Ecosystem Engineering: Sediment entrainment and flocculation mediated by microbial produced extracellular polymeric substances (EPS)
Microbial Ecology and Applied Microbiology
Final Report Abstract
Significance of the topic. Sediment dynamics shape aquatic habitats with huge ecological and economic implications and is greatly influenced by living organisms. This project funded by the DFG studies the biostabilisation potential of microbes and their secreted glue-like extracellular polymeric substances (EPS) in fine sediments to change their erosional behaviour; for the first time in freshwater habitats. The project addresses fundamental questions such as (a) the relevance of biostabilisation in lotic waters, (b) the influence of different environmental factors on biostabilisation, (c) the role of EPS in this process and (d) the impact of biostabilisation on the features and fate of eroded flocs. Work Progress. Firstly, a sophisticated experimental set-up consisting of flumes for biofilm cultivation was constructed allowing all the necessary manipulation and reproducibility of boundary conditions. To mimic the highly complex feedback mechanisms between fluid, biofilm and sediment appropriately, extensive prototype testing was required. Eventually, six identical straight flumes could be built where each of them has their own water circuits, temperature control as well as adjustable light intensities and flow velocities. Secondly, it was now possible to monitor regularly the natural-like growth of the biofilms by analysing various biological parameters such as microalgal biomass, bacterial cell numbers and EPS quantity and quality. For the latter, first trials in EPS protein elucidation using SDS-page resulted in promising protein fingerprints. Furthermore, microalgal community compositions, mainly diatoms, as well as eukaryotic and prokaryotic genetic diversity were investigated. The molecular approaches had to be optimized for our samples in testing various DNA extraction kits, PCR and DGGE protocols as well as different 16S rDNA primers/18S primers before performing statistical analysis and further sequencing. Thirdly, the techniques to determine biofilm adhesiveness and fine sediment stability were further optimized. The MagPI system (Magnetic Particle Induction) to monitor non-destructively adhesiveness with high spatial and temporal resolution has been developed further to better understand the functioning principle, ensure proper inter-calibration between different laboratories, improve the construction of the electromagnets and reduce subjectivity as well as help data accuracy by introducing a semi-automatised system (MagPI-IP Image processing). The erosion flume (SETEG) is used to measure overall sediment stability and we developed new reproducible protocols to determine the erosional behaviour of biostabilised sediment beds that have not been addressed before. Finally, set-up for floc characterization has been established by adapting the Gust Microcosm for floc erosion, constructing an appropriate settling column and implementing a sophisticated MATLAB code routine for a scientific sound floc evaluation. Significant findings. The first experiment in August 2012 proofed the comparability of biofilm growth and functions in all six flumes at identical abiotic boundary conditions. In the following, 8 further longterm experiments (duration between 4 and 6 weeks) were conducted over different seasons focusing on the impact of flow velocity and light intensity on biofilm development and biostabilisation. In summary, we could show that (a) stabilisation of fine sediments due to biofilm growth is indeed important in freshwater habitats (increase of sediment stability up to 11 times). While medium/high illumination resulted in biofilms with maximal stabilisation capacity due to microalgal growth, high flow velocity caused delayed biofilm growth and stabilisation (b). The microbial capacity to stabilize the sediment could be clearly related to EPS production especially regarding the secretion of EPS proteins (c) but also to the microbial community composition. Over the seasons, there were distinct shifts in microbial key-players and high degree of competition and specialisation to influence biostabilisation (d). Apparently, the occurrence of bacterial species being capable of producing high amounts of EPS as well as filaments (e.g. proteobacteria Rhodoferax) and sessile EPS-attached microalgal species (e.g. diatom Achnantidium) resulted in highest biostabilisation. The biologically-influenced flocs showed that a broad range of geometries and bulk densities to result in settling velocities that are significantly different from those assumed by classical equations for transport modelling (e).
Publications
- (2013). On the Way to implement Biofilm induced Sediment Stability in morphological Modeling. 35th IAHR World Congress. Chengdu, China
Thom, M., Schmidt, H., Wieprecht, S. und S.U. Gerbersdorf
- (2014). When Geomorphology meets Ecology: Considerations at Microscale. In Ecohydraulics Conference Proceedings. Trondheim, Norway
Gerbersdorf, S. U., Thesenvitz, C., Schmidt, H., Thom, M. & Wieprecht, S.
- (2015). A multi-disciplinarily designed mesocosm to address the complex flow-sedimentecology tripartite relationship on the microscale. Environmental Sciences Europe, 27(1), 1
Schmidt, H., Thom, M., Matthies, K., Behrens, S., Obst, U., Wieprecht, S., & Gerbersdorf, S. U.
(See online at https://doi.org/10.1186/s12302-014-0037-y) - (2015). Biostabilisation of fluvial sediments: An improved to device to address an old problem. In E-proceedings of the 36th IAHR World Congress. The Hague, Netherlands
Thom, M., Schmidt, H., Wieprecht, S., & Gerbersdorf, S. U.
(See online at https://dx.doi.org/10.13140/RG.2.1.4901.5521) - (2015). Biostabilization of cohesive sediments: revisiting the role of abiotic conditions, physiology and diversity of microbes, polymeric secretion, and biofilm architecture. Geobiology 13, 68-97
Gerbersdorf, S.U. und S. Wieprecht
(See online at https://doi.org/10.1111/gbi.12115) - (2015). Seasonal Biostabilisation and Erosion Behavior of Fluvial Biofilms Under Different Hydrodynamic and Light Conditions. International Journal of Sediment Research, 30, 273-284. Paper Award at the ISRS Stuttgart
Thom, M., Schmidt, H., Gerbersdorf, S. U., & Wieprecht, S.
(See online at https://doi.org/10.1016/j.ijsrc.2015.03.015) - (2016). The effect of seasonality upon the development of lotic biofilms and microbial biostabilisation. Freshwater Biology, 61(6), 963-978
Schmidt, H., Thom, M., King, L., Wieprecht, S., & Gerbersdorf, S. U.
(See online at https://doi.org/10.1111/fwb.12760) - (2016). The role of surface adhesion in biostabilisation processes, extended abstract. In Proceedings of the International Symposium on River Sedimentation ISRS. Stuttgart, Germany
Thom, M., Schmidt, H., Wieprecht, S., & Gerbersdorf, S. U.
