TY - JOUR A1 - Hering, Robert A1 - Hauptfleisch, Morgan A1 - Jago, Mark A1 - Smith, Taylor A1 - Kramer-Schadt, Stephanie A1 - Stiegler, Jonas A1 - Blaum, Niels T1 - Don't stop me now: Managed fence gaps could allow migratory ungulates to track dynamic resources and reduce fence related energy loss JF - Frontiers in Ecology and Evolution N2 - In semi-arid environments characterized by erratic rainfall and scattered primary production, migratory movements are a key survival strategy of large herbivores to track resources over vast areas. Veterinary Cordon Fences (VCFs), intended to reduce wildlife-livestock disease transmission, fragment large parts of southern Africa and have limited the movements of large wild mammals for over 60 years. Consequently, wildlife-fence interactions are frequent and often result in perforations of the fence, mainly caused by elephants. Yet, we lack knowledge about at which times fences act as barriers, how fences directly alter the energy expenditure of native herbivores, and what the consequences of impermeability are. We studied 2-year ungulate movements in three common antelopes (springbok, kudu, eland) across a perforated part of Namibia's VCF separating a wildlife reserve and Etosha National Park using GPS telemetry, accelerometer measurements, and satellite imagery. We identified 2905 fence interaction events which we used to evaluate critical times of encounters and direct fence effects on energy expenditure. Using vegetation type-specific greenness dynamics, we quantified what animals gained in terms of high quality food resources from crossing the VCF. Our results show that the perforation of the VCF sustains herbivore-vegetation interactions in the savanna with its scattered resources. Fence permeability led to peaks in crossing numbers during the first flush of woody plants before the rain started. Kudu and eland often showed increased energy expenditure when crossing the fence. Energy expenditure was lowered during the frequent interactions of ungulates standing at the fence. We found no alteration of energy expenditure when springbok immediately found and crossed fence breaches. Our results indicate that constantly open gaps did not affect energy expenditure, while gaps with obstacles increased motion. Closing gaps may have confused ungulates and modified their intended movements. While browsing, sedentary kudu's use of space was less affected by the VCF; migratory, mixed-feeding springbok, and eland benefited from gaps by gaining forage quality and quantity after crossing. This highlights the importance of access to vast areas to allow ungulates to track vital vegetation patches. KW - veterinary cordon fence KW - ungulate KW - fence ecology KW - resource-tracking KW - energy expenditure KW - accelerometer KW - GPS KW - wildlife and habitat management Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2022.907079 SN - 2296-701X SP - 1 EP - 18 PB - Frontiers CY - Lausanne, Schweiz ER - TY - JOUR A1 - Hering, Robert A1 - Hauptfleisch, Morgan A1 - Kramer-Schadt, Stephanie A1 - Stiegler, Jonas A1 - Blaum, Niels T1 - Effects of fences and fence gaps on the movement behavior of three southern African antelope species JF - Frontiers in Conservation Science N2 - Globally, migratory ungulates are affected by fences. While field observational studies reveal the amount of animal–fence interactions across taxa, GPS tracking-based studies uncover fence effects on movement patterns and habitat selection. However, studies on the direct effects of fences and fence gaps on movement behavior, especially based on high-frequency tracking data, are scarce. We used GPS tracking on three common African antelopes (Tragelaphus strepsiceros, Antidorcas marsupialis, and T. oryx) with movement strategies ranging from range residency to nomadism in a semi-arid, Namibian savanna traversed by wildlife-proof fences that elephants have regularly breached. We classified major forms of ungulate–fence interaction types on a seasonal and a daily scale. Furthermore, we recorded the distances and times spent at fences regarding the total individual space use. Based on this, we analyzed the direct effects of fences and fence gaps on the animals’ movement behavior for the previously defined types of animal–fence interactions. Antelope-fence interactions peaked during the early hours of the day and during seasonal transitions when the limiting resource changed between water and forage. Major types of ungulate–fence interactions were quick, trace-like, or marked by halts. We found that the amount of time spent at fences was highest for nomadic eland. Migratory springbok adjusted their space use concerning fence gap positions. If the small home ranges of sedentary kudu included a fence, they frequently interacted with this fence. For springbok and eland, distance traveled along a fence declined with increasing utilization of a fence gap. All species reduced their speed in the proximity of a fence but often increased their speed when encountering the fence. Crossing a fence led to increased speeds for all species. We demonstrate that fence effects mainly occur during crucial foraging times (seasonal scale) and during times of directed movements (daily scale). Importantly, we provide evidence that fences directly alter antelope movement behaviors with negative implications for energy budgets and that persistent fence gaps can reduce the intensity of such alterations. Our findings help to guide future animal–fence studies and provide insights for wildlife fencing and fence gap planning. KW - fence ecology KW - veterinary cordon fence KW - ungulate KW - movement speed KW - fence interaction KW - GPS KW - Africa KW - wildlife conservation Y1 - 2022 U6 - https://doi.org/10.3389/fcosc.2022.959423 SN - 2673-611X VL - 3 SP - 1 EP - 19 PB - Frontiers CY - Lausanne, Schweiz ER - TY - JOUR A1 - Irob, Katja A1 - Blaum, Niels A1 - Baldauf, Selina A1 - Kerger, Leon A1 - Strohbach, Ben A1 - Kanduvarisa, Angelina A1 - Lohmann, Dirk A1 - Tietjen, Britta T1 - Browsing herbivores improve the state and functioning of savannas BT - A model assessment of alternative land-use strategies JF - Ecology and evolution N2 - Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle-dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land-use strategies on a Namibian savanna: grazer- versus browser-dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land-use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing-dominated land-use strategies, land-use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services. KW - browsing KW - ecohydrology KW - land use KW - plant community KW - savanna KW - wildlife KW - management Y1 - 2022 U6 - https://doi.org/10.1002/ece3.8715 SN - 2045-7758 VL - 12 IS - 3 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Groh, Jannis A1 - Diamantopoulos, Efstathios A1 - Duan, Xiaohong A1 - Ewert, Frank A1 - Heinlein, Florian A1 - Herbst, Michael A1 - Holbak, Maja A1 - Kamali, Bahareh A1 - Kersebaum, Kurt-Christian A1 - Kuhnert, Matthias A1 - Nendel, Claas A1 - Priesack, Eckart A1 - Steidl, Jörg A1 - Sommer, Michael A1 - Pütz, Thomas A1 - Vanderborght, Jan A1 - Vereecken, Harry A1 - Wallor, Evelyn A1 - Weber, Tobias K. D. A1 - Wegehenkel, Martin A1 - Weihermüller, Lutz A1 - Gerke, Horst H. T1 - Same soil, different climate: Crop model intercomparison on translocated lysimeters JF - Vadose zone journal N2 - Crop model intercomparison studies have mostly focused on the assessment of predictive capabilities for crop development using weather and basic soil data from the same location. Still challenging is the model performance when considering complex interrelations between soil and crop dynamics under a changing climate. The objective of this study was to test the agronomic crop and environmental flux-related performance of a set of crop models. The aim was to predict weighing lysimeter-based crop (i.e., agronomic) and water-related flux or state data (i.e., environmental) obtained for the same soil monoliths that were taken from their original environment and translocated to regions with different climatic conditions, after model calibration at the original site. Eleven models were deployed in the study. The lysimeter data (2014-2018) were from the Dedelow (Dd), Bad Lauchstadt (BL), and Selhausen (Se) sites of the TERENO (TERrestrial ENvironmental Observatories) SOILCan network. Soil monoliths from Dd were transferred to the drier and warmer BL site and the wetter and warmer Se site, which allowed a comparison of similar soil and crop under varying climatic conditions. The model parameters were calibrated using an identical set of crop- and soil-related data from Dd. Environmental fluxes and crop growth of Dd soil were predicted for conditions at BL and Se sites using the calibrated models. The comparison of predicted and measured data of Dd lysimeters at BL and Se revealed differences among models. At site BL, the crop models predicted agronomic and environmental components similarly well. Model performance values indicate that the environmental components at site Se were better predicted than agronomic ones. The multi-model mean was for most observations the better predictor compared with those of individual models. For Se site conditions, crop models failed to predict site-specific crop development indicating that climatic conditions (i.e., heat stress) were outside the range of variation in the data sets considered for model calibration. For improving predictive ability of crop models (i.e., productivity and fluxes), more attention should be paid to soil-related data (i.e., water fluxes and system states) when simulating soil-crop-climate interrelations in changing climatic conditions. Y1 - 2022 U6 - https://doi.org/10.1002/vzj2.20202 SN - 1539-1663 VL - 21 IS - 4 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Dunker, Susanne A1 - Boyd, Matthew A1 - Durka, Walter A1 - Erler, Silvio A1 - Harpole, W. Stanley A1 - Henning, Silvia A1 - Herzschuh, Ulrike A1 - Hornick, Thomas A1 - Knight, Tiffany A1 - Lips, Stefan A1 - Mäder, Patrick A1 - Švara, Elena Motivans A1 - Mozarowski, Steven A1 - Rakosy, Demetra A1 - Römermann, Christine A1 - Schmitt-Jansen, Mechthild A1 - Stoof-Leichsenring, Kathleen A1 - Stratmann, Frank A1 - Treudler, Regina A1 - Virtanen, Risto A1 - Wendt-Potthoff, Katrin A1 - Wilhelm, Christian T1 - The potential of multispectral imaging flow cytometry for environmental monitoring JF - Cytometry part A N2 - Environmental monitoring involves the quantification of microscopic cells and particles such as algae, plant cells, pollen, or fungal spores. Traditional methods using conventional microscopy require expert knowledge, are time-intensive and not well-suited for automated high throughput. Multispectral imaging flow cytometry (MIFC) allows measurement of up to 5000 particles per second from a fluid suspension and can simultaneously capture up to 12 images of every single particle for brightfield and different spectral ranges, with up to 60x magnification. The high throughput of MIFC has high potential for increasing the amount and accuracy of environmental monitoring, such as for plant-pollinator interactions, fossil samples, air, water or food quality that currently rely on manual microscopic methods. Automated recognition of particles and cells is also possible, when MIFC is combined with deep-learning computational techniques. Furthermore, various fluorescence dyes can be used to stain specific parts of the cell to highlight physiological and chemical features including: vitality of pollen or algae, allergen content of individual pollen, surface chemical composition (carbohydrate coating) of cells, DNA- or enzyme-activity staining. Here, we outline the great potential for MIFC in environmental research for a variety of research fields and focal organisms. In addition, we provide best practice recommendations. KW - environmental monitoring KW - imaging flow cytometry KW - plant traits Y1 - 2022 U6 - https://doi.org/10.1002/cyto.a.24658 SN - 1552-4922 SN - 1552-4930 VL - 101 IS - 9 SP - 782 EP - 799 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Cao, Xianyong A1 - Chen, Jianhui A1 - Tian, Fang A1 - Xu, Qinghai A1 - Herzschuh, Ulrike A1 - Telford, Richard A1 - Huang, Xiaozhong A1 - Zheng, Zhuo A1 - Shen, Caiming A1 - Li, Wenjia T1 - Long-distance modern analogues bias results of pollen-based precipitation reconstructions JF - Science bulletin Y1 - 2022 U6 - https://doi.org/10.1016/j.scib.2022.01.003 SN - 2095-9273 SN - 2095-9281 VL - 67 IS - 11 SP - 1115 EP - 1117 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Schulte, Luise A1 - Meucci, Stefano A1 - Stoof-Leichsenring, Kathleen R. A1 - Heitkam, Tony A1 - Schmidt, Nicola A1 - von Hippel, Barbara A1 - Andreev, Andrei A. A1 - Diekmann, Bernhard A1 - Biskaborn, Boris A1 - Wagner, Bernd A1 - Melles, Martin A1 - Pestryakova, Lyudmila A. A1 - Alsos, Inger G. A1 - Clarke, Charlotte A1 - Krutovsky, Konstantin A1 - Herzschuh, Ulrike T1 - Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA JF - Communications biology N2 - Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution. Y1 - 2022 U6 - https://doi.org/10.1038/s42003-022-03455-0 SN - 2399-3642 VL - 5 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Cao, Xianyong A1 - Tian, Fang A1 - Herzschuh, Ulrike A1 - Ni, Jian A1 - Xu, Qinghai A1 - Li, Wenjia A1 - Zhang, Yanrong A1 - Luo, Mingyu A1 - Chen, Fahu T1 - Human activities have reduced plant diversity in eastern China over the last two millennia JF - Global change biology N2 - Understanding the history and regional singularities of human impact on vegetation is key to developing strategies for sustainable ecosystem management. In this study, fossil and modern pollen datasets from China are employed to investigate temporal changes in pollen composition, analogue quality, and pollen diversity during the Holocene. Anthropogenic disturbance and vegetation's responses are also assessed. Results reveal that pollen assemblages from non-forest communities fail to provide evidence of human impact for the western part of China (annual precipitation less than 400 mm and/or elevation more than 3000 m.a.s.l.), as inferred from the stable quality of modern analogues, principal components, and diversity of species and communities throughout the Holocene. For the eastern part of China, the proportion of fossil pollen spectra with good modern analogues increases from ca. 50% to ca. 80% during the last 2 millennia, indicating an enhanced intensity of anthropogenic disturbance on vegetation. This disturbance has caused the pollen spectra to become taxonomically less diverse over space (reduced abundances of arboreal taxa and increased abundances of herbaceous taxa), highlighting a reduced south-north differentiation and divergence from past vegetation between regions in the eastern part of China. We recommend that care is taken in eastern China when basing the development of ecosystem management strategies on vegetation changes in the region during the last 2000 years, since humans have significantly disturbed the vegetation during this period. KW - analogue quality KW - human-vegetation interaction KW - land use KW - latitudinal KW - zonation KW - plant diversity KW - pollen Y1 - 2022 U6 - https://doi.org/10.1111/gcb.16274 SN - 1354-1013 SN - 1365-2486 VL - 28 IS - 16 SP - 4962 EP - 4976 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Compart, Julia A1 - Zimmermann, Vincent A1 - Alseekh, Saleh A1 - Fernie, Alisdair R. A1 - Fettke, Jörg T1 - Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.) JF - Food chemistry N2 - Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield. KW - carbohydrate KW - mesocarp KW - metabolites KW - oil palm KW - oil yield KW - sucrose; KW - starch Y1 - 2022 U6 - https://doi.org/10.1016/j.foodchem.2022.133361 SN - 0308-8146 SN - 1873-7072 VL - 393 PB - Elsevier CY - New York, NY [u.a.] ER - TY - JOUR A1 - Zielhofer, Christoph A1 - Schmidt, Johannes A1 - Reiche, Niklas A1 - Tautenhahn, Marie A1 - Ballasus, Helen A1 - Burkart, Michael A1 - Linstädter, Anja A1 - Dietze, Elisabeth A1 - Kaiser, Knut A1 - Mehler, Natascha T1 - The lower Havel River Region (Brandenburg, Germany) BT - a 230-Year-Long historical map record indicates a decrease in surface water areas and groundwater levels JF - Water N2 - Instrumental data show that the groundwater and lake levels in Northeast Germany have decreased over the past decades, and this process has accelerated over the past few years. In addition to global warming, the direct influence of humans on the local water balance is suspected to be the cause. Since the instrumental data usually go back only a few decades, little is known about the multidecadal to centennial-scale trend, which also takes long-term climate variation and the long-term influence by humans on the water balance into account. This study aims to quantitatively reconstruct the surface water areas in the Lower Havel Inner Delta and of adjacent Lake Gulpe in Brandenburg. The analysis includes the calculation of surface water areas from historical and modern maps from 1797 to 2020. The major finding is that surface water areas have decreased by approximately 30% since the pre-industrial period, with the decline being continuous. Our data show that the comprehensive measures in Lower Havel hydro-engineering correspond with groundwater lowering that started before recent global warming. Further, large-scale melioration measures with increasing water demands in the upstream wetlands beginning from the 1960s to the 1980s may have amplified the decline in downstream surface water areas. KW - long-term hydrological changes KW - historical maps KW - review of written KW - sources KW - preindustrial to industrial period KW - hydro-engineering history; KW - effects of global warming KW - drying trend KW - wetlands KW - drainage works to KW - create cropland KW - Lower Havel River Region KW - Brandenburg KW - Germany Y1 - 2022 U6 - https://doi.org/10.3390/w14030480 SN - 2073-4441 VL - 14 IS - 3 PB - MDPI CY - Basel ER - TY - JOUR A1 - Kamali, Bahareh A1 - Jahanbakhshi, Farshid A1 - Dogaru, Diana A1 - Dietrich, Jörg A1 - Nendel, Claas A1 - AghaKouchak, Amir T1 - Probabilistic modeling of crop-yield loss risk under drought: a spatial showcase for sub-Saharan Africa JF - Environmental research letters N2 - Assessing the risk of yield loss in African drought-affected regions is key to identify feasible solutions for stable crop production. Recent studies have demonstrated that Copula-based probabilistic methods are well suited for such assessment owing to reasonably inferring important properties in terms of exceedance probability and joint dependence of different characterization. However, insufficient attention has been given to quantifying the probability of yield loss and determining the contribution of climatic factors. This study applies the Copula theory to describe the dependence between drought and crop yield anomalies for rainfed maize, millet, and sorghum crops in sub-Saharan Africa (SSA). The environmental policy integrated climate model, calibrated with Food and Agriculture Organization country-level yield data, was used to simulate yields across SSA (1980-2012). The results showed that the severity of yield loss due to drought had a higher magnitude than the severity of drought itself. Sensitivity analysis to identify factors contributing to drought and high-temperature stresses for all crops showed that the amount of precipitation during vegetation and grain filling was the main driver of crop yield loss, and the effect of temperature was stronger for sorghum than for maize and millet. The results demonstrate the added value of probabilistic methods for drought-impact assessment. For future studies, we recommend looking into factors influencing drought and high-temperature stresses as individual/concurrent climatic extremes. KW - Copula theory KW - crop model KW - drought stress KW - joint probability KW - risk Y1 - 2022 U6 - https://doi.org/10.1088/1748-9326/ac4ec1 SN - 1748-9326 VL - 17 IS - 2 PB - IOP Publishing CY - Bristol ER - TY - JOUR A1 - Hoang, Yen A1 - Gryzik, Stefanie A1 - Hoppe, Ines A1 - Rybak, Alexander A1 - Schädlich, Martin A1 - Kadner, Isabelle A1 - Walther, Dirk A1 - Vera, Julio A1 - Radbruch, Andreas A1 - Groth, Detlef A1 - Baumgart, Sabine A1 - Baumgrass, Ria T1 - PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments JF - Frontiers in immunology N2 - Recently, mass cytometry has enabled quantification of up to 50 parameters for millions of cells per sample. It remains a challenge to analyze such high-dimensional data to exploit the richness of the inherent information, even though many valuable new analysis tools have already been developed. We propose a novel algorithm "pattern recognition of immune cells (PRI)" to tackle these high-dimensional protein combinations in the data. PRI is a tool for the analysis and visualization of cytometry data based on a three or more-parametric binning approach, feature engineering of bin properties of multivariate cell data, and a pseudo-multiparametric visualization. Using a publicly available mass cytometry dataset, we proved that reproducible feature engineering and intuitive understanding of the generated bin plots are helpful hallmarks for re-analysis with PRI. In the CD4(+)T cell population analyzed, PRI revealed two bin-plot patterns (CD90/CD44/CD86 and CD90/CD44/CD27) and 20 bin plot features for threshold-independent classification of mice concerning ineffective and effective tumor treatment. In addition, PRI mapped cell subsets regarding co-expression of the proliferation marker Ki67 with two major transcription factors and further delineated a specific Th1 cell subset. All these results demonstrate the added insights that can be obtained using the non-cluster-based tool PRI for re-analyses of high-dimensional cytometric data. KW - multi-parametric analysis KW - re-analysis KW - combinatorial protein KW - expression KW - high-dimensional cytometry data KW - mass cytometry data KW - pattern perception Y1 - 2022 U6 - https://doi.org/10.3389/fimmu.2022.849329 SN - 1664-3224 VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Esmaeilishirazifard, Elham A1 - Usher, Louise A1 - Trim, Carol A1 - Denise, Hubert A1 - Sangal, Vartul A1 - Tyson, Gregory H. A1 - Barlow, Axel A1 - Redway, Keith F. A1 - Taylor, John D. A1 - Kremyda-Vlachou, Myrto A1 - Davies, Sam A1 - Loftus, Teresa D. A1 - Lock, Mikaella M. G. A1 - Wright, Kstir A1 - Dalby, Andrew A1 - Snyder, Lori A. S. A1 - Wuster, Wolfgang A1 - Trim, Steve A1 - Moschos, Sterghios A. T1 - Bacterial adaptation to venom in snakes and arachnida JF - Microbiology spectrum N2 - Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane-disrupting activity against multidrug-resistant bacteria. However, venomous bite wound infections are common in developing nations. Investigating the envenomation organ and venom microbiota of five snake and two spider species, we observed venom community structures that depend on the host venomous animal species and evidenced recovery of viable microorganisms from black-necked spitting cobra (Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Among the bacterial isolates recovered from N. nigricollis, we identified two venom-resistant, novel sequence types of Enterococcus faecalis whose genomes feature 16 virulence genes, indicating infectious potential, and 45 additional genes, nearly half of which improve bacterial membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. IMPORTANCE Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Here, we provide evidence on venom microbiota across snakes and arachnida and report on the convergent evolution mechanisms that can facilitate adaptation to black-necked cobra venom in two independent E. faecalis strains, easily misidentified by biochemical diagnostics. Therefore, since inoculation with viable and virulence gene-harboring bacteria can occur during envenomation, acute infection risk management following envenomation is warranted, particularly for immunocompromised and malnourished victims in resource-limited settings. These results shed light on how bacteria evolve for survival in one of the most extreme environments on Earth and how venomous bites must be also treated for infections. KW - drug resistance evolution KW - extremophiles KW - genome analysis KW - microbiome KW - multidrug resistance KW - venom Y1 - 2022 U6 - https://doi.org/10.1128/spectrum.02408-21 SN - 2165-0497 VL - 10 IS - 3 PB - American Society for Microbiology CY - Birmingham, Ala. ER - TY - JOUR A1 - Vences, Miguel A1 - Köhler, Jörn A1 - Crottini, Angelica A1 - Hofreiter, Michael A1 - Hutter, Carl R. A1 - du Preez, Louis A1 - Preick, Michaela A1 - Rakotoarison, Andolalao A1 - Rancilhac, Loïs A1 - Raselimanana, Achille P. A1 - Rosa, Gonçalo M. A1 - Scherz, Mark D. A1 - Glaw, Frank T1 - An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar JF - Vertebrate zoology N2 - The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar's eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar's North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d'Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy. KW - Amphibia KW - Anura KW - archival DNA KW - Mantellidae KW - new species KW - phylogeography Y1 - 2022 U6 - https://doi.org/10.3897/vz.72.e78830 SN - 1864-5755 SN - 2625-8498 VL - 72 SP - 271 EP - 309 PB - Senckenberg Gesellschaft für Naturforschung CY - Frankfurt am Main ER - TY - JOUR A1 - Sporbert, Maria A1 - Jakubka, Desiree A1 - Bucher, Solveig Franziska A1 - Hensen, Isabell A1 - Freiberg, Martin A1 - Heubach, Katja A1 - König, Andreas A1 - Nordt, Birgit A1 - Plos, Carolin A1 - Blinova, Ilona A1 - Bonn, Aletta A1 - Knickmann, Barbara A1 - Koubek, Tomáš A1 - Linstädter, Anja A1 - Mašková, Tereza A1 - Primack, Richard B. A1 - Rosche, Christoph A1 - Shah, Manzoor A. A1 - Stevens, Albert-Dieter A1 - Tielbörger, Katja A1 - Träger, Sabrina A1 - Wirth, Christian A1 - Römermann, Christine T1 - Functional traits influence patterns in vegetative and reproductive plant phenology - a multi-botanical garden study JF - New phytologist N2 - Phenology has emerged as key indicator of the biological impacts of climate change, yet the role of functional traits constraining variation in herbaceous species' phenology has received little attention. Botanical gardens are ideal places in which to investigate large numbers of species growing under common climate conditions. We ask whether interspecific variation in plant phenology is influenced by differences in functional traits. We recorded onset, end, duration and intensity of initial growth, leafing out, leaf senescence, flowering and fruiting for 212 species across five botanical gardens in Germany. We measured functional traits, including plant height, absolute and specific leaf area, leaf dry matter content, leaf carbon and nitrogen content and seed mass and accounted for species' relatedness. Closely related species showed greater similarities in timing of phenological events than expected by chance, but species' traits had a high degree of explanatory power, pointing to paramount importance of species' life-history strategies. Taller plants showed later timing of initial growth, and flowered, fruited and underwent leaf senescence later. Large-leaved species had shorter flowering and fruiting durations. Taller, large-leaved species differ in their phenology and are more competitive than smaller, small-leaved species. We assume climate warming will change plant communities' competitive hierarchies with consequences for biodiversity. KW - botanical gardens KW - first flowering day KW - growing season length KW - leaf KW - traits KW - PhenObs phenological network KW - phylogeny Y1 - 2022 U6 - https://doi.org/10.1111/nph.18345 SN - 0028-646X SN - 1469-8137 VL - 235 IS - 6 SP - 2199 EP - 2210 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Derežanin, Lorena A1 - Blažytė, Asta A1 - Dobrynin, Pavel A1 - Duchêne, David A. A1 - Grau, José Horacio A1 - Jeon, Sungwon A1 - Kliver, Sergei A1 - Koepfli, Klaus-Peter A1 - Meneghini, Dorina A1 - Preick, Michaela A1 - Tomarovsky, Andrey A1 - Totikov, Azamat A1 - Fickel, Jörns A1 - Förster, Daniel W. T1 - Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae JF - Molecular ecology N2 - Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance. KW - adaptation KW - gene family evolution KW - genomics KW - mustelids KW - positive KW - selection KW - structural variation Y1 - 2022 U6 - https://doi.org/10.1111/mec.16443 SN - 0962-1083 SN - 1365-294X VL - 31 IS - 10 SP - 2898 EP - 2919 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Garbulowski, Mateusz A1 - Smolinska, Karolina A1 - Çabuk, Uğur A1 - Yones, Sara A. A1 - Celli, Ludovica A1 - Yaz, Esma Nur A1 - Barrenas, Fredrik A1 - Diamanti, Klev A1 - Wadelius, Claes A1 - Komorowski, Jan T1 - Machine learning-based analysis of glioma grades reveals co-enrichment JF - Cancers N2 - Simple Summary Gliomas are heterogenous types of cancer, therefore the therapy should be personalized and targeted toward specific pathways. We developed a methodology that corrected strong batch effects from The Cancer Genome Atlas datasets and estimated glioma grade-specific co-enrichment mechanisms using machine learning. Our findings created hypotheses for annotations, e.g., pathways, that should be considered as therapeutic targets. Gliomas develop and grow in the brain and central nervous system. Examining glioma grading processes is valuable for improving therapeutic challenges. One of the most extensive repositories storing transcriptomics data for gliomas is The Cancer Genome Atlas (TCGA). However, such big cohorts should be processed with caution and evaluated thoroughly as they can contain batch and other effects. Furthermore, biological mechanisms of cancer contain interactions among biomarkers. Thus, we applied an interpretable machine learning approach to discover such relationships. This type of transparent learning provides not only good predictability, but also reveals co-predictive mechanisms among features. In this study, we corrected the strong and confounded batch effect in the TCGA glioma data. We further used the corrected datasets to perform comprehensive machine learning analysis applied on single-sample gene set enrichment scores using collections from the Molecular Signature Database. Furthermore, using rule-based classifiers, we displayed networks of co-enrichment related to glioma grades. Moreover, we validated our results using the external glioma cohorts. We believe that utilizing corrected glioma cohorts from TCGA may improve the application and validation of any future studies. Finally, the co-enrichment and survival analysis provided detailed explanations for glioma progression and consequently, it should support the targeted treatment. KW - glioma KW - machine learning KW - batch effect KW - TCGA KW - co-enrichment KW - rough sets Y1 - 2022 U6 - https://doi.org/10.3390/cancers14041014 SN - 2072-6694 VL - 14 IS - 4 PB - MDPI CY - Basel ER - TY - JOUR A1 - Potente, Giacomo A1 - Léveillé-Bourret, Étienne A1 - Yousefi, Narjes A1 - Choudhury, Rimjhim Roy A1 - Keller, Barbara A1 - Diop, Seydina Issa A1 - Duijsings, Daniël A1 - Pirovano, Walter A1 - Lenhard, Michael A1 - Szövényi, Péter A1 - Conti, Elena T1 - Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism JF - Molecular biology and evolution : MBE N2 - Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula? KW - genome architecture KW - supergene KW - heterostyly KW - evolutionary genomics KW - chromosome-scale genome assembly KW - primula Y1 - 2022 U6 - https://doi.org/10.1093/molbev/msac035 SN - 0737-4038 SN - 1537-1719 VL - 39 IS - 2 PB - Oxford Univ. Press CY - Oxford ER - TY - GEN A1 - Huu, Cuong Nguyen A1 - Plaschil, Sylvia A1 - Himmelbach, Axel A1 - Kappel, Christian A1 - Lenhard, Michael T1 - Female self-incompatibility type in heterostylous Primula is determined by the brassinosteroid-inactivating cytochrome P450 CYP734A50 T2 - Current biology N2 - Most flowering plants are hermaphrodites, with flowers having both male and female reproductive organs. One widespread adaptation to limit self-fertilization is self-incompatibility (SI), where self-pollen fails to fertilize ovules.(1,2) In homomorphic SI, many morphologically indistinguishable mating types are found, although in heteromorphic SI, the two or three mating types are associated with different floral morphologies.(3-6) In heterostylous Primula, a hemizygous supergene determines a short-styled S-morph and a long-styled L-morph, corresponding to two different mating types, and full seed set only results from inter morph crosses.(7-9) Style length is controlled by the brassinosteroid (BR)-inactivating cytochrome P450 CYP734A50,(10) yet it remains unclear what defines the male and female incompatibility types. Here, we show that CYP734A50 also determines the female incompatibility type. Inactivating CYP734A50 converts short S-morph styles into long styles with the same incompatibility behavior as L-morph styles, and this effect can be mimicked by exogenous BR treatment. In vitro responses of S-and L-morph pollen grains and pollen tubes to increasing BR levels could only partly explain their different in vivo behavior, suggesting both direct and indirect effects of the different BR levels in S-versus L-morph stigmas and styles in controlling pollen performance. This BR-mediated SI provides a novel mechanism for preventing self-fertilization. The joint control of morphology and SI by CYP734A50 has important implications for the evolutionary buildup of the heterostylous syndrome and provides a straightforward explanation for why essentially all of the derived self-compatible homostylous Primula species are long homostyles.(11) KW - heteromorphic self-incompatibility KW - heterostyly KW - Primula forbesii KW - brassinosteroid KW - CYP734A50 KW - supergene KW - pleiotropy Y1 - 2022 U6 - https://doi.org/10.1016/j.cub.2021.11.046 SN - 0960-9822 SN - 1879-0445 VL - 32 IS - 3 SP - 671 EP - 676, E1-E5 PB - Cell Press CY - Cambridge, Mass. ER - TY - JOUR A1 - Oberkofler, Vicky A1 - Bäurle, Isabel T1 - Inducible epigenome editing probes for the role of histone H3K4 methylation in Arabidopsis heat stress memory JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - A temperature-inducible epigenome editing system to knock down histone methylation can be used to study the role of histone H3K4 methylation during heat stress memory in Arabidopsis.
Histone modifications play a crucial role in the integration of environmental signals to mediate gene expression outcomes. However, genetic and pharmacological interference often causes pleiotropic effects, creating the urgent need for methods that allow locus-specific manipulation of histone modifications, preferably in an inducible manner. Here, we report an inducible system for epigenome editing in Arabidopsis (Arabidopsis thaliana) using a heat-inducible dCas9 to target a JUMONJI (JMJ) histone H3 lysine 4 (H3K4) demethylase domain to a locus of interest. As a model locus, we target the ASCORBATE PEROXIDASE2 (APX2) gene that shows transcriptional memory after heat stress (HS), correlating with H3K4 hyper-methylation. We show that dCas9-JMJ is targeted in a HS-dependent manner to APX2 and that the HS-induced overaccumulation of H3K4 trimethylation (H3K4me3) decreases when dCas9-JMJ binds to the locus. This results in reduced HS-mediated transcriptional memory at the APX2 locus. Targeting an enzymatically inactive JMJ protein in an analogous manner affected transcriptional memory less than the active JMJ protein; however, we still observed a decrease in H3K4 methylation levels. Thus, the inducible targeting of dCas9-JMJ to APX2 was effective in reducing H3K4 methylation levels. As the effect was not fully dependent on enzyme activity of the eraser domain, the dCas9-JMJ fusion protein may act in part independently of its demethylase activity. This underlines the need for caution in the design and interpretation of epigenome editing studies. We expect our versatile inducible epigenome editing system to be especially useful for studying temporal dynamics of chromatin modifications. Y1 - 2022 U6 - https://doi.org/10.1093/plphys/kiac113 SN - 0032-0889 SN - 1532-2548 VL - 189 IS - 2 SP - 703 EP - 714 PB - Oxford University Press CY - Oxford ER -