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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. Diatoms, large bloom-forming marine microorganisms, build frustules out of silicate, which ballasts the cells and aids their export to the deep ocean. This unique physiology forges an important link between the marine silicon and carbon cycles. However, the effect of ocean acidification on the silicification of diatoms is unclear. Here we show that diatom silicification strongly diminishes with increased acidity in a natural Antarctic community. Analyses of single cells from within the community reveal that the effect of reduced pH on silicification differs among taxa, with several species having significantly reduced silica incorporation at CO2 levels equivalent to those projected for 2100. These findings suggest that, before the end of this century, ocean acidification may influence the carbon and silicon cycle by both altering the composition of the diatom assemblages and reducing cell ballasting, which will probably alter vertical flux of these elements to the deep ocean.

Antarctic waters are amongst the most vulnerable in the world to ocean acidification due to their cold temperatures, naturally low levels of calcium carbonate and upwelling that brings deep CO\(_2\)-rich waters to the surface. A meta-analysis demonstrated groups of Antarctic marine biota in waters south of 60°S have a range of tolerances to ocean acidification. Invertebrates and phytoplankton showed negative effects above 500 μatm and 1000 μatm CO\(_2\) respectively, while bacteria appear tolerant to elevated CO\(_2\). Phytoplankton studied as part of a natural microbial community were found to be more sensitive than those studied as a single species in culture. This highlights the importance of community and ecosystem level studies, which incorporate the interaction and competition among species and trophic levels, to accurately assess the effects of ocean acidification on the Antarctic ecosystem. Antarctic marine microbes (comprising phytoplankton, protozoa and bacteria) drive ocean productivity, nutrient cycling and mediate trophodynamics and the biological pump. While they appear vulnerable to changes in ocean chemistry, little is known about the nature and magnitude of their responses to ocean acidification, especially for natural communities. To address this lack of information, a six level, dose-response ocean acidification experiment was conducted in Prydz Bay, East Antarctica, using 650 L incubation tanks (minicosms). The minicosms were filled with Antarctic nearshore water and adjusted to a gradient of carbon dioxide (CO\(_2\)) from 343 to 1641 μatm. Microscopy and phylogenetic marker gene sequence analysis found the microbial community composition altered at CO\(_2\) levels above approximately 1000 μatm. The CO\(_2\)- induced responses of icroeukaryotes (>20 μm) and nanoeukaryotes (2 to 20 μm) were taxon-specific. For diatoms the response of taxa was related to cell size with micro-sized diatoms (>20 μm) increasing in abundance with moderate CO\(_2\) (506 to 634 μatm), while above this level their abundance declined. In contrast, nano-size diatoms (