Recirculating Aquaculture Systems (RAS) offer control over physicochemical and biological factors impacting aquaculture success. One understudied facet of RASs is the water microbiome. Oyster larval microbiomes are shaped by their aquatic microbiomes. Understanding the dynamics of and the factors shaping RAS microbiome may provide insights to how the microbiome can be a tool for optimizing larval production. This study’s goals were to investigate the microbiome stability of a RAS rearing oyster larvae across time and space, determine impacts of larval presence on the microbiome, and examine connections between larvae production outcomes and microbiome stability. Water samples were collected weekly from four compartments in the Thad Cochran Marine Aquaculture Center’s RAS at the University of Southern Mississippi during three runs spanning May-October 2019 (168 days), June-October 2020 (115 days), and May-October 2021 (165 days). Sequencing was done using the V6-V8 variable regions of the 16S rRNA gene targeting bacteria. Water quality parameters and larval survival-assessments were collected. The RAS achieved stable physiocochemical conditions and microbiomes by the third run. Each compartment, with a specific function in water-reclamation/larval rearing, contained distinct microbiomes. Larval presence was not a factor shaping any compartment’s microbiome. Connections between larvae and the Raceway (first water-reclamation stage) microbiome elevated over time, and instability loosely correlated with declining larval performance. Establishing baseline microbiomes present in closed-systems and further exploring connections between production and RAS microbiomes would enhance knowledge of RAS microbiome dynamics. The better the RAS microbiome is understood, the more valuable a tool in aquaculture it can be.
","abstract_html":"<p>Recirculating Aquaculture Systems (RAS) offer control over physicochemical and biological factors impacting aquaculture success. One understudied facet of RASs is the water microbiome. Oyster larval microbiomes are shaped by their aquatic microbiomes. Understanding the dynamics of and the factors shaping RAS microbiome may provide insights to how the microbiome can be a tool for optimizing larval production. This study’s goals were to investigate the microbiome stability of a RAS rearing oyster larvae across time and space, determine impacts of larval presence on the microbiome, and examine connections between larvae production outcomes and microbiome stability. Water samples were collected weekly from four compartments in the Thad Cochran Marine Aquaculture Center’s RAS at the University of Southern Mississippi during three runs spanning May-October 2019 (168 days), June-October 2020 (115 days), and May-October 2021 (165 days). Sequencing was done using the V6-V8 variable regions of the 16S rRNA gene targeting bacteria. Water quality parameters and larval survival-assessments were collected. The RAS achieved stable physiocochemical conditions and microbiomes by the third run. Each compartment, with a specific function in water-reclamation/larval rearing, contained distinct microbiomes. Larval presence was not a factor shaping any compartment’s microbiome. Connections between larvae and the Raceway (first water-reclamation stage) microbiome elevated over time, and instability loosely correlated with declining larval performance. Establishing baseline microbiomes present in closed-systems and further exploring connections between production and RAS microbiomes would enhance knowledge of RAS microbiome dynamics. The better the RAS microbiome is understood, the more valuable a tool in aquaculture it can be.</p>","abstract_has_math":false,"creators":["Townsend, Isabelle"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Masters Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Dr. Leila Hamdan","Dr. Chet Rakocinski","Dr. Kristina Mojica"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-08-01T07:00:00Z","date_published":"2024-08-01T07:00:00Z","updated_at":"2026-07-24T05:45:40Z","subjects":["microbiome","RAS","crassostrea virginica larvae","microbial stability","aquaculture","Bioinformatics","Environmental Microbiology and Microbial Ecology","Molecular Biology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://aquila.usm.edu/masters_theses/1060","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Dr. Leila Hamdan","Dr. Chet Rakocinski","Dr. Kristina Mojica"]},{"key":"dc:creator","label":"Author","values":["Townsend, Isabelle"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2024-06-14T07:00:00Z"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Masters Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["microbiome","RAS","crassostrea virginica larvae","microbial stability","aquaculture","Bioinformatics","Environmental Microbiology and Microbial Ecology","Molecular Biology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://aquila.usm.edu/masters_theses/1060"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Recirculating Aquaculture Systems (RAS) offer control over physicochemical and biological factors impacting aquaculture success. One understudied facet of RASs is the water microbiome. Oyster larval microbiomes are shaped by their aquatic microbiomes. Understanding the dynamics of and the factors shaping RAS microbiome may provide insights to how the microbiome can be a tool for optimizing larval production. This study’s goals were to investigate the microbiome stability of a RAS rearing oyster larvae across time and space, determine impacts of larval presence on the microbiome, and examine connections between larvae production outcomes and microbiome stability. Water samples were collected weekly from four compartments in the Thad Cochran Marine Aquaculture Center’s RAS at the University of Southern Mississippi during three runs spanning May-October 2019 (168 days), June-October 2020 (115 days), and May-October 2021 (165 days). Sequencing was done using the V6-V8 variable regions of the 16S rRNA gene targeting bacteria. Water quality parameters and larval survival-assessments were collected. The RAS achieved stable physiocochemical conditions and microbiomes by the third run. Each compartment, with a specific function in water-reclamation/larval rearing, contained distinct microbiomes. Larval presence was not a factor shaping any compartment’s microbiome. Connections between larvae and the Raceway (first water-reclamation stage) microbiome elevated over time, and instability loosely correlated with declining larval performance. Establishing baseline microbiomes present in closed-systems and further exploring connections between production and RAS microbiomes would enhance knowledge of RAS microbiome dynamics. The better the RAS microbiome is understood, the more valuable a tool in aquaculture it can be.
"]},{"key":"dc:title","label":"Title","values":["Investigation of the Microbiome of a Recirculating Aquaculture System (RAS) for Crassostrea virginica Larvae"]}]}],"canonical_facts":{"dc:contributor":["Dr. Leila Hamdan","Dr. Chet Rakocinski","Dr. Kristina Mojica"],"dc:creator":["Townsend, Isabelle"],"dc:date.available":["2024-06-14T07:00:00Z"],"dc:description.abstract":["Recirculating Aquaculture Systems (RAS) offer control over physicochemical and biological factors impacting aquaculture success. One understudied facet of RASs is the water microbiome. Oyster larval microbiomes are shaped by their aquatic microbiomes. Understanding the dynamics of and the factors shaping RAS microbiome may provide insights to how the microbiome can be a tool for optimizing larval production. This study’s goals were to investigate the microbiome stability of a RAS rearing oyster larvae across time and space, determine impacts of larval presence on the microbiome, and examine connections between larvae production outcomes and microbiome stability. Water samples were collected weekly from four compartments in the Thad Cochran Marine Aquaculture Center’s RAS at the University of Southern Mississippi during three runs spanning May-October 2019 (168 days), June-October 2020 (115 days), and May-October 2021 (165 days). Sequencing was done using the V6-V8 variable regions of the 16S rRNA gene targeting bacteria. Water quality parameters and larval survival-assessments were collected. The RAS achieved stable physiocochemical conditions and microbiomes by the third run. Each compartment, with a specific function in water-reclamation/larval rearing, contained distinct microbiomes. Larval presence was not a factor shaping any compartment’s microbiome. Connections between larvae and the Raceway (first water-reclamation stage) microbiome elevated over time, and instability loosely correlated with declining larval performance. Establishing baseline microbiomes present in closed-systems and further exploring connections between production and RAS microbiomes would enhance knowledge of RAS microbiome dynamics. The better the RAS microbiome is understood, the more valuable a tool in aquaculture it can be.
"],"dc:identifier":["https://aquila.usm.edu/masters_theses/1060"],"dc:subject":["microbiome","RAS","crassostrea virginica larvae","microbial stability","aquaculture","Bioinformatics","Environmental Microbiology and Microbial Ecology","Molecular Biology"],"dc:title":["Investigation of the Microbiome of a Recirculating Aquaculture System (RAS) for Crassostrea virginica Larvae"],"thesis:degree_level":["Masters Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T05:45:40Z"}