Papers by Shantelle Smith
Biogeochemical data - 2017 Winter Cruise Atlantic-Indian Southern Ocean
Nutrient data from underway (surface, ~7 m) and CTD (surface only, ~10 m) samples. Nutrients incl... more Nutrient data from underway (surface, ~7 m) and CTD (surface only, ~10 m) samples. Nutrients include ammonium, nitrate, nitrite, urea, phosphate, and silicate concentrations. Particulate organic nitrogen and carbon concentrations, chlorophyll-a concentrations, inorganic carbon uptake rates, and nitrogen (nitrate, ammonium, urea) uptake rates are included - all for two size classes: >0.3 microns and >2.7 microns. Ammonium oxidation rates are also provided. Plankton abundances are provided for various groups (microplankton enumerated with microscopy and nano- and picoplankton enumerated using flow cytometry). Cruise: 28 June - 13 July 2017; R/V <em>SA Agulhas II </em>(VOY025); Cape Town to the Marginal Ice Zone; WOCE IO6 line.
Cruise Scientific Report associated with the Weddell Sea Expedition, 2019. Edited by J. A. Dowdes... more Cruise Scientific Report associated with the Weddell Sea Expedition, 2019. Edited by J. A. Dowdeswell (Chief Scientist).
Importing, processing, and plotting of shipboard ADCP data in R
First release. This code can be applied to any dataset of ADCP (Acoustic Doppler Current Profiler... more First release. This code can be applied to any dataset of ADCP (Acoustic Doppler Current Profiler) data from shipboard instrumentation. There is capacity for the importing of 'x' number of input files. The ADCP data is used to create velocity and distance (from first sampling point; used as a substitute for latitude/longitude - it is ideal for a ship track that does not follow a longitude or latitude). The absolute velocity is calculated from the relative current velocity and the ship's average speed. We use the ggplot2 package, supplemented by the scales and metR packages, to create a section plot of absolute current velocity.
Supplementary material to "Biogeochemical controls on wintertime ammonium accumulation in the surface layer of the Southern Ocean
The Weddell Sea (WS) represents a point of origin in the Southern Ocean where globally-important ... more The Weddell Sea (WS) represents a point of origin in the Southern Ocean where globally-important water masses form. Biological activities in WS surface waters thus affect large-scale ocean biogeochemistry. During summer 2018/2019, we measured net primary production (NPP), nitrogen (nitrate, ammonium, urea) uptake, and nitrification in the western WS at the Antarctic Peninsula (AP) and Larsen C Ice Shelf (LCIS), in the southwestern Weddell Gyre (WG), and at Fimbul Ice Shelf (FIS) in the southeastern WS. The highest average rates of NPP and greatest nutrient drawdown occurred at LCIS. Here, the phytoplankton community was dominated by colonial Phaeocystis antarctica, with diatoms increasing in abundance later in the season as sea-ice melt increased. At the other stations, NPP was variable, and diatoms known to enhance carbon export (e.g., Thalassiosira spp.) were dominant. Euphotic zone nitrification was always below detection, such that nitrate uptake could be used as a proxy for carbon export potential, which was highest in absolute terms at LCIS and the AP. Surprisingly, the highest f-ratios occurred near FIS rather than LCIS (average of 0.73 ± 0.09 versus 0.47 ± 0.08). We attribute this to partial ammonium inhibition of nitrate uptake at LCIS (where ammonium concentrations were 0.6 ± 0.4 μM, versus 0.05 ± 0.1 μM at FIS) driven by increased heterotrophy following the accumulation of nitrate-fuelled phytoplankton biomass in early summer. Across the WS, carbon export appears to be driven by a combination of physical, chemical, and biological factors, with the highest export flux occurring at the ice shelves and lowest in the central WG.
Abstract. The production and consumption of ammonium (NH4+) are essential upper-ocean nitrogen cy... more Abstract. The production and consumption of ammonium (NH4+) are essential upper-ocean nitrogen cycle pathways, yet in the Southern Ocean where NH4+ has been observed to accumulate in surface waters, its mixed-layer cycling remains poorly understood. For surface samples collected between Cape Town and the marginal ice zone (MIZ) in winter 2017, we found that NH4+ concentrations were five-fold higher than is typical for summer, and lower north than south of the Subantarctic Front (SAF; 0.01–0.26 µM versus 0.19–0.70 µM). Our observations confirm that NH4+ accumulates in the Southern Ocean’s winter mixed layer, particularly in polar waters. NH4+ uptake rates were highest near the Polar Front (PF; 12.9 ± 0.4 nM day−1) and in the Subantarctic Zone (10.0 ± 1.5 nM day−1), decreasing towards the MIZ (3.0 ± 0.8 nM day−1) despite high ambient NH4+ concentrations, likely due to low sea surface temperatures and light availability. By contrast, rates of NH4+ oxidation were higher south than north...
Air‐Sea Ammonia Fluxes Calculated From High‐Resolution Summertime Observations Across the Atlantic Southern Ocean
Geophysical Research Letters
<p>Oceanic ammonia emissions are the largest natural source of ammonia globally, but the ma... more <p>Oceanic ammonia emissions are the largest natural source of ammonia globally, but the magnitude of the air-sea flux in remote regions absent human influence remains uncertain. Here, we measured the concentration of surface ocean ammonium and atmospheric ammonia gas every two hours across a latitudinal transect (34.5&#186;S to 61&#186;S) of the Atlantic Southern Ocean during summer. Surface ocean ammonium concentrations ranged from undetectable to 0.36&#160;&#181;M and ammonia gas concentrations ranged from 0.6 to 5.1 nmol m<sup>-3</sup>. Calculated ammonia fluxes ranged from -2.5 to -91 pmol m<sup>-2</sup> s<sup>-1</sup>, and were consistently from the atmosphere into the ocean, even in regions where surface ocean ammonium concentrations were relatively high. As expected, temperature was the dominant control on the air-sea ammonia flux across the latitudinal transect. However, a sensitivity analysis suggests that seasonality in the surface Southern Ocean nitrogen cycle may have a major influence on the direction of the ammonia flux.</p>
Productivity and carbon export potential in the Weddell Sea, with a focus on the waters near Larsen C Ice Shelf
&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp... more &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Net primary production (NPP) is indicative of the energy available to an ecosystem, which is central to ecological functioning and biological carbon cycling. The Southern Ocean&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#8217;s Weddell Sea (WS) represents a point of origin where water masses form and exchange with the atmosphere, thereby setting the physical and chemical conditions of much of the global ocean. The WS is particularly understudied near Larsen C Ice Shelf (LCIS) where harsh sea-ice conditions persist year-round. We measured size-fractionated rates of NPP, nitrogen (N; as nitrate, ammonium, and urea) uptake, and nitrification, and characterized the phytoplankton community at 19 stations in summer 2018/2019, mainly near LCIS, with a few stations in the open Weddell Gyre (WG) and at Fimbul Ice Shelf (FIS). Throughout the study region, NPP and N uptake were dominated by nanophytoplankton (3-20 &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#956;m), with microphytoplankton (&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;20 &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#956;m) becoming more abundant later in the season, particularly at FIS. Here, we observed high phytoplankton biomass and diversity, and the community was dominated by diatoms known to enhance carbon export (e.g., &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;em&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Thalassiosira spp&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/em&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;.). At LCIS, by contrast, the community comprised mainly &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;em&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Phaeocystis Antarctica&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/em&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;. In the open WG, a population of small and weakly-silicified diatoms of the genus &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;em&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Corethron&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/em&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; dominated the phytoplankton community. Here, euphotic zone-integrated uptake rates were similar to those at LCIS even though the depth-specific rates were lower. Mixed-layer nitrification was below detection at all stations such that nitrate uptake can be used as a proxy for carbon export potential &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;em&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;sensu&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/em&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; the new production paradigm &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#8211; this was highest near FIS in late summer. Our observations can be explained by melting sea ice near the ice shelves that supplies iron and enhances water column stratification, thus alleviating iron and/or light limitation of phytoplankton and allowing them to consume the abundant surface macronutrients. That the sea ice melted completely at FIS but not LCIS may explain why late-summer productivity and carbon export potential were highest near FIS, more than double the rates measured in early summer and near LCIS. The early-to-late summer progression near the ice shelves contrasts that of the open Southern Ocean where iron is depleted by late summer, driving a shift towards smaller phytoplankton that facilitate less carbon export.&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;
Changing Biogeochemistry of the Southern Ocean and Its Ecosystem Implications
Frontiers in Marine Science
The Southern Ocean plays a critical role in regulating global climate as a major sink for atmosph... more The Southern Ocean plays a critical role in regulating global climate as a major sink for atmospheric carbon dioxide (CO2), and in global ocean biogeochemistry by supplying nutrients to the global thermocline, thereby influencing global primary production and carbon export. Biogeochemical processes within the Southern Ocean regulate regional primary production and biological carbon uptake, primarily through iron supply, and support ecosystem functioning over a range of spatial and temporal scales. Here, we assimilate existing knowledge and present new data to examine the biogeochemical cycles of iron, carbon and major nutrients, their key drivers and their responses to, and roles in, contemporary climate and environmental change. Projected increases in iron supply, coupled with increases in light availability to phytoplankton through increased near-surface stratification and longer ice-free periods, are very likely to increase primary production and carbon export around Antarctica. Biological carbon uptake is likely to increase for the Southern Ocean as a whole, whilst there is greater uncertainty around projections of primary production in the Sub-Antarctic and basin-wide changes in phytoplankton species composition, as well as their biogeochemical consequences. Phytoplankton, zooplankton, higher trophic level organisms and microbial communities are strongly influenced by Southern Ocean biogeochemistry, in particular through nutrient supply and ocean acidification. In turn, these organisms exert important controls on biogeochemistry through carbon storage and export, nutrient recycling and redistribution, and benthic-pelagic coupling. The key processes described in this paper are summarised in the Graphical Abstract. Climate-mediated changes in Southern Ocean biogeochemistry over the coming decades are very likely to impact primary production, sea-air CO2 exchange and ecosystem functioning within and beyond this vast and critically important ocean region. Graphical Abstract Infographic summarising the key processes described in this paper. Drawn by Dr. Stacey McCormack, University of Tasmania.
Clean Air Journal
South Africa has a unique geographic advantage that affords regular access to the Southern Ocean,... more South Africa has a unique geographic advantage that affords regular access to the Southern Ocean, as well as a technical advantage in the Department of Environmental Affairs-owned state-of-the-art ice-breaker, the R/V SA Agulhas II, as an integrated research and training platform. Atmospheric chemistry research in South Africa has the potential to leverage these advantages and make significant contributions to the rapidly integrating Earth systems science (terrestrial-atmospheric-oceanic-ice) and climate change research space. Recently, a group of University of Cape Town (UCT) postgraduate students studying Oceanography and Atmospheric Sciences had the opportunity to participate in the 58th South African National Antarctic Expedition (SANAE 58) and the international 2019 Weddell Sea Expedition (WSE) (https://weddellseaexpedition. org). The R/V SA Agulhas II left Cape Town on December 6, 2018, voyaged 11 000 km, and returned on March 15, 2019. M.Sc. students Kurt Spence and Shantelle Smith and Ph.D. student Jessica Burger, members of Dr. Katye Altieri's marine atmosphere biogeochemistry research group at UCT, led the atmospheric chemistry research campaign on the ship. Sizesegregated aerosol samples were collected daily using a cascade impactor, while an Ambient Ion Monitor-Ion Chromatograph (AIM-IC) system measured hourly gas-phase (ammonia, nitric acid, sulfuric acid) and aerosol-phase (sodium, chloride, nitrate, sulfate, ammonium) concentrations. The students returned with ~220 aerosol filters to extract and analyze, and 600 hours of AIM-IC data to process. This campaign was just the first of many atmospheric chemistry research opportunities afforded by the R/V SA Agulhas II and the NRF's South African National Antarctic Programme (SANAP). The Southern Ocean Seasonal Experiment (SCALE; www.scale.org. za), funded by the Department of Science and Technology, will take place in 2019 with dedicated science cruises planned for winter and spring, and SANAE 59 is scheduled for the summer of 2019/2020. In addition to Dr. Altieri's research group from UCT, these cruises will include international partners from Plymouth Marine Laboratory and GEOMAR measuring volatile organic compounds, dimethylsulfide, isoprene, and other trace gases. There are opportunities to join the exciting atmospheric chemistry research happening on the R/V SA Agulhas II through SCALE or future research cruises.
Winter biogenic silica and diatom distributions in the Indian sector of the Southern Ocean
Deep Sea Research Part I: Oceanographic Research Papers
Abstract Spring and summer Southern Ocean phytoplankton communities have been well characterized,... more Abstract Spring and summer Southern Ocean phytoplankton communities have been well characterized, but winter communities are often overlooked. Diatoms are a major contributor to Southern Ocean particulate organic carbon (POC) production and export, and exert a strong control on Antarctic surface and Subantarctic thermocline nutrient concentrations, thus influencing the low-latitude nutrient supply. Understanding diatom distribution, seasonal community progression, and diatom-nutrient interactions is vital for improving biogeochemical models, particularly as climate change alters polar phytoplankton communities. We investigated the distribution of nanophytoplankton (≥3 μm) and their associated biogeochemical environments along 30°E across the Indian Southern Ocean (Subtropical Zone; STZ to Antarctic Zone; AZ) in July 2017. Phytoplankton productivity inferred from chlorophyll-a was low compared to previously-published summertime values. Mixed-layer nitrate (NO3−) and phosphate (PO43−) concentrations were similar to existing summer measurements, likely due to a combination of deep mixing and biological uptake, while silicic acid (Si(OH)4) was high relative to summer, particularly south of the Polar Front (PF). The PF emerged as an important biogeochemical boundary separating relatively high chlorophyll-a, flagellate-dominated northern waters from southern waters characterized by low chlorophyll-a and diatom-dominated communities. Mixed layer-integrated biogenic silica (bSi) decreased 12-fold from the southern AZ to the STZ, resulting in a strong south-north gradient in bSi-per-chl-a (from 3.6 to 0.1 mol/g) and bSi-per-POC (from 0.22 to 0.016 mol mol−1). We attribute this to a high abundance of heavily-silicified diatom species (e.g., Fragilariopsis spp., which dominated the AZ diatom community) and a limited contribution of other phytoplankton to chlorophyll-a and POC to the south – indeed, diatoms constituted 5–67% of the total POC south of the PF and only 3–7% to the north. While mixed-layer Si(OH)4 concentrations decreased more than NO3− across the PF, likely due to preferential Si(OH)4 consumption by iron-limited diatoms, our data imply a lower ratio of Si(OH)4 to NO3− uptake compared to summer. This suggests that iron limitation may be less severe in the AZ in winter, at least in the west Indian sector. We conclude that AZ diatoms impact the low-latitude nutrient supply and are potentially important for carbon export in winter, despite the lower productivity of the Southern Ocean during this season.
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Papers by Shantelle Smith