Fungal Communities in the Decay of Wood

Long-term Dynamics of Fungal Communities Inhabiting Decaying Stumps of Quercus robur

We studied the diversity, composition, and long-term dynamics of wood-inhabiting fungi in Quercus robur stumps left after commercial tree harvesting in Lithuania. Sampling of wood was carried out at three sites and from stumps, which were 10-, 20-, 30-, 40-, and 50-year-old. DNA was isolated from wood samples and fungal communities analyzed using high-throughput sequencing. Results showed that stump age had a limited effect on fungal diversity. The development of fungal communities in oak stums was found to be a slow process as fungal communities remained similar for decades, while larger changes were only detected in older stumps. The most common fungi were Eupezizella sp. (18.4%), Hyphodontia pallidula (12.9%), Mycena galericulata (8.3%), and Lenzites betulinus (7.1%). Fistulina hepatica, which is a red-listed wood-decay oak fungus, was also detected at a low relative abundance in stump wood. In the shortage of suitable substrate, oak stumps may provide habitats for long-term survival of different fungal species, including red-listed and oak-related fungi.

MycoPins: a metabarcoding-based method to monitor fungal colonization of fine woody debris

The MycoPins method described here is a rapid and affordable protocol to monitor early colonization events in communities of wood-inhabiting fungi in fine woody debris. It includes easy to implement field sampling techniques and sample processing, followed by data processing, and analysis of the development of early dead wood fungal communities. The method is based on fieldwork from a time series experiment on standard sterilized colonization targets followed by the metabarcoding analysis and automated molecular identification of species. This new monitoring method through its simplicity, moderate costs, and scalability paves a way for a broader and scalable project pipeline. MycoPins establishes a standard routine for research stations or regularly visited field sites for monitoring of fungal colonization of woody substrates. The routine uses widely available consumables and therefore presents a unifying method for monitoring of fungi of this type.

Legacies of invertebrate exclusion and tree secondary metabolites control fungal communities in dead wood

During decomposition of organic matter, microbial communities may follow different successional trajectories depending on the initial environment and colonizers. The timing and order of the species arrival (assembly history) can lead to divergent communities through priority effects. We explored how assembly history and resource quality affected fungal communities and decay rate of decomposing wood, 1.5 and 4.5 years after tree felling. Additionally, we investigated the effect of invertebrate exclusion during the first two summers. We measured initial resource quality of bark and wood of aspen (Populus tremula) logs and surveyed the fungal communities by DNA metabarcoding at different times during succession. We found that gradients in fungal community composition were related to resource quality and discuss how this may reflect different fungal life history strategies. As with previous studies, the initial amount of bark tannins was negatively correlated with wood decomposition rate over 4.5 years. The initial fungal community explained variation in community composition after 1.5, but not 4.5 years, of succession. Although the assembly history of initial colonizers may cause alternate trajectories in successional communities, our results indicate that the communities may converge with the arrival of secondary colonizers. We also identified a strong legacy of invertebrate exclusion on fungal communities, even after 4.5 years of succession, thereby adding crucial knowledge on the importance of invertebrates in affecting fungal community development. By measuring and manipulating aspects of assembly history and resource quality that have rarely been studied, we expand our understanding of the complexity of fungal community dynamics.

Effect of ligninolytic axenic and coculture white-rot fungi on rice straw chemical composition and in vitro fermentation characteristics

The study sought to investigate the potentials of axenic cultures of Pleurotus ostreatus, Phanerochaete chrysosporium and their coculture (P. chrysosporium and P. ostreatus) to break down lignin and to enhance the rumen fermentability of rice straw. Rice straw was fermented by two lignin-degrading fungi, namely, P. ostreatus, P. chrysosporium and its coculture (P. ostreatus and P. chrysosporium) with uninoculated straw as control under solid-state fermentation employing a completely randomized research design. The coculture exhibited a mutual intermingling plus inhibition interaction. The fungi treatment increased the crude protein from (5.1%) in the control to (6.5%, 6.6%, and 6.7%) in the P. ostreatus, P. chrysosporium and coculture respectively. The coculture treated straw had a lower lignin content (5.3%) compared to the P. chrysosporium (6.2%) with the P. ostreatus recording the least (3.3%) lignin fraction. Treatment of rice straw with coculture improved the in vitro dry matter digestibility (68.1%), total volatile fatty acids (35.3 mM), and total gas (57.4 ml/200 mg) compared to P. chrysosporium (45.1%, 32.2 mM, 44.4 ml/200 mg) but was second to P. ostreatus (75.3%, 38.3 mM, 65.6 ml/200 mg). Instead of an anticipated synergistic effect from the coculture, a competitive antagonistic effect was rather observed at the end of the study, a condition that can be attributed to the coculture behavior.

A non-linear effect of the spatial structure of the soil ectomycorrhizal spore bank on the performance of pine seedlings

The spatial structure of the environment is known to affect ecological processes. Unlike the spatial structure of negative interactions, such as competition and predation, the role of spatial structure in positive interaction has received less attention. We tested how the spatial structure of spores of ectomycorrhizal fungi (EMF) in the soil affects the growth of Aleppo pine (Pinus halepensis) seedlings. Spores were spatially distributed at four different levels of patchiness (1 patch, 4 patches, 8 patches and complete mixing) in 4 L pots (all pots received the same total amount of spores). Based on previous findings, we hypothesized that plant performance would gradually increase from the single patch treatment to the complete mixing. However, we found a non-linear response to patchiness. Specifically, plants were largest in the single patch and complete mixing while those in the 4 and 8 patch treatments were the smallest. This non-monotonic response, which might be the result of spatially determined colonization timing or community composition, suggests that the spatial structure of EMF spores has a complex effect on seedling growth.

The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production

Lignocellulose is a promising feedstock for biofuel production as a renewable, carbohydrate-rich and globally abundant source of biomass. However, challenges faced include environmental and/or financial costs associated with typical lignocellulose pretreatments needed to overcome the natural recalcitrance of the material before conversion to biofuel. Anaerobic fungi are a group of underexplored microorganisms belonging to the early diverging phylum Neocallimastigomycota and are native to the intricately evolved digestive system of mammalian herbivores. Anaerobic fungi have promising potential for application in biofuel production processes due to the combination of their highly effective ability to hydrolyse lignocellulose and capability to convert this substrate to H2 and ethanol. Furthermore, they can produce volatile fatty acid precursors for subsequent biological conversion to H2 or CH4 by other microorganisms. The complex biological characteristics of their natural habitat are described, and these features are contextualised towards the development of suitable industrial systems for in vitro growth. Moreover, progress towards achieving that goal is reviewed in terms of process and genetic engineering. In addition, emerging opportunities are presented for the use of anaerobic fungi for lignocellulose pretreatment; dark fermentation; bioethanol production; and the potential for integration with methanogenesis, microbial electrolysis cells and photofermentation.

Biological active matter aggregates: Inspiration for smart colloidal materials

Aggregations of social organisms exhibit a remarkable range of properties and functionalities. Multiple examples, such as fire ants or slime mold, show how a population of individuals is able to overcome an existential threat by gathering into a solid-like aggregate with emergent functionality. Surprisingly, these aggregates are driven by simple rules, and their mechanisms show great parallelism among species. At the same time, great effort has been made by the scientific community to develop active colloidal materials, such as microbubbles or Janus particles, which exhibit similar behaviors. However, a direct connection between these two realms is still not evident, and it would greatly benefit future studies. In this review, we first discuss the current understanding of living aggregates, point out the mechanisms in their formation and explore the vast range of emergent properties. Second, we review the current knowledge in aggregated colloidal systems, the methods used to achieve the aggregations and their potential functionalities. Based on this knowledge, we finally identify a set of over-arching principles commonly found in biological aggregations, and further suggest potential future directions for the creation of bio-inspired colloid aggregations.

Fungal community structure of fallen pine and oak wood at different stages of decomposition in the Qinling Mountains, China

Historically, intense forest hazards have resulted in an increase in the quantity of fallen wood in the Qinling Mountains. Fallen wood has a decisive influence on the nutrient cycling, carbon budget and ecosystem biodiversity of forests, and fungi are essential for the decomposition of fallen wood. Moreover, decaying dead wood alters fungal communities. The development of high-throughput sequencing methods has facilitated the ongoing investigation of relevant molecular forest ecosystems with a focus on fungal communities. In this study, fallen wood and its associated fungal communities were compared at different stages of decomposition to evaluate relative species abundance and species diversity. The physical and chemical factors that alter fungal communities were also compared by performing correspondence analysis according to host tree species across all stages of decomposition. Tree species were the major source of differences in fungal community diversity at all decomposition stages, and fungal communities achieved the highest levels of diversity at the intermediate and late decomposition stages. Interactions between various physical and chemical factors and fungal communities shared the same regulatory mechanisms, and there was no tree species-specific influence. Improving our knowledge of wood-inhabiting fungal communities is crucial for forest ecosystem conservation.

Trichoderma viride Laccase Plays a Crucial Role in Defense Mechanism against Antagonistic Organisms

Fungal laccases are involved in a variety of physiological functions such as delignification, morphogenesis, and parasitism. In addition to these functions, we suggest that fungal laccases are involved in defense mechanisms. When the laccase secreting Trichoderma viride was grown in the presence of a range of microorganisms including bacteria and fungi, laccase secretion was enhanced in response to antagonistic organisms alone. In addition, growth of antagonistic microbes was restricted by the secreting fungi. Besides, our study for the first time shows the inability of the secreting fungi (T. viride) to compete with antagonistic organism when laccase activity is inhibited, further emphasizing its involvement in rendering a survival advantage to the secreting organism. When laccase inhibitor was added to the media, the zone of inhibition exerted by the antagonist organism was more pronounced and consequently growth of T. viride was significantly restricted. Based on these observations we accentuate that, laccase plays an important role in defense mechanism and provides endurance to the organism when encountered with an antagonistic organism in its surrounding.

Dung-inhabiting fungi: a potential reservoir of novel secondary metabolites for the control of plant pathogens

Coprophilous fungi are a large group of saprotrophic fungi mostly found in herbivore dung. The number of these fungi undergoing investigation is continually increasing, and new species and genera continue to be described. Dung-inhabiting fungi play an important ecological role in decomposing and recycling nutrients from animal dung. They produce a large array of bioactive secondary metabolites and have a potent enzymatic arsenal able to utilise even complex molecules. Bioactive secondary metabolites are actively involved in interaction with and defence against other organisms whose growth can be inhibited, resulting in an enhanced ecological fitness of producer strains. Currently, these antibiotics and bioactive secondary metabolites are of interest in medicine in particular, while very little information is available concerning their potential use in agriculture. This review introduces the ecology of dung-inhabiting fungi, with particular emphasis on the production of antibiotic compounds as a means to compete with other microorganisms. Owing to the fast pace of technological progress, new approaches to predicting the biosynthesis of bioactive metabolites are proposed. Coprophilous fungi should be considered as elite candidate organisms for the discovery of novel antifungal compounds, above all in view of their exploitation for crop protection.

Involutin is an Fe3+ reductant secreted by the ectomycorrhizal fungus Paxillus involutus during Fenton-based decomposition of organic matter

Ectomycorrhizal fungi play a key role in mobilizing nutrients embedded in recalcitrant organic matter complexes, thereby increasing nutrient accessibility to the host plant. Recent studies have shown that during the assimilation of nutrients, the ectomycorrhizal fungus Paxillus involutus decomposes organic matter using an oxidative mechanism involving Fenton chemistry (Fe²⁺ + H₂O₂ + H⁺ → Fe³⁺ + ˙OH + H₂O), similar to that of brown rot wood-decaying fungi. In such fungi, secreted metabolites are one of the components that drive one-electron reductions of Fe³⁺ and O₂, generating Fenton chemistry reagents. Here we investigated whether such a mechanism is also implemented by P. involutus during organic matter decomposition. Activity-guided purification was performed to isolate the Fe³⁺-reducing principle secreted by P. involutus during growth on a maize compost extract. The Fe³⁺-reducing activity correlated with the presence of one compound. Mass spectrometry and nuclear magnetic resonance (NMR) identified this compound as the diarylcyclopentenone involutin. A major part of the involutin produced by P. involutus during organic matter decomposition was secreted into the medium, and the metabolite was not detected when the fungus was grown on a mineral nutrient medium. We also demonstrated that in the presence of H₂O₂, involutin has the capacity to drive an in vitro Fenton reaction via Fe³⁺ reduction. Our results show that the mechanism for the reduction of Fe³⁺ and the generation of hydroxyl radicals via Fenton chemistry by ectomycorrhizal fungi during organic matter decomposition is similar to that employed by the evolutionarily related brown rot saprotrophs during wood decay.

Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.

Potential of biofilm-based biofuel production

Biofilm technology has been extensively applied to wastewater treatment, but its potential application in biofuel production has not been explored. Current technologies of converting lignocellulose materials to biofuel are hampered by costly processing steps in pretreatment, saccharification, and product recovery. Biofilms may have a potential to improve efficiency of these processes. Advantages of biofilms include concentration of cell-associated hydrolytic enzymes at the biofilm-substrate interface to increase reaction rates, a layered microbial structure in which multiple species may sequentially convert complex substrates and coferment hexose and pentose as hydrolysates diffuse outward, and the possibility of fungal-bacterial symbioses that allow simultaneous delignification and saccharification. More importantly, the confined microenvironment within a biofilm selectively rewards cells with better phenotypes conferred from intercellular gene or signal exchange, a process which is absent in suspended cultures. The immobilized property of biofilm, especially when affixed to a membrane, simplifies the separation of biofuel from its producer and promotes retention of biomass for continued reaction in the fermenter. Highly consolidated bioprocessing, including delignification, saccharification, fermentation, and separation in a single reactor, may be possible through the application of biofilm technology. To date, solid-state fermentation is the only biofuel process to which the advantages of biofilms have been applied, even though it has received limited attention and improvements. The transfer of biofilm technology from environmental engineering has the potential to spur great innovations in the optimization of biofuel production.

Effects of propagule density and survival strategies on establishment and growth: further investigations in the phylloplane fungal model system

This work builds on an earlier culture study where we determined that species diversity of competing saprotrophic phyllpolane fungi had only a negligible effect on the establishment and coexistence of a target fungus, Pestalotia vaccinii. Here, we explore preliminary evidence suggesting that spore density is a more important contributing factor to colonization and coexistence. We examine the influence of propagule density in vitro on establishment and growth of select members of the phylloplane of Vaccinium macrocarpon (American cranberry). To evaluate the response of the weak pathogen P. vaccinii to changes in competitors spore density, we chose saprotrophs from the previous investigation that had the greatest inhibitory effect on the establishment of P. vaccinii (Curvularia lunata), an intermediate inhibitory effect (Alternaria alternata) and the least inhibitory effect (Penicillium sp.). A constant target spore concentration of 50 viable spores of P. vaccinii was pit against densities of the three individual competitors ranging between 12 and 200 spores. As viable propagule density increased, establishment and coexistence of P. vaccinii significantly decreased, with C. lunata and A. alternata decreasing the growth of P. vaccinii more than Penicillium sp. Concomitantly, both C. lunata and Penicillium sp. were not significantly affected by overall spore density but were significantly affected by the presence of P. vaccinii. A. alternata, on the other hand, was not significantly influenced by the presence of P. vaccinii but was significantly affected by overall spore density. An in vitro investigation into the effect of interspecific competition on mycelial growth suggests how different survival strategies and community assembly rules might influence both growth and development. Growth of P. vaccinii was significantly less when interacting with C. lunata than when interacting with either A. alternata or Penicillium sp. Conversely, P. vaccinii had the greatest effect on the growth of C. lunata, less of an effect on the growth of A. alternata, and the least effect on Penicillium sp.

Identification and analysis of differentially expressed cDNAs during nonself-competitive interaction between Phlebiopsis gigantea and Heterobasidion parviporum

The molecular factors regulating interspecific interaction between the saprotrophic biocontrol fungus Phlebiopsis gigantea and the conifer pathogen Heterobasidion parviporum were investigated. We constructed cDNA libraries and used expressed sequence tag analysis for the identification and characterization of genes expressed during the self and nonself-hyphal interaction. cDNA clones from either the pathogen or biocontrol agent were arrayed on nylon membrane filters and differentially screened with cDNA probes made from mycelia forming the barrage zone during nonself-interactions, mycelia growing outside the barrage zones or monocultures. BlastX analysis of the differentially expressed clones led to the identification of genes with diverse functions, including those with potential as virulence factors, such as hydrophobins. Because of the high sequence conservation (r2 = 0.81) between P. gigantea and H. parviporum, a selected number of genes from either fungus were used to monitor the expression profile under varying interaction conditions by virtual northern blot. The results are discussed with respect to the potential role of the induced genes during the nonself-competitive interaction for space and nutrients between P. gigantea and H. parviporum.

Microfungus communities of white spruce and trembling aspen logs at different stages of decay in disturbed and undisturbed sites in the boreal mixedwood region of Alberta

Fallen logs of trembling aspen (Populus tremuloides Michx.) and white spruce (Picea glauca (Moench) Voss) at various stages of decomposition were sampled from undisturbed and 1-, 14-, and 28-year-old post-fire and post-harvest sites in northern Alberta and studied for differences in the associated microfungus communities. Wood samples were plated directly onto each of six different media and, from these, fungal species were identified and enumerated over a 24-month period. Approximately 10 000 isolates were obtained, representing 292 species of filamentous microfungi, including 41 ascomycetes, 29 zygomycetes, and 222 mitosporic fungi. The most commonly isolated species were Trichoderma viride (Gray) Pers., Rhinocladiella atrovirens Nannf., Penicillium pinophilum Hedgcock, and Mortierella ramanniana (Moller) Linnem. Cluster analysis and ordination of microfungus communities in logs showed that the tree species of the log had the greatest influence on the species composition of communities. Fungus community composition was also correlated with the stage of decomposition. Species richness was highest in logs from undisturbed sites and lowest in logs from the most recently disturbed sites. Species diversity (Shannon-Weaver) was only slightly higher at undisturbed sites than at disturbed sites. The most significant environmental factor was log moisture, which increased proportionately with stage of decomposition and was significantly correlated with climatic factors.Key words: ecology, fungi, ordination, succession, species richness, diversity.

Interspecific combative interactions between wood-decaying basidiomycetes

Competition is the most common type of interaction occurring between wood-decaying higher fungi. Since competition for nutrients in organic resources is effectively brought about by competition for space, the common division into interference and exploitation competition is not very appropriate. Fungal competition can be divided into primary resource capture (obtaining uncolonized resources) and secondary resource capture (combat to obtain resources already colonized by other fungi). Combative mechanisms include antagonism at a distance, hyphal interference, mycoparasitism and gross mycelial contact. Interactions can result in deadlock or replacement, and a hierarchy of combative ability can be discerned amongst fungi that inhabit particular resources, but within this hierarchy there exists intransitivity, modification of outcome by other species and abiotic variables. Interactions can dramatically alter mycelial function, and have potential as biological control agents of fungal pathogens of trees and in service timber.

Tansley Review No. 19 Environmental and endogenous controls of developmental pathways: variation and its significance in the forest pathogen, Heterobasidion annosum

Cultural studies of the forest root pathogen Heterobasidion annosum (Fr.) Bref. have shown that the mycelium of the fungus possesses a high degree of developmental versatility, being able to grow in a variety of distinctive functional modes. Consequently the fungus can alternate between conidiogenous and meiotic reproductive pathways, rapid, sparsely branched and slow, densely branched mycelial extension, nutritive and non-nutritive modes, and'juvenile'and 'senescent'phases. This ability is probably of considerable importance in natural infection cycles and provides an interesting model for examining interrelationships between developmental regulation and host-pathogen interactions generally. It also raises important questions about the interface between environmental and endogenous controls of developmental pathways. CONTENTS Summary 245 I. Introduction 245 II. Spore germination and mycelial extension 246 III. Production of non-nutritive mycelium 249 IV. Sporophore production, senescence, somatic incompatibility and extracellular enzyme production 251 V. Discussion 254 Acknowledgements 255 References 255.