An accurate description of Aspergillus niger organic acid batch fermentation through dynamic metabolic modelling

Abstract Background Aspergillus niger fermentation has provided the chief source of industrial citric acid for over 50 years. Traditional strain development of this organism was achieved through random mutagenesis, but advances in genomics have enabled the development of genome-scale metabolic modelling that can be used to make predictive improvements in fermentation performance. The parent citric acid-producing strain of A. niger, ATCC 1015, has been described previously by a genome-scale metabolic model that encapsulates its response to ambient pH. Here, we report the development of a novel double optimisation modelling approach that generates time-dependent citric acid fermentation using dynamic flux balance analysis. Results The output from this model shows a good match with empirical fermentation data. Our studies suggest that citric acid production commences upon a switch to phosphate-limited growth and this is validated by fitting to empirical data, which confirms the diauxic growth behaviour and the role of phosphate storage as polyphosphate. Conclusions The calibrated time-course model reflects observed metabolic events and generates reliable in silico data for industrially relevant fermentative time series, and for the behaviour of engineered strains suggesting that our approach can be used as a powerful tool for predictive metabolic engineering

Evidence for Active Uptake and Deposition of Si-based defenses in Tall Fescue

Silicon (Si) is taken up from the soil as monosilicic acid by plant roots, transported to leaves and deposited as phytoliths, amorphous silica (SiO2) bodies, which are a key component of anti-herbivore defense in grasses. Silicon transporters have been identified in many plant species, but the mechanisms underpinning Si transport remain poorly understood. Specifically, the extent to which Si uptake is a passive process, driven primarily by transpiration, or has both passive and active components remains disputed. Increases in foliar Si concentration following herbivory suggest plants may exercise some control over Si uptake and distribution. In order to investigate passive and active controls on Si accumulation, we examined both genetic and environmental influences on Si accumulation in the forage grass Festuca arundinacea. We studied three F. arundinacea varieties that differ in the levels of Si they accumulate. Varieties not only differed in Si concentration, but also in increases in Si accumulation in response to leaf damage. The varietal differences in Si concentration generally reflected differences in stomatal density and stomatal conductance, suggesting passive, transpiration-mediated mechanisms underpin these differences. Bagging plants after damage was employed to minimize differences in stomatal conductance between varieties and in response to damage. This treatment eliminated constitutive differences in leaf Si levels, but did not impair the damage-induced increases in Si uptake: damaged, bagged plants still had more leaf Si than undamaged, bagged plants in all three varieties. Preliminary differential gene expression analysis revealed that the active Si transporter Lsi2 was highly expressed in damaged unbagged plants compared with undamaged unbagged plants, suggesting damage-induced Si defenses are regulated at gene level. Our findings suggest that although differences in transpiration may be partially responsible for varietal differences in Si uptake, they cannot explain damage-induced increases in Si uptake and deposition, suggesting that wounding causes changes in Si uptake, distribution and deposition that likely involve active processes and changes in gene expression. Introductio

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost- derived consortia

Microbial communities (MCs) create complex metabolic networks in natural habitats and respond to environmental changes by shifts in the community structure. Although members of MCs are often not amenable for cultivation in pure culture, it is possible to obtain a greater diversity of species in the laboratory setting when microorganisms are grown as mixed cultures. In order to mimic the environmental conditions, an appropriate growth medium must be applied. Here, we examined the hypothesis that a greater diversity of microorganisms can be sustained under nutrient-limited conditions. Using a 16 S rRNA amplicon metagenomic approach, we explored the structure of a compost-derived MC. During a five-week time course the MC grown in minimal medium with sugarcane bagasse (SCB) as a sole carbon source showed greater diversity and enrichment in lignocellulose-degrading microorganisms. In contrast, a MC grown in nutrient rich medium with addition of SCB had a lower microbial diversity and limited number of lignocellulolytic species. Our approach provides evidence that factors such as nutrient availability has a significant selective pressure on the biodiversity of microorganisms in MCs. Consequently, nutrient-limited medium may displace bacterial generalist species, leading to an enriched source for mining novel enzymes for biotechnology applications

Lytic Polysaccharide Monooxygenases as Chitin-Specific Virulence Factors in Crayfish Plague

he oomycete pathogen Aphanomyces astaci, also known as "crayfish plague", is an obligate fungal-like parasite of freshwater crustaceans and is considered responsible for the ongoing decline of native European crayfish populations. A. astaci is thought to secrete a wide array of effectors and enzymes that facilitate infection, however their molecular mechanisms have been poorly characterized. Here, we report the identification of AA15 lytic polysaccharide monooxygenases (LPMOs) as a new group of secreted virulence factors in A. astaci. We show that this enzyme family has greatly expanded in A. astaci compared to all other oomycetes, and that it may facilitate infection through oxidative degradation of crystalline chitin, the most abundant polysaccharide found in the crustacean exoskeleton. These findings reveal new roles for LPMOs in animal-pathogen interactions, and could help inform future strategies for the protection of farmed and endangered species

Mechanical, chemical, biological : Moving towards closed-loop bio-based recycling in a circular economy of sustainable textiles

The textile industry is facing increasing criticism because of its intensive use of resources –both natural and fossil derived– and the negative environmental and societal impacts associated with the manufacturing, use and disposal of clothes. This has led to a desire to move towards a circular economy for textiles that will implement recycling concepts and technologies to protect resources, the environment and people. So far, recycling processes have been focused on the chemical and mechanical reuse of textile fibres. In contrast, bio-based processes for textile production and recycling have received little attention, beyond end-of-life composting. However, the selectivity and benign processing conditions associated with bio-based technologies hold great promise for circularising the textile life cycle and reducing the environmental impacts of textile production and processing. Developing circular and sustainable systems for textile production requires a revolutionary system approach that encompasses the choice of material and finishes being designed for recycling at the end of life, and in this context bio-based processes can help provide the means to maintain materials in a closed loop. This paper reviews established methods in mechanical and chemical recycling processes in closed-loop textile recycling of all fibre types, as well as bio-based processes that demonstrate open-loop textile recycling. Fermentation and enzymatic processes have been demonstrated for the production of all types of textiles, which in combination with enzymatic deconstruction of end of life cellulosic textiles could allow them to be recycled indefinitely. Within the context of the circular economy, bio-based processes could extend mechanical and chemical textile recycling mechanisms in the technical cycle, enabling greater circularity of textiles in the biological cycle before composting takes place

Revealing the insoluble metasecretome of lignocellulosedegrading microbial communities

AbstractMicrobial communities metabolize plant biomass using secreted enzymes; however, identifying extracellular proteins tightly bound to insoluble lignocellulose in these microbiomes presents a challenge, as the rigorous extraction required to elute these proteins also lyses the microbes associated with the plant biomass releasing intracellular proteins that contaminate the metasecretome. Here we describe a technique for targeting the extracellular proteome, which was used to compare the metasecretome and meta-surface-proteome of two lignocellulose-degrading communities grown on wheat straw and rice straw. A combination of mass spectrometry-based proteomics coupled with metatranscriptomics enabled the identification of a unique secretome pool from these lignocellulose-degrading communities. This method enabled us to efficiently discriminate the extracellular proteins from the intracellular proteins by improving detection of actively secreted and transmembrane proteins. In addition to the expected carbohydrate active enzymes, our new method reveals a large number of unknown proteins, supporting the notion that there are major gaps in our understanding of how microbial communities degrade lignocellulosic substrates.</jats:p

Co-expression Network Analysis of Diverse Wheat Landraces Reveals Marker of Early Thermotolerance and Candidate Master-regulator of Thermotolerance Genes

Bread wheat (Triticum aestivum L.) is a crop, relied on by billions of people around the world as a major source of both income and calories. Rising global temperatures, however, pose a genuine threat to the livelihood of these people, as wheat growth and yields are extremely vulnerable to damage by heat stress. Here we present the YoGI wheat landrace panel, comprised of 342 accessions which show remarkable phenotypic and genetic diversity thanks to their adaptation to different climates. We quantified the abundance of 110,790 transcripts from the panel and used these data to conduct weighted co-expression network analysis and identify hub genes in modules associated with abiotic stress tolerance. We found that the expression of three hub genes, all heat shock proteins (HSPs), were significantly correlated with early thermotolerance in a validation panel of landraces. These hub genes belonged to the same module, with one (TraesCS4D01G207500.1) likely regulating the expression of the other two hub genes, as well as a suite of other HSPs and heat stress transcription factors (Hsfs). In this work, therefore, we identify three validated hub genes, whose expression can serve as markers of thermotolerance during early development, and suggest that TraesCS4D01G207500.1 is a potential master regulator of HSP and Hsf expression – presenting the YoGI landrace panel as an invaluable tool for breeders wishing to determine and introduce novel alleles into modern varieties, for the production of climate-resilient crops