Scaling Up Local Vegetable and Fruit Production in the Inland Northwest: Overcoming Constraints for Sustainable Agricultural Development Grant uri icon

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abstract

  • NON-TECHNICAL SUMMARY: Diseases are the major factor affecting economic viability and hampering sustained growth of the aquaculture industry. Over a 16 year period, the University of Idaho and the USDA-Agriculture Research Service have selectively bred rainbow trout that flourish when fed an all plant protein (high soy) diet. After eight generations, the selected strain exhibits rapid growth, altered intestinal morphology and higher survival in bacterial and viral challenge tests while fed an all plant protein diet compared to commercial strains of trout. We propose to exploit this unique trout strain to identify genetic mechanisms and to assess the influence of intestinal microbiota (IM) on disease resistance using high-throughput technologies and standard immunological assays.We will analyze IM under homeostatic, as well as disease challenged conditions, during early developmental stages that are critical for disease susceptibility and development of host-microbiota interactions. From this, we will be able to discern whether the IM and host gastrointestinal associated lymphatic tissue (GALT) are unique, in the absence of the diet-type and intestinal enteritis effects which confounded our previous results. In addition, we will further evaluate the IM and host intestinal gene expression in the context of both viral and bacterial disease challenges, to investigate the resilience of the selected strains' gut microbial ecology to the perturbation of exposure to virulent pathogens.We expect to produce evidence of the IM and/or the host genome as primary factors influencing disease resistance in the ARS-UI selected fish, by eliminating the dietary effects later in life that confound previous studies. This has widespread implications for rainbow trout and salmon farming, but also extends to other species produced in the USA and globally. Fish health and drug-free disease management were recently identified as a high priority for Idaho trout producers.

    OBJECTIVES: Diseases are the major factor affecting economic viability and hampering sustained growth of the aquaculture industry. Over a 16 year period, the University of Idaho and the USDA-Agriculture Research Service have selectively bred rainbow trout that flourish when fed an all plant protein (high soy) diet. After eight generations, the selected strain exhibits rapid growth, altered intestinal morphology and higher survival in bacterial and viral challenge tests while fed an all plant protein diet compared to commercial strains of trout. We propose to exploit this unique trout strain to identify genetic mechanisms and to assess the influence of intestinal microbiota (IM) on disease resistance using high-throughput technologies and standard immunological assays. We will analyze IM under homeostatic, as well as disease challenged conditions, during early developmental stages that are critical for disease susceptibility and development of host-microbiota interactions. From this, we will be able to discern whether the IM and host gastrointestinal associated lymphatic tissue (GALT) are unique, in the absence of the diet-type and intestinal enteritis effects which confounded our previous results. In addition, we will further evaluate the IM and host intestinal gene expression in the context of both viral and bacterial disease challenges, to investigate the resilience of the selected strains' gut microbial ecology to the perturbation of exposure to virulent pathogens. Such research will enable us to identify targeted hypotheses about the selected strain's host-microbiota interactions and specific microbial taxa for use in future funding opportunities.Our long-term goal is to develop management practices and therapeutic tools that enable more effective disease prevention through improved maintenance of fish homeostasis. The research proposed here will further explore the genetic effects on fish host-microbiota interactions using our unique select strain as a model, to characterize the role of the IM on immune function in rainbow trout, and to enable generation of refined hypotheses concerning microbial taxa found in the ARS-UI strain that may possess probiotic properties.Specific Objectives:Objective 1: Compare the homeostatic intestinal microbiota (IM) and intestinal gene expression of the ARS-UI selected strain of rainbow trout to that of a commercial reference strain, during critical early life stages. Our working hypothesis is that host (ARS-UI trout) immune response and regulation at early life stages leads to differences in IM, which then provide superior immune protection later in life.?Objective 2: Compare the association between overall survival, intestinal microbiota (IM) composition, and intestinal gene expression of the ARS-UI selected strain of rainbow trout, to that of a commercial reference strain, during exposure to a virulent virus or bacterium. Our working hypothesis is that specific microbes within the IM of the selected trout strain are more resilient to ecological perturbations such as exposure to virulent pathogens, which provide greater ecological exclusion of pathogens and leads to a more focused immune response from the host.

    APPROACH: In the first objective, we aim to identify differences in the compositional dynamics of the intestinal microbiome (IM) of the selected and non-selected fish strains at early-life stages. Previous research indicates that the IM serve an integral role in priming and shaping the immune responses of vertebrate animals early in life (12, 14, 15), and therefore exploring differences in the IM between these two fish strains early in life may explain the previous observation of improved immune responses in the selected strain. We will also assess host gene expression at the level of the intestine (GALT) to compare the immune response to, and/or regulation of, the IM in the ARS-UI selected strain to a commercial trout strain. In this objective, we anticipate that significant differences will be detected between the two strains of rainbow trout, both in the composition of the IM (beta diversity and differentially abundant microbes), as well as the host gene expression (DEGs).In the second objective, we plan to evaluate the effects of disease challenge (both viral and bacterial) on the two strains of fish and their respective IM to further elucidate the physiological mechanisms responsible for the superior disease resistance of ARS-UI trout. We will take a novel approach to explore the effects of these pathogens on the interaction between the host and their IM at the level of the intestinal mucosa (GALT) using our ARS-UI strain, allowing us to explore associations between IM, intestinal gene expression, and disease resistance.The results of this research and new knowledge gained will be disseminated through peer-reviewed manuscripts, student dissertation, and presentation to stakeholders and other researchers at annual meetings and conferences. The impact of the research will be accessed through the successful funding of future proposals built upon the results of this seed project, the successful defense and graduation of 1 Ph.D. student, and peer-reviewed scientific research articles published.

total award amount

  • 499,782

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