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Profiling the Southern Ocean’s microbial community

By Sarah Fawcett1, Rosemary Dorrington2, Tommy Bornman3,4, Stephanie De Villiers4,5, Issufo Halo6
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The Antarctic Circumnavigation Expedition (ACE) is the first project of the Swiss Polar Institute, a newly created entity founded by EPFL, the Swiss Institute of Forest, Snow and Landscape research WSL, ETHZ, the University of Bern and Editions Paulsen. It aims to enhance international relations and collaboration between countries, as well as to spark the interest of a new generation of young scientists and explorers in polar research.

From December 2016 to March 2017, scientific teams from all over the world will board the Russian research vessel Akademik Treshnikov for an unprecedented expedition around Antarctica. From biology to climatology to oceanography, researchers - including this South African-led team - will work in a number of interrelated fields aimed at safeguarding the future of this Continent.


Russian research vessel, Akademik Tryoshnikov (© AARI)

A better understanding of Antarctica is critical, not just for its preservation, but for the whole planet, because the polar regions are affected by climate change more than any other region on Earth. Moreover, they play a central role in providing oceans with strong underwater streams that regulate the world’s climate - from the poles to the Equator.

The Southern Ocean plays an important role in Earth’s climate, storing more heat and carbon dioxide (CO2) than any other ocean region.

The capacity of the global ocean to absorb CO2 is actually limited by the Southern Ocean because phytoplankton (the microscopic plants living in the sunlit upper ocean) do not fully consume the macronutrients (nitrogen and phosphorus) supplied to surface waters in this region. While this is generally thought to result from a combination of iron, light and silicate limitation, the role of biological factors such as phytoplankton, bacterial and zooplankton (“microbial”) communities is not well understood.


Planned route for the Antarctic Circumnavigation Expedition. A total of 22 projects will be undertaken by 50 researchers from six continents aboard the Russian research vessel, Akademik Treshnikov, as she travels around Antarctica during the austral summer of 2016/17

The Southern Ocean hosts numerous Subantarctic island systems, which supply iron and nutrients directly to surrounding oceanic waters through runoff and seal and bird activity, as well as indirectly through eddies that form in their vicinity. The importance of the islands relative to the open ocean for driving CO2 removal remains to be quantified.

Investigating the role of the microbial community

This research initiative seeks to investigate the role of the microbial community in driving CO2 drawdown by quantifying the importance of phytoplankton groups for organic carbon export, and evaluating the role of different nitrogen sources (such as nitrate mixed up from the deep ocean, ammonium recycled in surface waters, nitrogen supplied by island runoff and/or eddy transport) in shaping the microbial community diversity and structure.

Using measurements of nutrients, nitrogen isotopes, microbial diversity and metabolic activity, combined with a numerical model, we aim to develop an integrated view of the Subantarctic island systems in order to characterise their role in Southern Ocean productivity. In other words, Who is there? What are they doing? Why are they doing it?


Fin whale surfacing (© Richard Youd. Australian Antarctic Division)


The South African ice-breaking research vessel, the R/V SA Agulhas II, cruises through “pancake ice” in the Antarctic Zone of the Atlantic Southern Ocean. Pancake ice forms in rough waters from small, needle-like crystals; the “pancakes” will eventually cement together to form a coherent ice sheet (© Preston Kemeny, California Institute of Technology)


Phytoplankton chlorophyll fields in the Southern Ocean, as derived from satellite remote sensing observations (© NASA)

Postgraduate opportunities

A number of MSc and PhD opportunities are available as part of ACE Project XII (see descriptions below). Participation in this project requires that students be willing to spend time at sea. To apply, please send a single PDF document containing a letter of motivation, brief CV, your most recent academic transcript and contact information for two references to Dr Sarah Fawcett ( by 30 June 2016. No late applications will be accepted.

  1. Dynamics and seasonality of mesoscale eddies along the Subantarctic belt (supervisor: Dr Issufo Halo, Cape Peninsula University of Technology): This project will focus on using an automatic eddy detection algorithm to quantify mesoscale eddies in the Subantarctic region from an altimetry dataset. The study aims to understand the mechanisms of eddy formation and their physical structure through the water column. Their potential impact on the Subantarctic island ecosystem will also be assessed. Prerequisites: Applicants must have at least an Honours degree in Oceanography, Physics, Mathematics or similar.
  2. Microbial community dynamics in Subantarctic marine systems (supervisor: Professor R. Dorrington, Rhodes University; MSc and PhD studentships available): Background: Microorganisms (archaebacteria, bacteria, fungi, algae and viruses) represent by far the most abundant species on the planet and are critically important in driving both terrestrial and marine ecosystem functioning. Nutrient availability (particularly carbon and nitrogen sources) is the primary factor influencing microbial diversity and richness, while environmental conditions (pH, salinity) affect community structure. The aim of this project is to relate the diversity, structure and metabolic activity of microbial communities to nutrient cycling in Subantarctic marine ecosystems, focusing on the influence of island systems. Broad research question: What is the role of microbial communities in driving nutrient cycling in Subantarctic systems? “Who is there? What are they doing?” Prerequisites: Applicants must have at least an Honours degree in Microbiology with hands-on recombinant DNA experience. Research experience in molecular microbial ecology and/or next-generation sequence analysis will be an advantage.
  3. Phytoplankton and zooplankton dynamics in the Subantarctic (supervisors: Dr. T. Bornman, SAEON, NMMU; Dr. S. De Villiers, DEA, NMMU): An MSc project will investigate various aspects of zooplankton and phytoplankton dynamics in the Southern Ocean, in the context of nutrient cycling and primary production in the vicinity of Subantarctic island systems compared to open ocean mesoscale features. Prerequisites: Applicants must have at least an Honours degree in Marine Zoology or Botany. Research experience in plankton will be an advantage.
  4. Identifying the drivers of the Subantarctic biological pump (supervisor: Dr. S. Fawcett, UCT): The goal of this project is to evaluate the importance of different types of phytoplankton for organic carbon export by coupling flow cytometric sorting of different phytoplankton groups with high sensitivity nitrogen isotope analysis. Biomass isotope data will be interpreted in the context of nutrient concentration and nitrate isotope measurements. Prerequisites: Applicants must have at least an Honours degree in Oceanography, Chemistry, Environmental or Earth Science, or a similar field. Research experience in a chemistry/biology laboratory and/or in shipboard oceanography will be an advantage.


1Department of Oceanography, University of Cape Town;
2 Department of Biochemistry and Microbiology, Rhodes University;
3 Elwandle Coastal Node, South African Environmental Observation Network;
4 Nelson Mandela Metropolitan University;
5 Oceans and Coasts, Department of Environmental Affairs;
6 Cape Peninsula University of Technology

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