Chapter 7 Interactions between saprotrophic fungi

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.

Enhancement of laccase production by Cerrena unicolor through fungal interspecies interaction and optimum conditions determination

The present study aimed to identify a pair of fungal strains that promote laccase production in the co-cultivation of white-rot basidiomycetes and to determine the optimum conditions to enhance enzyme synthesis under co-fermentation of mandarin peels. Co-cultivation of Cerrena unicolor with Trametes versicolor, Lenzites betulina, and Panus lecomtei led to up-regulation of laccase activity. Moreover, interspecific interaction of Cerrena unicolor and Trametes versicolor induced the production of two new laccase isoenzymes. By contrast, interactions of Cerrena unicolor with Trametes coccineus and Trametes hirsuta resulted in a multiple decreased ability of Cerrena unicolor to produce laccase. Co-cultivation of Cerrena unicolor with other fungi 3- to 12-fold down-regulated manganese peroxidase (MnP) activity. The outcomes of these fungal interactions are closely related to the initial concentration and availability of the nutrients, the partners' inoculum ratio, time, and sequence of their inoculation. Co-cultivation of Cerrena unicolor and Trametes versicolor in fermenter resulted in the accumulation of 476 U/mL laccase and 1.12 U/mL MnP.

Decay stages of wood and associated fungal communities characterise diversity-decomposition relationships

The biodiversity–ecosystem function relationship is a central topic in ecology. Fungi are the dominant decomposers of organic plant material in terrestrial ecosystems and display tremendous species diversity. However, little is known about the fungal diversity–decomposition relationship. We evaluated fungal community assemblies and substrate quality in different stages of wood decay to assess the relationships between fungal species richness and weight loss of wood substrate under laboratory conditions. Wood-inhabiting fungal communities in the early and late stages of pine log decomposition were used as a model. Colonisation with certain species prior to inoculation with other species resulted in four-fold differences in fungal species richness and up to tenfold differences in the rate of wood substrate decomposition in both early- and late-decaying fungal communities. Differences in wood substrate quality had a significant impact on species richness and weight loss of wood and the relationships between the two, which were negative or neutral. Late communities showed significantly negative species richness–decay relationships in wood at all decay stages, whereas negative relationships in early communities were significant only in the intermediate decay stage. Our results suggest that changes in fungal communities and wood quality during wood decomposition affect the fungal diversity–decomposition relationship.

Substrate Preference Determines Macrofungal Biogeography in the Greater Mekong Sub-Region

The availability and the quality of substrates are important drivers of macrofungal biogeography, and thus macrofungal species occurrence is potentially dependent on the availability of different substrates. However, few studies have explored the properties of macrofungal substrates and assessed the relationship between macrofungal diversity and substrate diversity at a landscape level. To address this issue, we conducted a landscape-scale survey of basidiocarp substrates in the Greater Mekong Subregion (GMS). A total of 957 macrofungal species distributed across 73 families and 189 genera were collected. Substrates of these macrofungi were categorized into four main groups (namely, litter, soil, root, and rare substrates) and referenced into 14 sub-substrate types (such as branches, leaves, and fruit). The results revealed that 50% of the observed macrofungal species were symbiotrophs living in ectomycorrhizal association with plant hosts, 30% were saprotrophs decomposing plant litter, 15% lived in soil organic matter, and 5% lived in rare substrates. The most abundant root symbiotic fungi were members of Russula, whereas most litter saprotrophic fungi belonged to Marasmius. Macrofungi commonly favored a single substrate. This specificity was not affected by changes in vegetation or climate. Less than 1% of macrofungi (e.g., Marasmius aff. maximus) could live on multiple substrates. Most of these unusual macrofungi were characterized as highly mobile and were generally found in successional areas. In secondary forests, our survey indicated that significant correlations exist between substrate preference and taxonomic diversity, reflected as higher substrate diversity generally accompanied by higher macrofungal diversity. In conclusion, substrate preference is an important factor driving macrofungal composition and distribution in the GMS. Macrofungi that thrive on multiple substrates constitute pioneer groups that have an important role in establishing macrofungal communities in new habitats. These observations have furthered our understanding of how substrate preferences could explain macrofungal biogeography.

Dynamics of Metabolite Induction in Fungal Co-cultures by Metabolomics at Both Volatile and Non-volatile Levels

Fungal co-cultivation has emerged as a promising way for activating cryptic biosynthetic pathways and discovering novel antimicrobial metabolites. For the success of such studies, a key element remains the development of standardized co-cultivation methods compatible with high-throughput analytical procedures. To efficiently highlight induction processes, it is crucial to acquire a holistic view of intermicrobial communication at the molecular level. To tackle this issue, a strategy was developed based on the miniaturization of fungal cultures that allows for a concomitant survey of induction phenomena in volatile and non-volatile metabolomes. Fungi were directly grown in vials, and each sample was profiled by head space solid phase microextraction gas chromatography mass spectrometry (HS-SPME-GC-MS), while the corresponding solid culture medium was analyzed by liquid chromatography high resolution mass spectrometry (LC-HRMS) after solvent extraction. This strategy was implemented for the screening of volatile and non-volatile metabolite inductions in an ecologically relevant fungal co-culture of Eutypa lata (Pers.) Tul. & C. Tul. (Diatrypaceae) and Botryosphaeria obtusa (Schwein.) Shoemaker (Botryosphaeriaceae), two wood-decaying fungi interacting in the context of esca disease of grapevine. For a comprehensive evaluation of the results, a multivariate data analysis combining Analysis of Variance and Partial Least Squares approaches, namely AMOPLS, was used to explore the complex LC-HRMS and GC-MS datasets and highlight dynamically induced compounds. A time-series study was carried out over 9 days, showing characteristic metabolite induction patterns in both volatile and non-volatile dimensions. Relevant links between the dynamics of expression of specific metabolite production were observed. In addition, the antifungal activity of 2-nonanone, a metabolite incrementally produced over time in the volatile fraction, was assessed against Eutypa lata and Botryosphaeria obtusa in an adapted bioassay set for volatile compounds. This compound has shown antifungal activity on both fungi and was found to be co-expressed with a known antifungal compound, O-methylmellein, induced in solid media. This strategy could help elucidate microbial inter- and intra-species cross-talk at various levels. Moreover, it supports the study of concerted defense/communication mechanisms for efficiently identifying original antimicrobials.

Threesomes destabilise certain relationships: multispecies interactions between wood decay fungi in natural resources

Understanding interspecific interactions is key to explaining and modelling community development and associated ecosystem function. Most interactions research has focused on pairwise combinations, overlooking the complexity of multispecies communities. This study investigated three-way interactions between saprotrophic fungi in wood and across soil, and indicated that pairwise combinations are often inaccurate predictors of the outcomes of multispecies competition in wood block interactions. This inconsistency was especially true of intransitive combinations, resulting in increased species coexistence within the resource. Furthermore, the addition of a third competitor frequently destabilised the otherwise consistent outcomes of pairwise combinations in wood blocks, which occasionally resulted in altered resource decomposition rates, depending on the relative decay abilities of the species involved. Conversely, interaction outcomes in soil microcosms were unaffected by the presence of a third combatant. Multispecies interactions promoted species diversity within natural resources, and made community dynamics less consistent than could be predicted from pairwise interaction studies.

Location, location, location: priority effects in wood decay communities may vary between sites

Priority effects are known to have a major influence on fungal community development in decomposing wood, but it has not yet been established whether these effects are consistent between different geographical locations. Here, beech (Fagus sylvatica) wood disks that had been pre-colonized with three wood decay basidiomycetes were placed in seven woodland sites with similar characteristics for 12-24 months, and the successor communities profiled using culture-based techniques coupled with amplicon sequencing. On the majority of sites, assembly history differed as a result of primary versus secondary resource capture only (i.e. different communities developed in uncolonized control disks compared with those that had been pre-colonized), but on certain sites distinct successor communities followed each pre-colonizer species. This study provides preliminary evidence that differences in abiotic factors and species pools between sites can cause spatial variation in how priority effects influence wood decay communities.

Spore sensitivity to sunlight and freezing can restrict dispersal in wood-decay fungi

Assessment of the costs and benefits of dispersal is central to understanding species' life-history strategies as well as explaining and predicting spatial population dynamics in the changing world. While mortality during active movement has received much attention, few have studied the costs of passive movement such as the airborne transport of fungal spores. Here, we examine the potential of extreme environmental conditions to cause dispersal mortality in wood-decay fungi. These fungi play a key role as decomposers and habitat creators in forest ecosystems and the populations of many species have declined due to habitat loss and fragmentation. We measured the effect of simulated solar radiation (including ultraviolet A and B) and freezing at -25°C on the spore germinability of 17 species. Both treatments but especially sunlight markedly reduced spore germinability in most species, and species with thin-walled spores were particularly light sensitive. Extrapolating the species' laboratory responses to natural irradiance conditions, we predict that sunlight is a relevant source of dispersal mortality at least at larger spatial scales. In addition, we found a positive effect of spore size on spore germinability, suggesting a trade-off between dispersal distance and establishment. We conclude that freezing and particularly sunlight can be important sources of dispersal mortality in wood-decay fungi which can make it difficult for some species to colonize isolated habitat patches and habitat edges.

Ecological understanding of root-infecting fungi using trait-based approaches

Classification schemes have been popular to tame the diversity of root-infecting fungi. However, the usefulness of these schemes is limited to descriptive purposes. We propose that a shift to a multidimensional trait-based approach to disentangle the saprotrophic-symbiotic continuum will provide a better framework to understand fungal evolutionary ecology. Trait information reflecting the separation of root-infecting fungi from free-living soil relatives will help to understand the evolutionary process of symbiosis, the role that species interactions play in maintaining their large diversity in soil and in planta, and their contributions at the ecosystem level. Methodological advances in several areas such as microscopy, plant immunology, and metatranscriptomics represent emerging opportunities to populate trait databases.

Nitrogen and carbon reallocation in fungal mycelia during decomposition of boreal forest litter

Boreal forests are characterized by spatially heterogeneous soils with low N availability. The decomposition of coniferous litter in these systems is primarily performed by basidiomycete fungi, which often form large mycelia with a well-developed capacity to reallocate resources spatially- an advantageous trait in heterogeneous environments. In axenic microcosm systems we tested whether fungi increase their biomass production by reallocating N between Pinus sylvestris (Scots pine) needles at different stages of decomposition. We estimated fungal biomass production by analysing the accumulation of the fungal cell wall compound chitin. Monospecific systems were compared with systems with interspecific interactions. We found that the fungi reallocated assimilated N and mycelial growth away from well-degraded litter towards fresh litter components. This redistribution was accompanied by reduced decomposition of older litter. Interconnection of substrates increased over-all fungal C use efficiency (i.e. the allocation of assimilated C to biomass rather than respiration), presumably by enabling fungal translocation of growth-limiting N to litter with higher C quality. Fungal connection between different substrates also restricted N-mineralization and production of dissolved organic N, suggesting that litter saprotrophs in boreal forest ecosystems primarily act to redistribute rather than release N. This spatial integration of different resource qualities was hindered by interspecific interactions, in which litters of contrasting quality were colonised by two different basidiomycete species. The experiments provide a detailed picture of how resource reallocation in two decomposer fungi leads to a more efficient utilisation of spatially separated resources under N-limitation. From an ecosystem point of view, such economic fungal behaviour could potentially contribute to organic matter accumulation in the litter layers of boreal forests.