However, the operational success of recirculating aquaculture systems (RAS) depends directly on system microbial community activities. In RAS, each component environment is engineered for a specific microbial niche for waste management, as the water continuously flowing through the system must be processed before returning to the rearing tank. In this study, we compared waste management component microbiomes (rearing tank water, pH correction tank, solid-waste clarifier, biofilter, and degassing tower) within a commercial-scale freshwater RAS by high-throughput 16S rRNA gene sequencing. To assess consistency among freshwater RAS microbiomes, we also compared the microbial community compositions of six aquaculture and aquaponic farms. Community assemblages reflected site and source water relationships, and the presence of a hydroponic subsystem was a major community determinant. In contrast to the facility-specific community composition, some sequence variants, mainly classified into Flavobacterium, Cetobacterium, the family Sphingomonadaceae, and nitrifying guilds of ammonia-oxidizing archaea and Nitrospira, were common across all facilities. The findings of this study suggest that, independently of system design, core taxa exist across RAS rearing similar fish species but that system design informs the individual aquatic microbiome assemblages. Future RAS design would benefit from understanding the roles of these core taxa and then capitalizing on their activities to further reduce system waste/added operational controls. IMPORTANCE Recirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and AP rely on microbial consortia for maintaining water quality and promoting fish/plant health, but little is known about the microorganisms actually present. This lack of knowledge prevents optimization of designs and operational controls to target the growth of beneficial microbial species or consortia. The significance of our research is in identifying the common microorganisms that inhabit production RAS and AP and the operational factors that influence which microorganisms colonize and become abundant. Identifying these organisms is a first step toward advanced control of microbial activities that improve reproducibility and reduce costs.
format	article
author	Ryan P. Bartelme Matthew C. Smith Osvaldo J. Sepulveda-Villet Ryan J. Newton
author_facet	Ryan P. Bartelme Matthew C. Smith Osvaldo J. Sepulveda-Villet Ryan J. Newton
author_sort	Ryan P. Bartelme
title	Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems
title_short	Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems
title_full	Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems
title_fullStr	Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems
title_full_unstemmed	Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems
title_sort	component microenvironments and system biogeography structure microorganism distributions in recirculating aquaculture and aquaponic systems
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/8ea6c4d9ef714e1b8bf481ba1d7c90d4
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Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

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