Publication Date:
2024-05-24
Description:
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant
in most marine environments. Molecular methods such as metabarcoding have
revealed a high, yet undescribed diversity of Foraminifera. However, so far only one
molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies
on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial
cytochrome oxidase I (COI) and identification of Foraminifera species were recently
published. Here we test the performance of these primers for the amplification of
whole foraminiferal communities, and compare their performance to that of the highly
degenerate LerayXT primers, which amplify the same COI region in a wide range
of eukaryotes. We applied metabarcoding to 48 samples taken along three transects
spanning a North Sea beach in the Netherlands from dunes to the low tide level,
and analysed both sediment samples and meiofauna samples, which contained taxa
between 42 mm and 1 mm in body size obtained by decantation from sand samples.
We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference
library containing 32 species of Foraminifera, and used this to taxonomically annotate
our community metabarcoding data. Our analyses show that the highly degenerate
LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are
highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera
and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea,
and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in
Foraminifera community composition along the beach transects from high tide to
low tide level, and a dominance of single-chambered monothalamid Foraminifera.
Our results highlight that COI metabarcoding can be a powerful tool for assessing
Foraminiferal communities.
Keywords:
Foraminifera
;
Metabarcoding
;
Beach
;
Community composition
;
Intertidal
;
Molecular
;
biodiversity
Repository Name:
National Museum of Natural History, Netherlands
Type:
info:eu-repo/semantics/article
Format:
application/pdf
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