Helmholtz-Zentrum für Umweltforschung
Recent publications
Rhamnolipids are biosurfactants produced by bacteria belonging to the Pseudomonas genus. They are discussed to complex heavy metal cations stronger than cations of Fe, Ca, Mg. It is therefore suggested to employ rhamnolipids in phytoextraction where their addition to soil should result in preferential complexation of heavy metals that can be taken up by plants, thus enabling rapid and ecological clean-up of contaminated soil. In order to test this concept, we evaluated the rhamnolipid-mediated phytoextraction of heavy metal from soil collected from the vicinity of a copper smelter. The following aspects were investigated: i) selectivity of rhamnolipids towards Cu, Zn, Pb, Cd and Fe during soil washing; ii) phytoextraction efficiency of each ion with respect to the effective concentration of rhamnolipids; iii) possible phytotoxic effects; iv) effect of micro-sized polystyrene amendment. The experiments evaluated soil washing efficiency, BCR (Community Bureau of Reference) sequential extraction to determine the impact of rhamnolipids on the mobility of metal ions, phytoextraction with maize (Zea mays L.) and phytotoxic effects based on dry matter, chlorophyll fluorescence and content. The obtained results indicated that rhamnolipids lack desired selectivity towards heavy metal ions as Fe was complexed more efficiently by 80 % of the available rhamnolipids compared to priority pollutants like Zn, Cu, Pb, which were complexed by only 20 % of the tested rhamnolipids. With increased concentration of rhamnolipids, the soil washing efficiency increased and shifted in favour of Fe, reaching values of approx. 469 mg for Fe and only 118 mg in total of all tested heavy metals. Phytoextraction also favoured the accumulation of Fe, while Cd was not removed from the soil even at the highest applied rhamnolipid concentrations. Considering the selectivity of rhamnolipids and the costs associated with their production, our results suggest the need to search for other alternative (bio)surfactants with better selectivity and lower price.
Laccases (EC1.10.3.2) have attracted growing attention in bioremediation research due to their high reactivity and substrate versatility. In this study, three genes for potential novel laccases were identified in an enrichment culture from contaminated field soil and recombinantly expressed in E. coli. Two of them, designated as PlL and BaL, were biochemically characterized regarding their optimal pH and temperature, kinetic parameters, and substrate versatility. In addition, lacasse PlL from Parvibaculum lavamentivorans was tested on historically contaminated soil. Treatment with PlL led to a significantly higher reduction of total petroleum hydrocarbons (83% w/w) compared to the microbial control (74% w/w). Hereby, PlL was especially effective in degrading hydrocarbons >C17. Their residual concentration was by 43% w/w lower than in the microbial treatment. In comparison to the laccase from Myceliophthora thermophila (MtL), PlL treatment was not significantly different for the fraction >C17 but resulted in a 30% (w/w) lower residual concentration for hydrocarbons <C18. In general, PlL can promote the degradation of petroleum hydrocarbons. As a consequence, it can be applied to reduce remediation time by duly achieving remediation target concentrations needed for site closure.
Cable bacteria are multicellular, filamentous bacteria that use internal conductive fibers to transport electrons over centimeter distances from donors within anoxic sediment layers to oxygen at the surface. We extracted the fibers and used them as free‐standing bio‐based electrodes to investigate their electrocatalytic behavior. The fibers catalyzed the reversible interconversion of oxygen and water, and an electric current was running through the fibers even when the potential difference was generated solely by a gradient of oxygen concentration. Oxygen reduction as well as oxygen evolution were confirmed by optical measurements. Within living cable bacteria, oxygen reduction by direct electrocatalysis on the fibers and not by membrane‐bound proteins readily explains exceptionally high cell‐specific oxygen consumption rates observed in the oxic zone, while electrocatalytic water oxidation may provide oxygen to cells in the anoxic zone.
Biodegradable plastics are one of the possible solutions for reducing plastic waste, yet the mechanisms and organisms involved in their degradation in the aquatic environment remain understudied. In this study, we have enriched a microbial community from North Sea water and sediment, capable of growing on the polyester poly(butylene succinate). This culture was grown on two other biodegradable polyesters, polycaprolactone and a poly(butylene adipate-co-terephthalate) blend. The differences between microbial community structure and biodegradation activity on these three polymers were determined by metagenomics, metaproteomics, and respirometry analysis. In this study, we observed that the polymer type drives the community structure and determines its biodegradation capability. When the PBS-enriched culture grew on the poly(butylene adipate- co -terephthalate) blend, the community was more diverse, yet showed the lowest biodegradation percentage, while poly(butylene succinate) and polycaprolactone resulted in a less diverse community but much higher biodegradation activity. The dominating species were Alcanivorax sp., Thalassobius sp., or Pseudomonas sp., depending on the substrate. In general, we have observed that Gammaproteobacteria were more abundant and active within the biofilm on the polymers and Alphaproteobacteria within the free-living fraction of the enrichments. Three putative hydrolases were recombinantly expressed and their hydrolytic activity on all polymers tested was verified. In conclusion, we showed that all three plastics can be biodegraded by bacteria naturally occurring within the marine environment. IMPORTANCE Biodegradable plastics can be used in applications where the end product cannot be efficiently recycled due to high levels of contaminations, e.g., food or soil. Some of these plastics have a dedicated end of life, such as composting, but their degradation in the marine environment is poorly understood. In this study we showed that marine microbial communities can degrade a range of biodegradable polymers with different physical and chemical properties and use these as a sole carbon source for growth. We have also provided insights into the degradation mechanisms using a combined metagenomic and metaproteomic approach. In addition, we have identified three new enzymes that are capable of degrading both aliphatic polymers and aliphatic-aromatic copolymers, which can be used for biotechnological applications.
Groundwater is the primary source of drinking water for Kabul city residents, and it is also widely utilized for industrial and agricultural purposes. Identification of the major hydrogeochemical processes is significantly important for sustainable groundwater management in Western Kabul Plain (WKP) aquifer. In this research, the physicochemical results and isotopic ratios of water-stable isotopes of 13 groundwater and river water samples from the WKP were collected in April 2021 and employed to assess the hydrogeochemical processes using multivariate statistics and self-organizing map (SOM). The results of this study indicated that Ca–(Mg–Na)–HCO3 is the dominant type of hydro-chemical facies in the WKP aquifer. The findings revealed that all water samples originated from modern meteoric precipitation and the aquifer is mainly recharged from Kabul and Paghman rivers. The sampling locations were divided into three clusters based on Q-mode hierarchical cluster analysis and SOM models. The factor analysis and SOM models indicated that groundwater chemistry in the WKP aquifer is primarily controlled by the dissolution of calcite, dolomite, gypsum, halite, weathering of silicates, and ion exchange. The factor analysis and SOM models showed that NO3̄ concentrations principally originated from anthropogenic activities. The findings of this research may contribute to sustainable groundwater resource management in Kabul city.
To reach their net-zero targets, countries will have to compensate hard-to-abate CO emissions through carbon dioxide removal (CDR). Yet, current assessments rarely include socio-cultural or institutional aspects or fail to contextualize CDR options for implementation. Here we present a context-specific feasibility assessment of CDR options for the example of Germany. We assess fourteen CDR options, including three chemical carbon capture options, six options for bioenergy combined with carbon capture and storage (BECCS), and five options that aim to increase ecosystem carbon uptake. The assessment addresses technological, economic, environmental, institutional, social-cultural and systemic considerations using a traffic-light system to evaluate implementation opportunities and hurdles. We find that in Germany CDR options like cover crops or seagrass restoration currently face comparably low implementation hurdles in terms of technological, economic, or environmental feasibility and low institutional or social opposition but show comparably small CO removal potentials. In contrast, some BECCS options that show high CDR potentials face significant techno-economic, societal and institutional hurdles when it comes to the geological storage of CO. While a combination of CDR options is likely required to meet the net-zero target in Germany, the current climate protection law includes a limited set of options. Our analysis aims to provide comprehensive information on CDR hurdles and possibilities for Germany for use in further research on CDR options, climate, and energy scenario development, as well as an effective decision support basis for various actors.
Groundwater protection and contaminated site remediation efforts continue to be hampered by the difficulty in characterizing physical properties in the subsurface at a resolution that is sufficiently high for practical investigations. For example, conventional well-based field methods, such as pumping tests, have proven to be of limited effectiveness for obtaining information, such as the transmissive and storage characteristics of a formation and the rate at which groundwater flows, across different layers in a heterogeneous aquifer system. In this chapter, we describe a series of developments that are intended to improve our discipline’s capability for high-resolution characterization of subsurface conditions in shallow, unconsolidated settings. These developments include high-resolution methods for hydraulic conductivity ( K ) characterization based on direct push (DP) technology (e.g., DP electrical conductivity probe, DP permeameter, DP injection logger, Hydraulic Profiling Tool (HPT), and High-Resolution K tool), K and porosity characterization by nuclear magnetic resonance (NMR), and groundwater flux characterization by monitoring the movement of thermal or chemical tracers through distributed temperature sensing (DTS) equipment or the point velocity probe (PVP). Each of these approaches is illustrated using field or laboratory examples, and a brief discussion is provided on their advantages, limitations, as well as suggestions for future developments.
Sporadic Parkinson’s Disease (sPD) is a progressive neurodegenerative disorder caused by multiple genetic and environmental factors. Mitochondrial dysfunction is one contributing factor, but its role at different stages of disease progression is not fully understood. Here, we showed that neural precursor cells and dopaminergic neurons derived from induced pluripotent stem cells (hiPSCs) from sPD patients exhibited a hypometabolism. Further analysis based on transcriptomics, proteomics, and metabolomics identified the citric acid cycle, specifically the α-ketoglutarate dehydrogenase complex (OGDHC), as bottleneck in sPD metabolism. A follow-up study of the patients approximately 10 years after initial biopsy demonstrated a correlation between OGDHC activity in our cellular model and the disease progression. In addition, the alterations in cellular metabolism observed in our cellular model were restored by interfering with the enhanced SHH signal transduction in sPD. Thus, inhibiting overactive SHH signaling may have potential as neuroprotective therapy during early stages of sPD.
Phototrophic microorganisms, like cyanobacteria, are gaining attention as host organisms for biocatalytic processes with light as energy source and water as electron source. Redox enzymes, especially oxygenases, can profit from in‐situ supply of co‐substrates, i.e., reduction equivalents and O2, by the photosynthetic light reaction. The electron transfer downstream of PS I to heterologous electron consuming enzymes in principle can involve NADPH, NADH, and/or ferredoxin, whereas most direct and efficient transfer is desirable. Here, we use the model organism Synechocystis sp. PCC 6803 to investigate, to what extent host and/or heterologous constituents are involved in electron transfer to a heterologous Cytochrome P450 monooxygenase from Acidovorax sp. CHX100. Interestingly, in this highly active light‐fueled cycloalkane hydroxylating biocatalyst, host‐intrinsic enzymes were found capable of completely substituting the function of the Acidovorax ferredoxin reductase. To a certain extent (20%), this also was true for the Acidovorax ferredoxin. These results indicate the presence of a versatile set of electron carriers in cyanobacteria, enabling efficient and direct coupling of electron consuming reactions to photosynthetic water oxidation. This will both simplify and promote the use of phototrophic microorganisms for sustainable production processes.
Leaky urban drainage networks (UDNs) exfiltrating wastewater can contaminate aquifers. Detailed knowledge on spatiotemporal distributions of water-dissolved, sewer-borne contaminants in groundwater is essential to protect urban aquifers and to optimize monitoring systems. We evaluated the effect of UDN layouts on the spreading of sewer-borne contaminants in groundwater using a parsimonious approach. Due to the UDN’s long-term leakage behavior and the existence of non-degradable sewer-borne contaminants (equivalent to a conservative and constant contaminant source), we employed a concept of horizontal line sources to mimic the UDN layout. This does not require the consideration of bio-degradation processes or temporal delay and effectively bypasses the vadose zone, thus reducing computational requirements associated with a full simulation of leakages. We used a set of synthetic leakage scenarios which were generated using fractals and are based on a real-world UDN layout. We investigated the effects of typical leakage rates, varying groundwater flow directions, and UDN’s layouts on the shape of the contaminant plume, disregarding the resulted concentration. Leakage rates showed minimal effects on the total covered plume area, whereas 89% of the variance of the plume’s geometry is explained by both the UDN’s layout (e.g., length and level of complexity) and groundwater flow direction. We demonstrated the potential of applying this approach to identify possible locations of groundwater observation wells using a real UDN layout. This straightforward and parsimonious method can serve as an initial step to strategically identify optimal monitoring systems locations within urban aquifers, and to improve sewer asset management at city scale. Supplementary Information The online version contains supplementary material available at 10.1007/s10661-023-12027-6.
Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user‐friendly tool tailored for those familiar with Unix command‐line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual‐isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open‐source software available at https://github.com/mdsufz/MuDoGeR . Additionally, MuDoGeR is also available as a Singularity container.
Deriving gross & net primary productivity (GPP & NPP) and carbon turnover time of forests from remote sensing remains challenging. This study presents a novel approach to estimate forest productivity by combining radar remote sensing measurements, machine learning and an individual-based forest model. In this study, we analyse the role of different spatial resolutions on predictions in the context of the Radar BIOMASS mission (by ESA). In our analysis, we use the forest gap model FORMIND in combination with a boosted regression tree (BRT) to explore how spatial biomass distributions can be used to predict GPP, NPP and carbon turnover time (τ) at different resolutions. We simulate different spatial biomass resolutions (4 ha, 1 ha and 0.04 ha) in combination with different vertical resolutions (20, 10 and 2 m). Additionally, we analysed the robustness of this approach and applied it to disturbed and mature forests. Disturbed forests have a strong influence on the predictions which leads to high correlations (R² > 0.8) at the spatial scale of 4 ha and 1 ha. Increased vertical resolution leads generally to better predictions for productivity (GPP & NPP). Increasing spatial resolution leads to better predictions for mature forests and lower correlations for disturbed forests. Our results emphasize the value of the forthcoming BIOMASS satellite mission and highlight the potential of deriving estimates for forest productivity from information on forest structure. If applied to more and larger areas, the approach might ultimately contribute to a better understanding of forest ecosystems.
Providing an anodic potential in a bio‐electrochemical system to the obligate aerobe Pseudomonas putida enables anaerobic survival and allows the cells to overcome redox imbalances. In this setup, the bacteria could be exploited to produce chemicals via oxidative pathways at high yield. However, the absence of anaerobic growth and low carbon turnover rates remain as obstacles for the application of such an electro‐fermentation technology. Growth and carbon turnover start with carbon uptake into the periplasm and cytosol. P. putida KT2440 has three native transporting systems for glucose, each differing in energy and redox demand. This architecture previously led to the hypothesis that internal redox and energy constraints ultimately limit cytoplasmic carbon utilization in a bio‐electrochemical system. However, it remains largely unclear which uptake route is predominantly used by P. putida under electro‐fermentative conditions. To elucidate this, we created three gene deletion mutants of P. putida KT2440, forcing the cells to exclusively utilize one of the routes. When grown in a bio‐electrochemical system, the pathway mutants were heavily affected in terms of sugar consumption, current output and product formation. Surprisingly, however, we found that about half of the acetate formed in the cytoplasm originated from carbon that was put into the system via the inoculation biomass, while the other half came from the consumption of substrate. The deletion of individual sugar uptake routes did not alter significantly the secreted acetate concentrations among different strains even with different carbon sources. This means that the stoichiometry of the sugar uptake routes is not a limiting factor during electro‐fermentation and that the low rates might be caused by other reasons, for example energy limitations or a yet‐to‐be‐identified oxygen‐dependent regulatory mechanism.
Infrastructure deterioration threatens urban water security and the pursuit of Sustainable Development Goal 6 (SDG 6, “water for all”). One billion urban residents worldwide already face intermittent piped water access, making their public water supply unreliable and unequal. Thus, effective investments in water infrastructure improvements are critical. In a recent WRR paper, Jeuland et al. (2023, https://doi.org/10.1029/2022WR033897) evaluate the impacts of a large infrastructure improvement project on various water security metrics and assess the challenges of such an investigation. They apply a rigorous difference‐in‐difference approach to data from a US$275 million investment in upgrades to water supply and sewage networks in the Zarqa governorate in arid Jordan, analyzing its effects on households, businesses, farms, and the water utility. The authors find a range of moderate improvements to water access and re‐use metrics, including a significant reduction in reported shortages. Key water security indicators related to access intermittency, however, such as the supply duration per day and the expenditure on water deliveries by tanker trucks, saw little to no improvement. The findings reveal that the efforts required to overcome the insecurity and inequity of intermittent public water supply systems might be considerably larger than expected. This suggests an urgent need to further enhance both the accuracy of impact evaluation methods and the effectiveness of infrastructure investments to support the pursuit of SDG 6.
Concurrent extreme rainfall events, or synchronous extremes, during Indian Summer Monsoon Rainfall (ISMR), cause significant damage, but their spatiotemporal evolution remains unclear. Using the event synchronization approach to examine the synchronicity of extreme rainfall events from 1901 to 2019, we find that Central India consistently hosts strongly connected synchronous extreme hubs with localized connections, indicating the geographical trapping of these concurrent events in the region. We observe a moderate positive correlation between network cohesiveness and El Niño Southern Oscillations (ENSO), and a negative correlation between ENSO and link lengths, suggesting localized synchronicity during El Niño dominant decades and opposite patterns in La Niña periods. Despite increasing ISMR variability and spatial nonuniformity, the persistence of hubs and network attributes could offer insights for predicting synchronous extremes, informing effective adaptation and risk management strategies during the monsoon season.
Mycelial networks allow fungi to spread efficiently and traverse air-filled pores. By transporting nutrients from nutrient-rich and to nutrient-poor areas, they also promote bacterial growth and cometabolic degradation of contaminants. Mycelia likewise connect microhabitats and act as dispersal vectors (fungal highways) for aerobic and anaerobic bacteria. Co-transport with hyphal-riding bacteria allows phages to move in water-poor habitats and enhances the fitness of invading bacteria in host precolonised zones.
Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation‐tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient‐cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.
Forests can foster mental health and well‐being. Yet, the contribution of forest biodiversity remains unclear, and experimental research is needed to unravel pathways of biodiversity–health linkages. Here, we assess the role of tree species richness, both actual and perceived, and how stress reduction and attention restoration can serve as potential mediating pathways to achieve positive mental health and well‐being outcomes. We conducted an experimental, multicentric field study in three peri‐urban forests in Europe, employing a mixed design with 223 participants, that comprised 20‐min stays in forests with either low, medium or high tree species richness or a built control. Participants' short‐term mental health and well‐being and saliva cortisol as a biomarker of stress were measured before and after the intervention. Forest visits for 20 min were found to be beneficial for participants' short‐term mental health, short‐term mental well‐being, subjective stress, subjective directed attention and perceived restorativeness compared with a built environment. No differences were found for the physiological stress indicator saliva cortisol, which decreased in both the forest and the built environments. Increased perceived biodiversity—possibly linked to structural forest attributes—was significantly associated with well‐being outcomes, while no association was found for differences in actual tree species richness. Structural equation modelling indicates that higher levels of perceived biodiversity had an indirect effect on short‐term mental health and well‐being through enhancing perceived restorativeness. While we found no evidence of actual tree species richness effects, perceived biodiversity was associated with positive short‐term mental health and well‐being outcomes. Understanding these biodiversity–health linkages can inform conservation management and help develop effective nature‐based interventions for promoting public health through nature visits. Read the free Plain Language Summary for this article on the Journal blog.
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1,085 members
Hans-Hermann Thulke
  • Department of Ecological Modelling
Bernhard Karrasch
  • Department of River Ecology
Nico Jehmlich
  • Department of Molecular Systems Biology
Permoserstrasse 15, 04318, Leipzig, Sachsen, Germany
Head of institution
Prof. Dr. Dr. h.c. Georg Teutsch