A three-dimensional discrete lattice-based system for modeling the growth of aerial hyphae of filamentous fungi on solid surfaces: A tool for investigating micro-scale phenomena in solid-state fermentation

Host Material Viscoelasticity Determines Wrinkling of Fungal Films

Microbial organisms react to their environment and are able to change it through biological and physical processes. For example, fungi exhibit various growth morphologies depending on their host material. Here, we show how the rheological properties of the host material influence the fungal wrinkling morphology. Rheological data of the host material was set in relation to the growth morphology. On host material with high storage modulus, the fungal film was flat, whereas on host material with low storage modulus, the fungus showed a morphology made of folds and wrinkles. We combined our findings with mechanical instability theories and found that the formation of wrinkles and folds is dependent on the storage modulus of the host material. The connection between the wrinkling morphology and the storage modulus of the host material is shown with simple scaling theories. The amplitude, number of wrinkles, and wrinkle length follow geometrical laws, and the mechanical properties of the fungal film are expected to increase with increasing host material elasticity. The obtained results show the connection between living biological films, how they react to their surroundings, and the underlying physical mechanisms. They can provide a framework to further design fungal materials with specific surface morphologies.

A framework for an organelle-based mathematical modeling of hyphae

Background

Although highly desirable, a mechanistic explanation for the outstanding protein secretion capabilities of fungi such as Aspergilli is missing. As a result, a rational and predictive design of strains as cell factories for protein production is still out of reach. The analysis of the secretion apparatus is not only hampered by open issues concerning molecular cell biological processes, but as well by their spatial fragmentation and highly dynamic features. Whereas the former issues are addressed by many groups, an account of the space- and time-dependent processes, which is best done by means of mathematical models, is lacking. Up to now, mathematical models for hyphal organisms mainly focus on one of two extremes. Either macroscopic morphology, such as pellet or mycelium growth, is addressed, or a microscopic picture is drawn predicting, for instance, the form of a hyphal tip. How intra-hyphal transport and organelle distribution works, however, has not been tackled so far mathematically.

Results

The main result of this contribution is a generic modeling framework to describe the space- and time-dependent evolution of intracellular substances and organelles. It takes intrahyphal, passive and active transport of substances into account and explains exponential and then linear length growth by tugor-driven uptake of water. Experimentally observed increasing concentration levels of organelles towards the tip can be well explained within the framework without resorting to complex biological regulations. It is shown that the accumulation can be partly explained by geometrical constraints, besides a necessary deceleration of the active transport velocity. The model is formulated such that more intricate intracellular processes can be included.

Conclusions

Results from steady-state experiments are easy to be interpreted. In a hyphal network, however, new branches are produced at an exponential rate. Moreover, passive and active transport processes give rise to a spatial distribution of organelles and other cytoplasmatic constituents inside hyphae. As a result, most of the data obtained in experiments will be from a non-steady and space dependent state. A quantitative and mechanistic explanation of the processes occurring will only be possible if these dependencies are taking into account while evaluating experimental findings.

A model for growth of a single fungal hypha based on well-mixed tanks in series: simulation of nutrient and vesicle transport in aerial reproductive hyphae

Current models that describe the extension of fungal hyphae and development of a mycelium either do not describe the role of vesicles in hyphal extension or do not correctly describe the experimentally observed profile for distribution of vesicles along the hypha. The present work uses the n-tanks-in-series approach to develop a model for hyphal extension that describes the intracellular transport of nutrient to a sub-apical zone where vesicles are formed and then transported to the tip, where tip extension occurs. The model was calibrated using experimental data from the literature for the extension of reproductive aerial hyphae of three different fungi, and was able to describe different profiles involving acceleration and deceleration of the extension rate. A sensitivity analysis showed that the supply of nutrient to the sub-apical vesicle-producing zone is a key factor influencing the rate of extension of the hypha. Although this model was used to describe the extension of a single reproductive aerial hypha, the use of the n-tanks-in-series approach to representing the hypha means that the model has the flexibility to be extended to describe the growth of other types of hyphae and the branching of hyphae to form a complete mycelium.

Modeling the Growth of Filamentous Fungi at the Particle Scale in Solid-State Fermentation Systems

Solid-state fermentation (SSF) with filamentous fungi is a promising technique for the production of a range of biotechnological products and has the potential to play an important role in future biorefineries. The performance of such processes is intimately linked with the mycelial mode of growth of these fungi: Not only is the production of extracellular enzymes related to morphological characteristics, but also the mycelium can affect bed properties and, consequently, the efficiency of heat and mass transfer within the bed. A mathematical model that describes the development of the fungal mycelium in SSF systems at the particle scale would be a useful tool for investigating these phenomena, but, as yet, a sufficiently complete model has not been proposed. This review presents the biological and mass transfer phenomena that should be included in such a model and then evaluates how these phenomena have been modeled previously in the SSF and related literature. We conclude that a discrete lattice-based model that uses differential equations to describe the mass balances of the components within the system would be most appropriate and that mathematical expressions for describing the individual phenomena are available in the literature. It remains for these phenomena to be integrated into a complete model describing the development of fungal mycelia in SSF systems.

The Cell Factory Aspergillus Enters the Big Data Era: Opportunities and Challenges for Optimising Product Formation

Living with limits. Getting more from less. Producing commodities and high-value products from renewable resources including waste. What is the driving force and quintessence of bioeconomy outlines the lifestyle and product portfolio of Aspergillus, a saprophytic genus, to which some of the top-performing microbial cell factories belong: Aspergillus niger, Aspergillus oryzae and Aspergillus terreus. What makes them so interesting for exploitation in biotechnology and how can they help us to address key challenges of the twenty-first century? How can these strains become trimmed for better growth on second-generation feedstocks and how can we enlarge their product portfolio by genetic and metabolic engineering to get more from less? On the other hand, what makes it so challenging to deduce biological meaning from the wealth of Aspergillus -omics data? And which hurdles hinder us to model and engineer industrial strains for higher productivity and better rheological performance under industrial cultivation conditions? In this review, we will address these issues by highlighting most recent findings from the Aspergillus research with a focus on fungal growth, physiology, morphology and product formation. Indeed, the last years brought us many surprising insights into model and industrial strains. They clearly told us that similar is not the same: there are different ways to make a hypha, there are more protein secretion routes than anticipated and there are different molecular and physical mechanisms which control polar growth and the development of hyphal networks. We will discuss new conceptual frameworks derived from these insights and the future scientific advances necessary to create value from Aspergillus Big Data.