TY - JOUR A1 - Lukan, Tjaša A1 - Machens, Fabian A1 - Coll, Anna A1 - Baebler, Špela A1 - Messerschmidt, Katrin A1 - Gruden, Kristina T1 - Plant X-tender BT - an extension of the AssemblX system for the assembly and expression of multigene constructs in plants JF - PLOS ONE N2 - Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0190526 SN - 1932-6203 VL - 13 IS - 1 PB - Public Library of Science CY - San Fransisco ER - TY - JOUR A1 - Cisek, Richard A1 - Tokarz, Danielle A1 - Kontenis, Lukas A1 - Barzda, Virginijus A1 - Steup, Martin T1 - Polarimetric second harmonic generation microscopy BT - an analytical tool for starch bioengineering JF - Starch-Starke N2 - Second harmonic generation (SHG) is a nonlinear optical process that inherently generates signal in non-centrosymmetric materials, such as starch granules, and therefore can be used for label-free imaging. Both intensity and polarization of SHG are determined by material properties that are characterized by the nonlinear susceptibility tensor, ((2)). Examination of the tensor is performed for each focal volume of the image by measuring the outgoing polarization state of the SHG signal for a set of incoming laser beam polarizations. Mapping of nonlinear properties expressed as the susceptibility ratio reveals structural features including the organization of crystalline material within a single starch granule, and the distribution of structural properties in a population of granules. Isolated granules, as well as in situ starch, can be analyzed using polarimetric SHG microscopy. Due to the fast sample preparation and short imaging times, polarimetric SHG microscopy allows for a quick assessment of starch structure and permits rapid feedback for bioengineering applications. This article presents the basics of SHG theory and microscopy applications for starch-containing materials. Quantification of ultrastructural features within individual starch granules is described. New results obtained by polarization resolved SHG microscopy of starch granules are presented for various maize genotypes revealing heterogeneity within a single starch particle and between various granules. KW - Determination of crystallinity KW - Determination of hydration KW - Label-free imaging KW - Nonlinear optical microscopy KW - Structural determination Y1 - 2017 U6 - https://doi.org/10.1002/star.201700031 SN - 0038-9056 SN - 1521-379X VL - 70 IS - 1-2 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Wen, Xi A1 - Unger, Viktoria A1 - Jurasinski, Gerald A1 - Koebsch, Franziska A1 - Horn, Fabian A1 - Rehder, Gregor A1 - Sachs, Torsten A1 - Zak, Dominik A1 - Lischeid, Gunnar A1 - Knorr, Klaus-Holger A1 - Boettcher, Michael E. A1 - Winkel, Matthias A1 - Bodelier, Paul L. E. A1 - Liebner, Susanne T1 - Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions JF - Biogeosciences N2 - The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rRNA high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity (EC) was more than 3 times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5 mS cm(-1), respectively. Porewater concentrations of terminal electron acceptors (TEAs) varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid (re) establishment of methanogens and slow (re) establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting. Y1 - 2018 U6 - https://doi.org/10.5194/bg-15-6519-2018 SN - 1726-4170 SN - 1726-4189 VL - 15 IS - 21 SP - 6519 EP - 6536 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Stoessel, Daniel A1 - Schulte, Claudia A1 - dos Santos, Marcia C. Teixeira A1 - Scheller, Dieter A1 - Rebollo-Mesa, Irene A1 - Deuschle, Christian A1 - Walther, Dirk A1 - Schauer, Nicolas A1 - Berg, Daniela A1 - da Costa, Andre Nogueira A1 - Maetzler, Walter T1 - Promising Metabolite Profiles in the Plasma and CSF of Early Clinical JF - Frontiers in Aging Neuroscience N2 - Parkinson's disease (PD) shows high heterogeneity with regard to the underlying molecular pathogenesis involving multiple pathways and mechanisms. Diagnosis is still challenging and rests entirely on clinical features. Thus, there is an urgent need for robust diagnostic biofluid markers. Untargeted metabolomics allows establishing low-molecular compound biomarkers in a wide range of complex diseases by the measurement of various molecular classes in biofluids such as blood plasma, serum, and cerebrospinal fluid (CSF). Here, we applied untargeted high-resolution mass spectrometry to determine plasma and CSF metabolite profiles. We semiquantitatively determined small-molecule levels (<= 1.5 kDa) in the plasma and CSF from early PD patients (disease duration 0-4 years; n = 80 and 40, respectively), and sex-and age-matched controls (n = 76 and 38, respectively). We performed statistical analyses utilizing partial least square and random forest analysis with a 70/30 training and testing split approach, leading to the identification of 20 promising plasma and 14 CSF metabolites. The semetabolites differentiated the test set with an AUC of 0.8 (plasma) and 0.9 (CSF). Characteristics of the metabolites indicate perturbations in the glycerophospholipid, sphingolipid, and amino acid metabolism in PD, which underscores the high power of metabolomic approaches. Further studies will enable to develop a potential metabolite-based biomarker panel specific for PD KW - biomarker KW - untargeted metabolomics KW - neurodegeneration KW - plasma KW - CSF KW - machinelearning Y1 - 2018 U6 - https://doi.org/10.3389/fnagi.2018.00051 SN - 1663-4365 VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - GEN A1 - Autenrieth, Marijke A1 - Ernst, Anja A1 - Deaville, Rob A1 - Demaret, Fabien A1 - Ijsseldijk, Lonneke L. A1 - Siebert, Ursula A1 - Tiedemann, Ralph T1 - Putative origin and maternal relatedness of male sperm whales (Physeter macrocephalus) recently stranded in the North Sea T2 - Mammalian biology = Zeitschrift für Säugetierkunde N2 - The globally distributed sperm whale (Physeter macrocephalus) has a partly matrilineal social structure with predominant male dispersal. At the beginning of 2016, a total of 30 male sperm whales stranded in five different countries bordering the southern North Sea. It has been postulated that these individuals were on a migration route from the north to warmer temperate and tropical waters where females live in social groups. By including samples from four countries (n = 27), this event provided a unique chance to genetically investigate the maternal relatedness and the putative origin of these temporally and spatially co-occuring male sperm whales. To utilize existing genetic resources, we sequenced 422 bp of the mitochondrial control region, a molecular marker for which sperm whale data are readily available from the entire distribution range. Based on four single nucleotide polymorphisms (SNPs) within the mitochondrial control region, five matrilines could be distinguished within the stranded specimens, four of which matched published haplotypes previously described in the Atlantic. Among these male sperm whales, multiple matrilineal lineages co-occur. We analyzed the population differentiation and could show that the genetic diversity of these male sperm whales is comparable to the genetic diversity in sperm whales from the entire Atlantic Ocean. We confirm that within this stranding event, males do not comprise maternally related individuals and apparently include assemblages of individuals from different geographic regions. (c) 2017 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved. KW - Mitochondrial DNA KW - Maternal relationships KW - Population genetics KW - Migration KW - Marine mammals Y1 - 2018 U6 - https://doi.org/10.1016/j.mambio.2017.09.003 SN - 1616-5047 SN - 1618-1476 VL - 88 SP - 156 EP - 160 PB - Elsevier CY - München ER - TY - JOUR A1 - Käch, Heidi A1 - Mathe-Hubert, Hugo A1 - Dennis, Alice B. A1 - Vorburger, Christoph T1 - Rapid evolution of symbiont-mediated resistance compromises biological control of aphids by parasitoids JF - Evolutionary applications N2 - There is growing interest in biological control as a sustainable and environmentally friendly way to control pest insects. Aphids are among the most detrimental agricultural pests worldwide, and parasitoid wasps are frequently employed for their control. The use of asexual parasitoids may improve the effectiveness of biological control because only females kill hosts and because asexual populations have a higher growth rate than sexuals. However, asexuals may have a reduced capacity to track evolutionary change in their host populations. We used a factorial experiment to compare the ability of sexual and asexual populations of the parasitoid Lysiphlebus fabarum to control caged populations of black bean aphids (Aphis fabae) of high and low clonal diversity. The aphids came from a natural population, and one-third of the aphid clones harbored Hamiltonella defensa, a heritable bacterial endosymbiont that increases resistance to parasitoids. We followed aphid and parasitoid population dynamics for 3months but found no evidence that the reproductive mode of parasitoids affected their effectiveness as biocontrol agents, independent of host clonal diversity. Parasitoids failed to control aphids in most cases, because their introduction resulted in strong selection for clones protected by H.defensa. The increasingly resistant aphid populations escaped control by parasitoids, and we even observed parasitoid extinctions in many cages. The rapid evolution of symbiont-conferred resistance in turn imposed selection on parasitoids. In cages where asexual parasitoids persisted until the end of the experiment, they became dominated by a single genotype able to overcome the protection provided by H.defensa. Thus, there was evidence for parasitoid counteradaptation, but it was generally too slow for parasitoids to regain control over aphid populations. It appears that when pest aphids possess defensive symbionts, the presence of parasitoid genotypes able to overcome symbiont-conferred resistance is more important for biocontrol success than their reproductive mode. KW - aphids KW - Aphis fabae KW - biological control KW - defensive symbiosis KW - Hamiltonella defensa KW - Lysiphlebus fabarum KW - parasitoid KW - resistance Y1 - 2018 U6 - https://doi.org/10.1111/eva.12532 SN - 1752-4571 VL - 11 IS - 2 SP - 220 EP - 230 PB - Wiley CY - Hoboken ER - TY - GEN A1 - Uhlig, Katja A1 - Gehre, Christian P. A1 - Kammerer, Sarah A1 - Küpper, Jan-Heiner A1 - Coleman, Charles Dominic A1 - Püschel, Gerhard Paul A1 - Duschl, Claus T1 - Real-time monitoring of oxygen consumption of hepatocytes in a microbioreactor T2 - Toxicology letters Y1 - 2018 U6 - https://doi.org/10.1016/j.toxlet.2018.06.652 SN - 0378-4274 SN - 1879-3169 VL - 295 SP - S115 EP - S115 PB - Elsevier CY - Clare ER - TY - JOUR A1 - Cuadrat, Rafael R. C. A1 - Ionescu, Danny A1 - Davila, Alberto M. R. A1 - Grossart, Hans-Peter T1 - Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics JF - Frontiers in microbiology N2 - Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem. KW - metagenomics 2.0 KW - PKS KW - NRPS KW - freshwater KW - environmental genomics Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.00251 SN - 1664-302X VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - de Abreu e Lima, Francisco Anastacio A1 - Leifels, Lydia A1 - Nikoloski, Zoran T1 - Regression-based modeling of complex plant traits based on metabolomics data JF - Plant Metabolomics N2 - Bridging metabolomics with plant phenotypic responses is challenging. Multivariate analyses account for the existing dependencies among metabolites, and regression models in particular capture such dependencies in search for association with a given trait. However, special care should be undertaken with metabolomics data. Here we propose a modeling workflow that considers all caveats imposed by such large data sets. KW - Metabolomics KW - Plants KW - Trait KW - Regression KW - Prediction KW - Modeling KW - R programing language KW - R software packages Y1 - 2018 SN - 978-1-4939-7819-9 SN - 978-1-4939-7818-2 U6 - https://doi.org/10.1007/978-1-4939-7819-9_23 SN - 1064-3745 SN - 1940-6029 VL - 1778 SP - 321 EP - 327 PB - Humana Press Inc. CY - New York ER - TY - THES A1 - Mubeen, Umarah T1 - Regulation of central carbon and nitrogen metabolism by Target of Rapamycin (TOR) kinase in Chlamydomonas reinhardtii T1 - Regulation des zentralen Kohlen- und Stickstoff Stoffwechsels durch die Target of Rapamycin Kinase in der Grünalge Chlamydomonas reinhardtii N2 - The highly conserved protein complex containing the Target of Rapamycin (TOR) kinase is known to integrate intra- and extra-cellular stimuli controlling nutrient allocation and cellular growth. This thesis describes three studies aimed to understand how TOR signaling pathway influences carbon and nitrogen metabolism in Chlamydomonas reinhardtii. The first study presents a time-resolved analysis of the molecular and physiological features across the diurnal cycle. The inhibition of TOR leads to 50% reduction in growth followed by nonlinear delays in the cell cycle progression. The metabolomics analysis showed that the growth repression is mainly driven by differential carbon partitioning between anabolic and catabolic processes. Furthermore, the high accumulation of nitrogen-containing compounds indicated that TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression. In the second study the cause of the high accumulation of amino acids is explained. For this purpose, the effect of TOR inhibition on Chlamydomonas was examined under different growth regimes using stable 13C- and 15N-isotope labeling. The data clearly showed that an increased nitrogen uptake is induced within minutes after the inhibition of TOR. Interestingly, this increased N-influx is accompanied by increased activities of nitrogen assimilating enzymes. Accordingly, it was concluded that TOR inhibition induces de-novo amino acid synthesis in Chlamydomonas. The recognition of this novel process opened an array of questions regarding potential links between central metabolism and TOR signaling. Therefore a detailed phosphoproteomics study was conducted to identify the potential substrates of TOR pathway regulating central metabolism. Interestingly, some of the key enzymes involved in carbon metabolism as well as amino acid synthesis exhibited significant changes in the phosphosite intensities immediately after TOR inhibition. Altogether, these studies provide a) detailed insights to metabolic response of Chlamydomonas to TOR inhibition, b) identification of a novel process causing rapid upshifts in amino acid levels upon TOR inhibition and c) finally highlight potential targets of TOR signaling regulating changes in central metabolism. Further biochemical and molecular investigations could confirm these observations and advance the understanding of growth signaling in microalgae. N2 - Target of Rapamycin (TOR) ist das Zentralprotein eines hochkonservierten Proteinkomplexes, welcher Nährstoff- und Energie Ressourcen für zelluläre Wachstumsprozesse kontengiert. Diese Doktorarbeit beschreibt anhand dreier Studien, wie TOR zu diesem Zweck, in der Grünalge Chlamydomonas reinhardtii, den zentralen Stoffwechsel reguliert. Die erste Studie untersucht dazu das zeitaufgelöste Verhalten von Biomolekülen im Tagesverlauf synchronisiert wachsender Algen. Dabei konnte gezeigt werden, das der TOR Inhibitor Rapamycin das Wachstum um 50% reduziert und den Zellzyklus verzögert. Die Zellzyklus Verzögerung scheint dabei hauptsächlich durch veränderte Stoffwechselprozesse erklärt zu sein. Hierbei konnte gezeigt werden, dass TOR vor allem stickstoffhaltige Stoffwechselprodukte (z.B. Aminosäuren) kontrolliert, welche die Grundlage für Biomasseproduktion, Wachstum und den Zellzyklus bilden. Im Rahmen der zweiten Studie konnte dann der molekulare Mechanismus der Akkumulation der zellulären Aminosäuren aufgeklärt werden. Zu diesem Zweck wurden Fütterungsstudien mit 13C- und 15N-Isotopen durchgeführt. Die Ergebnisse dieser Fütterung konnten klar zeigen, dass die Inhibition von TOR zur verstärkten Aufnahme von Stickstoff in die Zelle und dessen Assimilierung in Aminosäuren führt. Die Aufdeckung dieses neuen, von TOR gesteuerten Prozesses eröffnete somit die Frage, wie die Signalkaskade von TOR zu den Enzymen der Aminosäuresynthese verläuft. Detaillierte phosphoproteomische Studien sollten dieser Frage nachgehen und Zielprotein der TOR Kinase zu identifizieren und regulierte Stoffwechselprozesses zu finden. Dabei stellte sich heraus, dass sowohl verschiedene Enzyme der Aminosäuresynthese als auch Enzyme des zentralen Stoffwechsels innerhalb weniger Minuten stark verändert wurden. Zusammenfassend kann man festhalten das die vorliegende Arbeit detaillierte Stoffwechselanalysen des Stoffwechsels nach einer TOR Inhibition aufdeckt. Hierbei ein neuer Mechanismus zur Regulation der Aminosäuresynthese, nach TOR Inhibition gezeigt werden konnte, welche durch systemische Regulation der Phosphorylierungsmuster zellulärer Proteine kontrolliert wird. Zusätzliche molekulare und biochemische Studien konnten weiterhin zeigen, dass wie TOR das zelluläre Wachstum der photosynthetischen Grünalge kontrolliert und somit steuert. KW - Target of Rapamycin kinase KW - Growth signaling KW - metabolism KW - phosphoproteomics KW - Chlamydomonas KW - Target of Rapamycin kinase KW - Wachstumssignale KW - Stoffwechsel KW - Phosphoproteomik KW - Chlamydomonas Y1 - 2018 ER - TY - GEN A1 - Synodinos, Alexios D. A1 - Eldridge, David A1 - Geißler, Katja A1 - Jeltsch, Florian A1 - Lohmann, Dirk A1 - Midgley, Guy A1 - Blaum, Niels T1 - Remotely sensed canopy height reveals three pantropical ecosystem states BT - a comment T2 - Ecology : a publication of the Ecological Society of America Y1 - 2017 U6 - https://doi.org/10.1002/ecy.1997 SN - 0012-9658 SN - 1939-9170 VL - 99 IS - 1 SP - 231 EP - 234 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Muhl, Rika M. W. A1 - Roelke, Daniel L. A1 - Zohary, Tamar A1 - Moustaka-Gouni, Maria A1 - Sommer, Ulrich A1 - Borics, Gabor A1 - Gaedke, Ursula A1 - Withrow, Frances G. A1 - Bhattacharyya, Joydeb T1 - Resisting annihilation BT - relationships between functional trait dissimilarity, assemblage competitive power and allelopathy JF - Ecology letters N2 - Allelopathic species can alter biodiversity. Using simulated assemblages that are characterised by neutrality, lumpy coexistence and intransitivity, we explore relationships between within-assemblage competitive dissimilarities and resistance to allelopathic species. An emergent behaviour from our models is that assemblages are more resistant to allelopathy when members strongly compete exploitatively (high competitive power). We found that neutral assemblages were the most vulnerable to allelopathic species, followed by lumpy and then by intransitive assemblages. We find support for our modeling in real-world time-series data from eight lakes of varied morphometry and trophic state. Our analysis of this data shows that a lake's history of allelopathic phytoplankton species biovolume density and dominance is related to the number of species clusters occurring in the plankton assemblages of those lakes, an emergent trend similar to that of our modeling. We suggest that an assemblage's competitive power determines its allelopathy resistance. KW - Allelopathy KW - exploitative competition KW - interference competition KW - intransitivity KW - lumpy coexistence KW - neutrality KW - species supersaturated assemblages Y1 - 2018 U6 - https://doi.org/10.1111/ele.13109 SN - 1461-023X SN - 1461-0248 VL - 21 IS - 9 SP - 1390 EP - 1400 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - De Lombaerde, Emiel A1 - Verheyen, Kris A1 - Perring, Michael P. A1 - Bernhardt-Roemermann, Markus A1 - Van Calster, Hans A1 - Brunet, Jorg A1 - Chudomelova, Marketa A1 - Decocq, Guillaume A1 - Diekmann, Martin A1 - Durak, Tomasz A1 - Hedl, Radim A1 - Heinken, Thilo A1 - Hommel, Patrick A1 - Jaroszewicz, Bogdan A1 - Kopecky, Martin A1 - Lenoir, Jonathan A1 - Macek, Martin A1 - Máliš, František A1 - Mitchell, Fraser J. G. A1 - Naaf, Tobias A1 - Newman, Miles A1 - Petřík, Petr A1 - Reczyńska, Kamila A1 - Schmidt, Wolfgang A1 - Swierkosz, Krzysztof A1 - Vild, Ondrej A1 - Wulf, Monika A1 - Baetena, Lander T1 - Responses of competitive understorey species to spatial environmental gradients inaccurately explain temporal changes JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - Understorey plant communities play a key role in the functioning of forest ecosystems. Under favourable environmental conditions, competitive understorey species may develop high abundances and influence important ecosystem processes such as tree regeneration. Thus, understanding and predicting the response of competitive understorey species as a function of changing environmental conditions is important for forest managers. In the absence of sufficient temporal data to quantify actual vegetation changes, space-for-time (SFT) substitution is often used, i.e. studies that use environmental gradients across space to infer vegetation responses to environmental change over time. Here we assess the validity of such SFT approaches and analysed 36 resurvey studies from ancient forests with low levels of recent disturbances across temperate Europe to assess how six competitive understorey plant species respond to gradients of overstorey cover, soil conditions, atmospheric N deposition and climatic conditions over space and time. The combination of historical and contemporary surveys allows (i) to test if observed contemporary patterns across space are consistent at the time of the historical survey, and, crucially, (ii) to assess whether changes in abundance over time given recorded environmental change match expectations from patterns recorded along environmental gradients in space. We found consistent spatial relationships at the two periods: local variation in soil variables and overstorey cover were the best predictors of individual species’ cover while interregional variation in coarse-scale variables, i.e. N deposition and climate, was less important. However, we found that our SFT approach could not accurately explain the large variation in abundance changes over time. We thus recommend to be cautious when using SFT substitution to infer species responses to temporal changes. KW - Temperate forest KW - Herb layer KW - Tree regeneration KW - Global change KW - Nitrogen deposition KW - Canopy KW - Spatiotemporal resurvey data KW - Cover abundance KW - Chronosequence KW - forestREplot Y1 - 2018 U6 - https://doi.org/10.1016/j.baae.2018.05.013 SN - 1439-1791 SN - 1618-0089 VL - 30 SP - 52 EP - 64 PB - Elsevier GMBH CY - München ER - TY - JOUR A1 - Göritz, Anna A1 - Berger, Stella A. A1 - Gege, Peter A1 - Grossart, Hans-Peter A1 - Nejstgaard, Jens C. A1 - Riedel, Sebastian A1 - Röttgers, Rüdiger A1 - Utschig, Christian T1 - Retrieval of water constituents from hyperspectral in-situ measurements under variable cloud cover BT - a case study at Lake Stechlin (Germany) JF - Remote sensing / Molecular Diversity Preservation International (MDPI) N2 - Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring. KW - remote sensing KW - inland water KW - hyperspectral measurements KW - in-situ KW - cloud KW - surface reflection KW - inversion KW - bio-optical modeling Y1 - 2018 U6 - https://doi.org/10.3390/rs10020181 SN - 2072-4292 VL - 10 IS - 2 PB - MDPI CY - Basel ER - TY - JOUR A1 - van Velzen, Ellen A1 - Gaedke, Ursula T1 - Reversed predator BT - prey cycles are driven by the amplitude of prey oscillations JF - Ecology and Evolution N2 - Ecoevolutionary feedbacks in predator–prey systems have been shown to qualitatively alter predator–prey dynamics. As a striking example, defense–offense coevolution can reverse predator–prey cycles, so predator peaks precede prey peaks rather than vice versa. However, this has only rarely been shown in either model studies or empirical systems. Here, we investigate whether this rarity is a fundamental feature of reversed cycles by exploring under which conditions they should be found. For this, we first identify potential conditions and parameter ranges most likely to result in reversed cycles by developing a new measure, the effective prey biomass, which combines prey biomass with prey and predator traits, and represents the prey biomass as perceived by the predator. We show that predator dynamics always follow the dynamics of the effective prey biomass with a classic ¼‐phase lag. From this key insight, it follows that in reversed cycles (i.e., ¾‐lag), the dynamics of the actual and the effective prey biomass must be in antiphase with each other, that is, the effective prey biomass must be highest when actual prey biomass is lowest, and vice versa. Based on this, we predict that reversed cycles should be found mainly when oscillations in actual prey biomass are small and thus have limited impact on the dynamics of the effective prey biomass, which are mainly driven by trait changes. We then confirm this prediction using numerical simulations of a coevolutionary predator–prey system, varying the amplitude of the oscillations in prey biomass: Reversed cycles are consistently associated with regions of parameter space leading to small‐amplitude prey oscillations, offering a specific and highly testable prediction for conditions under which reversed cycles should occur in natural systems. KW - coevolution KW - ecoevolutionary dynamics KW - predator-prey dynamics KW - top-down control Y1 - 2018 U6 - https://doi.org/10.1002/ece3.4184 SN - 2045-7758 SP - 1 EP - 13 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - van Velzen, Ellen A1 - Gaedke, Ursula T1 - Reversed predator-prey cycles are driven by the amplitude of prey oscillations JF - Ecology and evolution N2 - Ecoevolutionary feedbacks in predator-prey systems have been shown to qualitatively alter predator-prey dynamics. As a striking example, defense-offense coevolution can reverse predator-prey cycles, so predator peaks precede prey peaks rather than vice versa. However, this has only rarely been shown in either model studies or empirical systems. Here, we investigate whether this rarity is a fundamental feature of reversed cycles by exploring under which conditions they should be found. For this, we first identify potential conditions and parameter ranges most likely to result in reversed cycles by developing a new measure, the effective prey biomass, which combines prey biomass with prey and predator traits, and represents the prey biomass as perceived by the predator. We show that predator dynamics always follow the dynamics of the effective prey biomass with a classic 1/4-phase lag. From this key insight, it follows that in reversed cycles (i.e., -lag), the dynamics of the actual and the effective prey biomass must be in antiphase with each other, that is, the effective prey biomass must be highest when actual prey biomass is lowest, and vice versa. Based on this, we predict that reversed cycles should be found mainly when oscillations in actual prey biomass are small and thus have limited impact on the dynamics of the effective prey biomass, which are mainly driven by trait changes. We then confirm this prediction using numerical simulations of a coevolutionary predator-prey system, varying the amplitude of the oscillations in prey biomass: Reversed cycles are consistently associated with regions of parameter space leading to small-amplitude prey oscillations, offering a specific and highly testable prediction for conditions under which reversed cycles should occur in natural systems. KW - coevolution KW - ecoevolutionary dynamics KW - predator-prey dynamics KW - top-down control Y1 - 2018 U6 - https://doi.org/10.1002/ece3.4184 SN - 2045-7758 VL - 8 IS - 12 SP - 6317 EP - 6329 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Manzoni, Stefano A1 - Capek, Petr A1 - Porada, Philipp A1 - Thurner, Martin A1 - Winterdahl, Mattias A1 - Beer, Christian A1 - Bruchert, Volker A1 - Frouz, Jan A1 - Herrmann, Anke M. A1 - Lindahl, Bjorn D. A1 - Lyon, Steve W. A1 - Šantrůčková, Hana A1 - Vico, Giulia A1 - Way, Danielle T1 - Reviews and syntheses BT - Carbon use efficiency from organisms to ecosystems - definitions, theories, and empirical evidence JF - Biogeosciences N2 - The cycling of carbon (C) between the Earth surface and the atmosphere is controlled by biological and abiotic processes that regulate C storage in biogeochemical compartments and release to the atmosphere. This partitioning is quantified using various forms of C-use efficiency (CUE) - the ratio of C remaining in a system to C entering that system. Biological CUE is the fraction of C taken up allocated to biosynthesis. In soils and sediments, C storage depends also on abiotic processes, so the term C-storage efficiency (CSE) can be used. Here we first review and reconcile CUE and CSE definitions proposed for autotrophic and heterotrophic organisms and communities, food webs, whole ecosystems and watersheds, and soils and sediments using a common mathematical framework. Second, we identify general CUE patterns; for example, the actual CUE increases with improving growth conditions, and apparent CUE decreases with increasing turnover. We then synthesize > 5000CUE estimates showing that CUE decreases with increasing biological and ecological organization - from uni-cellular to multicellular organisms and from individuals to ecosystems. We conclude that CUE is an emergent property of coupled biological-abiotic systems, and it should be regarded as a flexible and scale-dependent index of the capacity of a given system to effectively retain C. Y1 - 2018 U6 - https://doi.org/10.5194/bg-15-5929-2018 SN - 1726-4170 SN - 1726-4189 VL - 15 IS - 19 SP - 5929 EP - 5949 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - He, Hai A1 - Edlich-Muth, Christian A1 - Lindner, Steffen N. A1 - Bar-Even, Arren T1 - Ribulose Monophosphate Shunt Provides Nearly All Biomass and Energy Required for Growth of E. coli JF - ACS Synthetic Biology N2 - The ribulose monophosphate (RuMP) cycle is a highly efficient route for the assimilation of reduced one-carbon compounds. Despite considerable research, the RuMP cycle has not been fully implemented in model biotechnological organisms such as Escherichia coli, mainly since the heterologous establishment of the pathway requires addressing multiple challenges: sufficient formaldehyde production, efficient formaldehyde assimilation, and sufficient regeneration of the formaldehyde acceptor, ribulose 5-phosphate. Here, by efficiently producing formaldehyde from sarcosine oxidation and ribulose 5-phosphate from exogenous xylose, we set aside two of these concerns, allowing us to focus on the particular challenge of establishing efficient formaldehyde assimilation via the RuMP shunt, the linear variant of the RuMP cycle. We have generated deletion strains whose growth depends, to different extents, on the activity of the RuMP shunt, thus incrementally increasing the selection pressure for the activity of the synthetic pathway. Our final strain depends on the activity of the RuMP shunt for providing the cell with almost all biomass and energy needs, presenting an absolute coupling between growth and activity of key RuMP cycle components. This study shows the value of a stepwise problem solving approach when establishing a difficult but promising pathway, and is a strong basis for future engineering, selection, and evolution of model organisms for growth via the RuMP cycle. KW - ribulose monophosphate cycle KW - methylotrophy KW - metabolic engineering KW - growth selection KW - carbon labeling KW - flux modeling KW - formaldehyde assimilation Y1 - 2018 U6 - https://doi.org/10.1021/acssynbio.8b00093 SN - 2161-5063 VL - 7 IS - 6 SP - 1601 EP - 1611 PB - ACS CY - Washington, DC ER - TY - JOUR A1 - Schwanhold, Nadine A1 - Iobbi-Nivol, Chantal A1 - Lehmann, Angelika A1 - Leimkühler, Silke T1 - Same but different BT - Comparison of two system-specific molecular chaperones for the maturation of formate dehydrogenases JF - PLoS one N2 - The maturation of bacterial molybdoenzymes is a complex process leading to the insertion of the bulky bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor into the apoenzyme. Most molybdoenzymes were shown to contain a specific chaperone for the insertion of the bis-MGD cofactor. Formate dehydrogenases (FDH) together with their molecular chaperone partner seem to display an exception to this specificity rule, since the chaperone FdhD has been proven to be involved in the maturation of all three FDH enzymes present in Escherichia colt. Multiple roles have been suggested for FdhD-like chaperones in the past, including the involvement in a sulfur transfer reaction from the L-cysteine desulfurase IscS to bis-MGD by the action of two cysteine residues present in a conserved CXXC motif of the chaperones. However, in this study we show by phylogenetic analyses that the CXXC motif is not conserved among FdhD-like chaperones. We compared in detail the FdhD-like homologues from Rhodobacter capsulatus and E. colt and show that their roles in the maturation of FDH enzymes from different subgroups can be exchanged. We reveal that bis-MGDbinding is a common characteristic of FdhD-like proteins and that the cofactor is bound with a sulfido-ligand at the molybdenum atom to the chaperone. Generally, we reveal that the cysteine residues in the motif CXXC of the chaperone are not essential for the production of active FDH enzymes. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0201935 SN - 1932-6203 VL - 13 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Yannelli, Florencia A. A1 - Karrer, Gerhard A1 - Hall, Rea A1 - Kollmann, Johannes A1 - Heger, Tina T1 - Seed density is more effective than multi-trait limiting similarity in controlling grassland resistance against plant invasions in mesocosms JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - QuestionDisturbed areas offer great opportunities for restoring native biodiversity, but they are also prone to invasion by alien plants. Following the limiting similarity hypothesis, we address the question of whether or not similarity of plant functional traits helps developing seed mixtures of native communities with high resistance to invasive species at an early stage of restoration. LocationCentre of Greenhouses and Laboratories Durnast, Technische Universitat Munchen, Freising, Germany. MethodsUsing a system of linear equations, we designed native communities maximizing the similarity between the native and two invasive species according to ten functional traits. We used native grassland plants, two invasive alien species that are often problematic in disturbed areas (i.e., Ambrosia artemisiifolia and Solidago gigantea) and trait information obtained from databases. The two communities were then tested for resistance against establishment of the two invaders separately in a greenhouse experiment. We measured height of the invasive species and above-ground biomass, along with leaf area index, 4 and 8months after sowing respectively. ResultsBoth invasive species were successfully reduced by the native community designed to suppress S. gigantea dominated by small-seeded species. These results could be considered as partial support for the limiting similarity hypothesis. However, given the success of this mixture against both invasive species, suppression was better explained by a seed density effect resulting from the smaller seed mass of the native species included in this mixture. Further, the dominance of a fast-developing competitive species could also contribute to its success. ConclusionsThere was no unequivocal support for the limiting similarity hypothesis in terms of the traits selected. Instead we found that increasing seeding density of native species and selecting species with a fast vegetative development is an effective way to suppress invasive plants during early stages of restoration. If limiting similarity is used to design communities for restoration, early life-history traits should be taken into account. KW - Achillea millefolium KW - Ambrosia artemisiifolia KW - biotic resistance KW - competition KW - density-driven suppression KW - disturbed areas KW - restoration KW - seed mixtures KW - Solidago gigantea Y1 - 2018 U6 - https://doi.org/10.1111/avsc.12373 SN - 1402-2001 SN - 1654-109X VL - 21 IS - 3 SP - 411 EP - 418 PB - Wiley CY - Hoboken ER -