Automated, continuous video microscopy tracking of hyphal growth

Full identification of a growing and branching network's spatio-temporal structures

Experimentally monitoring the kinematics of branching network growth is a tricky task, given the complexity of the structures generated in three dimensions. One option is to drive the network in such a way as to obtain two-dimensional growth, enabling a collection of independent images to be obtained. The density of the network generates ambiguous structures, such as overlaps and meetings, which hinder the reconstruction of the chronology of connections. In this paper, we propose a general method for global network reconstruction. Each network connection is defined by a unique label, enabling it to be tracked in time and space. In this work, we distinguish between lateral and apical branches on the one hand, and extremities on the other. Finally, we reconstruct the network after identifying and eliminating overlaps. This method is then applied to the model filamentous fungus Podospora anserina to reconstruct its growing thallus. We derive criteria for differentiating between apical and lateral branches. We find that the outer ring is favorably composed of apical branches, while densification within the network comes from lateral branches. From this, we derive the specific dynamics of each of the two types. Finally, in the absence of any latency phase during growth initiation, we can reconstruct a time based on the equality of apical and lateral branching collections. This makes it possible to directly compare the growth dynamics of different thalli.

Exploring discrete space-time models for information transfer: Analogies from mycelial networks to the cosmic web

Fungal mycelium networks are large scale biological networks along which nutrients, metabolites flow. Recently, we discovered a rich spectrum of electrical activity in mycelium networks, including action-potential spikes and trains of spikes. Reasoning by analogy with animals and plants, where travelling patterns of electrical activity perform integrative and communicative mechanisms, we speculated that waves of electrical activity transfer information in mycelium networks. Using a new discrete space-time model with emergent radial spanning-tree topology, hypothetically comparable mycelial morphology and physically comparable information transfer, we provide physical arguments for the use of such a model, and by considering growing mycelium network by analogy with growing network of matter in the cosmic web, we develop mathematical models and theoretical concepts to characterise the parameters of the information transfer.

Characterization of spatio-temporal dynamics of the constrained network of the filamentous fungus Podospora anserina using a geomatics-based approach

In their natural environment, fungi are subjected to a wide variety of environmental stresses which they must cope with by constantly adapting the architecture of their growing network. In this work, our objective was to finely characterize the thallus development of the filamentous fungus Podospora anserina subjected to different constraints that are simple to implement in vitro and that can be considered as relevant environmental stresses, such as a nutrient-poor environment or non-optimal temperatures. At the Petri dish scale, the observations showed that the fungal thallus is differentially affected (thallus diameter, mycelium aspect) according to the stresses but these observations remain qualitative. At the hyphal scale, we showed that the extraction of the usual quantities (i.e. apex, node, length) does not allow to distinguish the different thallus under stress, these quantities being globally affected by the application of a stress in comparison with a thallus having grown under optimal conditions. Thanks to an original geomatics-based approach based on the use of automatized Geographic Information System (GIS) tools, we were able to produce maps and metrics characterizing the growth dynamics of the networks and then to highlight some very different dynamics of network densification according to the applied stresses. The fungal thallus is then considered as a map and we are no longer interested in the quantity of material (hyphae) produced but in the empty spaces between the hyphae, the intra-thallus surfaces. This study contributes to a better understanding of how filamentous fungi adapt the growth and densification of their network to potentially adverse environmental changes.

Prediction and experimental evidence of different growth phases of the Podospora anserina hyphal network

Under ideal conditions, the growth of the mycelial network of a filamentous fungus is monotonous, showing an ever increasing complexity with time. The components of the network growth are very simple and based on two mechanisms: the elongation of each hypha, and their multiplication by successive branching. These two mechanisms are sufficient to produce a complex network, and could be localized only at the tips of hyphae. However, branching can be of two types, apical or lateral, depending on its location on the hyphae, therefore imposing the redistribution of the necessary material in the whole mycelium. From an evolutionary point of view, maintaining different branching processes, with additional energy needs for structure and metabolism, is intriguing. We propose in this work to discuss the advantages of each branching type using a new observable for the network growth, allowing us to compare growth configurations. For this purpose, we build on experimental observations of the Podospora anserina mycelium growth, enabling us to feed and constrain a lattice-free modeling of this network based on a binary tree. First, we report the set of statistics related to the branches of P. anserina that we have implemented into the model. Then, we build the density observable, allowing us to discuss the succession of growth phases. We predict that density over time is not monotonic, but shows a decay growth phase, clearly separated from an other one by a stationary phase. The time of appearance of this stable region appears to be driven solely by the growth rate. Finally, we show that density is an appropriate observable to differentiate growth stress.

Automation and artificial intelligence in filamentous fungi-based bioprocesses: A review

By utilizing their powerful metabolic versatility, filamentous fungi can be utilized in bioprocesses aimed at achieving circular economy. With the current digital transformation within the biomanufacturing sector, the interest of automating fungi-based systems has intensified. The purpose of this paper was therefore to review the potentials connected to the use of automation and artificial intelligence in fungi-based systems. Automation is characterized by the substitution of manual tasks with mechanized tools. Artificial intelligence is, on the other hand, a domain within computer science that aims at designing tools and machines with the capacity to execute functions that would usually require human aptitude. Process flexibility, enhanced data reliability and increased productivity are some of the benefits of integrating automation and artificial intelligence in fungi-based bioprocesses. One of the existing gaps that requires further investigation is the use of such data-based technologies in the production of food from fungi.

A fully automated pipeline for the dynamic at-line morphology analysis of microscale Aspergillus cultivation

Background

Morphology, being one of the key factors influencing productivity of filamentous fungi, is of great interest during bioprocess development. With increasing demand of high-throughput phenotyping technologies for fungi due to the emergence of novel time-efficient genetic engineering technologies, workflows for automated liquid handling combined with high-throughput morphology analysis have to be developed.

Results

In this study, a protocol allowing for 48 parallel microbioreactor cultivations of Aspergillus carbonarius with non-invasive online signals of backscatter and dissolved oxygen was established. To handle the increased cultivation throughput, the utilized microbioreactor is integrated into a liquid handling platform. During cultivation of filamentous fungi, cell suspensions result in either viscous broths or form pellets with varying size throughout the process. Therefore, tailor-made liquid handling parameters such as aspiration/dispense height, velocity and mixing steps were optimized and validated. Development and utilization of a novel injection station enabled a workflow, where biomass samples are automatically transferred into a flow through chamber fixed under a light microscope. In combination with an automated image analysis concept, this enabled an automated morphology analysis pipeline. The workflow was tested in a first application study, where the projected biomass area was determined at two different cultivation temperatures and compared to the microbioreactor online signals.

Conclusions

A novel and robust workflow starting from microbioreactor cultivation, automated sample harvest and processing via liquid handling robots up to automated morphology analysis was developed. This protocol enables the determination of projected biomass areas for filamentous fungi in an automated and high-throughput manner. This measurement of morphology can be applied to describe overall pellet size distribution and heterogeneity.

Visualizing three-dimensional fungal growth using light sheet fluorescence microscopy

The evaluation of morphology is fundamental to comprehend how fungi grow, develop, and interact with the environment. Although fungal growth has been extensively studied associated to two-dimensional geometries, lack of appropriate experimental tools has limited exploration of the complex three-dimensional (3D) structures exhibited by mycelia in more general contexts. In this paper, we report the construction of a light-sheet fluorescence microscope (LSFM) capable of performing time-lapse visualization of 3D biological structures (4D microscopy), and the use of this instrument to follow the dynamics of fungal growth. LSFM uses scanning of selective plane illumination and digital reconstruction to provide 3D images of the specimen. We describe the optical, electronic, and computational means to implement two-color LSFM, and provide detailed procedures for aligning and testing the setup. We successfully demonstrate use of both autofluorescence and specific tagging to image Trichoderma atroviride and Neurospora crassa strains growing in liquid media, over extended times (~12 h) and volumes (~400 × 1500 × 800 μm³) at single-hypha resolution. The excellent image contrast provided by LSFM enables us to visualize the dynamics of mycelial architecture, interactions among hyphae, and measure rates of 3D apical extension. Altogether, our work shows a powerful imaging tool to perform 3D morphological analysis of fungi, from hyphae to mycelium.

Fungal oxylipins direct programmed developmental switches in filamentous fungi

Filamentous fungi differentiate along complex developmental programs directed by abiotic and biotic signals. Currently, intrinsic signals that govern fungal development remain largely unknown. Here we show that an endogenously produced and secreted fungal oxylipin, 5,8-diHODE, induces fungal cellular differentiation, including lateral branching in pathogenic Aspergillus fumigatus and Aspergillus flavus, and appressorium formation in the rice blast pathogen Magnaporthe grisea. The Aspergillus branching response is specific to a subset of oxylipins and is signaled through G-protein coupled receptors. RNA-Seq profiling shows differential expression of many transcription factors in response to 5,8-diHODE. Screening of null mutants of 33 of those transcription factors identifies three transcriptional regulators that appear to mediate the Aspergillus branching response; one of the mutants is locked in a hypo-branching phenotype, while the other two mutants display a hyper-branching phenotype. Our work reveals an endogenous signal that triggers crucial developmental processes in filamentous fungi, and opens new avenues for research on the morphogenesis of filamentous fungi.

Fungi produce oxygenated fatty acids, or oxylipins, of unclear function. Here, Niu et al. show that an Aspergillus oxylipin induces various developmental processes in several fungi, including lateral branching in human pathogenic Aspergillus species, and appressorium formation in the plant pathogen Magnaporthe grisea.

Microfluidic monitoring of the growth of individual hyphae in confined environments

Soil fungi have the ability to form large mycelial networks. They rely on the resources available in the soil to produce biomass and are able to degrade complex biomolecules. Some of them can even degrade recalcitrant organic pollutants and are considered as promising candidates for soil bioremediation strategies. However, the success of this approach depends on the ability of fungi to colonize the soil matrix, where they encounter spatial and temporal variations of confinement, humidity and nutrient concentration. In this paper, we present a study of fungal growth at the scale of single hyphae in a microfluidic device, allowing fine control of nutrient and water supply. Time-lapse microscopy allowed simultaneous monitoring of the growth of dozens of hyphae of Talaromyces helicus, a soil isolate, and of the model fungus Neurospora crassa through parallel microchannels. The distributions of growth velocity obtained for each strain were compared with measurements obtained in macroscopic solid culture. For the two strains used in the study, confinement caused the growth velocity to drop in comparison with unconfined experiments. In addition, N. crassa was also limited in its growth by the nutrient supply, while the microfluidic culture conditions seemed better suited for T. helicus. Qualitative observations of fungi growing in microfluidic chambers without lateral confinement also revealed that side walls influence the branching behaviour of hyphae. This study is one of the first to consider the confinement degree within soil microporosities as a key factor of fungal growth, and to address its effect, along with physicochemical parameters, on soil colonization, notably for bioremediation purposes.

Hyphal network whole field imaging allows for accurate estimation of anastomosis rates and branching dynamics of the filamentous fungus Podospora anserina

The success of filamentous fungi in colonizing most natural environments can be largely attributed to their ability to form an expanding interconnected network, the mycelium, or thallus, constituted by a collection of hyphal apexes in motion producing hyphae and subject to branching and fusion. In this work, we characterize the hyphal network expansion and the structure of the fungus Podospora anserina under controlled culture conditions. To this end, temporal series of pictures of the network dynamics are produced, starting from germinating ascospores and ending when the network reaches a few centimeters width, with a typical image resolution of several micrometers. The completely automated image reconstruction steps allow an easy post-processing and a quantitative analysis of the dynamics. The main features of the evolution of the hyphal network, such as the total length L of the mycelium, the number of “nodes” (or crossing points) N and the number of apexes A, can then be precisely quantified. Beyond these main features, the determination of the distribution of the intra-thallus surfaces (S_i) and the statistical analysis of some local measures of N, A and L give new insights on the dynamics of expanding fungal networks. Based on these results, we now aim at developing robust and versatile discrete/continuous mathematical models to further understand the key mechanisms driving the development of the fungus thallus.

Advanced strategy for metabolite exploration in filamentous fungi

Filamentous fungi comprise an abundance of gene clusters that encode high-value metabolites, whereas affluent gene clusters remain silent during laboratory conditions. Complex cellular metabolism further limits these metabolite yields. Therefore, diverse strategies such as genetic engineering and chemical mutagenesis have been developed to activate these cryptic pathways and improve metabolite productivity. However, lower efficiencies of gene modifications and screen tools delayed the above processes. To address the above issues, this review describes an alternative design-construction evaluation optimization (DCEO) approach. The DCEO tool provides theoretical and practical principles to identify potential pathways, modify endogenous pathways, integrate exogenous pathways, and exploit novel pathways for their diverse metabolites and desirable productivities. This DCEO method also offers different tactics to balance the cellular metabolisms, facilitate the genetic engineering, and exploit the scalable metabolites in filamentous fungi.