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Development of an eDNA sample analysis workflow for estimation of myxozoan (Cnidaria) parasite biodiversity in river water samples

Grant number: 17/11823-9
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): October 01, 2017
Effective date (End): September 30, 2018
Field of knowledge:Agronomical Sciences - Veterinary Medicine - Preventive Veterinary Medicine
Principal Investigator:Antonio Augusto Mendes Maia
Grantee:Tiago Milanin
Supervisor: Jerri Lee Bartholomew
Host Institution: Faculdade de Zootecnia e Engenharia de Alimentos (FZEA). Universidade de São Paulo (USP). Pirassununga , SP, Brazil
Research place: Oregon State University (OSU), United States  
Associated to the scholarship:15/18807-3 - Detection of myxosporean in oligochaetes from fish farms of hybrid pintado (Pseudoplatystoma corruscans x Pseudoplatystoma reticulatum) in Mato Grosso do Sul state, Brazil, BP.PD


Myxozoans are a diverse group of spore-forming parasites that are an emerging threat to wild and farmed fish populations worldwide, including salmon, carp, catfish and flounder. As aquaculture and farming of native fish species expands, novel species of myxozoan parasites can cause economic problems, either by non-pathogenic species emerging as pests, or by unknown species making host jumps from wild to farmed populations. Thus, it is important to gather baseline parasite biodiversity data to better assess the risks for aquaculture. The historical approach for surveying, sampling and identifying myxozoan parasites is laborious, and involves catching and dissecting fish, then examining tissue microscopically. This project proposes the use of an alternative approach for better and faster estimation of myxozoan parasite diversity - direct sampling of myxozoans from water samples (i.e. environmental DNA, or eDNA). eDNA methods represent a powerful, efficient tool for understanding complex communities of aquatic parasites. For that, it will be develop a sample workflow to estimate myxozoan parasite diversity from filtered river water samples, using targeted sample enrichment by PCR and bead-based methods, followed by Next Generation Sequencing. Water from the Willamette Basin, in Oregon USA, which is a system where the number of myxozoan parasites has already been well established by conventional sampling, will be tested. This will be the first study to compare conventional species diversity data with results obtained from sequencing eDNA from the same environment. My goal is to develop a sample analysis workflow that gives more accurate estimates of myxozoan biodiversity, without the time consuming, laborious and fundamentally biased approach of collecting and dissecting fish. The proposal that we will develop during this internship in the USA can then be used in Brazil to survey rivers and aquatics environments for presence of myxozoan parasites, to better inform risk assessments and aquaculture planning. (AU)

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