Foraminifera are single-cell eukaryotes common in all marine environments and generally characterized by shells, more specifically termed “tests”, which can either be organic, agglutinated, calcareous, and rarely siliceous. The diversity of foraminifera is commonly assessed microscopically based on morphological features of their tests. However, recent genetic and metagenetic studies show that this morphology-based diversity is largely underestimated. Many cryptic species and numerous lineages uncharacterized morphologically have been revealed, especially among the class of monothalamous (single-chambered) foraminifera. Here, we use an environmental DNA metabarcoding approach to explore the foraminiferal community in the Ubatuba region, northern São Paulo State coast, South-eastern Brazil, where no genetic foraminiferal studies have ever been conducted before. Our analyses revealed 42 phylotypes, among which 9 were identified as globothalamids and 31 have been assigned to monothalamids. All reported phylotypes are new to science and none of them could be assigned to species or genotypes present in foraminiferal barcoding database. These results demonstrate a huge gap that exist in our knowledge of the Southwest Atlantic shallow-waters foraminiferal genetic diversity. Filling this gap would be necessary for more accurate assessment of foraminiferal diversity in general and more specifically if DNA-based methods are to be used to identify potential foraminiferal indicators for ecological and biomonitoring studies in the future.
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