Ecological and functional effects of fungal endophytes on wood decomposition

Two novel endophytic Tolypocladium species identified from native pines in south Florida

This study investigated the incidence and diversity of Tolypocladium within trunks of south Florida slash pines (Pinus densa). Thirty-five isolates were recovered from trunk tissue including living phloem, cambium, and sapwood. Two novel species of Tolypocladium (T. subtropicale and T. trecense) are described here based on morphological and molecular analysis of concatenated LSU, ITS, tef-1, tub, and RPB1 sequences. Our findings expand our understanding of the distribution, diversity, and ecology of this genus and confirm that it is widely spread as an endophyte across ecosystems and hosts. Strains collected in this survey will be used in future bioassays to determine their potential ecological roles as mycoparasites or entomopathogens. Citation: Soares JM, Karlsen-Ayala E, Salvador-Montoya CA, Gazis R (2023). Two novel endophytic Tolypocladium species identified from native pines in south Florida. Fungal Systematics and Evolution 11: 51-61. doi: 10.3114/fuse.2023.11.04.

Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats

Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine, and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9, and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that taxa either dispersed to both terrestrial and aquatic habitats, or that microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.

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.

Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms

Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps  of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata

Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.

Belowground community turnover accelerates the decomposition of standing dead wood

Standing dead trees (snags) decompose more slowly than downed dead wood and provide critical habitat for many species. The rate at which snags fall therefore influences forest carbon dynamics and biodiversity. Fall rates correlate strongly with mean annual temperature, presumably because warmer climates facilitate faster wood decomposition and hence degradation of the structural stability of standing wood. These faster decomposition rates coincide with turnover from fungal-dominated wood decomposer communities in cooler forests to co-domination by fungi and termites in warmer regions. A key question for projecting forest dynamics is therefore whether temperature effects on wood decomposition arise primarily because warmer conditions facilitate faster decomposer metabolism, or are also influenced indirectly by belowground community turnover (e.g. termites exert additional influence beyond fungal-plus-bacterial mediated decomposition). To test between these possibilities, we simulate standing dead trees with untreated, wooden posts and follow them in the field across five years at 12 sites, before measuring buried, soil-air interface and aerial post sections to quantify wood decomposition and organism activities. High termite activities at the warmer sites are associated with rates of post fall that are 3-times higher than at the cooler sites. Termites primarily consume buried wood, with decomposition rates greatest where termite activities are highest. However, where higher microbial and termite activities co-occur, they appear to first compensate for one another and then slow decomposition rates at their highest activities, suggestive of interference competition. If the range of microbial- and termite co-domination of wood decomposer communities expands under climate warming, our data suggest that expansion will accelerate snag fall with consequent effects on forest carbon cycling and biodiversity in forests previously dominated by microbial decomposers.

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.

Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics during Quercus petraea decomposition

In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years from Quercus petraea wood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.

Insufficient sampling constrains our characterization of plant microbiomes

Plants host diverse microbial communities, but there is little consensus on how we sample these communities, and this has unknown consequences. Using root and leaf tissue from showy milkweed (Asclepias speciosa), we compared two common sampling strategies: (1) homogenizing after subsampling (30 mg), and (2) homogenizing bulk tissue before subsampling (30 mg). We targeted bacteria, arbuscular mycorrhizal (AM) fungi and non-AM fungi in roots, and foliar fungal endophytes (FFE) in leaves. We further extracted DNA from all of the leaf tissue collected to determine the extent of undersampling of FFE, and sampled FFE twice across the season using strategy one to assess temporal dynamics. All microbial groups except AM fungi differed in composition between the two sampling strategies. Community overlap increased when rare taxa were removed, but FFE and bacterial communities still differed between strategies, with largely non-overlapping communities within individual plants. Increasing the extraction mass 10 × increased FFE richness ~ 10 ×, confirming the severe undersampling indicated in the sampling comparisons. Still, seasonal patterns in FFEs were apparent, suggesting that strong drivers are identified despite severe undersampling. Our findings highlight that current sampling practices poorly characterize many microbial groups, and increased sampling intensity is necessary for increase reproducibility and to identify subtler patterns in microbial distributions.

Effects of bird aggregation on the soil properties and microbial community diversity of urban forest fragments

Forest fragments in urban parks provide important habitat for birds. However, the guano deposited by large aggregations of birds in such fragments can dramatically change soil properties, which in turn, can alter soil microbial community composition, potentially affecting the forests' composition and survival. To investigate the effects of bird aggregations on the soil of fragmented urban forests, we compared the soil properties and microbial communities of two forested islands, one in Liuhuahu park and the other in Wanzuitou park, Guangzhou, where large numbers of birds aggregate yearly to nest. Comparison to sites without bird aggregations suggests that decades of guano deposition appears to have caused soil acidification and an increase in soil nutrients. The relative abundance of the soil bacterial phylum Actinobacteria and the soil fungal phylum Ascomycota were significantly lower in soil under bird aggregations. The aerobic nitrite oxidation, nitrate reduction and cellulolysis bacterial guilds were significantly less abundant under bird aggregations in Liuhuahu park. The wood saprotroph fungi guild was significantly less abundant under the bird aggregation in Liuhuahua park and the pathogenic fungi guild significantly more abundant in Wanzuitou park. Soil properties, including TN, NO₃^--N, TOC and pH, explained the variation in Ascomycota and Basidiomycota abundance, and the alpha-diversity of the fungal community. Microbial community variation could potentially slow the rate of decomposition and disease resistance of plant in these forests. We suggest that sufficient contiguous forest should be maintained in urban areas to reduce the density of bird aggregations in isolated forest fragments.

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

Using Wood Rot Phenotypes to Illuminate the "Gray" Among Decomposer Fungi

Wood-decomposing fungi use distinct strategies to deconstruct wood that can significantly vary carbon release rates and fates. White and brown rot-type fungi attack lignin as a prerequisite to access carbohydrates (white rot) or selectively remove carbohydrates (brown rot). Soft rot fungi use less well-studied mechanisms to deconstruct wood (e.g., cavitation and erosion). These fungi often co-exist in nature, creating a balance in carbon turnover that could presumably “tip” in a changing climate. There is no simple genetic marker, however, to distinguish fungi by rot types, and traditional black and white distinctions (brown and white, in this case) cannot explain a spectrum of “gray” carbon loss possibilities. In this study, we tested 39 wood-degrading fungal strains along this spectrum of rot types. We tracked wood mass loss and chemical changes in aspen blocks in early- to mid-decay stages, including three signatures of fungal nutritional mode measured from wood rather than from fungus: dilute alkali solubility, water-soluble monosaccharides, and lignin loss (%) relative to density loss (%) (L/D). Results were then plotted relative to rot types and correlated with gene counts, combining new data with past results in some cases. Results yielded a novel distinction in soluble monosaccharide patterns for brown rot fungi, and reliable distinctions between white and brown rot fungi, although soft rot fungi were not as clearly distinguished as suggested in past studies. Gene contents (carbohydrate-active enzymes and peroxidases) also clearly distinguished brown and white rot fungi, but did not offer reliable correlation with lignin vs. carbohydrate selectivity. These results support the use of wood residue chemistry to link fungal genes (with known or unknown function) with emergent patterns of decomposition. Wood signatures, particularly L/D, not only confirm the rot type of dominant fungi, but they offer a more nuanced, continuous variable to which we can correlate genomic, transcriptomic, and secretomic evidence rather than limit it to functional categories as distinct “bins.”

Plant communities mediate the interactive effects of invasion and drought on soil microbial communities

Soil microbiomes could play a major role in ecosystem responses to escalating anthropogenic global change. However, we currently have a poor understanding of how soil microbes will respond to interacting global change factors and if responses will be mediated by changes in plant community structure. We used a field experiment to assess changes in soil fungal and bacterial communities in response to plant invasion, experimental drought, and their combination. In addition, we evaluated the relative importance of direct versus indirect pathways of invasion and drought through changes in associated plant communities with structural equation models. We found that fungal communities were interactively structured by invasion and drought, where fungal richness was lowest with invasion under ambient conditions but highest with invasion under drought conditions. Bacterial richness was lower under drought but unaffected by invasion. Changes in the plant community, including lower plant richness and higher root biomass, moderated the direct effects of invasion on microbial richness. Fungal and bacterial functional groups, including pathogens, mutualists, and nitrogen metabolizers, were also influenced by plant community changes. In sum, plant communities mediated the effects of interacting global change drivers on soil microbial community structure, with significant potential consequences for community dynamics and ecosystem functions.

Characteristics of microbial eukaryotic community recovery in eutrophic water by using ecological floating beds

Ecological floating beds can rapidly remove nutrients (nitrogen and phosphorus) from eutrophic water, but we still know little about whether this process can simultaneously recover microbial eukaryotic communities. To fill this gap, planktonic microbial eukaryotic communities were investigated using 18S rRNA high-throughput gene sequencing during nutrient removal by floating beds of Canna indica L. We found that nutrient concentrations were high in both the control and treatment groups during period 1 (days 0-5) but rapidly decreased in the treatment group during period 2 (days 6-9) and period 3 (days 10-18). However, the microbial eukaryotic species richness and community compositions were similar between the control and treatment groups during periods 1 and 2 but showed small differences during period 3. The microbial eukaryotic co-occurrence networks between the control and treatment groups also showed similar degree centrality and interconnected eukaryotic members. We found that some abundant fungi species significantly responded to nutrient variations, but a large number of abundant ciliates were insensitive to nutrient removal. Our findings suggest that ecological floating beds can rapidly remove nutrients in eutrophic waters but that it is difficult to quickly and simultaneously improve microbial eukaryotic communities. This result reveals the critical influence of nutrient pollution on aquatic ecosystems and therefore on long-term and comprehensive aquatic habitat restoration, as aquatic macrophyte recoveries should be conducted after nutrient controls have been implemented.

Fungal functional ecology: bringing a trait-based approach to plant-associated fungi

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun^Fun ). Fun^Fun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers

Fungi dominate the turnover of wood, Earth’s largest pool of aboveground terrestrial carbon. Fungi first evolved this capacity by degrading lignin to access and hydrolyze embedded carbohydrates (white rot). Multiple lineages, however, adapted faster reactive oxygen species (ROS) pretreatments to loosen lignocellulose and selectively extract sugars (brown rot). This brown rot “shortcut” often coincided with losses (>60%) of conventional lignocellulolytic genes, implying that ROS adaptations supplanted conventional pathways. We used comparative transcriptomics to further pursue brown rot adaptations, which illuminated the clear temporal expression shift of ROS genes, as well as the shift toward synthesizing more GHs in brown rot relative to white rot. These imply that gene regulatory shifts, not simply ROS innovations, were key to brown rot fungal evolution. These results not only reveal an important biological shift among these unique fungi, but they may also illuminate a trait that restricts brown rot fungi to certain ecological niches.

Fungi dominate the recycling of carbon sequestered in woody biomass. This process of organic turnover was first evolved among “white rot” fungi that degrade lignin to access carbohydrates and later evolved multiple times toward more efficient strategies to selectively target carbohydrates—“brown rot.” The brown rot adaption was often explained by mechanisms to deploy reactive oxygen species (ROS) to oxidatively attack wood structures. However, its genetic basis remains unclear, especially in the context of gene contractions of conventional carbohydrate-active enzymes (CAZYs) relative to white rot ancestors. Here, we hypothesized that these apparent gains in brown rot efficiency despite gene losses were due, in part, to upregulation of the retained genes. We applied comparative transcriptomics to multiple species of both rot types grown across a wood wafer to create a gradient of progressive decay and to enable tracking temporal gene expression. Dozens of “decay-stage-dependent” ortho-genes were isolated, narrowing a pool of candidate genes with time-dependent regulation unique to brown rot fungi. A broad comparison of the expression timing of CAZY families indicated a temporal regulatory shift of lignocellulose-oxidizing genes toward early stages in brown rot compared to white rot, enabling the segregation of oxidative treatment ahead of hydrolysis. These key brown rot ROS-generating genes with iron ion binding functions were isolated. Moreover, transcription energy was shifted to be invested on the retained GHs in brown rot fungi to strengthen carbohydrate conversion. Collectively, these results support the hypothesis that gene regulation shifts played a pivotal role in brown rot adaptation.