Abyssal DNA: Eukaryotic Diversity in Atlantic Equatorial Deep-Sea Sediments Assessed Through DNA Metabarcoding

Gontijo, Natana Rabelo; Gonçalves, Vívian Nicolau; Neto, Arthur Ayres; Vieira, Rosemary; Caram, Tainá Napoleão; Malheiros, Marina Martins; Lopes, Fabyano A .C.; Silva, Micheline C.; Azevedo, Allana Queiroz; Gonçalves, Thauana Rodrigues; Jovane, Luigi; Convey, Peter ORCID: https://orcid.org/0000-0001-8497-9903; Câmara, Paulo E.A.S.; Rosa, Luiz Henrique. 2025 Abyssal DNA: Eukaryotic Diversity in Atlantic Equatorial Deep-Sea Sediments Assessed Through DNA Metabarcoding. DNA, 5 (3). 17, pp. 10.3390/dna5030045

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Abstract/Summary

Background/Objectives: We evaluated eukaryotic diversity in two cores obtained from abyssal sediments collected at depths of 4280 m and 4444 m in the equatorial Atlantic, between the Fernando de Noronha and São Pedro and São Paulo archipelagos, using a DNA metabarcoding approach applied to environmental DNA (eDNA) samples. Results: In total, we detected 248,905 DNA reads that were assigned to 65 amplicon sequence variants (ASVs) in the two core sediments (176,073 DNA reads and 59 ASVs were detected in sediment obtained at 4280 m depth, and 72,832 DNA reads and 14 ASVs were detected in the core at 4444 m). These represented three Kingdoms and five phyla: Fungi (Ascomycota and Basidiomycota), Viridiplantae (Chlorophyta and Streptophyta) and Chromista (Ciliophora), in rank abundance order. Ascomycota was the dominant phylum, followed by Basidiomycota. Didymella sp., Cladosporium sp., Scopulariopsis sp., Alternaria eichhorniae, Curvularia sp., Hortaea werneckii, Penicillium sp. (Ascomycota) and Malassezia globosa (Basidiomycota) were the most abundant taxa. Pseudochlorella pyrenoidosa (Chlorophyta) was the most abundant representative of Viridiplantae detected, and Spirotrachelostyla tani (Ciliophora) was the only Chromista detected, both present as minor components of the assigned eukaryotic diversity and only in the 4280 m core. The eukaryotic assemblages displayed moderate diversity indices, and those from the deeper core (4444 m depth) displayed the highest diversity values. Few assigned taxa were present in both samples. The two cores differed in their geological characteristics, consistent with their location in different depositional basins. The core obtained at 4280 m depth, located further north and more isolated from the adjacent continent by two fracture zones, appears to receive less terrigenous sediment input. In contrast, the core obtained at 4444 m depth is under greater continental influence and receives more terrigenous input from the continent. These geological and geographic differences may contribute to the varying eukaryotic eDNA diversities found. Results: Our metabarcoding study revealed the presence of a sediment eukaryotic community dominated by fungi. This included assigned ASVs representing groups with different ecological roles, such as cosmopolitan and phytopathogenic members and extremophiles, some of which may be able to survive and function in the polyextreme deep-sea abyssal conditions. Abyssal sediments present a potential habitat for studying organisms at the edge of viable conditions for life on Earth. eDNA metabarcoding provides a promising technique for detecting cryptic and uncultured biodiversity compared to traditional approaches, opening avenues for further ecological, evolutionary and biotechnological studies.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.3390/dna5030045
Additional Keywords:	Atlantic Ocean, environmental DNA, extremophiles, marine sediment, taxonomy
Date made live:	19 Sep 2025 11:35 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/538978

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