Faecal metabarcoding is widely used for mammalian diet analysis. However, most extraction protocols are designed to target high molecular weight genomic DNA, making short sequences of digested DNA challenging to extract. Here, we evaluate prey DNA metrics in baleen whale scat from a phosphate buffer DNA extraction method along with two commercial extraction kits (the QIAamp Fast DNA Stool Mini Kit and the PowerSoil kit) with the following variations: 1) different durations of incubation in a phosphate buffer (1 hour and 24 hours), 2) processing of both pellet and supernatant from phosphate buffer incubation, and 3) two different concentrations of DNA binding buffer to examine prey DNA. We found that the choice of extraction protocol influenced richness, diversity and composition of eukaryotes (18S rDNA) and crustaceans (Crust16S mtDNA) detected in SRW faecal samples. The PowerSoil protocol performed well for both markers, delivering the highest target richness for 18S rDNA and highest diversity for Crust16S mtDNA, while the pellet of the phosphate buffer yielded the highest richness for Crust16S mtDNA. The phosphate buffer supernatant protocols produced the lowest results for richness and diversity. Taxonomic composition in the supernatant alone was influenced by the duration of incubation and the concentration of binding buffer and was also distinct from the corresponding pellet. Our results reinforce the importance of having clear targets prior to selecting a method for faecal metabarcoding, as the specific aims (e.g. identifying richness versus diversity) will inform the choice of extraction protocol.

Antarctic Bottom Water (AABW) production supplies the deep limb of the global overturning circulation and ventilates the deep ocean. While the Weddell and Ross Seas are recognised as key sites for AABW production, additional sources have been discovered in coastal polynya regions around East Antarctica, Vincennes Bay being the latest. Vincennes Bay, despite encompassing two distinct polynya regions, is considered the weakest source, producing Dense Shelf Water (DSW) only just dense enough to contribute to the lighter density classes of AABW found offshore. Importantly, the network of local glaciers and upstream Totten Ice Shelf system are all reportedly thinning and the freshwater input from such melting is likely to influence water mass structure. Accordingly, Vincennes Bay presents an interesting test case for DSW/AABW sensitivity to climate-driven changes in Antarctic coastal oceanography. Here we provide the first detailed observations of the Vincennes Bay shelf region and surrounds, using CTD data from instrumented elephant seals in late summer/early fall. We find that Vincennes Bay has East Antarctica’s warmest recorded intrusions of modified Circumpolar Deep Water (mCDW), intrusions that both hinder sea-ice production and contribute salt to new DSW formation. Warm mCDW is also observed to be driving basal melt in Vincennes Bay, as seal CTD data provide the first direct observational evidence for inflow of basal melt to this region. As the most marginal of AABW sources, Vincennes Bay is a particularly useful region for assessment of the sensitivity of AABW production to changes in climate.