Helmholtz-Zentrum für Umweltforschung
Recent publications
Urban green space (UGS) is a complex and highly dynamic interface between people and nature. The existing methods of quantifying and evaluating UGS are mainly implemented on the surface features at a landscape scale, and most of them are insufficient to thoroughly reflect the spatial-temporal relationships, especially the internal characteristics changes at a small scale and the neighborhood spatial relationship of UGS. This paper thus proposes a method to evaluate the internal dynamics and neighborhood heterogeneity of different types of UGS in Leipzig using the gray level co-occurrence matrix (GLCM) index. We choose GLCM variance, contrast, and entropy to analyze five main types of UGS through a holistic description of their vegetation growth, spatial heterogeneity, and internal orderliness. The results show that different types of UGS have distinct characteristics due to the changes of surrounding buildings and the distance to the built-up area. Within a one-year period, seasonal changes in UGS far away from built-up areas are more obvious. As for the larger and dense urban forests, they have the lowest spatial heterogeneity and internal order. On the contrary, the garden areas present the highest heterogeneity. In this study, the GLCM index depicts the seasonal alternation of UGS on the temporal scale and shows the spatial form of each UGS, being in line with local urban planning contexts. The correlation analysis of indices also proves that each type of UGS has its distinct temporal and spatial characteristics. The GLCM is valid in assessing the internal characteristics and relationships of various UGS at the neighborhood scales, and using the methodology developed in our study, more studies and field experiments could be fulfilled to investigate the assessment accuracy of our GLCM index approach and to further enhance the scientific understanding on the internal features and ecological functions of UGS.
The biomass of invertebrate detritivores is an important driver of multiple ecosystem functions, yet little is known about how it changes in the context of global change. Taking Collembola communities as our focal groups, we conducted a study at the Global Change Experimental Facility (GCEF) in central Germany to assess how climate change (i.e., increased temperature by ∼0.55 °C across seasons, and the altered precipitation patterns by ∼9 % increase in spring and autumn, and ∼21 % reduction in summer) and intensive land use (i.e., from extensively-used grassland to conventional cropland) would shift the biomass patterns of Collembola and their different life forms. Our results show that the biomass of different Collembola life forms differed in their response to the changes in climate and land use. Specifically, the population biomass of surface-dwelling Collembola significantly decreased under future climate scenario and intensive land use, while the biomass of soil-living Collembola responded less. Importantly, Collembola biomass was decreased by (i) climate change-induced body size shrinkage, and (ii) intensive land use-induced density reduction. These results suggest that different environmental change drivers are able to reduce soil microarthropod biomass via dissimilar mechanisms.
Soil structure plays a central role in many soil processes that are environmentally relevant. Intermittent freezing of the soil over winter is an important abiotic disturbance in temperate climates and its effects on soil structure depend on the soil’s preexistent structural strength and cohesion. Management choices such as tillage and plant cover after harvest strongly influence soil structure, and therefore the soil’s response to freeze-thaw. We examined the effects of 5 freeze-thaw cycles (FT) on the µCT-detectable structure of intact topsoil cores (Ø=100 mm, h=80 mm) from a long-term rotation and tillage experiment in Denmark. The cores were divided among two tillage treatments and two plant cover treatments, corresponding to a gradient of structural strength: CT-B<CT-V<NT-B<NT-V (CT=conventional tillage, NT=no-till, B=bare fallow and V=winter rye volunteers). We classified the µCT-detectable macropore volume in four size ranges (Full Range, <300 µm, 300–1020 µm and >1020 µm) and analyzed the macroporosity (Vt), mean macropore diameter (dm) and mean Euclidian distance to the nearest macropore (EDm). Additionally, we analyzed the effects of tillage and plant cover on several µCT-derived geometric parameters in Full Range. Overall, NT-B and NT-V resulted in lower macroporosity than in CT-B and CT-V. Similarly, we found fewer, less branched macropores with shorter mean branch length in NT compared to CT for both plant cover treatments. However, we propose that µCT-derived geometric parameters might be confounded by the overlapping influence of relatively few, complex and voluminous coarse macropores and the more abundant, less complex very fine macropores. Freeze-thaw, in turn, caused crumbling of soil around coarse macropores, reducing Vt and dm in Full Range and reducing Vt in the > 1020 µm range. Additionally, FT caused significant increases in Vt and reductions in dm and EDm in the < 300 µm range, indicating creation of new very fine macropores and expansion of previously indiscernible macropores. Overall, the effects of FT were reduced in NT (for equal plant cover treatments) and V (for equal tillage treatments), indicating greater resilience against FT in both cases.
Scenario analysis is a useful technique to inform landscape planning of social-ecological systems by modelling future trends in ecosystem service supply and distribution. This is especially critical in floodplain agroecosystems of rural areas, which are at risk of losing riparian forest corridors due to increasing land use conversion for agricultural production and other ecosystem services due to rural abandonment. However, few studies investigating the effects of land management combine social and ecological modelling in scenario analyses. We estimated the supply of 16 ecosystem services under five alternative scenarios along two gradients: agricultural intensification of the floodplain and active ecological restoration of the riparian forest. We used redundancy analyses to detect ecosystem service bundles and interviews to identify societal gains and losses associated with each management scenario. Our results show how land management influences both the supply and distribution of ecosystem services. Scenarios promoting active ecological restoration supplied more services and benefited a larger range of societal sectors than scenarios focused on provisioning services. We also found two consistent bundles across scenarios, one related to less intensive food supply and another one related to outdoor activities. Interestingly, additional services were included in these bundles in the different scenarios, reflecting land management effects. Landscape scale management promoting both the conservation of ecosystem functioning and the sustainable use of provisioning services could supply a more balanced set of ecosystem services and benefit a larger number of societal sectors, contributing to more equitable and sustainable futures in rural areas. © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
As the only oxygenic phototrophs among prokaryotes, cyanobacteria employ intricate mechanisms to regulate common metabolic pathways. These mechanisms include small protein inhibitors exerting their function by protein-protein interaction with key metabolic enzymes and regulatory small RNAs (sRNAs). Here we show that the sRNA NsiR4, which is highly expressed under nitrogen limiting conditions, interacts with the mRNA of the recently described small protein PirA in the model strain Synechocystis sp. PCC 6803. In particular, NsiR4 targets the pirA 5'UTR close to the ribosome binding site. Heterologous reporter assays confirmed that this interaction interferes with pirA translation. PirA negatively impacts arginine synthesis under ammonium excess by competing with the central carbon/nitrogen regulator PII that binds to and thereby activates the key enzyme of arginine synthesis, N-acetyl-L-glutamate-kinase (NAGK). Consistently, ectopic nsiR4 expression in Synechocystis resulted in lowered PirA accumulation in response to ammonium upshifts, which also affected intracellular arginine pools. As NsiR4 and PirA are inversely regulated by the global nitrogen transcriptional regulator NtcA, this regulatory axis enables fine tuning of arginine synthesis and conveys additional metabolic flexibility under highly fluctuating nitrogen regimes. Pairs of small protein inhibitors and of sRNAs that control the abundance of these enzyme effectors at the post-transcriptional level appear as fundamental building blocks in the regulation of primary metabolism in cyanobacteria.
Nowadays, utilizing shallow geothermal energy for heating and cooling buildings has received increased interest in the building sector. Among different technologies, large borehole heat exchanger arrays are widely employed to supply heat to various types of buildings. Recently, a 16-borehole array was constructed to extract shallow geothermal energy to provide heat to a newly-developed public building in Berlin. To guarantee the quality of the numerical model and reveal its sensitivity to different subsurface conditions, model simulations were conducted for 25 years with two finite element simulators, namely the open-source code OpenGeoSys and the widely applied commercial software FEFLOW. Given proper numerical settings, the simulation results from OpenGeoSys and FEFLOW are in good agreement. However, further analysis reveals differences with respect to borehole inflow temperature calculation implemented in the two software. It is found that FEFLOW intrinsically uses the outflow temperature from the previous time step to determine the current inflow temperature, which makes it capable of much faster simulation by avoiding iterations within a single time step. In comparison, OpenGeoSys always updates the inflow and outflow temperature based on their current time step values. Because the updates are performed after each iteration, it delivers more accurate results with the expense of longer simulation time. Based on this case study, OpenGeoSys is a valid alternative to FEFLOW for modeling ground source heat pump systems. For modellers working in this field, it is thus recommended to adopt small enough time step size, so that potential numerical error can be avoided.
Background Transcription factors (TFs) are proteins controlling the flow of genetic information by regulating cellular gene expression. A better understanding of TFs in a bacterial community context may open novel revenues for exploring gene regulation in ecosystems where bacteria play a key role. Here we describe PredicTF, a platform supporting the prediction and classification of novel bacterial TF in single species and complex microbial communities. PredicTF is based on a deep learning algorithm. Results To train PredicTF, we created a TF database (BacTFDB) by manually curating a total of 11,961 TF distributed in 99 TF families. Five model organisms were used to test the performance and the accuracy of PredicTF. PredicTF was able to identify 24–62% of the known TFs with an average precision of 88% in our five model organisms. We demonstrated PredicTF using pure cultures and a complex microbial community. In these demonstrations, we used (meta)genomes for TF prediction and (meta)transcriptomes for determining the expression of putative TFs. Conclusion PredicTF demonstrated high accuracy in predicting transcription factors in model organisms. We prepared the pipeline to be easily implemented in studies profiling TFs using (meta)genomes and (meta)transcriptomes. PredicTF is an open-source software available at https://github.com/mdsufz/PredicTF .
Background Persistence is a key criterion for the risk assessment of chemicals. In degradation tests, microbial biodegradation of labeled test chemicals leads to the incorporation of the label in microbial biomass, resulting in biogenic non-extractable residues (bioNER), which are not considered as harmful in persistence assessment. The amount of bioNER can be estimated using the microbial turnover to biomass (MTB) model. MTB estimates the biomass growth during productive degradation of a compound from theoretical growth yield and CO2-formation and gives an upper and a lower value for bioNER formation. The aim of this study is use available experimental data for bioNER to assess the validity, accuracy and precision of the MTB method as new tool in persistence assessment. Results We collected experimental data in order to test accuracy and precision of this estimation method. In total, 16 experimental studies were found in literature where bioNER was experimentally quantified. Hereof, 13 studies used the amount of label recovered from total amino acid (tAA) content as proxy for bioNER. Unfortunately, the comparison with experimental data was difficult due to the variety of employed methods. A conversion factor is required to extrapolate from tAA on bioNER, and this factor may vary during the experiment and between experiments. The bioNER formation for all compounds tested was calculated with the MTB method, and the outcome was compared to measured tAA as proxy for bioNER. The relation between predicted and measured bioNER was significant, but no better correlation was obtained than with CO2 to tAA. The mean absolute error of the prediction (low MTB versus tAA) was 5% applied label (range 0.3 to 16%). Some deviation between measured results and calculated bioNER could be contributed to uncertainties in the experimental determination, as shown by variance in replicates (bromoxynil) or high background of label in sterile samples (sulfadiazine). Conclusions MTB thus provides a robust model for determining of the potential amounts of biomass and bioNER formed from the degradation of organic chemicals.
Cardiosphere-derived cells (CDCs) generated from human cardiac biopsies have been shown to have disease-modifying bioactivity in clinical trials. Paradoxically, CDCs’ cellular origin in the heart remains elusive. We studied the molecular identity of CDCs using single-cell RNA sequencing (sc-RNAseq) in comparison to cardiac non-myocyte and non-hematopoietic cells (cardiac fibroblasts/CFs, smooth muscle cells/SMCs and endothelial cells/ECs). We identified CDCs as a distinct and mitochondria-rich cell type that shared biological similarities with non-myocyte cells but not with cardiac progenitor cells derived from human-induced pluripotent stem cells. CXCL6 emerged as a new specific marker for CDCs. By analysis of sc-RNAseq data from human right atrial biopsies in comparison with CDCs we uncovered transcriptomic similarities between CDCs and CFs. By direct comparison of infant and adult CDC sc-RNAseq data, infant CDCs revealed GO-terms associated with cardiac development. To analyze the beneficial effects of CDCs (pro-angiogenic, anti-fibrotic, anti-apoptotic), we performed functional in vitro assays with CDC-derived extracellular vesicles (EVs). CDC EVs augmented in vitro angiogenesis and did not stimulate scarring. They also reduced the expression of pro-apoptotic Bax in NRCMs. In conclusion, CDCs were disclosed as mitochondria-rich cells with unique properties but also with similarities to right atrial CFs. CDCs displayed highly proliferative, secretory and immunomodulatory properties, characteristics that can also be found in activated or inflammatory cell types. By special culture conditions, CDCs earn some bioactivities, including angiogenic potential, which might modify disease in certain disorders.
The chemical pollution crisis severely threatens human and environmental health globally. To tackle this challenge the establishment of an overarching international science–policy body has recently been suggested. We strongly support this initiative based on the awareness that humanity has already likely left the safe operating space within planetary boundaries for novel entities including chemical pollution. Immediate action is essential and needs to be informed by sound scientific knowledge and data compiled and critically evaluated by an overarching science–policy interface body. Major challenges for such a body are (i) to foster global knowledge production on exposure, impacts and governance going beyond data-rich regions (e.g., Europe and North America), (ii) to cover the entirety of hazardous chemicals, mixtures and wastes, (iii) to follow a one-health perspective considering the risks posed by chemicals and waste on ecosystem and human health, and (iv) to strive for solution-oriented assessments based on systems thinking. Based on multiple evidence on urgent action on a global scale, we call scientists and practitioners to mobilize their scientific networks and to intensify science–policy interaction with national governments to support the negotiations on the establishment of an intergovernmental body based on scientific knowledge explaining the anticipated benefit for human and environmental health.
Acute myeloid leukemia (AML) patients suffer dismal prognosis upon treatment resistance. To study functional heterogeneity of resistance, we generated serially transplantable patient-derived xenograft (PDX) models from one patient with AML and twelve clones thereof, each derived from a single stem cell, as proven by genetic barcoding. Transcriptome and exome sequencing segregated clones according to their origin from relapse one or two. Undetectable for sequencing, multiplex fluorochrome-guided competitive in vivo treatment trials identified a subset of relapse two clones as uniquely resistant to cytarabine treatment. Transcriptional and proteomic profiles obtained from resistant PDX clones and refractory AML patients defined a 16-gene score that was predictive of clinical outcome in a large independent patient cohort. Thus, we identified novel genes related to cytarabine resistance and provide proof of concept that intra-tumor heterogeneity reflects inter-tumor heterogeneity in AML.
Background The cattle sector is the most important economic production unit of the Irish farming and agri-food sector. Despite its relevance, there has been limited quantitative information about the structure of differing cattle production types and of the connections between them. This paper addresses this gap by providing, for the first time, an overview of the Irish cattle population structured by enterprise type. Methods & Results We collected data from the cattle register for the period 2015 to 2019 and assigned registered herds to one of 18 different herd types using a recently published herd type classification approach. This allows, for the first time, to exploring changes in enterprise types and subtypes over time, and describing the movements between these subtypes and from these subtypes to slaughter. Conclusions The overview and associated classification presented in this study will form the basis for a number of future comparative studies, including cross-sectoral assessments of profitability, estimation of the extent of animal health losses on Irish cattle farms or structural analysis of Greenhouse Gas (GHG) emissions across production systems.
Background Sleep is important for healthy functioning in children. Numerous genetic and environmental factors, from conception onwards, may influence this phenotype. Epigenetic mechanisms such as DNA methylation have been proposed to underlie variation in sleep or may be an early-life marker of sleep disturbances. We examined if DNA methylation at birth or in school age is associated with parent-reported and actigraphy-estimated sleep outcomes in children. Methods We meta-analysed epigenome-wide association study results. DNA methylation was measured from cord blood at birth in 11 cohorts and from peripheral blood in children (4–13 years) in 8 cohorts. Outcomes included parent-reported sleep duration, sleep initiation and fragmentation problems, and actigraphy-estimated sleep duration, sleep onset latency and wake-after-sleep-onset duration. Results We found no associations between DNA methylation at birth and parent-reported sleep duration (n = 3658), initiation problems (n = 2504), or fragmentation (n = 1681) (p values above cut-off 4.0 × 10–8). Lower methylation at cg24815001 and cg02753354 at birth was associated with longer actigraphy-estimated sleep duration (p = 3.31 × 10–8, n = 577) and sleep onset latency (p = 8.8 × 10–9, n = 580), respectively. DNA methylation in childhood was not cross-sectionally associated with any sleep outcomes (n = 716–2539). Conclusion DNA methylation, at birth or in childhood, was not associated with parent-reported sleep. Associations observed with objectively measured sleep outcomes could be studied further if additional data sets become available.
Background The European environmental risk assessment of plant protection products considers aquatic model ecosystem studies (microcosms/mesocosms, M/M) as suitable higher tier approach to assess treatment-related effects and to derive regulatory acceptable concentrations (RAC). However, it is under debate to what extent these artificial test systems reflect the risks of pesticidal substances with potential harmful effects on natural macroinvertebrate communities, and whether the field communities are adequately protected by the results of the M/M studies. We therefore compared the composition, sensitivity and vulnerability of benthic macroinvertebrates established in control (untreated) groups of 47 selected M/M studies with natural stream communities at 26 reference field sites. Results Since 2013 the number of benthic macroinvertebrate taxa present in M/M studies has increased by 39% to a mean of 38 families per study. However, there is only an average of 4 families per study that comply with the recommendations provided by EFSA (EFSA J 11:3290, 2013), i.e.: (i) allowing statistical identification of treatment-related effects of at least 70% according to the minimum detectable difference (here criteria are slightly modified) and (ii) belonging to insects or crustaceans (potentially sensitive taxa for pesticidal substances). Applying the criterion of physiological sensitivity according to the SPEAR pesticides concept, the number of families decreases from 4 to 2.3 per study. Conclusions Most taxa established in recent M/M studies do not suitably represent natural freshwater communities. First, because their abundances are often not sufficient for statistical detection of treatment-related effects in order to determine an appropriate endpoint and subsequent RAC. Recommendations are given to improve the detectability of such effects and their reliability. Second, the taxa often do not represent especially sensitive or vulnerable taxa in natural communities in terms of their traits. The uncertainties linked to vulnerable taxa in M/M studies are especially high considering their representativity for field assemblages and the comparability of factors determining their recovery time. Thus considering recovery for deriving a RAC (i.e., ERO-RAC) is not recommended. In addition, this paper discusses further concerns regarding M/M studies in a broader regulatory context and recommends the development of alternative assessment tools and a shift towards a new paradigm.
Background Bioaccumulation of hydrophobic organic compounds (HOCs) along freshwater food chains is a major environmental concern as top predators in food webs are relevant for human consumption. To characterize and manage the associated risks, considerable numbers of organisms are sampled regularly for monitoring purposes. However, ethical and financial issues call for an alternative, more generic and more robust approach for assessing the internal exposure of fish that circumvents large variability in biota sampling due to interindividual differences. Passive sampling devices (PSDs) offer a fugacity-based approach for pollutant enrichment from different abiotic environmental compartments with a subsequent estimation of bioaccumulation in fish which we explored and compared to HOC concentrations in fish as determined using traditional approaches. Results In this study, concentrations in silicone-based PSDs applied to the water phase and suspended particulate matter (SPM) of a river polluted with HOCs were used to estimate the concentration in model lipids at thermodynamic equilibrium with either environmental compartment. For comparison, muscle tissue of seven fish species (trophic level 1.8 to 2.8) was extracted using traditional exhaustive solvent extraction, and the lipid-normalized concentrations of HOCs were determined. The PSD-based data from SPM proved to be a more conservative estimator for HOCs accumulated in fish than those from water. Body length of the fish was found to be more suitable to describe increasing accumulation of HOCs than their trophic level as derived from stable isotope analysis and might offer a suitable alternative for future studies. Conclusions By combining fugacity-based sampling in the abiotic environment, translation into corresponding concentrations in model lipids and body length as an indicator for increasing bioaccumulation in fish, we present a suggestion for a robust approach that may be a meaningful addition to conventional monitoring methods. This approach potentially increases the efficiency of existing monitoring programs without the need to regularly sacrifice vertebrate species. Graphical Abstract
Lock-in mechanisms are major hurdles to sustainability transitions. Scholars identified various types of lock-ins; however, their dynamics and interactions remain underexplored. Using the case of food packaging, this study enhances the conceptual understanding and empirical analysis of lock-ins and their interactions from a socio-technical perspective. We analyze the material, institutional, behavioral, and discursive configuration and the shallow and deep lock-ins reinforcing the persistent dominance of single-use over reusable food packaging in Germany. Additionally, we explore the lock-in interactions both within and between the socio-technical elements. Hence, we introduce archetypical interlock-ins and lock-in clusters pointing to core trends of resistance towards reusable packaging alternatives. This study advances the lock-in concept for future socio-technical analyses while guiding the illumination of the complex dynamics of stability, the assessment of current sustainability transition interventions, and the search for potential unlocking strategies to enable change.
A major impediment to effective cellular therapies in solid tumors is the limited access of therapeutic cells to the tumor site. One strategy to overcome this challenge is to endow T cells with chemotactic properties required to access tumor tissue. Here, we present a chimeric antigen receptor (CAR)-modified T cell strategy centered around enhanced T cell trafficking. We outline isolation, activation, and transduction of human T cells, as well as techniques for assessing migratory and cytotoxic capacity of CAR-T cells. For complete details on the use and execution of this protocol, please refer to Lesch et al. (2021).
There is a global concern of pollinator declines and linked ecosystem service losses. However, although land-use changes are a primary threat to biodiversity, how land-use change affects pollinator communities, pollination networks and fruit-set of food crops is poorly understood. The impact of land-use changes is especially understudied in tropical systems, even though most tropical crops are highly dependent on animal pollination. Using 40 sites to investigate diurnal and nocturnal flower visitors in small-scale agroecosystems across land-use gradients in Thailand and tropical South-western China, we show that habitat structure shapes pollinator communities at local (floral species richness) and landscape level (percentage of tree plantation in a 500 m radius and percentage forest in a 5 km radius), influencing both the species richness of pollinators and their visitation rates. These, in turn, alter plant-pollinator network structure: community-level specialization increases with floral species richness and percentage of forest cover. However, the specialization decreases with percentage of tree plantation, illustrating that natural habitat better supports specialized species. Furthermore, fruit-sets of several crops were affected by land-use. Notably, fruit-set of mango was positively associated with the percentage of forest cover in the surrounding landscape. These findings reveal how land-use influence pollinator communities and highlight how natural habitats may safeguard ecosystem services.
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1,046 members
Hans-Hermann Thulke
  • Department of Ecological Modelling
Bernhard Karrasch
  • Department of River Ecology
Nico Jehmlich
  • Department of Molecular Systems Biology
Claudia Schuetze
  • Department of Monitoring and Exploration Technologies
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Permoserstrasse 15, 04318, Leipzig, Sachsen, Germany
Head of institution
Prof. Dr. Dr. h.c. Georg Teutsch
Website
www.ufz.de