The Enigmatic Universe of the Herbivore Gut

The herbivore gut is a fascinating ecosystem exquisitely adapted to plant biomass degradation. Within this ecosystem, anaerobic fungi invade biomass and secrete hydrolytic enzymes. In a recent study, Solomon et al. characterized three anaerobic fungi by transcriptomics, proteomics, and functional analyses to identify novel components essential for plant biomass deconstruction

Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi.

Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi:Insights, Challenges, and Opportunities

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit

Bruchmechanische Charakterisierung der Adhäsion an Polymer/Glas-Grenzflächen

Die mechanischen Eigenschaften von Verbundwerkstoffen und Werkstoffverbunden werden in erheblichem Maß durch die Eigenschaften der Grenzfläche bestimmt. Oftmals ist die Grenzfläche sogar das schwächste Element. Eine zuverlässige Beschreibung der mechanischen Grenzflächenqualität ist von großer Bedeutung für die Wahl optimaler Werkstoffkombinationen und Kontaktbildungsverfahren. Bei mechanisch-technologischen Charakterisierungsmethoden unterliegen die Zielgrößen, wie etwa die Grenzflächenscherfestigkeit, oftmals einer starken Streuung. In der vorliegenden Arbeit wird deshalb das Konzept der linearelastischen Bruchmechanik zur Grenzflächencharakterisierung herangezogen. Für die dazu notwendige Spannungsanalyse des Prüfkörpers mit einem öffnungsdominierten Grenzflächenriß werden FE-Modelle erstellt. Im Nachgang zu Experiment und Datenreduktion werden die Voraussetzungen für die Anwendbarkeit des linear-elastischen Konzeptes verifiziert. Da die Grenzflächenzähigkeit c G empfindlich von der Zweiachsigkeit ψ des örtlichen Beanspruchungszustandes abhängt, wird eine Belastungseinrichtung konzipiert, mit der ψ im gesamten, der linear-elastischen Bruchmechanik zugänglichen Mixed-Mode-Intervall stufenlos variiert werden kann. Ergänzend zur Bestimmung der (ψ ) c G -Grenzflächenbruchkurve wurde das Rißwachstum lichtmikroskopisch verfolgt und der Einfluß thermischer Eigenspannungen abgeschätzt. An nicht-linearen FE-Modellen wird der Einfluß des Rißuferkontaktes sowie des plastischen Fließens als Kleinbereichstörung auf die Modenabhängigkeit der Grenzflächenbruchenergie untersucht. In beiden Beispielen wird durch Annahme von Verzerrungskriterien im Inneren der jeweiligen Nichtlinearitätszone eine Verbindung zwischen Festigkeitslehre und Bruchmechanik hergestellt. Für den Fall der Kleinbereichplastizität werden außerdem die Ligamentnormalspannungen im Rahmen eines weakest-link-Modells für rißbehaftete Körper bewertet.Es zeigt sich, daß die U-Gestalt der (ψ ) c G -Grenzflächenbruchkurve qualitativ nachvollzogen werden kann, wenn man die Ligamentnormalspannungen als rißtreibende Kraft bewertet.The performance of material compounds and composite materials may be highly influenced by the mechanical properties of the interface between the adjoining materials. Many times the interfaces is even the system´s weakest element. A reliable assessment of the interface´s mechanical properties is crucial for the optimum choice of materials and joining methods. Characterisation methods based on a strength of materials approach often are subject to considerable scatter. Therefore, in the present work interfacial characterisation is based on a fracture mechanical approach. The stress analysis of the bimaterial sample with an open, i.e tractionfree interfacial crack is performed with FEM. In a second step based on experimental data, the applicability of the linear-elastic fracture mechanical concept is verified a posteriori. Since interfacial toughness appears to be highly dependent of the biaxiality angle ψ of the local stress state, a loading device has been designed, which allows to continuously vary ψ within the full range accessible to LEFM. In addition, the propagation of the interfacial crack was tracked with an optical microscope. Finally, the influence of thermal residual stress on the U-shaped (ψ ) c G interfacial fracture toughness curve is estimated. Beyond linear-elastic FE modelling, the relation between small scale crack face contact as well as small scale plasticity and the mode dependence of interfacial fracture toughness is explored. In both cases a deformation failure criterion is assumed on a structural level situated well within the respective nonlinearity zone in order to explore the way, how local stress redistribution due to contained geometric and material nonlinearity effects might translate itself into the mode-dependence of interfacial fracture toughness measured on the structural level of the enclosing linear-elastic K-dominance zone. For small scale plasticity, in addition, the role of the elastic-plastic ligament normal stresses is considered within the framework of the weakest link model. It turns out, that the U-shape of the (ψ ) c G -curve may be reproduced qualitatively, if one assumes the ligament normal stresses to be the dominant crack driving forces

Bruchmechanische Charakterisierung der Adhäsion an Polymer/Glas-Grenzflächen

Die mechanischen Eigenschaften von Verbundwerkstoffen und Werkstoffverbunden werden in erheblichem Maß durch die Eigenschaften der Grenzfläche bestimmt. Oftmals ist die Grenzfläche sogar das schwächste Element. Eine zuverlässige Beschreibung der mechanischen Grenzflächenqualität ist von großer Bedeutung für die Wahl optimaler Werkstoffkombinationen und Kontaktbildungsverfahren. Bei mechanisch-technologischen Charakterisierungsmethoden unterliegen die Zielgrößen, wie etwa die Grenzflächenscherfestigkeit, oftmals einer starken Streuung. In der vorliegenden Arbeit wird deshalb das Konzept der linearelastischen Bruchmechanik zur Grenzflächencharakterisierung herangezogen. Für die dazu notwendige Spannungsanalyse des Prüfkörpers mit einem öffnungsdominierten Grenzflächenriß werden FE-Modelle erstellt. Im Nachgang zu Experiment und Datenreduktion werden die Voraussetzungen für die Anwendbarkeit des linear-elastischen Konzeptes verifiziert. Da die Grenzflächenzähigkeit c G empfindlich von der Zweiachsigkeit ψ des örtlichen Beanspruchungszustandes abhängt, wird eine Belastungseinrichtung konzipiert, mit der ψ im gesamten, der linear-elastischen Bruchmechanik zugänglichen Mixed-Mode-Intervall stufenlos variiert werden kann. Ergänzend zur Bestimmung der (ψ ) c G -Grenzflächenbruchkurve wurde das Rißwachstum lichtmikroskopisch verfolgt und der Einfluß thermischer Eigenspannungen abgeschätzt. An nicht-linearen FE-Modellen wird der Einfluß des Rißuferkontaktes sowie des plastischen Fließens als Kleinbereichstörung auf die Modenabhängigkeit der Grenzflächenbruchenergie untersucht. In beiden Beispielen wird durch Annahme von Verzerrungskriterien im Inneren der jeweiligen Nichtlinearitätszone eine Verbindung zwischen Festigkeitslehre und Bruchmechanik hergestellt. Für den Fall der Kleinbereichplastizität werden außerdem die Ligamentnormalspannungen im Rahmen eines weakest-link-Modells für rißbehaftete Körper bewertet.Es zeigt sich, daß die U-Gestalt der (ψ ) c G -Grenzflächenbruchkurve qualitativ nachvollzogen werden kann, wenn man die Ligamentnormalspannungen als rißtreibende Kraft bewertet.The performance of material compounds and composite materials may be highly influenced by the mechanical properties of the interface between the adjoining materials. Many times the interfaces is even the system´s weakest element. A reliable assessment of the interface´s mechanical properties is crucial for the optimum choice of materials and joining methods. Characterisation methods based on a strength of materials approach often are subject to considerable scatter. Therefore, in the present work interfacial characterisation is based on a fracture mechanical approach. The stress analysis of the bimaterial sample with an open, i.e tractionfree interfacial crack is performed with FEM. In a second step based on experimental data, the applicability of the linear-elastic fracture mechanical concept is verified a posteriori. Since interfacial toughness appears to be highly dependent of the biaxiality angle ψ of the local stress state, a loading device has been designed, which allows to continuously vary ψ within the full range accessible to LEFM. In addition, the propagation of the interfacial crack was tracked with an optical microscope. Finally, the influence of thermal residual stress on the U-shaped (ψ ) c G interfacial fracture toughness curve is estimated. Beyond linear-elastic FE modelling, the relation between small scale crack face contact as well as small scale plasticity and the mode dependence of interfacial fracture toughness is explored. In both cases a deformation failure criterion is assumed on a structural level situated well within the respective nonlinearity zone in order to explore the way, how local stress redistribution due to contained geometric and material nonlinearity effects might translate itself into the mode-dependence of interfacial fracture toughness measured on the structural level of the enclosing linear-elastic K-dominance zone. For small scale plasticity, in addition, the role of the elastic-plastic ligament normal stresses is considered within the framework of the weakest link model. It turns out, that the U-shape of the (ψ ) c G -curve may be reproduced qualitatively, if one assumes the ligament normal stresses to be the dominant crack driving forces

Cavity growth in soft adhesives

The growth process of cavities nucleated at the interface between a rigid surface and a soft adhesive layer has been investigated with a probe method. A tensile stress was applied to the highly confined layer resulting in a negative hydrostatic pressure in the layer. The statistics of appearance and rate of growth of cavities as a function of applied negative stress were monitored with a CCD camera. If large germs of cavities were initially present, most of the cavities became optically visible above a critical level of stress independent of layer thickness. Cavities grew simultaneously and at the same expansion rate as a function of applied stress. In the absence of large germs, cavities became optically visible one after another, reaching a limiting size controlled by the thickness of the layer independently and very rapidly. Although, for each sample, we observed a statistical distribution of critical stress levels where a cavity expanded, the mean cavitation stress depended both on surface topography and more surprisingly on layer thickness. We believe that this new and somewhat surprising result can be interpreted with a model for the growth of small germs in finite size layers (J. Dollhofer, A. Chiche, V. Muralidharan et al., Int. J. Solids Struct. 41, 6111 (2004)). This model is mainly based on the dual notion of an energy activated transition from an unexpanded metastable state to an expanded stable state and to the proportionality of the activation energy with the elastic energy stored in the adhesive layer

Quality assurance of compost and digestate

Establishing a quality assurance system for compost and digestate from bio-waste can help to decrease the amount of biodegradable waste being landfilled and to increase material recycling. Germany has been successfully operating such a system since 1989, comprising also an organisation with the competence to control the quality of compost and digestate and to award a quality label, the Bundesgütegemeinschaft Kompost e.V. This brochure introduces to the quality assurance system of compost and digestate in Germany. It provides information, inter alia, on the legal framework related to bio-waste in the EU and in Germany, on involved organisations and on requirements