Focal point of research activities: Environmental Systems
Summary:
Interdisciplinary studies are required when investigating environmental systems. This field brings together expertise from the fields of engineering,
microbiology and chemistry to better understand systems such as the biostabilisation of river and reservoir systems.
Key research questions address the following aspects. Firstly, the seasonal and spatial variation in the biostabilisation of fine sediment dynamics
is investigated. Secondly, once sediment is eroded from the bed, the influence of microbial biostabilisation on the characteristics of the entrained
material, or flocs, is addressed. The impact on floc characteristics, in turn, influences the transport or fate of fine material in these watercourses.
The biostabilisation working group (BIOSTAB) focuses on the significance of different microorganisms, to taxa and species level, on the
biostabilisation of sediment, as well as the reciprocal influence of hydrodynamic conditions and the biofilm topography and architecture.
Furthermore, the influence of micropollutants on the functionality and growth of biofilm is investigated. All of the above findings should provide
contextual data to implement microbial biostabilisation in future numerical sediment transport models.
Figure 1: Microbial biostabilisation plays a significant role in all aspects of the erosion, transport deposition and
consolidation (ETDC) cycle of fine cohesive sediments. Microbially produced polymers bind sediment particles together to increase the
resistance of the sediment bed to erosion. Once sediment is eroded, the fate of the entrained material is influenced by the microbial
activity, which alters floc characteristics and thus the transport and deposition of the fine material back to the sediment bed. The
sediment bed is also subject to consolidation processes that modify the biological matrix, chemically and physically which can further
promote the binding between particles. Source: Gerbersdorf and Wieprecht, Review Paper, Geobiology, 2015.
The department 1 / research group BIOSTAB has unique test facilities for the growth of biofilms under controlled conditions which mimic natural
regimes of light, temperature and hydrodynamics. These were built as part of the DFG project GE 1932 / 3-1 and consist of 6 independent but identical
flume systems. Further details of the flumes are available in the following publications: Schmidt et al., ESEU, 2015 and
Thom et al., Wasserwirtschaft 6, 2012
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Figure 2: A) Three independent flume systems housed in a large container which allow the natural growth of biofilms on
various substrates under controlled environmental conditions. B) The removable cartridges in the test area of the flume with biofilm growth.
The research group BIOSTAB examines in detail the following aspects / research areas:
The colonisation of surfaces by microbial organisms can result in a diverse biofilm. Pioneer bacteria will settle on a surface which then
promotes the attachment of protozoa and microalgae. The bacterial community is determined through a variety of molecular and genetic techniques
(PCR, FISH, DGGE) in collaboration with Prof. Werner Manz, Institute for Integrated Science, University of Koblenz-Landau; PD Dr. Michael
Schweikert from the Institute of Biomaterials and Biomolecular Systems (IBBS), University of Stuttgart and with Prof . Dr. Ursula Obst, KIT
Institute of Functional interfaces.
Figure 3: The graphic illustrates the multicultural life within a biofilm consisting of heterotrophic bacteria, cyanobacteria, diatoms, green algae, fungi and protozoa. The left circle indicates the trophic relations of the microorganisms in the “Microbial Loop”, the latter ensures a high efficiency in carbon transfer to higher trophic levels. Source: Gerbersdorf and Wieprecht, Review Paper, Geobiology, 2015
The microalgae present in biofilms are determined both qualitatively and quantitatively in collaboration with Dr Lydia King, Freiburg (diatoms)
and Prof. Dan Dietrich, Human and Environmental Toxicology, University of Konstanz (Cyanobacteria / blue-green algae).
Figure 4: DGGE gel of a natural bacterial community from a biofilm taken from the River Enz, Baden-Württemberg.
The diversity, specialisation and habitat capacity can all be determined from examination of the band patterns.
Image: Holger Schmidt.
Figure 5: Electron microscopy (EM) image of benthic microalgae (diatoms) which illustrates the Achnanthes minutissimum
attaches to the sediment particles by stalks made from extracellular polymeric substances (EPS). Image: Dr Lydia King.
Although the biofilm matrix is mainly composed of water (>90%), other important components such as extracellular DNA, sugars, proteins and
lipids are present, as well as many combinations such as glycoproteins. These substances are collectively termed “extracellular polymeric
substances or EPS” as they are secreted by the micro-organisms present as opposed to the internal components of the cells. In order to carefully
separate the extracellular and intracellular components, relatively ‘gentle’ extraction methods are used (Cation Exchange Resin or CER), followed
by quantitative and photometric determination of the main components of the colloidal fraction of EPS in the wet lab of BIOSTAB.
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Figure 6: Low Temperature Scanning Electron Microscopy (LTSEM) image. A) Glass beads before any growth of a biofilm. B) Glass
beads after a few days of biofilm growth illustrating the binding capacity of the EPS between particles. Source: H. Lubarsky, C. Hubas, M.
Chocho?ek, F. Larson, W. Manz, D.M. Paterson, and S.U. Gerbersdorf, PLoS One, 2010.
The presence of EPS and micro-organisms on a sediment bed can increase the adhesion or ‘stickiness’ of the surface. This adhesion is important for
the stability of the sediment and for the trapping and binding of particles from the overlying water column during deposition. This adhesion is
measured using the Magnetic Particle Induction (MagPI) method (Figure 7).
Figure 7: Schematic diagram of two alternative MagPI systems. An electromagnet (left) and a permanent magnet (right).
Ferromagnetic particles are placed on top of the biofilm and the force required to retrieve these particles is a direct measure of biofilm
adhesion. Source: F. Larson, H. Lubarsky, S.U. Gerbersdorf, and D.M. Paterson, L & O Methods, 2009.
In order to determine the influence of biostabilisation on the critical erosion threshold of sediments beds, the SETEG flume (An in-house built flow
channel) is used. Herewith, the biofilm surface is exposed to the flow within the channel (open bottom) and the flow velocity is enhanced in defined
increments until bed failure occurs. From hydraulic calibration the bottom shear stress is known as a function of the controlled flow rate.
This can be extended by e.g. lifting sediment cores up by a motor to measure erosion as a function of depth at shear stresses up to 15 Pa.
In addition, the erosion rate can be determined using the Sediment Erosion Rate Detection by Computerised Image Analysis (SEDCIA) system.
SEDCIA calculates the erosion rate based on the differences in surface elevation detected by lasers aimed at the sediment surface (See the MMM
research group pages for more information (Forschungsschwerpunkt MMM ).
The biofilm rich sediment beds can also be inserted into an annular erosion chamber (Gust microcosm, Figure 8). Once the biofilm and sediment
has been resuspended this material can be collected and further analysed. As the sediment is now bound with EPS it no longer erodes as
individual particles, instead aggregates of sediment particles plus organic matter/biofilm are released into the water column as ‘flocs’.
These flocs are known to behave differently from the constituent mineral components. The differences in floc characteristics can be detected
by carefully transferring the flocs to a settling chamber in which individual flocs are imaged using CCS camera (Figure 9) and characteristics
evaluated using a self-developed Matlab code (Daniela Santolamazza, Master Thesis, 2013).
Figure 8: The Gust microcosm. A homogenous shear stress can be applied to the sediment bed inserted in the chamber,
by means of a rotating disc and pump system. This evenly eroded the sediment bed. More technical details information in:
Gust & Mueller, 1997.
Figure 9: Multiple images of individual eroded flocs settling through a column can be captured by the CCD camera and
recorded on the attached software. Image: Titus Kimani Githua, Master Thesis, 2014.
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