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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Research Project #438312

Research Project: Characterization of the Microbiome of Aquaculture Production Systems and Development of Intervention Strategies to Improve Animal Health

Location: Cool and Cold Water Aquaculture Research

Project Number: 8082-32000-007-02-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2020
End Date: Jun 30, 2021

Objective:
Identify factors in production system microbiomes that can be used in strategies to improve animal health. Sub-objective 3.a Determine the microbial composition during biofilm development in raceways. Sub-objective 3.b Reduce the amount of Fc and Fp in biofilms. Sub-objective 3.c identify molecular mechanisms by which bacteria can invade biofilms formed by F. columnare or F. psychrophilum.

Approach:
The research is using a combination of synergistic approaches: metagenomics, bacteriology, microscopy and genetics to identify factors that can be used to improve animal health. In Subobjective 3.a, it will be determined how the microbiome of active trout raceways changes over time. DNA will be extracted from filtered water samples and surface swabs from the walls and baffles inside raceways. The 16S rRNA gene will be sequenced to determine the composition of the microbiome and detect Flavobacterium columnare and F. psychrophilum, two important pathogens of rainbow trout. Fluorescent in situ hybridization will be performed on biofilms to determine the three-dimensional composition of the biofilms. A temporal analysis will reveal when and where F. columnare and F. psychrophilum invade the biofilms. Biofilm formation will be simulated in the lab and different substrates will be assessed for their effect on biofilm formation. Subobjective 3.b. will assess how the maturity of the biofilm affects the ability of F. columnare and F. psychrophilum to invade biofilms. In addition, there will be tests of 50 different bacteria cultured from the farm of a stakeholder for their ability to interfere with the ability of F. columnare and F. pychrophilum to form biofilms. Sub-objective 3.c. will identify molecular mechanisms by which bacteria can invade biofilms formed by F. columnare or F. psychrophilum. IN-Seq, a novel transposon mutagenesis approach will be used to determine which transposon mutations in a population of mutants are selected for or against while invading biofilms formed by F. columnare or F. psychrophilum. Mutations will be characterized by moving them into a wild type background, complementing them with the wild type gene and confirming the phenotypes. Together these approaches aim at identifying and developing methods to disrupt pathogen containing biofilms. Results from this research will improve animal well-being, reduce antibiotic use and increase trout production efficiency and profitability.