Doctoral Programme on Marine Ecosystem Health and Conservation
 The MARES Researchers and their Research
Microbial community functioning at hypoxia: identification of the key players of nitrogen and sulfur cycles and their role in the ecosystem with manipulation experiments
PhD Code: MARES_12_13:
  • Host institute 1: P16 - Hellenic Centre for Marine Research (HCMR)
  • Host institute 2: P2 - Universität Bremen
  • Host institute 3: P1 - Ghent University (PhD promoter).
Research fields:
  • T1 - Future Oceans: temperature changes - hypoxia - acidifation
  • T2 - Understanding biodiversity effects on the functioning of marine ecosystems
  • Vincx Magda
  • Friedrich Michael W.
  • Karakassis Ioannis (
Contact Person and email: Arvanitidis Christos -

Subject description
Scientific background
Microorganisms drive biogeochemical processes that are critical for maintaining the planet in a habitable state (Falkowski et al., 2008); they are instrumental to the structure and functioning of marine ecosystems and to the chemistry of the ocean due to their essential part in the cycling of the elements and in the recycling of the organic matter. They play also an essential role in the operations of the trophic networks by perpetually interacting with the other biological components (Glöckner et al., 2012).
It is well known that increased hypoxia has an effect on the biogeochemical cycles of nutrients. Severe hypoxia and total lack of oxygen (anoxia) can lead to the production of hydrogen sulfide, which results from anaerobic mineralization of organic matter by sulfate reducing bacteria (Grote et al., 2012).
Chemolithotrophic prokaryotes are known to oxidize inorganic reduced compounds, such as ammonia or hydrogen sulfide and other reduced sulfur substances (Friedrich et al., 2001). Therefore, this prokaryotic activity greatly impacts biogeochemical cycles, especially nitrogen and sulfur cycles. In these reductive environments, chemolithoautotrophs benefit from their ability to grow by assimilating carbon dioxide (CO2).
Objectives and Methodology
The aim of this project is to study the effect of the microbial community assemblages, and specifically chemolithoautotrophic prokaryotes, on the biogeochemical cycles of hypoxic ecosystems. In particular, this project aims at understanding the coupling between of the oxidation reactions with the reduction reactions for nitrogen and sulfur. This study will experimentally investigate the contribution of different types of sulfur/sulfide oxidizers (aerobic, nitrate reducing, photosynthetic) on the removal of hydrogen sulfide in marine environments and their possible competition towards the various energy sources. Also, this project aims at understanding how sulfate reducers compete with each other for the available sulfate, when the latter is insufficient for complete oxidation of organic compounds, given that sulfate reducers can use a wide range of other electron acceptors.
The null hypothesis of this study is that the growth and functional potential of chemolithotrophic prokaryotes is irrelevant of the ecosystem’s available energy sources. Also, another hypothesis to be tested is that the removal of the toxic hydrogen sulfide is equally successful in all the different types of oxidation.
The area under study will be Amvrakikos Gulf (Ionian Sea, Western Greece). The experimental approach will include field work to collect environmental samples and conduct microcosm experiments, which will allow the manipulation of various environmental factors and the study of the system’s response under different electron donors. The results of the study are important to the stakeholders and the end-users of this productive ecosystem because of the long-term dystrophic crises occurring in the lagoons which are responsible for severe decreases in fish production.
Furthermore, bacterial strains will be isolated from the sediment samples and their growth rate will be tested in a variety of electron donors and acceptors. For the quantification of the chemolithoautotrophic bacteria, catalyzed reporter deposition (CARD)-FISH probes will be used, combined with microautoradiography (MICRO-CARDFISH) to assess the specific uptake of radiolabeled bicarbonate by prokaryotic cells. This technique will allow the quantification of chemolithoautotrophic bacteria in the samples and it will also allow their spatial distribution to be visualized.
Moreover, Quantitative real-time PCR will be used to study the expression of the different functional genes that drive the chemolithotrophic bacterial metabolism.
The construction of metagenomic libraries will allow the description of the whole microbial community and it will reveal its functional potential.
Consortium description and feasibility
This PhD subject involves close collaboration between two research partners, the Hellenic Centre for Marine Research (HCMR) and the University of Bremen. The combined scientific expertise of the partners and the use of infrastructure will largely facilitate the accomplishment of the project in a three year framework.
  • Falkowski P.G., Fenchel T., Delong E.F. (2008). The microbial engines that drive Earth’s biogeochemical cycles. Science 320: 1034–1039
  • Friedrich C.G., Rother D., Bardischewsky F., Quentmeier A., Fischer J. (2001). Oxidation of Reduced Inorganic Sulfur Compounds by Bacteria: Emergence of a Common Mechanism? Applied and Environmental Microbiology 67 (7): 2873-2882
  • Glöckner F.O., Stal L.J., Sandaa R.-A., Gasol J.M., O’Gara F., Hernandez F., Labrenz M., Stoica E., Varela M.M., Bordalo A., Pitta P. (2012). Marine Microbial Diversity and its role in Ecosystem Functioning and Environmental Change. Marine Board Position Paper 17. Calewaert, J.B. and McDonough N. (Eds.). Marine Board-ESF, Ostend, Belgium.
  • Grote J., Schott T., Bruckner C.G., Glöckner F.O., Josta G. et al. (2012). Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proc Natl Acad Sci USA 109 (2): 506–510
Employment Details
Fixed term employment contract (including social security).

Expected outcomes
1) Three scientific publications in international peer-reviewed journals. 2) Participation to one international and one national conference. 3) Outreach activities with the stakeholders and the public at large.

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Last update on 04/12/2019 -
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