Contrasting taxonomic and phylogenetic diversity responses to forest modifications: comparisons of taxa and successive plant life stages in South african scarp forest
Eike Lena Neuschulz
- The degradation of natural forests to modified forests threatens subtropical and tropical biodiversity worldwide. Yet, species responses to forest modification vary considerably. Furthermore, effects of forest modification can differ, whether with respect to diversity components (taxonomic or phylogenetic) or to local (α-diversity) and regional (β-diversity) spatial scales. This real-world complexity has so far hampered our understanding of subtropical and tropical biodiversity patterns in human-modified forest landscapes. In a subtropical South African forest landscape, we studied the responses of three successive plant life stages (adult trees, saplings, seedlings) and of birds to five different types of forest modification distinguished by the degree of within-forest disturbance and forest loss. Responses of the two taxa differed markedly. Thus, the taxonomic α-diversity of birds was negatively correlated with the diversity of all plant life stages and, contrary to plant diversity, increased with forest disturbance. Conversely, forest disturbance reduced the phylogenetic α-diversity of all plant life stages but not that of birds. Forest loss neither affected taxonomic nor phylogenetic diversity of any taxon. On the regional scale, taxonomic but not phylogenetic β-diversity of both taxa was well predicted by variation in forest disturbance and forest loss. In contrast to adult trees, the phylogenetic diversity of saplings and seedlings showed signs of contemporary environmental filtering. In conclusion, forest modification in this subtropical landscape strongly shaped both local and regional biodiversity but with contrasting outcomes. Phylogenetic diversity of plants may be more threatened than that of mobile species such as birds. The reduced phylogenetic diversity of saplings and seedlings suggests losses in biodiversity that are not visible in adult trees, potentially indicating time-lags and contemporary shifts in forest regeneration. The different responses of taxonomic and phylogenetic diversity to forest modifications imply that biodiversity conservation in this subtropical landscape requires the preservation of natural and modified forests.
Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses
Maria A. Nilsson
- The ancestors to the Australian marsupials entered Australia around 60 (54-72) million years ago from Antarctica, and radiated into the four living orders Peramelemorphia, Dasyuromorphia, Diprotodontia and Notoryctemorphia. The relationship between the four Australian marsupial orders has been a long-standing question, because different phylogenetic studies were not able to consistently reconstruct the same topology. Initial in silico analysis of the Tasmanian devil genome and experimental screening in the seven marsupial orders revealed 20 informative transposable element insertions for resolving the inter- and intraordinal relationships of Australian and South American orders. However, the retrotransposon insertions support three conflicting topologies regarding Peramelemorphia, Dasyuromorphia and Notoryctemorphia, indicating that the split between the three orders may be best understood as a network. This finding is supported by a phylogenetic re-analysis of nuclear gene sequences, using a consensus network approach that allows depicting hidden phylogenetic conflict, otherwise lost when forcing the data into a bifurcating tree. The consensus network analysis agrees with the transposable element analysis in that all possible topologies regarding Peramelemorphia, Dasyuromorphia, and Notoryctemorphia in a rooted four-taxon topology are equally well supported. In addition, retrotransposon insertion data supports the South American order Didelphimorphia being the sistergroup to all other living marsupial orders. The four Australian orders originated within three million years at the Cretaceous-Paleogene boundary. The rapid divergences left conflicting phylogenetic information in the genome possibly generated by incomplete lineage sorting or introgressive hybridisation, leaving the relationship among Australian marsupial orders unresolvable as a bifurcating process million years later.
Forests, savannas, and grasslands: bridging the knowledge gap between ecology and dynamic global vegetation models
Stefan C. Dekker
Peter M. van Bodegom
Steven I. Higgins
Christian H. Reick
Miguel Ángel de Zavala
- The forest, savanna, and grassland biomes, and the transitions between them, are expected to undergo major changes in the future due to global climate change. Dynamic global vegetation models (DGVMs) are very useful for understanding vegetation dynamics under the present climate, and for predicting its changes under future conditions. However, several DGVMs display high uncertainty in predicting vegetation in tropical areas. Here we perform a comparative analysis of three different DGVMs (JSBACH, LPJ-GUESS-SPITFIRE and aDGVM) with regard to their representation of the ecological mechanisms and feedbacks that determine the forest, savanna, and grassland biomes, in an attempt to bridge the knowledge gap between ecology and global modeling. The outcomes of the models, which include different mechanisms, are compared to observed tree cover along a mean annual precipitation gradient in Africa. By drawing on the large number of recent studies that have delivered new insights into the ecology of tropical ecosystems in general, and of savannas in particular, we identify two main mechanisms that need improved representation in the examined DGVMs. The first mechanism includes water limitation to tree growth, and tree–grass competition for water, which are key factors in determining savanna presence in arid and semi-arid areas. The second is a grass–fire feedback, which maintains both forest and savanna presence in mesic areas. Grasses constitute the majority of the fuel load, and at the same time benefit from the openness of the landscape after fires, since they recover faster than trees. Additionally, these two mechanisms are better represented when the models also include tree life stages (adults and seedlings), and distinguish between fire-prone and shade-tolerant forest trees, and fire-resistant and shade-intolerant savanna trees. Including these basic elements could improve the predictive ability of the DGVMs, not only under current climate conditions but also and especially under future scenarios.
Combined transcript, proteome, and metabolite analysis of transgenic maize seeds engineered for enhanced carotenoid synthesis reveals pleotropic effects in core metabolism
- The aim of this study was to assess whether endosperm-specific carotenoid biosynthesis influenced core metabolic processes in maize embryo and endosperm and how global seed metabolism adapted to this expanded biosynthetic capacity. Although enhancement of carotenoid biosynthesis was targeted to the endosperm of maize kernels, a concurrent up-regulation of sterol and fatty acid biosynthesis in the embryo was measured. Targeted terpenoid analysis, and non-targeted metabolomic, proteomic, and transcriptomic profiling revealed changes especially in carbohydrate metabolism in the transgenic line. In-depth analysis of the data, including changes of metabolite pools and increased enzyme and transcript concentrations, gave a first insight into the metabolic variation precipitated by the higher up-stream metabolite demand by the extended biosynthesis capacities for terpenoids and fatty acids. An integrative model is put forward to explain the metabolic regulation for the increased provision of terpenoid and fatty acid precursors, particularly glyceraldehyde 3-phosphate and pyruvate or acetyl-CoA from imported fructose and glucose. The model was supported by higher activities of fructokinase, glucose 6-phosphate isomerase, and fructose 1,6-bisphosphate aldolase indicating a higher flux through the glycolytic pathway. Although pyruvate and acetyl-CoA utilization was higher in the engineered line, pyruvate kinase activity was lower. A sufficient provision of both metabolites may be supported by a by-pass in a reaction sequence involving phosphoenolpyruvate carboxylase, malate dehydrogenase, and malic enzyme.
The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina
- Background: Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota.
Results: The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned.
Conclusions: The current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production.
Habilitationsordnung der Mathematisch-Naturwissenschaftlichen Fachbereiche der Johann Wolfgang Goethe-Universität Frankfurt am Main vom 4. Februar 1992 : genehmigt durch Beschluss des Präsidiums der Johann Wolfgang Goethe-Universität Frankfurt am Main am 19. November 2013
Herstellung eines Phaffia rhodozyma : Stamms mit verstärkter Astaxanthin-Synthese über gezielte genetische Modifikation chemisch mutagenisierter Stämme
- Ziel dieser Arbeit war es erstmals durch eine Kombination aus chemischer Mutagenese und gezielter genetischer Modifikation (hier: „metabolic engineering“) einen Phaffia-Stamm herzustellen, welcher über die Mutagenese hinaus über eine weiter verstärkte Astaxanthin-Synthese verfügt.
Die von „DSM Nutritional Products“ bereitgestellten chemischen Mutanten wurden analysiert und über einen Selektionsprozess auf Pigmentstabilität und Wachstum hin optimiert, da die Stämme aus cryogenisierter Dauerkultur starke Pigmentinstabilitäten und ein verzögertes Wachstum aufwiesen.
Über eine exploratorische Phase wurde die Carotinoidsynthese analysiert und festgestellt, dass in den Mutanten keine Einzelreaktionen betroffen sind, welche für die Heraufregulierung der Carotinoidsynthese in den Mutanten verantwortlich sind. Hierbei wurden Limitierungen identifiziert und diese durch Transformation von Expressionsplasmiden mit geeigneten Genen aufgehoben, um damit eine noch effizientere Metabolisierung von Astaxanthin-Vorstufen hin zu Astaxanthin zu erreichen. Eine Überexpression der Phytoensynthase/Lycopinzyklase crtYB resultierte in einem gesteigerten Carotinoidgehalt bei gleichbleibendem Astaxanthin- Anteil. Durch eine zweite Transformation mit einer Expressionskassette für die Astaxanthin-Synthase asy konnte der Carotinoidgehalt weiter gesteigert und zusätzlich eine Limitierung der Metabolisierung von Astaxanthin-Vorstufen behoben werden, sodass die Transformante nahezu alle Intermediate der Astaxanthinsynthese zu Astaxanthin metabolisieren konnte (Gassel et al. 2013). Es konnte gezeigt werden, dass auch in den Mutanten, aus Experimenten mit dem Wildtyp bekannte, Limitierungen identifiziert und ausgeglichen werden konnten.
Investigation of the biosynthesis of bacterial natural products
- Natural products (NPs) have been a rich source for pharmaceutically used anti-infectives and other drugs. However, the application of anti-infectives inevitably causes the development of resistant and multiresistant pathogens, which have to be treated with novel anti-infectives. The industrial research for novel anti-infectives has been concentrating on members of the bacterial Actinomycetales for a long time. Due to several reasons, e.g. the rediscovery of already known NPs, pharmaceutical companies abandoned their NP-research and focused on drug development based on combinatorial chemistry. However, the limited structural diversity of merely synthetic compound libraries has not been a fruitful source for bioactive compounds. Hence the discovery of novel bioactive NPs as a source for anti-infectives is still of economical and humanitarian interest and will remain to be an important branch of research in the future. One strategy to circumvent the rediscovery of bioactive NPs is the analysis of yet unexplored bacterial taxa. Based on this assumption, this work aimed at the discovery of novel NPs from the entomopathogenic bacterial genera Xenorhabdus and Photorhabdus and other promising taxa, as well as the investigation of their biosynthesis. ...
Lateralization of Travelling Wave Response in the Hearing Organ of Bushcrickets
Arun Palghat Udayashankar
- Travelling waves are the physical basis of frequency discrimination in many vertebrate and invertebrate taxa, including mammals, birds, and some insects. In bushcrickets (Tettigoniidae), the crista acustica is the hearing organ that has been shown to use sound-induced travelling waves. Up to now, data on mechanical characteristics of sound-induced travelling waves were only available along the longitudinal (proximal-distal) direction. In this study, we use laser Doppler vibrometry to investigate in-vivo radial (anterior-posterior) features of travelling waves in the tropical bushcricket Mecopoda elongata. Our results demonstrate that the maximum of sound-induced travelling wave amplitude response is always shifted towards the anterior part of the crista acustica. This lateralization of the travelling wave response induces a tilt in the motion of the crista acustica, which presumably optimizes sensory transduction by exerting a shear motion on the sensory cilia in this hearing organ.
pH- and sodium-induced changes in a sodium/proton antiporter
- We examined substrate-induced conformational changes in MjNhaP1, an archaeal electroneutral Na+/H+-antiporter resembling the human antiporter NHE1, by electron crystallography of 2D crystals in a range of physiological pH and Na+ conditions. In the absence of sodium, changes in pH had no major effect. By contrast, changes in Na+ concentration caused a marked conformational change that was largely pH-independent. Crystallographically determined, apparent dissociation constants indicated ∼10-fold stronger Na+ binding at pH 8 than at pH 4, consistent with substrate competition for a common ion-binding site. Projection difference maps indicated helix movements by about 2 Å in the 6-helix bundle region of MjNhaP1 that is thought to contain the ion translocation site. We propose that these movements convert the antiporter from the proton-bound, outward-open state to the Na+-bound, inward-open state. Oscillation between the two states would result in rapid Na+/H+ antiport.