The Mycelium as a Network

Enhancement of soil aggregation and physical properties through fungal amendments under varying moisture conditions

Soil structure and aggregation are crucial for soil functionality, particularly under drought conditions. Saprobic soil fungi, known for their resilience in low moisture conditions, are recognized for their influence on soil aggregate dynamics. In this study, we explored the potential of fungal amendments to enhance soil aggregation and hydrological properties across different moisture regimes. We used a selection of 29 fungal isolates, recovered from soils treated under drought conditions and varying in colony density and growth rate, for single-strain inoculation into sterilized soil microcosms under either low or high moisture (≤-0.96 and -0.03 MPa, respectively). After 8 weeks, we assessed soil aggregate formation and stability, along with soil properties such as soil water content, water hydrophobicity, sorptivity, total fungal biomass and water potential. Our findings indicate that fungal inoculation altered soil hydrological properties and improved soil aggregation, with effects varying based on the fungal strains and soil moisture levels. We found a positive correlation between fungal biomass and enhanced soil aggregate formation and stabilization, achieved by connecting soil particles via hyphae and modifying soil aggregate sorptivity. The improvement in soil water potential was observed only when the initial moisture level was not critical for fungal activity. Overall, our results highlight the potential of using fungal inoculation to improve the structure of agricultural soil under drought conditions, thereby introducing new possibilities for soil management in the context of climate change.

Towards establishing a fungal economics spectrum in soil saprobic fungi

Trait-based frameworks are promising tools to understand the functional consequences of community shifts in response to environmental change. The applicability of these tools to soil microbes is limited by a lack of functional trait data and a focus on categorical traits. To address this gap for an important group of soil microorganisms, we identify trade-offs underlying a fungal economics spectrum based on a large trait collection in 28 saprobic fungal isolates, derived from a common grassland soil and grown in culture plates. In this dataset, ecologically relevant trait variation is best captured by a three-dimensional fungal economics space. The primary explanatory axis represents a dense-fast continuum, resembling dominant life-history trade-offs in other taxa. A second significant axis reflects mycelial flexibility, and a third one carbon acquisition traits. All three axes correlate with traits involved in soil carbon cycling. Since stress tolerance and fundamental niche gradients are primarily related to the dense-fast continuum, traits of the 2nd (carbon-use efficiency) and especially the 3rd (decomposition) orthogonal axes are independent of tested environmental stressors. These findings suggest a fungal economics space which can now be tested at broader scales.

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.

From purposeless residues to biocomposites: A hyphae made connection

Biocomposites create attractive alternatives to match packing needs with available agricultural residues. Growing native fungal strains developed a mycelium biocomposite over a mixture of Peach Palm Fruit Peel Flour and Sugar Cane Bagasse Wet Dust. A methodology was proposed to analyze their main characteristics: 1) morphological, 2) chemical, and 3) biodegradability. 1) SEM analysis evidenced the structural change of the dried vs pressed material and mycelium morphology for both species. 2) The ratio lignin:carbohydrate showed that P. ostreatus degrades the cellulose-hemicellulose fraction of the substrate at a higher rate than T. elegans, and 3) the curve BMP indicated that these materials are readily biodegradable with a maximum yield of 362,50 mL biogas/g VS. An innovative tangible valorization strategy based on mass balances is also presented: from just 50 kg of peel flour, up to 1840 units can be manufactured, which could pave the way for a more sustainable future.

Foraging strategies of fungal mycelial networks: responses to quantity and distance of new resources

Fungal mycelial networks are essential for translocating and storing water, nutrients, and carbon in forest ecosystems. In particular, wood decay fungi form mycelial networks that connect various woody debris on the forest floor. Understanding their foraging strategies is crucial for complehending the role of mycelium in carbon and nutrient cycling in forests. Previous studies have shown that mycelial networks initiate migration from the original woody resource (inoculum) to a new woody resource (bait) if the latter is sufficiently large but not if it is small. However, the impact of energetic costs during foraging, such as the distance to the bait, has not been considered. In the present study, we conducted full-factorial experiments with two factors, bait size (4 and 8 cm3) and distance from the inoculum (1 and 15 cm). An inoculum wood block, colonized by the wood decay fungus Phanerochaete velutina, was placed in one corner of a bioassay dish (24 cm × 24 cm) filled with unsterilized soil. Once the mycelium grew onto the soil to a distance >15 cm from the inoculum, a sterilized new bait wood block (of either size) was placed on the soil at one of the two distances to be colonized by the mycelia from the inoculum. After 50 days of incubation, the baits were harvested, and their dried weight was measured to calculate the absolute weight loss during incubation. The inoculum wood blocks were retrieved and placed on a new soil dish to determine whether the mycelium would grow out onto the soil again. If no growth occurred within 8 days of additional incubation, we concluded that the mycelium had migrated from the inoculum to the bait. The results showed that mycelia in inocula coupled with baits positioned 1 cm away migrated to the baits more frequently than those with baits positioned 15 cm away. A structural equation model revealed that bait weight loss (energy gain) and hyphal coverage on the soil (foraging cost) significantly influenced mycelial migration decisions. These findings suggest that fungal mycelia may employ their own foraging strategies based on energetic benefits.

Landscape-scale mapping of soil fungal distribution: proposing a new NGS-based approach

Soil fungi play an indispensable role in the functioning of terrestrial habitats. Most landscape-scale studies of soil fungal diversity try to identify the fungal taxa present at a study site and define the relationships between their abundance and environmental factors. The specific spatial distribution of these fungi over the site, however, is not addressed. Our study's main objective is to propose a novel approach to landscape-scale mapping of soil fungi distribution using next generation sequencing and geographic information system applications. Furthermore, to test the proposed approach and discuss its performance, we aimed to conduct a case study mapping the spatial distribution of soil fungi on the Wielka Żuława island. The case study was performed on the Wielka Żuława island in northern Poland, where soil samples were collected every 100 m in an even grid. The fungal taxa and their relative abundance in each sample were assessed using the Illumina platform. Using the data obtained for the sampled points, maps of soil fungi spatial distribution were generated using three common interpolators: inverted distance weighted (IDW), B-spline, and ordinary Kriging. The proposed approach succeeded in creating maps of fungal distribution on Wielka Żuława. The most abundant groups of soil fungi were Penicillium on the genus level, Aspergillaceae on the family level, and ectomycorrhizal fungi on the trophic group level. Ordinary Kriging proved to be the most accurate at predicting relative abundance values for the groups of fungi significantly spatially autocorrelated at the sampled scale. For the groups of fungi not displaying spatial autocorrelation at the sampled scale, IDW provided the most accurate predictions of their relative abundance. Although less accurate at predicting exact relative abundance values, B-spline performed best in delineating the spatial patterns of soil fungi distribution. The proposed approach to landscape-scale mapping of soil fungi distribution could provide new insights into the ecology of soil fungi and terrestrial ecosystems in general. Producing maps of predicted fungal distribution in landscape-scale soil fungi diversity studies would also facilitate the reusability and replicability of the results. Outside the area of research, mapping the distribution of soil fungi could prove helpful in areas such as agriculture and forestry, nature conservation, and urban planning.

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.

Three-dimensional printing of mycelium hydrogels into living complex materials

Biological living materials, such as animal bones and plant stems, are able to self-heal, regenerate, adapt and make decisions under environmental pressures. Despite recent successful efforts to imbue synthetic materials with some of these remarkable functionalities, many emerging properties of complex adaptive systems found in biology remain unexplored in engineered living materials. Here, we describe a three-dimensional printing approach that harnesses the emerging properties of fungal mycelia to create living complex materials that self-repair, regenerate and adapt to the environment while fulfilling an engineering function. Hydrogels loaded with the fungus Ganoderma lucidum are three-dimensionally printed into lattice architectures to enable mycelial growth in a balanced exploration and exploitation pattern that simultaneously promotes colonization of the gel and bridging of air gaps. To illustrate the potential of such mycelium-based living complex materials, we three-dimensionally print a robotic skin that is mechanically robust, self-cleaning and able to autonomously regenerate after damage.

Ten decadal advances in fungal biology leading towards human well-being

Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of -OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.

Prediction and experimental evidence of the optimisation of the angular branching process in the thallus growth of Podospora anserina

Based upon apical growth and hyphal branching, the two main processes that drive the growth pattern of a fungal network, we propose here a two-dimensions simulation based on a binary-tree modelling allowing us to extract the main characteristics of a generic thallus growth. In particular, we showed that, in a homogeneous environment, the fungal growth can be optimized for exploration and exploitation of its surroundings with a specific angular distribution of apical branching. Two complementary methods of extracting angle values have been used to confront the result of the simulation with experimental data obtained from the thallus growth of the saprophytic filamentous fungus Podospora anserina. Finally, we propose here a validated model that, while being computationally low-cost, is powerful enough to test quickly multiple conditions and constraints. It will allow in future works to deepen the characterization of the growth dynamic of fungal network, in addition to laboratory experiments, that could be sometimes expensive, tedious or of limited scope.

Morphology and Transport in Eukaryotic Cells

Transport of intracellular components relies on a variety of active and passive mechanisms, ranging from the diffusive spreading of small molecules over short distances to motor-driven motion across long distances. The cell-scale behavior of these mechanisms is fundamentally dependent on the morphology of the underlying cellular structures. Diffusion-limited reaction times can be qualitatively altered by the presence of occluding barriers or by confinement in complex architectures, such as those of reticulated organelles. Motor-driven transport is modulated by the architecture of cytoskeletal filaments that serve as transport highways. In this review, we discuss the impact of geometry on intracellular transport processes that fulfill a broad range of functional objectives, including delivery, distribution, and sorting of cellular components. By unraveling the interplay between morphology and transport efficiency, we aim to elucidate key structure-function relationships that govern the architecture of transport systems at the cellular scale. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A review on the potential of filamentous fungi for microbial self-healing of concrete

Concrete is the most used construction material worldwide due to its abundant availability and inherent ease of manufacturing and application. However, the material bears several drawbacks such as the high susceptibility for crack formation, leading to reinforcement corrosion and structural degradation. Extensive research has therefore been performed on the use of microorganisms for biologically mediated self-healing of concrete by means of CaCO₃ precipitation. Recently, filamentous fungi have been recognized as high-potential microorganisms for this application as their hyphae grow in an interwoven three-dimensional network which serves as nucleation site for CaCO₃ precipitation to heal the crack. This potential is corroborated by the current state of the art on fungi-mediated self-healing concrete, which is not yet extensive but valuable to direct further research. In this review, we aim to broaden the perspectives on the use of fungi for concrete self-healing applications by first summarizing the major progress made in the field of microbial self-healing of concrete and then discussing pioneering work that has been done with fungi. Starting from insights and hypotheses on the types and principles of biomineralization that occur during microbial self-healing, novel potentially promising candidate species are proposed based on their abilities to promote CaCO₃ formation or to survive in extreme conditions that are relevant for concrete. Additionally, an overview will be provided on the challenges, knowledge gaps and future perspectives in the field of fungi-mediated self-healing concrete.

Environmental factors shaping bacterial, archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California

The flanking regions of Guaymas Basin, a young marginal rift basin located in the Gulf of California, are covered with thick sediment layers that are hydrothermally altered due to magmatic intrusions. To explore environmental controls on microbial community structure in this complex environment, we analyzed site- and depth-related patterns of microbial community composition (bacteria, archaea, and fungi) in hydrothermally influenced sediments with different thermal conditions, geochemical regimes, and extent of microbial mats. We compared communities in hot hydrothermal sediments (75-100°C at ~40 cm depth) covered by orange-pigmented Beggiatoaceae mats in the Cathedral Hill area, temperate sediments (25-30°C at ~40 cm depth) covered by yellow sulfur precipitates and filamentous sulfur oxidizers at the Aceto Balsamico location, hot sediments (>115°C at ~40 cm depth) with orange-pigmented mats surrounded by yellow and white mats at the Marker 14 location, and background, non-hydrothermal sediments (3.8°C at ~45 cm depth) overlain with ambient seawater. Whereas bacterial and archaeal communities are clearly structured by site-specific in-situ thermal gradients and geochemical conditions, fungal communities are generally structured by sediment depth. Unexpectedly, chytrid sequence biosignatures are ubiquitous in surficial sediments whereas deeper sediments contain diverse yeasts and filamentous fungi. In correlation analyses across different sites and sediment depths, fungal phylotypes correlate to each other to a much greater degree than Bacteria and Archaea do to each other or to fungi, further substantiating that site-specific in-situ thermal gradients and geochemical conditions that control bacteria and archaea do not extend to fungi.

Timing of Resource Addition Affects the Migration Behavior of Wood Decomposer Fungal Mycelia

Studies of fungal behavior are essential for a better understanding of fungal-driven ecological processes. Here, we evaluated the effects of timing of resource (bait) addition on the behavior of fungal mycelia when it remains in the inoculum and when it migrates from it towards a bait, using cord-forming basidiomycetes. Experiments allowed mycelium to grow from an inoculum wood across the surface of a soil microcosm, where it encountered a new wood bait 14 or 98 d after the start of growth. After the 42-d colonization of the bait, inoculum and bait were individually moved to a dish containing fresh soil to determine whether the mycelia were able to grow out. When the inoculum and bait of mycelia baited after 14 d were transferred to new soil, there was 100% regrowth from both inoculum and bait in Pholiota brunnescens and Phanerochaete velutina, indicating that no migration occurred. However, when mycelium was baited after 98 d, 3 and 4 out of 10 replicates of P. brunnescens and P. velutina, respectively, regrew only from bait and not from inoculum, indicating migration. These results suggest that prolonged periods without new resources alter the behavior of mycelium, probably due to the exhaustion of resources.

From lignocellulose to plastics: Knowledge transfer on the degradation approaches by fungi

In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation.

Fungi and viruses as important players in microbial mats

Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.

An Argument for an Ecosystemic AI: Articulating Connections across Prehuman and Posthuman Intelligences

As an art collective Cesar & Lois develops projects that examine sociotechnical systems, attempting to challenge anthropocentric technological pathways while linking to intelligences sourced in biological circuitry. As artists we imagine new configurations for what we understand as (social, economic, technological) networks and intelligences. With this ecosystemic approach we consider the possibility of an artificial intelligence (AI) that supports well-being in a broad sense, accommodating relationships across different layers of living worlds and involving local and global communities of all kinds. This thinking is grounded in research by theorists across disciplines, including communications and media theory, microbiology, anthropology, decolonial studies, social ecology, sociology and environmental psychology. At a time when human beings and their ecosystems face grave threats due to climate change and a global pandemic, we are rethinking the basis for our AIs, and for the resulting decision-making on behalf of societies and ecosystems. Creative projects by Cesar & Lois provide alternative conceptual models for thinking across networks, reframing the artists’ and potentially viewers’ understanding of what motivates and shapes societies. Referencing a series of artworks and the theories that underpin them, this article envisages a sociotechnical framework that takes into account ecosystems and challenges the philosophical orientations that guide society. Degenerative Cultures is an artwork in which the artists overlap microbiological organisms, AI and human systems as a speculative restructuring of networks across human and nonhuman entities. The push for ecosystemic technologies and intelligences is linked to the expansion of community to include planetary constituents, such as nonhuman beings and environments. The artists posit that such ecosystemic networks would be capable of taking into account the planet’s human societies as well as nonhuman species and their environments, broadening the concept of community well-being and shifting the technological architecture to meet the complex needs of the planet and its constituent parts. The experimental series, [ECO]nomic Revolution, layers Physarum polycephalum, or slime mold, over the mapped demographics of human cities. The species polycephalum references multi-brains, and implies a decentralized logic, which for the non-neurological microbiological network translates to the sharing of nutrients and regulated growth across a culture. Assuming a perspective based in the arts, this proposition imagines a shift from the dominant conceptions of AI as an individual intelligence and frames it as part of a network that necessarily includes ecosystems. We envision the creation of sociotechnical systems that could be modeled on networked lifeforms that have optimized themselves across millions of years, like the organism Physarum polycephalum, which occurs globally in moist environments, or like those microbial populations within and outside of human bodies, whose percussive biological processing interacts with and alters many layers of lifeforms. We argue that an environmentally responsive intelligence based on relationships across living systems potentially serves a broad community composed of diverse human populations, nonhuman beings and ecosystems.

Getting around the cell: physical transport in the intracellular world

Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.

A mechanistic explanation of the transition to simple multicellularity in fungi

Development of multicellularity was one of the major transitions in evolution and occurred independently multiple times in algae, plants, animals, and fungi. However recent comparative genome analyses suggest that fungi followed a different route to other eukaryotic lineages. To understand the driving forces behind the transition from unicellular fungi to hyphal forms of growth, we develop a comparative model of osmotrophic resource acquisition. This predicts that whenever the local resource is immobile, hard-to-digest, and nutrient poor, hyphal osmotrophs outcompete motile or autolytic unicellular osmotrophs. This hyphal advantage arises because transporting nutrients via a contiguous cytoplasm enables continued exploitation of remaining resources after local depletion of essential nutrients, and more efficient use of costly exoenzymes. The model provides a mechanistic explanation for the origins of multicellular hyphal organisms, and explains why fungi, rather than unicellular bacteria, evolved to dominate decay of recalcitrant, nutrient poor substrates such as leaf litter or wood.

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.

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.

Comparative genomics reveals the origin of fungal hyphae and multicellularity

Hyphae represent a hallmark structure of multicellular fungi. The evolutionary origins of hyphae and of the underlying genes are, however, hardly known. By systematically analyzing 72 complete genomes, we here show that hyphae evolved early in fungal evolution probably via diverse genetic changes, including co-option and exaptation of ancient eukaryotic (e.g. phagocytosis-related) genes, the origin of new gene families, gene duplications and alterations of gene structure, among others. Contrary to most multicellular lineages, the origin of filamentous fungi did not correlate with expansions of kinases, receptors or adhesive proteins. Co-option was probably the dominant mechanism for recruiting genes for hypha morphogenesis, while gene duplication was apparently less prevalent, except in transcriptional regulators and cell wall - related genes. We identified 414 novel gene families that show correlated evolution with hyphae and that may have contributed to its evolution. Our results suggest that hyphae represent a unique multicellular organization that evolved by limited fungal-specific innovations and gene duplication but pervasive co-option and modification of ancient eukaryotic functions.

Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks

The world's ecosystems are characterized by an unequal distribution of resources [1]. Trade partnerships between organisms of different species-mutualisms-can help individuals cope with such resource inequality [2-4]. Trade allows individuals to exchange commodities they can provide at low cost for resources that are otherwise impossible or more difficult to access [5, 6]. However, as resources become increasingly patchy in time or space, it is unknown how organisms alter their trading strategies [7, 8]. Here, we show how a symbiotic fungus mediates trade with a host root in response to different levels of resource inequality across its network. We developed a quantum-dot-tracking technique to quantify phosphorus-trading strategies of arbuscular mycorrhizal fungi simultaneously exposed to rich and poor resource patches. By following fluorescent nanoparticles of different colors across fungal networks, we determined where phosphorus was hoarded, relocated, and transferred to plant hosts. We found that increasing exposure to inequality stimulated trade. Fungi responded to high resource variation by (1) increasing the total amount of phosphorus distributed to host roots, (2) decreasing allocation to storage, and (3) differentially moving resources within the network from rich to poor patches. Using single-particle tracking and high-resolution video, we show how dynamic resource movement may help the fungus capitalize on value differences across the trade network, physically moving resources to areas of high demand to gain better returns. Such translocation strategies can help symbiotic organisms cope with exposure to resource inequality.

Bidirectional Propagation of Signals and Nutrients in Fungal Networks via Specialized Hyphae

Intercellular distribution of nutrients and coordination of responses to internal and external cues via endogenous signaling molecules are hallmarks of multicellular organisms. Vegetative mycelia of multicellular fungi are syncytial networks of interconnected hyphae resulting from hyphal tip growth, branching, and fusion. Such mycelia can reach considerable dimensions and, thus, different parts can be exposed to quite different environmental conditions. Our knowledge about the mechanisms by which fungal mycelia can adjust nutrient gradients or coordinate their defense response to fungivores is scarce, in part due to limitations in technologies currently available for examining different parts of a mycelium over longer time periods at the microscopic level. Here, we combined a tailor-made microfluidic platform with time-lapse fluorescence microscopy to visualize the dynamic response of the vegetative mycelium of a basidiomycete to two different stimuli. The microfluidic platform allows simultaneous monitoring at both the colony and single-hypha level. We followed the dynamics of the distribution of a locally administered nutrient analog and the defense response to spatially confined predation by a fungivorous nematode. Although both responses of the mycelium were constrained locally, we observed long-distance propagation for both the nutrient analog and defense response in a subset of hyphae. This propagation along hyphae occurred in both acropetal and basipetal directions and, intriguingly, the direction was found to alternate every 3 hr in an individual hypha. These results suggest that multicellular fungi have, as of yet, undescribed mechanisms to coordinate the distribution of nutrients and their behavioral response upon attack by fungivores.

Bacterial-fungal interactions: ecology, mechanisms and challenges

Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.

Harnessing fungi to mitigate CH4 in natural and engineered systems

Methane (CH₄) is a powerful greenhouse gas emitted from natural and anthropogenic sources, and its emission rates vary among sources as a function of environment, microbial respiration, and feedbacks. Biological CH₄ flux from natural and engineered systems is typically represented simply as generation of CH₄ by methanogens minus oxidation by methanotrophs. In many cases, however, CH₄ flux is modulated by transport and solubility mechanisms that occur before oxidation or other chemical transformation. The ability of fungi to directly oxidize CH₄ remains unclear; however, their hydrophobic growths extending above microbial biofilms can improve surface area and sorption of hydrophobic gases. This can improve overall oxidation rates in a biofilm simply by improving phase transfer dynamics and bioavailability to bacterial or archaeal associates. This indirect facilitation is not necessarily intuitive, but there has been a recent emerging interest in harnessing these fungal abilities in engineering bioreactors and filtration systems designed to capture and oxidize CH₄. These dynamics may be playing a similar facilitative role in natural CH₄ oxidation, where fungi may indirectly influence carbon mineralization and methanogen/methanotroph communities, and/or directly oxidize and dissolve gaseous CH₄. This review highlights these unique roles for fungi in determining net CH₄ oxidation rates, and it summarizes the potential to harness fungi to mitigate CH₄ emissions.