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This study provides a snapshot of the largely understudied meiobenthic and nematode communities in the Prince Gustav Channel (PGC) and Duse Bay (DB). We compared five stations sampled at different water depths along the shelf and investigated their meiobenthic community structure. We approached nematode biodiversity combining traditional taxonomic identification and high throughput sequencing (HTS), with the use of Amplicon Sequence Variants (ASVs). Additionally, we characterized the environment by primary production proxies, grain size and seasonal ice conditions. Our results suggest that the availability of organic matter and its freshness are responsible for the high densities found at all depths. However, potential factors influencing the high local and regional variability of meiofauna density and biodiversity are less clear. A bathymetric transect consisting of three stations in DB (200, 500, and 1,000 m depth) showed increasing pigment concentrations in the first centimeters of the sediment vertical profile with increasing water depth, whereas the meiofauna densities showed the opposite trend. The deepest station of DB seems to function as a sink for fine material as supported by the higher silt fraction and higher organic matter concentrations. When comparing the two basins in the PGC (1,000 and 1,250 m) and the one in DB (1,000 m), differences in terms of environmental variables, meiofaunal densities, and composition were observed. The deepest basin in PGC is located further South (closer to the highly unstable Larsen area), and marked differences with the other basins suggest that it might be experiencing different conditions as a result of its presence near the summer ice margin and its more elongated topography. Both, the shallowest and the deepest stations showed the highest number of unique sequences, suggesting a more biodiverse nematode assemblage. The morphological identification did not show significant differences in the biodiversity of all stations, differently from the ASVs approach. However, the lack of reference sequences in online databases and the thickness of nematode’s cuticule are still important issues to consider as they potentially lead to underestimations of biodiversity and functional traits.

Combining Traditional Taxonomy and Metabarcoding: Assemblage Structure of Nematodes in the Shelf Sediments of the Eastern Antarctic Peninsula