Refine
Has Fulltext
- yes (48) (remove)
Year of publication
- 2019 (48) (remove)
Document Type
- Postprint (26)
- Doctoral Thesis (22)
Is part of the Bibliography
- yes (48)
Keywords
- biodiversity (4)
- Biodiversität (3)
- Capsella (2)
- Klimawandel (2)
- Räuber-Beute (2)
- animal personality (2)
- climate change (2)
- coexistence (2)
- ecology (2)
- plant diversity (2)
Institute
- Institut für Biochemie und Biologie (48) (remove)
Background: Artificial light at night (ALAN) is one form of human-induced rapid environmental changes (HIREC) and is strongly interfering with natural dark–light cycles. Some personality types within a species might be better suited to cope with environmental change and therefore might be selected upon under ongoing urbanization.
Results: We used LED street lamps in a large outdoor enclosure to experimentally investigate the effects of ALAN on activity patterns, movement and interaction of individuals of two species, the bank vole (Myodes glareolus) and the striped field mouse (Apodemus agrarius). We analyzed effects combined with individual boldness score. Both species reduced their activity budget during daylight hours. While under natural light conditions home ranges were larger during daylight than during nighttime, this difference vanished under ALAN. Conspecifics showed reduced home range overlap, proximity and activity synchrony when subjected to nighttime illumination. Changes in movement patterns in reaction to ALAN were not associated with differences in boldness score of individuals.
Conclusions: Our results suggest that light pollution can lead to changes in movement patterns and individual interactions in small mammals. This could lead to fitness consequences on the population level.
The natural abundance of Coiled Coil (CC) motifs in cytoskeleton and extracellular matrix proteins suggests that CCs play an important role as passive (structural) and active (regulatory) mechanical building blocks. CCs are self-assembled superhelical structures consisting of 2-7 α-helices. Self-assembly is driven by hydrophobic and ionic interactions, while the helix propensity of the individual helices contributes additional stability to the structure. As a direct result of this simple sequence-structure relationship, CCs serve as templates for protein design and sequences with a pre-defined thermodynamic stability have been synthesized de novo. Despite this quickly increasing knowledge and the vast number of possible CC applications, the mechanical function of CCs has been largely overlooked and little is known about how different CC design parameters determine the mechanical stability of CCs. Once available, this knowledge will open up new applications for CCs as nanomechanical building blocks, e.g. in biomaterials and nanobiotechnology.
With the goal of shedding light on the sequence-structure-mechanics relationship of CCs, a well-characterized heterodimeric CC was utilized as a model system. The sequence of this model system was systematically modified to investigate how different design parameters affect the CC response when the force is applied to opposing termini in a shear geometry or separated in a zipper-like fashion from the same termini (unzip geometry). The force was applied using an atomic force microscope set-up and dynamic single-molecule force spectroscopy was performed to determine the rupture forces and energy landscape properties of the CC heterodimers under study. Using force as a denaturant, CC chain separation is initiated by helix uncoiling from the force application points. In the shear geometry, this allows uncoiling-assisted sliding parallel to the force vector or dissociation perpendicular to the force vector. Both competing processes involve the opening of stabilizing hydrophobic (and ionic) interactions. Also in the unzip geometry, helix uncoiling precedes the rupture of hydrophobic contacts.
In a first series of experiments, the focus was placed on canonical modifications in the hydrophobic core and the helix propensity. Using the shear geometry, it was shown that both a reduced core packing and helix propensity lower the thermodynamic and mechanical stability of the CC; however, with different effects on the energy landscape of the system. A less tightly packed hydrophobic core increases the distance to the transition state, with only a small effect on the barrier height. This originates from a more dynamic and less tightly packed core, which provides more degrees of freedom to respond to the applied force in the direction of the force vector. In contrast, a reduced helix propensity decreases both the distance to the transition state and the barrier height. The helices are ‘easier’ to unfold and the remaining structure is less thermodynamically stable so that dissociation perpendicular to the force axis can occur at smaller deformations.
Having elucidated how canonical sequence modifications influence CC mechanics, the pulling geometry was investigated in the next step. Using one and the same sequence, the force application points were exchanged and two different shear and one unzipping geometry were compared. It was shown that the pulling geometry determines the mechanical stability of the CC. Different rupture forces were observed in the different shear as well as in the unzipping geometries, suggesting that chain separation follows different pathways on the energy landscape. Whereas the difference between CC shearing and unzipping was anticipated and has also been observed for other biological structures, the observed difference for the two shear geometries was less expected. It can be explained with the structural asymmetry of the CC heterodimer. It is proposed that the direction of the α-helices, the different local helix propensities and the position of a polar asparagine in the hydrophobic core are responsible for the observed difference in the chain separation pathways. In combination, these factors are considered to influence the interplay between processes parallel and perpendicular to the force axis.
To obtain more detailed insights into the role of helix stability, helical turns were reinforced locally using artificial constraints in the form of covalent and dynamic ‘staples’. A covalent staple bridges to adjacent helical turns, thus protecting them against uncoiling. The staple was inserted directly at the point of force application in one helix or in the same terminus of the other helix, which did not experience the force directly. It was shown that preventing helix uncoiling at the point of force application reduces the distance to the transition state while slightly increasing the barrier height. This confirms that helix uncoiling is critically important for CC chain separation. When inserted into the second helix, this stabilizing effect is transferred across the hydrophobic core and protects the force-loaded turns against uncoiling. If both helices were stapled, no additional increase in mechanical stability was observed. When replacing the covalent staple with a dynamic metal-coordination bond, a smaller decrease in the distance to the transition was observed, suggesting that the staple opens up while the CC is under load.
Using fluorinated amino acids as another type of non-natural modification, it was investigated how the enhanced hydrophobicity and the altered packing at the interface influences CC mechanics. The fluorinated amino acid was inserted into one central heptad of one or both α-helices. It was shown that this substitution destabilized the CC thermodynamically and mechanically. Specifically, the barrier height was decreased and the distance to the transition state increased. This suggests that a possible stabilizing effect of the increased hydrophobicity is overruled by a disturbed packing, which originates from a bad fit of the fluorinated amino acid into the local environment. This in turn increases the flexibility at the interface, as also observed for the hydrophobic core substitution described above. In combination, this confirms that the arrangement of the hydrophobic side chains is an additional crucial factor determining the mechanical stability of CCs.
In conclusion, this work shows that knowledge of the thermodynamic stability alone is not sufficient to predict the mechanical stability of CCs. It is the interplay between helix propensity and hydrophobic core packing that defines the sequence-structure-mechanics relationship. In combination, both parameters determine the relative contribution of processes parallel and perpendicular to the force axis, i.e. helix uncoiling and uncoiling-assisted sliding as well as dissociation. This new mechanistic knowledge provides insight into the mechanical function of CCs in tissues and opens up the road for designing CCs with pre-defined mechanical properties. The library of mechanically characterized CCs developed in this work is a powerful starting point for a wide spectrum of applications, ranging from molecular force sensors to mechanosensitive crosslinks in protein nanostructures and synthetic extracellular matrix mimics.
How much do we really lose?
(2019)
Natural landscape elements (NLEs) in agricultural landscapes contribute to biodiversity and ecosystem services, but are also regarded as an obstacle for large‐scale agricultural production. However, the effects of NLEs on crop yield have rarely been measured. Here, we investigated how different bordering structures, such as agricultural roads, field‐to‐field borders, forests, hedgerows, and kettle holes, influence agricultural yields. We hypothesized that (a) yield values at field borders differ from mid‐field yields and that (b) the extent of this change in yields depends on the bordering structure.
We measured winter wheat yields along transects with log‐scaled distances from the border into the agricultural field within two intensively managed agricultural landscapes in Germany (2014 near Göttingen, and 2015–2017 in the Uckermark).
We observed a yield loss adjacent to every investigated bordering structure of 11%–38% in comparison with mid‐field yields. However, depending on the bordering structure, this yield loss disappeared at different distances. While the proximity of kettle holes did not affect yields more than neighboring agricultural fields, woody landscape elements had strong effects on winter wheat yields. Notably, 95% of mid‐field yields could already be reached at a distance of 11.3 m from a kettle hole and at a distance of 17.8 m from hedgerows as well as forest borders.
Our findings suggest that yield losses are especially relevant directly adjacent to woody landscape elements, but not adjacent to in‐field water bodies. This highlights the potential to simultaneously counteract yield losses close to the field border and enhance biodiversity by combining different NLEs in agricultural landscapes such as creating strips of extensive grassland vegetation between woody landscape elements and agricultural fields. In conclusion, our results can be used to quantify ecocompensations to find optimal solutions for the delivery of productive and regulative ecosystem services in heterogeneous agricultural landscapes.
Water is essential to life and thus, an essential resource. However, freshwater resources are limited and their maintenance is crucial. Pollution with chemicals and pathogens through urbanization and a growing population impair the quality of freshwater. Furthermore, water can serve as vector for the transmission of pathogens resulting in water-borne illness.
The Interdisciplinary Research Group III – "Water" of the Leibniz alliance project INFECTIONS‘21 investigated water as a hub for pathogens focusing on Clostridioides difficile and avian influenza A viruses that may be shed into the water. Another aim of this study was to characterize the bacterial communities in a wastewater treatment plant (WWTP) of the capital Berlin, Germany to further assess potential health risks associated with wastewater management practices.
Bacterial communities of WWTP inflow and effluent differed significantly. The proportion of fecal/enteric bacteria was relatively low and OTUs related to potential enteric pathogens were largely removed from inflow to effluent. However, a health risk might exist as an increased relative abundance of potential pathogenic Legionella spp. such as L. lytica was observed. Three Clostridioides difficile isolates from wastewater inflow and an urban bathing lake in Berlin (‗Weisser See‘) were obtained and sequenced. The two isolates from the wastewater did not carry toxin genes, whereas the isolate from the lake was positive for the toxin genes. All three isolates were closely related to human strains. This indicates a potential, but rather sporadic health risk. Avian influenza A viruses were detected in 38.8% of sediment samples by PCR, but virus isolation failed. An experiment with inoculated freshwater and sediment samples showed that virus isolation from sediment requires relatively high virus concentrations and worked much better in Madin-Darby Canine Kidney (MDCK) cell cultures than in embryonated chicken eggs, but low titre of influenza contamination in freshwater samples was sufficient to recover virus.
In conclusion, this work revealed potential health risks coming from bacterial groups with pathogenic potential such as Legionella spp. whose relative abundance is higher in the released effluent than in the inflow of the investigated WWTP. It further indicates that water bodies such as wastewater and lake sediments can serve as reservoir and vector, even for non-typical water-borne or water-transmitted pathogens such as C. difficile.
Microplastics (MP) constitute a widespread contaminant all over the globe. Rivers and wastewater treatment plants (WWTP) transport annually several million tons of MP into freshwaters, estuaries and oceans, where they provide increasing artificial surfaces for microbial colonization. As knowledge on MP-attached communities is insufficient for brackish ecosystems, we conducted exposure experiments in the coastal Baltic Sea, an in-flowing river and a WWTP within the drainage basin. While reporting on prokaryotic and fungal communities from the same set-up previously, we focus here on the entire eukaryotic communities. Using high-throughput 18S rRNA gene sequencing, we analyzed the eukaryotes colonizing on two types of MP, polyethylene and polystyrene, and compared them to the ones in the surrounding water and on a natural surface (wood). More than 500 different taxa across almost all kingdoms of the eukaryotic tree of life were identified on MP, dominated by Alveolata, Metazoa, and Chloroplastida. The eukaryotic community composition on MP was significantly distinct from wood and the surrounding water, with overall lower diversity and the potentially harmful dinoflagellate Pfiesteria being enriched on MP. Co-occurrence networks, which include prokaryotic and eukaryotic taxa, hint at possibilities for dynamic microbial interactions on MP. This first report on total eukaryotic communities on MP in brackish environments highlights the complexity of MP-associated biofilms, potentially leading to altered microbial activities and hence changes in ecosystem functions.
Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world’s largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales, and
Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm.
The unprecedented increase in atmospheric concentrations of carbon dioxide (CO2) and other greenhouse gases (GHG) by anthropogenic activities since the Industrial Revolution impacts on various earth system processes, commonly referred to as `climate change´ (CC). CC faces aquatic ecosystems with extreme abiotic perturbations that potentially alter the interrelations between functional autotrophic and heterotrophic plankton groups. These relations, however, modulate biogeochemical cycling and mediate the functioning of aquatic ecosystems as C sources or sinks to the atmosphere. The aim of this thesis was therefore to investigate how different aspects of CC influence community composition and functioning of pelagic heterotrophic bacteria. These organisms constitute a major component of biogeochemical cycling and largely determine the balance between autotrophic and heterotrophic processes.
Due to the vast amount of potential CC impacts, this thesis focuses on the following two aspects: (1) Increased exchange of CO2 across the atmosphere-water interface and reaction of CO2 with seawater leads to profound shifts in seawater carbonate chemistry, commonly termed as `ocean acidification´ (OA), with consequences for organism physiology and the availability of dissolved inorganic carbon (DIC) in seawater. (2) The increase in atmospheric GHG concentration impacts on the efficiency with which the Earth cools to space, affecting global surface temperature and climate. With ongoing CC, shifts in frequency and severity of episodic weather events, such as storms, are expected that in particular might affect lake ecosystems by disrupting thermal summer stratification. Both aspects of CC were studied at the ecosystem-level in large-volume mesocosm experiments by using the Kiel Off-shore Mesocosms for Future Ocean Simulations (KOSMOS) deployed at different coastal marine locations, and the LakeLab facility in Lake Stechlin.
We evaluated the impact of OA on heterotrophic bacterial metabolism in a brackish coastal ecosystem during low-nutrient summer months in the Baltic Sea. There are several in situ experiments that already assessed potential OA-induced changes in natural plankton communities at diverse spatial and seasonal conditions. However, most studies were performed at high phytoplankton biomass conditions, partly provoked by nutrient amendments. Our study highlights potential OA effects at low-nutrient conditions that are representative for most parts of the ocean and of particular interest in current OA research. The results suggest that during extended periods at low-nutrient concentrations, increasing pCO2 levels indirectly impact the growth balance of heterotrophic bacteria via trophic bacteria-phytoplankton interactions and shift the ecosystem to a more autotrophic system.
Further work investigated how OA affects heterotrophic bacterial dissolved organic matter (DOM) transformation in two mesocsom studies, performed at different nutrient conditions. We observed similar succession patterns for individual compound pools during a phytoplankton bloom and subsequent accumulation of these compounds irrespective of the pCO2 treatment. Our results indicate that OA-induced changes in the dynamics of bacterial DOM transformation and potential impacts on DOM quality are unlikely. In addition, there have been no indications that in dependence of nutrient conditions, different amounts of photosynthetic organic matter are channelled into the more recalcitrant DOM pool. This provides novel insights into the general dynamics of the marine DOM pool.
A fourth enclosure experiment in oligo-mesotrophic Lake Stechlin assessed the impact of a severe summer storm on lake bacterial communities during thermal stratification by artificially mixing. Mixing disrupted and lowered the thermocline, increasing the upper mixed layer and substantially changed water physical-chemical variables. Deep water entrainment and associated changes in water physical-chemical variables significantly affected relative bacterial abundances for about one week. Afterwards a pronounced cyanobacterial bloom developed in response to mixing which affected community assembly of heterotrophic bacteria. Colonization and mineralization of senescent phytoplankton cells by heterotrophic bacteria largely determined C-sequestration to the sediment. About six weeks after mixing, bacterial communities and measured activity parameters converged to control conditions. As such, summer storms have the potential to affect bacterial communities for a prolonged period during summer stratification. The results highlight effects on community assembly and heterotrophic bacterial metabolism that are associated to entrainment of deep water into the mixed water layer and assess consequences of an episodic disturbance event for the coupling between bacterial metabolism and autochthonous DOM production in large volume clear-water lakes.
Altogether, this doctoral thesis reveales substantial sensitivities of heterotrophic bacterial metabolism and community structure in response to OA and a simulated summer storm event, which should be considered when assessing the impact of climate change on marine and lake ecosystems.
Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.