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In soils and sediments there is a strong coupling between local biogeochemical processes and the distribution of water, electron acceptors, acids and nutrients. Both sides are closely related and affect each other from small scale to larger scales. Soil structures such as aggregates, roots, layers or macropores enhance the patchiness of these distributions. At the same time it is difficult to access the spatial distribution and temporal dynamics of these parameter. Noninvasive imaging techniques with high spatial and temporal resolution overcome these limitations. And new non-invasive techniques are needed to study the dynamic interaction of plant roots with the surrounding soil, but also the complex physical and chemical processes in structured soils. In this study we developed an efficient non-destructive in-situ method to determine biogeochemical parameters relevant to plant roots growing in soil. This is a quantitative fluorescence imaging method suitable for visualizing the spatial and temporal pH changes around roots. We adapted the fluorescence imaging set-up and coupled it with neutron radiography to study simultaneously root growth, oxygen depletion by respiration activity and root water uptake. The combined set up was subsequently applied to a structured soil system to map the patchy structure of oxic and anoxic zones induced by a chemical oxygen consumption reaction for spatially varying water contents. Moreover, results from a similar fluorescence imaging technique for nitrate detection were complemented by a numerical modeling study where we used imaging data, aiming to simulate biodegradation under anaerobic, nitrate reducing conditions.
In this thesis, I investigated the factors influencing the growth and vertical distribution of planktonic algae in extremely acidic mining lakes (pH 2-3). In the focal study site, Lake 111 (pH 2.7; Lusatia, Germany), the chrysophyte, Ochromonas sp., dominates in the upper water strata and the chlorophyte, Chlamydomonas sp., in the deeper strata, forming a pronounced deep chlorophyll maximum (DCM). Inorganic carbon (IC) limitation influenced the phototrophic growth of Chlamydomonas sp. in the upper water strata. Conversely, in deeper strata, light limited its phototrophic growth. When compared with published data for algae from neutral lakes, Chlamydomonas sp. from Lake 111 exhibited a lower maximum growth rate, an enhanced compensation point and higher dark respiration rates, suggesting higher metabolic costs due to the extreme physico-chemical conditions. The photosynthetic performance of Chlamydomonas sp. decreased in high-light-adapted cells when IC limited. In addition, the minimal phosphorus (P) cell quota was suggestive of a higher P requirement under IC limitation. Subsequently, it was shown that Chlamydomonas sp. was a mixotroph, able to enhance its growth rate by taking up dissolved organic carbon (DOC) via osmotrophy. Therefore, it could survive in deeper water strata where DOC concentrations were higher and light limited. However, neither IC limitation, P availability nor in situ DOC concentrations (bottom-up control) could fully explain the vertical distribution of Chlamydomonas sp. in Lake 111. Conversely, when a novel approach was adopted, the grazing influence of the phagotrophic phototroph, Ochromonas sp., was found to exert top-down control on its prey (Chlamydomonas sp.) reducing prey abundance in the upper water strata. This, coupled with the fact that Chlamydomonas sp. uses DOC for growth, leads to a pronounced accumulation of Chlamydomonas sp. cells at depth; an apparent DCM. Therefore, grazing appears to be the main factor influencing the vertical distribution of algae observed in Lake 111. The knowledge gained from this thesis provides information essential for predicting the effect of strategies to neutralize the acidic mining lakes on the food-web.