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Diatom frustules record the variations of seawater Ge/Si, a ratio related to continental weathering, early diagenesis, and biological productivity. To investigate the geochemistry of germanium and the possibility of using opal Ge/Si as a proxy of changes in Ge and Si budgets in high latitude Antarctic marginal sea, nine surface sediment samples and one sediment core were collected from Prydz Bay during Chinese Antarctic Expeditions from 2005 to 2009. Diatom opal was separated and purified from sediment samples, and opal Ge/Si was determined. The results showed that (Ge/Si) opal ranged from 0.48 to 0.78 μmol mol−1 (0.60 ± 0.09 μmol mol−1) in Prydz Bay. (Ge/Si) opal from sites in the open sea and at the edge of the Amery Ice Shelf are comparable to modern oceanic seawater, while it is relatively low on the continental shelf. The variations in (Ge/Si) opal were not significantly influenced by biological fractionation during diatom uptake, but were related to changes in external input or authigenic loss of Ge. An authigenic sink of Ge was detected at all sites and accounted for 20% ~ 52% of Ge in bulk sediments. Authigenic precipitation of Ge is generally controlled by precipitation of Fe-rich minerals, but is also influenced by biogenic opal delivery in the centre of the bay where siliceous productivity is extremely high. The higher (Ge/Si) opal relative to those on the continental shelf is suggested to be caused by Ge supplementation from oceanic water in the open sea area and by high input of glacial debris from ice-melting at the edge of the Amery Ice Shelf. • (Ge/Si) opal in the open sea area and at the edge of Amery Ice Shelf (AIS) are comparable to modern oceanic ratio. • Oceanic water supplement and high glacial debris input control (Ge/Si)opal in the open sea and AIS edge areas respectively. • Authigenic precipitation of Ge is responsible for the low ratios on the shelf region. • Authigenic Ge sink is controlled by precipitation Fe-rich minerals, but also influenced by opal delivery in the centre bay. [ABSTRACT FROM AUTHOR]