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

Type Article
Date 2020-07
Language English
Author(s) Clerissi Camille1, 2, Guillou Laure3, Escoubas Jean Michel4, Toulza Eve5
Affiliation(s) 1 : IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
2 : PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
3 : Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, Roscoff, France
4 : IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Montpellier, France
5 : IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
Source Bmc Microbiology (1471-2180) (Springer Science and Business Media LLC), 2020-07 , Vol. 20 , N. 1 , P. 193 (13p.)
DOI 10.1186/s12866-020-01860-1
Keyword(s) Holobiont, Metabarcoding, Microbiome, Ostreoida, Crassostrea
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.

Full Text
File Pages Size Access
Publisher's official version 13 2 MB Open access
Additional file 1: Table S1. Microbiota samples 10 KB Open access
Additional file 2: Figure S1. Sequences of high taxonomic ranks (oysters, Embryophyceae, protists) within oyster sample 12 MB Open access
Additional file 3: Table S2. Number of sequences. Values correspond to 18SV1V2EX/18SV4BP. 19 KB Open access
Additional file 4: Figure S2. Rarefaction analyses. 910 KB Open access
Additional file 5: Table S3. OTU annotations and abundances for 18SV1V2EX samples. 1 MB Open access
Additional file 6: Table S4. OTU annotations and abundances for 18SV4BP samples. 614 KB Open access
Additional file 7: Figure S3. Comparison of amplicon sizes between 18SV1V2EX and 18SV4BP 203 KB Open access
Additional file 8: Table S5. Metadata and alpha diversity indices. Alpha diversity values correspond to 18SV1V2EX/18SV4BP. NA: not analysed (protist sequences< 5160). 21 KB Open access
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