Environmental controls of benthic nitrogen cycling in Lake Lugano South Basin, Switzerland – Pathways, rates, isotopic signatures and microbial communities

Cojean , Adeline N.Y.. Environmental controls of benthic nitrogen cycling in Lake Lugano South Basin, Switzerland – Pathways, rates, isotopic signatures and microbial communities. 2020, Doctoral Thesis, University of Basel, Faculty of Science.


Official URL: https://edoc.unibas.ch/79088/

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Nitrogen (N) is a key constituent of biomolecules required by all living organisms so understanding of its fluxes and in situ environmental availability is of crucial importance. In aquatic ecosystems, N availability regulates primary production and, to an extent, mass and energy transfer between trophic levels. Naturally, the vast reservoir of atmospheric N2 is only available to highly specialized diazotrophic microbes, but development and broad implementation of the Haber–Bosch process produces 450 million tons of nitrogen fertilizer per year from the N2 in the atmosphere, thereby changing the global N cycle entirely. Excessive loadings of reactive N (i.e., NO3-, NH4+) from fertilizer overuse have dramatically disturbed Earth ecosystems and inland waters in particular. One of the immediate consequences of P and N pollution in lakes and in the ocean is excessive biomass production, which supplies large amounts of highly labile organic matter to the sediments. Subsequent microbial degradation of this surplus organic matter quickly reduced the oxygen (O2) availability leading to proliferation of hypoxia and anoxia in bottom waters.
Anaerobic respiration by microorganisms can remove significant quantities of reactive N from the system, specifically in the sediments where rates of microbial N processing are highest. Anaerobic denitrification and ammonium oxidation (anammox), which convert fixed N to N2, are globally the most important sinks for reactive N. In contrast, anaerobic dissimilatory nitrate reduction to ammonium (DNRA) hampers the removal of nitrogen and instead leads to recycling of nutrients (e.g. NH4+) in the water column. The relative partitioning between N-removal and its recycling plays a critical role in modulating eutrophication and is highly relevant for regulating the N budget of lakes and the ocean. However, our current understanding of the nitrogen cycling in lacustrine sediments, and in particular the exact biogeochemical controls on the relative partitioning between these N-transformation processes remains limited. Recent discovery of new N-transforming microorganisms with previously unknown metabolisms and unexpected links with other biogeochemical cycling (e.g. iron, manganese, sulfur and methane) implies that despite, decades of research, aquatic nitrogen cycling still hides mysteries. Lake Lugano (South Basin) is a monomictic eutrophic system, and thus an excellent model system to disentangle the relative importance of numerous microbial redox-driven transformations and identify their environmental controls. The main goal of my PhD project was to quantify the different benthic N-transformation processes and understand the potential environmental controls on their relative contribution to N reduction, and associated NO3- isotopic signatures. In addition, we investigated the microbial community’s structure and its seasonal dynamics at the surface sediments.
The results highlight the overall importance of the biogeochemical controls O2, sediment reactivity, Fe2+ and H2S on the partitioning between N-loss and N-recycling, as well as on N isotopic signatures associated with NO3- reduction. Denitrification was the main anaerobic N-transformation processes in the sediments. The relative contribution of DNRA to total NO3- reduction varied from 31 to 52% depending on the season. In contrast, anammox contributed only about 1%. We demonstrated the major importance of oxygenation in controlling the fate of N in incubation experiments using natural sediments subject to fluctuating oxygen concentrations. Denitrification was favored over DNRA at relatively low oxygen concentrations (≤ 1 µM O2). In contrast N-processing via DNRA was prevalent at higher O2 levels. The O2 penetration depth was found to control the NO3- isotopic signatures in overlying water, through effects on nitrification (aerobic oxidation of NH4+ to NO3-) in particular. Finally, we showed that the availability of Fe2+ and H2S regulated the balance between denitrification and DNRA. Generally, at low Fe2+ (≤ 250 µM) and free H2S (≤ 80 µM) levels, denitrification was favored over DNRA, while DNRA was stimulated when Fe2+ concentration exceeded 700 µM. In contrast, Mn2+ did not play an important role in regulating the fate of benthic N.
Among bacterial functional groups, only sulfate-reducing, sulfur-oxidizing and methanotrophic bacteria were affected by seasonally changing redox conditions at the sediment-water interface. The annual water-column turnover and subsequent oxygenation of bottom waters likely decreases Fe2+ and H2S availability in surface sediments, which may enhance NO3- removal to N2 at the oxic-anoxic interface layer. On the other hand, DNRA is less O2 sensitive than denitrification, and water-column mixing may enhance NH4+ release from the sediments. Therefore, the experimental results suggest the importance of fluctuating environmental conditions in regulating the partitioning between N-loss and N-recycling in freshwater sediments, however, it remains difficult to predict how these environmental changes act together to possibly shift the balance between the different N-cycling processes and to regulate the overall fixed N-elimination rate in lake sediments.
Advisors:Lehmann, Moritz F
Committee Members:Stief, Peter
Faculties and Departments:05 Faculty of Science > Departement Umweltwissenschaften > Geowissenschaften > Aquatic and Isotope Biogeochemistry (Lehmann)
UniBasel Contributors:Lehmann, Moritz F
Item Type:Thesis
Thesis Subtype:Doctoral Thesis
Thesis no:13971
Thesis status:Complete
Number of Pages:X, 207
Identification Number:
  • urn: urn:nbn:ch:bel-bau-diss139718
edoc DOI:
Last Modified:02 Mar 2021 05:30
Deposited On:01 Mar 2021 14:57

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