Polynyas, or recurring areas of seasonally open water surrounded by sea ice, are foci for energy and material transfer between the atmosphere and the polar ocean. They are also climate sensitive, with both sea ice extent and glacial melt influencing their productivity. The Amundsen Sea Polynya (ASP) is the greenest polynya in the Southern Ocean, with summertime chlorophyll a concentrations exceeding 20 µg L−1. During the Amundsen Sea Polynya International Research Expedition (ASPIRE) in austral summer 2010–11, we aimed to determine the fate of this high algal productivity. We collected water column profiles for total dissolved inorganic carbon (DIC) and nutrients, particulate and dissolved organic matter, chlorophyll a, mesozooplankton, and microbial biomass to make a carbon budget for this ecosystem. We also measured primary and secondary production, community respiration rates, vertical particle flux and fecal pellet production and grazing. With observations arranged along a gradient of increasing integrated dissolved inorganic nitrogen drawdown (ΔDIN; 0.027–0.74 mol N m−2), changes in DIC in the upper water column (ranging from 0.2 to 4.7 mol C m−2) and gas exchange (0–1.7 mol C m−2) were combined to estimate early season net community production (sNCP; 0.2–5.9 mol C m−2) and then compared to organic matter inventories to estimate export. From a phytoplankton bloom dominated by Phaeocystis antarctica, a high fraction (up to ∼60%) of sNCP was exported to sub-euphotic depths. Microbial respiration remineralized much of this export in the mid waters. Comparisons to short-term (2–3 days) drifting traps and a year-long moored sediment trap capturing the downward flux confirmed that a relatively high fraction (3–6%) of the export from ∼100 m made it through the mid waters to depth. We discuss the climate-sensitive nature of these carbon fluxes, in light of the changing sea ice cover and melting ice sheets in the region.

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The West Antarctic Peninsula (WAP) is a climatically sensitive region where periods of strong warming have caused significant changes in the marine ecosystem and food-web processes. Tight coupling between phytoplankton and higher trophic levels implies that the coastal WAP is a bottom-up controlled system, where changes in phytoplankton dynamics may largely impact other food-web components. Here, we analysed the inter-decadal time series of year-round chlorophyll- (Chl) collected from three stations along the coastal WAP: Carlini Station at Potter Cove (PC) on King George Island, Palmer Station on Anvers Island and Rothera Station on Adelaide Island. There were trends towards increased phytoplankton biomass at Carlini Station (PC) and Palmer Station, while phytoplankton biomass declined significantly at Rothera Station over the studied period. The impacts of two relevant climate modes to the WAP, the El Niño-Southern Oscillation and the Southern Annular Mode, on winter and spring phytoplankton biomass appear to be different among the three sampling stations, suggesting an important role of local-scale forcing than large-scale forcing on phytoplankton dynamics at each station. The inter-annual variability of seasonal bloom progression derived from considering all three stations together captured ecologically meaningful, seasonally co-occurring bloom patterns which were primarily constrained by water-column stability strength. Our findings highlight a coupled link between phytoplankton and physical and climate dynamics along the coastal WAP, which may improve our understanding of overall WAP food-web responses to climate change and variability.This article is part of the theme issue 'The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change'.

An inherent issue in high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations, making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxon cooccurrence patterns substantially different from those derived using relative abundances. We found that the method provided results consistent with the traditional CHEMTAX analysis of pigments and total bacterial counts by flow cytometry. Using the internal standard method, we also showed that chloroplast 16S rRNA gene data in microbial surveys can be used to estimate abundances of certain eukaryotic phototrophs such as cryptophytes and diatoms. In Phaeocystis, scatter in the 16S/18S rRNA gene ratio may be explained by physiological adaptation to environmental conditions. We conclude that the internal standard method, when applied to rRNA gene microbial community profiling, is quantitative and that its application will substantially improve our understanding of microbial ecosystems. IMPORTANCE High-throughput-sequencing-based marine microbiome profiling is rapidly expanding and changing how we study the oceans. Although powerful, the technique is not fully quantitative; it provides taxon counts only in relative abundances. In order to address this issue, we present a method to quantitatively estimate microbial abundances per unit volume of seawater filtered by spiking known amounts of internal DNA standards into each sample. We validated this method by comparing the calculated abundances to other independent estimates, including chemical markers (pigments) and total bacterial cell counts by flow cytometry. The internal standard approach allows us to quantitatively estimate and compare marine microbial community profiles, with important implications for linking environmental microbiomes to quantitative processes such as metabolic and biogeochemical rates.