Evaluation and optimization of an eDNA metabarcoding assay for detection of freshwater myxozoan communities

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F23%3A00583120" target="_blank" >RIV/60077344:_____/23:00583120 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60076658:12310/23:43907250

Výsledek na webu

<a href="https://onlinelibrary.wiley.com/doi/10.1002/edn3.380" target="_blank" >https://onlinelibrary.wiley.com/doi/10.1002/edn3.380</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/edn3.380" target="_blank" >10.1002/edn3.380</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Evaluation and optimization of an eDNA metabarcoding assay for detection of freshwater myxozoan communities

Popis výsledku v původním jazyce

The environmental DNA (eDNA) metabarcoding approach has become a useful tool for detecting the species diversity of different animal groups, including parasites. Myxozoa (Malacosporea and Myxosporea) represent a unique group of morphologically simplified endoparasites that mainly infest fish and whose diversity remains largely unexplored. Metabarcoding of DNA from the aquatic environment is a promising non-invasive method that allows us to assess myxozoan biodiversity at a given site. This is essential not only for describing myxozoan communities, but also for the development of disease control methods. Using an alignment of 330 sequences, we employed in silico PCR to score primer pairs, designed to amplify the V4 region of the SSU rDNA of different myxosporean sublineages comprising the entire diversity of oligochaete-infecting (freshwater) myxosporeans. We selected eight clade-specific primer sets for metabarcoding, avoiding amplification of DNA from other organisms present in eutrophic freshwaters. The metabarcoding approach used in the analysis of eDNA sediment samples detected a high myxosporean diversity even in small sample volumes (in total 44 OTUs). Furthermore, metabarcoding analysis of myxosporeans in fish tissue samples selected for primer testing revealed 91 different myxosporean OTUs, more than double the number obtained by classical PCR screening and Sanger sequencing with general myxozoan primers and almost seven times higher detection than by microscopic examination. Our results further suggest quantitative sampling requirements for realistic future diversity estimates by comparing OTUs from fish tissue metabarcoding and eDNA samples. The use of specific primer sets enabled the detection of a high proportion of myxosporean reads (63–100%) in all datasets, even in highly eutrophic habitats. This shows our metabarcoding approach as an excellent tool for non-invasive and sensitive detection of myxosporean biodiversity in aquatic sediments, potentially useful for monitoring myxozoan disease agents that threaten economically important fish in aquaculture.

Název v anglickém jazyce

Evaluation and optimization of an eDNA metabarcoding assay for detection of freshwater myxozoan communities

Popis výsledku anglicky

The environmental DNA (eDNA) metabarcoding approach has become a useful tool for detecting the species diversity of different animal groups, including parasites. Myxozoa (Malacosporea and Myxosporea) represent a unique group of morphologically simplified endoparasites that mainly infest fish and whose diversity remains largely unexplored. Metabarcoding of DNA from the aquatic environment is a promising non-invasive method that allows us to assess myxozoan biodiversity at a given site. This is essential not only for describing myxozoan communities, but also for the development of disease control methods. Using an alignment of 330 sequences, we employed in silico PCR to score primer pairs, designed to amplify the V4 region of the SSU rDNA of different myxosporean sublineages comprising the entire diversity of oligochaete-infecting (freshwater) myxosporeans. We selected eight clade-specific primer sets for metabarcoding, avoiding amplification of DNA from other organisms present in eutrophic freshwaters. The metabarcoding approach used in the analysis of eDNA sediment samples detected a high myxosporean diversity even in small sample volumes (in total 44 OTUs). Furthermore, metabarcoding analysis of myxosporeans in fish tissue samples selected for primer testing revealed 91 different myxosporean OTUs, more than double the number obtained by classical PCR screening and Sanger sequencing with general myxozoan primers and almost seven times higher detection than by microscopic examination. Our results further suggest quantitative sampling requirements for realistic future diversity estimates by comparing OTUs from fish tissue metabarcoding and eDNA samples. The use of specific primer sets enabled the detection of a high proportion of myxosporean reads (63–100%) in all datasets, even in highly eutrophic habitats. This shows our metabarcoding approach as an excellent tool for non-invasive and sensitive detection of myxosporean biodiversity in aquatic sediments, potentially useful for monitoring myxozoan disease agents that threaten economically important fish in aquaculture.

Druh

J_SC - Článek v periodiku v databázi SCOPUS

CEP obor

—

OECD FORD obor

10618 - Ecology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Environmental DNA

ISSN

2637-4943

e-ISSN

2637-4943

Svazek periodika

5

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

14

Strana od-do

312-325

Kód UT WoS článku

—

EID výsledku v databázi Scopus

2-s2.0-85146095628