Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers

• Published in: BMC Microbiology
• Main Authors: Camille Clerissi, Laure Guillou, Jean-Michel Escoubas, Eve Toulza
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2020
• Subjects: Holobiont; Metabarcoding; Microbiome; Ostreoida; Crassostrea; Microbiology; QR1-502; Pacific; Crassostrea gigas; Pacific oyster
• Online Access: https://doi.org/10.1186/s12866-020-01860-1; https://doaj.org/article/68e395d6232a43ad9d90d97e7089eedd

Abstract Background Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far. Results To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples. Conclusions Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles.