Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories

Cairns, Timothy C.; Zheng, Xiaomei; Zheng, Ping; Sun, Jibin; Meyer, Vera

doi:10.1186/s13068-019-1400-4

Cited by 94 publications

(109 citation statements)

References 144 publications

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“…Depending on the predominant morphology in a submerged fungal culture, the substances produced by the organism can differ significantly. As fungal growth and protein secretion are coupled processes, it is for example known that the highest protein secretion normally occurs during rapid hyphal growth, which takes place in disperse mycelia and the outer layers of fungal pellets where nutrient supply is not limited (Cairns, Zheng, Zheng, Sun, & Meyer, ). On the other hand, the production of secondary metabolites peaks when the producing organism shows an extremely low or zero growth (Brakhage, ).…”

Section: Introductionmentioning

confidence: 99%

From three‐dimensional morphology to effective diffusivity in filamentous fungal pellets

Schmideder

Barthel

Müller

et al. 2019

Biotech & Bioengineering

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Filamentous fungi are exploited as cell factories in biotechnology for the production of proteins, organic acids, and natural products. Hereby, fungal macromorphologies adopted during submerged cultivations in bioreactors strongly impact the productivity. In particular, fungal pellets are known to limit the diffusivity of oxygen, substrates, and products. To investigate the spatial distribution of substances inside fungal pellets, the diffusive mass transport must be locally resolved. In this study, we present a new approach to obtain the effective diffusivity in a fungal pellet based on its three-dimensional morphology. Freeze-dried Aspergillus niger pellets were studied by X-ray microcomputed tomography, and the results were reconstructed to obtain three-dimensional images. After processing these images, representative cubes of the pellets were subjected to diffusion computations. The effective diffusion factor and the tortuosity of each cube were calculated using the software GeoDict. Afterwards, the effective diffusion factor was correlated with the amount of hyphal material inside the cubes (hyphal fraction). The obtained correlation between the effective diffusion factor and hyphal fraction shows a large deviation from the correlations reported in the literature so far, giving new and more accurate insights. This knowledge can be used for morphological optimization of filamentous pellets to increase the yield of biotechnological processes.

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Section: Introductionmentioning

confidence: 99%

From three‐dimensional morphology to effective diffusivity in filamentous fungal pellets

Schmideder

Barthel

Müller

et al. 2019

Biotech & Bioengineering

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“…Beginning in 1999, reuse of standard measures, materials, and methods began to prove useful for synthetic biology; but, the resulting impacts of standardization with and of living matter have not yet matched other technology-enabled sectors [72][73][74][75][76][77][78][79] . Although humans have long-partnered with filamentous fungi there are yet to emerge any standards supporting the use and reuse of wood-degrading fungi in mycologically-based bioproduction [80][81][82][83] .…”

Section: Introductionmentioning

confidence: 99%

Enabling community-based metrology for wood-degrading fungi

Perez

Luccioni

Gaut

et al. 2019

Preprint

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Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on solid-state fermentation and wood-degrading fungi can enable more direct means of manufacture. However, such practices are often ad hoc and not readily reproducible. We sought to develop standard reference strains, substrates, measurements, and methods sufficient to begin to enable reliable reuse of mycological materials and products. Specifically, we show that a widely-available and globallyregularized consumer product (Pringles™) can support the growth of wood-degrading fungi, and that growth on Pringles™ can be correlated with growth on a fully-traceable and compositionally characterized substrate (NIST Reference Material 8492 Eastern Cottonwood Biomass). So established, five laboratories were able to compare measurements of wood-fungus performance via a simple radial extension growth rate assay. Reliable reuse of materials, measures, and methods is necessary to enable distributed bioproduction processes that can be adopted at all scales, from local to industrial. cells, known as hyphae, chitinous-composite cell walls, vast repertoire of degradative enzymes and secondary metabolites, and interconnected networks of cells, known as mycelium, that form through a combination of apical growth, hyphal branching, and regulated self-fusion 22-31 . Growing mycelium penetrate and degrade the substrate upon which the organism lives and uptake and shuttle nutrients throughout complex hyphal networks 23 .Mushrooms, the reproductive structures of wood-degrading filamentous fungi, are widely-used as foodstuffs and as a source of medicines and are consequentially revered by many cultures [30][31][32] .Additionally, mycological materials made from the tissues of mushrooms are used in meat replacements, filtration and remediation of contaminated water, packaging materials, furniture, textiles for the fashion industry, architectural design, art, materials for super capacitors and batteries, anti-viral therapeutics for bees, and nanoparticle synthesis 35,36,45,46,[37][38][39][40][41][42][43][44] . Most commercial mycological materials are fabricated by placing an organism and substrate mixture into a preformed mold and allowing the mycelium to process the substrate via solid-state fermentation. The process itself is typically halted via thermal inactivation followed by downstream processing.Recent studies have elucidated the impacts that choice of organism, genetic modification, substrate composition, and environmental conditions have on the macroscopic properties of mycelium-based materials [47][48][49][50][51][52][53][54] . Most organisms now used to produce mycelium materials are of the class Agaricomycete in the division Basidiomycota. The Agaricomycete are less-extensively studied and developed as some of their Ascomycota counterparts, such as ...

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“…Beginning in 1999, reuse of standard measures, materials, and methods began to prove useful for synthetic biology; but, the resulting impacts of standardization with and of living matter have not yet matched other technology-enabled sectors [73][74][75][76][77][78][79][80]. Although humans have long-partnered with filamentous fungi there are yet to emerge any standards supporting the coordinated reuse of wood-degrading fungi in mycologically-based bioproduction [81][82][83][84].…”

mentioning

confidence: 99%

Enabling community-based metrology for wood-degrading fungi

Perez

Luccioni

Kamakaka

et al. 2020

Fungal Biol Biotechnol

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Background: Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on solid-state fermentation and wood-degrading fungi could enable more direct means of manufacture. However, basic methods for cultivating wood-degrading fungi are often ad hoc and not readily reproducible. Here, we developed standard reference strains, substrates, measurements, and methods sufficient to begin to enable reliable reuse of mycological materials and products in simple laboratory settings. Results:We show that a widely-available and globally-regularized consumer product (Pringles ™ ) can support the growth of wood-degrading fungi, and that growth on Pringles ™ -broth can be correlated with growth on media made from a fully-traceable and compositionally characterized substrate (National Institute of Standards and Technology Reference Material 8492 Eastern Cottonwood Whole Biomass Feedstock). We also establish a Relative Extension Unit (REU) framework that is designed to reduce variation in quantification of radial growth measurements. So enabled, we demonstrate that five laboratories were able to compare measurements of wood-fungus performance via a simple radial extension growth rate assay, and that our REU-based approach reduced variation in reported measurements by up to ~ 75%. Conclusions:Reliable reuse of materials, measures, and methods is necessary to enable distributed bioproduction processes that can be adopted at all scales, from local to industrial. Our community-based measurement methods incentivize practitioners to coordinate the reuse of standard materials, methods, strains, and to share information supporting work with wood-degrading fungi.

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Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories

Cited by 94 publications

References 144 publications

From three‐dimensional morphology to effective diffusivity in filamentous fungal pellets

From three‐dimensional morphology to effective diffusivity in filamentous fungal pellets

Enabling community-based metrology for wood-degrading fungi

Enabling community-based metrology for wood-degrading fungi

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