Wood-decomposing Fungi Research Articles

Forest restoration benefits common and rare wood-decomposing fungi with a delay

Decline in the amount of dead wood deteriorates habitats for saproxylic organisms globally. This could be compensated by restoration, but it is poorly understood how created dead wood corresponds to the habitat requirements of saproxylic species. Using a large-scale field experiment of 30 restoration sites across Finland, we studied the long-term (5–15 years) effects of dead wood creation on wood-decomposing fungi (polypores) in Norway spruce and Scots pine dominated forests. All studied conservation areas had been used for timber production prior to conservation. The average amount and diversity of woody debris was higher on the restoration treatments than on the non-restored controls. Altogether, 56 polypore species were recorded. Restoration treatments had 1.4 and 8 times more species and observations than controls. Eight red-listed polypore species were observed, six on the restored plots (four only from the created dead wood) and two on the controls. Species composition of polypore assemblages differed between the restoration and control treatments, as well as between the spruce- and pine-dominated forests. Following restoration, temporal changes in the polypore assemblages were clear but only partly related to dead wood creation. Unlike previous short-term studies, our results show that dead wood creation by felling and ring-barking trees benefits not only common but also indicator and red-listed polypore species; indeed, 15 years after restoration all red-listed species occurred on created dead wood. As some red-listed species occurred solely on naturally fallen trees five to ten years after restoration, created dead wood alone cannot substitute for natural dead wood.

Fungi associated with the basidiomes of Hymenochaetaceae (Agaricomycetes, Basidiomycota) in the Amazon

The Hymenochaetaceae are basidiomycete, wood-decomposing fungi that are found in different habitats, including the Amazon region, and can be parasitized or live in association with some plant organisms. This study investigated the cultivable fungi associated with the basidiomes of Hymenochaetaceae collected in different areas of the Brazilian Amazon. In all, 107 specimens of Hymenochaetaceae were collected and 203 strains of associated fungi were obtained, which were grouped into 16 morphogroups, with Trichoderma and Aspergillus being the most representative. A total of 19 strains were identified using the molecular method, which made it easier to find their possible biotechnological applications cited in the literature. This investigation has enabled new discoveries that may be inspire further studies that explore microbial resources through co-culture and the relationship between macrofungi and their associated fungi.

Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates.

Unlike 'white rot' (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, 'brown rot' (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R2 = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R2 = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities.

A positive feedback to climate change: The effect of temperature on the respiration of key wood-decomposing fungi does not decline with time.

Heterotrophic soil microorganisms are responsible for ~50% of the carbon dioxide released by respiration from the terrestrial biosphere each year. The respiratory response of soil microbial communities to warming, and the control mechanisms, remains uncertain, yet is critical to understanding the future land carbon (C)-climate feedback. Individuals of nine species of fungi decomposing wood were exposed to 90 days of cooling to evaluate the medium-term effect of temperature on respiration. Overall, the effect of temperature on respiration increased in the medium term, with no evidence of compensation. However, the increasing effect of temperature on respiration was lost after correcting for changes in biomass. These results indicate that C loss through respiration of wood-decomposing fungi will increase beyond the direct effects of temperature on respiration, potentially promoting greater C losses from terrestrial ecosystems and a positive feedback to climate change.

Growth, morphology, and formation of cinnabarin in Pycnoporus cinnabarinus in relation to different irradiation spectra

BackgroundThe demand for natural pigments in general, and for fungi-derived pigments in particular, is constantly rising. Wood-decomposing fungi represent a promising source for natural pigments and they are usually easy to cultivate in pure culture. One of them, i.e., Pycnoporus cinnabarinus, offers a highly interesting spectrum of bioactivity, partly due to the formation of the orange–red pigment cinnabarin. However, apart from a few studies addressing its diverse potential biotechnological applications, there is still a large gap of knowledge concerning the influence of light on the formation of cinnabarin. The aim of this work was to investigate the effect of different irradiations on the cinnabarin content, the growth, and the morphology of three different P. cinnabarinus strains. We used highly standardized irradiation conditions and cultivation techniques in combination with newly developed methods for the extraction and direct quantification of cinnabarin.ResultsRed, green, blue, and UV-A irradiation (mean irradiance Ee = 1.5 ± 0.18 W m−2) had considerable effects on the growth and colony appearance of all three P. cinnabarinus strains tested. The cinnabarin content determined was, thus, dependent on the irradiation wavelength applied, allowing strain-specific thresholds to be defined. Irradiation with wavelengths below this strain-specific threshold corresponded to a lower cinnabarin content, at least at the intensity applied. The orange–red pigment appeared by light microscopy as incrusted extracellular plaques present on the hyphal walls. Highly efficient vegetative propagation occurred by arthroconidia, and we observed the tendency that this asexual reproduction was (i) most frequent in the dark but (ii) never occurred under UV-A exposure.Conclusion This study highlights a differential photo-dependence of growth, morphology, and cinnabarin formation in P. cinnabarinus. This confirms that it is advisable to consider the wavelength of the light used in future biotechnological productions of natural pigments.Graphical abstract

Preservation, diagenetic transformation and paleoecological significance of fungal saccharides from lignites and fossil wood

Fungi are a common component of terrestrial ecosystems, although their preservation as molecular fossils is relatively rare. Saccharides, such as arabitol, mannitol and trehalose, are important in biochemical processes, and are the dominant compounds in fungi, lichens and yeasts. Here we present gas chromatography–mass spectrometry (GC–MS) analysis of fungal saccharides in brown coal extracts and compare their distribution to extant white, brown, and soft-rot fungi. Distribution differs depending on the type of decay in modern and fossil wood-decomposing fungi. An arabitol/(arabitol + trehalose) ratio higher than 0.6 for extant and fossil fungi is diagnostic for soft and brown rot, while values below 0.4 are characteristic of white rot fungi. Values between 0.4 and 0.6 suggest a mixed origin of fungal saccharides. The observed differences may shed light on the type of fungal activity, in particular relatated to climatic conditions of the Cenozoic.We conclude that saccharides can be good indicators, sensitive to climate change, of wood degradation by fungi in thermally immature organic matter. As a case study, early Cenozoic lignites were formed on low latitudes in the tropics during or near the Paleocene/Eocene thermal maximum, as extant soft rot fungi can withstand extremes of temperature and humidity. The presence of these fungi is confirmed by the dominance of arabitol over trehalose in most of the Lower Cenozoic lignites and arabitol/(arabitol + trehalose) ratio values higher than 0.6. In contrast, Miocene detritic coals, which were formed in temperate to subtropical climates, contain saccharides derived from a mixture of different fungi with white rot predominance.

A new, morphologically and ecologically unusual Lasioseius mite (Acari: Blattisociidae) associated with Diaperis boleti (Coleoptera, Tenebrionidae) and wood-decomposing fungi in Slovakia

On the basis of females and males found on the adult beetles of the mycophagous tenebrionid Diaperis boleti (L.) and on the polypore fungi Fomitopsis betulina, Laetiporus sulphureus, and Cerioporus squamosus infested with this beetle, which serve as a specific phoretic host for the new species, a new blattisociid mite, Lasioseius boleti sp. nov. was described. The new species is characterised by a pronounced sexual dimorphism of the dorsal chaetotaxy, which is unusual for the genus, and by several features more typical of other highly specialized fungicoles among the mesostigmatic mites than of other species of Lasioseius Berlese, such as the genera Hoploseius Berlese (Blattisociidae), Mycomelichares Mašán and Joharchi (Melicharidae), and Bulbolaelaps Faraji, Zare and Rahmani (Digamasellidae). The new species is unusual among the known congeners mainly because of its unusual bionomy, sexual dimorphism, presence of unequal setae that vary greatly in length and form in both sexes, moderately shortened peritremes, sharp cheliceral teeth, and brush-like tritosternum.

Urbanization filters woodpecker assemblages: Habitat specialization limits population abundance of dead wood dependent organisms in the urban landscape

Although urban landscapes are regarded as unsuitable for dead wood dependent organisms, some species, including woodpeckers, commonly occur in cities. As the availability of trees and dead wood resources is a primary dimension of the habitat-niche for most woodpeckers, we hypothesized that increasing habitat specialization (decreasing habitat-niche-volume) would limit species abundance within an urban landscape. We surveyed the woodpecker assemblage in the urban landscape, and for seven species we quantified the habitat-niche relying on four dimensions (the availability of trees, snags, fallen logs and dead tree branches). Then, we analysed the habitat preferences and habitat-niche partitioning of the woodpecker assemblage. For each species, we calculated the habitat-niche-volume and tested whether this trait correlated with species abundance in the urban landscape. Woodpeckers selected habitats with a high availability of either trees or dead wood (especially dead tree branches). The habitat-niches partially overlapped, but varied between species in terms of the availability of trees, dead tree branches, snags or fallen logs. The habitat-niche-volume varied among species and was positively associated with species abundance in the urban landscape. The regional abundance of species, body size and relative brain size did not affect the abundance of urban woodpecker populations. Our study highlights that urbanization filters woodpecker assemblages by limiting habitat-specialists and promoting habitat-generalists. We suggest that the alteration of woodpecker assemblages in the urban landscape may have a cascading effect on entire assemblages of dead wood dependent organisms, including cavity-nesters, saproxylic insects and wood-decomposing fungi. Urban development, which limits dead wood resources, is therefore a serious threat to biodiversity, whereas sustainable management of urban green spaces, e.g. the preservation of dead wood, may mitigate biodiversity loss.

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.

Is the Survivability of Silver Fir under Condition of Strong Ungulate Pressure Related to Mycobiota of Bark-Stripping Wounds?

The aim of the research was to check whether the healing of bark-stripping wounds of the silver fir tree trunks reduces the share of wood-decomposing fungi, which may be the result of inter-species interactions. The study carried out in Gorce National Park in Polish Western Carpathians analyzed drill holes of sapwood from three types of wounds (fresh, healed and old) on fir trunks with a diameter at breast height (DBH) of 4.0–16.9 cm as a result of bark-stripping by red deer (Cervus elaphus). In the wood of fresh wounds Alternaria alternata (Fr.) Keissl. and Arthrinium arundinis (Corda) Dyko & B. Sutton had the largest share in mycobiota. Phompsis spp. and the species Sydowia polyspora (Bref. & Tavel) E. Müll. and Epicoccum nigrum Link were also isolated. The dominants in old wounds were Eutypa spp., Phomopsis spp. and Cylindrobasidium evolvens (Fr.) Jülich. Healed wounds were dominated by Trichoderma atroviride P. Karst, a fungus antagonistic to many fungal pathogens. Such properties are shared by A. arundinis, especially common in fresh wound wood. It seems that these fungi support the process of wounded tree regeneration (healing of wounds) and limit the activity of wood-decaying fungi in old age, which makes fir survival very high. Thus, even a strong red deer pressure cannot be considered the basic factor determining the dynamics of fir in this part of the Carpathians.

Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs.

The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.

Prescribed burning reduces species richness of wood-decay fungi in the forests of northwest Arkansas.

The present study, which was carried out at three localities in the Ozark Mountains of northwest Arkansas, investigated the effects of prescribed burning on wood-decomposing fungi using samples of decaying woody debris (DWD) placed in plastic incubation chambers. One of the localities had not been subjected to recent prescribed burning, whereas the other localities contained both an unburned area as well as an area recently subjected to burning. In all three localities, small pieces of decaying woody debris (DWD) were collected, placed in the incubation chambers and the latter kept moist for any extended period of time. Pieces of DWD collected in the areas subjected to burning typically displayed evidence of considerable charring. Fruiting bodies appearing in the incubation chambers were removed and identified by sequencing of ribosomal DNA region. A total of 101 specimens representing 80 different taxa were recorded in the entire investigation, but the numbers of both specimens and taxa were appreciably higher for the unburned collecting sites. As such, the data obtained indicate that prescribed burning lowers the species richness of the wood-decomposing fungi associated with DWD at a particular locality. The unique aspect of the present study was the use of incubation chambers to characterize the taxa of fungi associated with CWD.

Abundance and phenology of macrofungal fruiting bodies in central and northern Japan

To understand how ectomycorrhizal (ECM), wood-decomposing (WDC) and litter-decomposing (LDC) fungi differ in abundance and fruiting season, fruiting-body production was monitored by counting their number and/or measuring their biomass in deciduous broad-leaved and coniferous forests in Ishikawa (central Japan) and Hokkaido (northern Japan). ECM fungi were dominant in forests of both types in Ishikawa and a Larix kaempheri forest in Tomakomai (Hokkaido), whereas WDC fungi were dominant in a deciduous broad-leaved forest in Sapporo (Hokkaido). ECM and WDC fungi usually showed two abundance peaks in Kanazawa (Ishikawa), mid-summer and autumn for ECM fungi and spring or summer and autumn for WDC fungi, whereas LDC fungi usually showed one peak in autumn. In Tomakomai, the abundance peak appeared later in ECM fungi but earlier in LDC and WDC fungi in comparison with Kanazawa. The mode of resource acquisition is assumed as one of factors that affect the seasonal timing of fruiting-body production. On the other hand, highly positive correlations were often observed between precipitation in Jun or Aug and the fruiting-body production in summer and/or autumn in the survey in Kanazawa, suggesting that precipitation could affect the fruiting-body production a few months later. • Ectomycorrhizal fungi (ECM) showed two production peaks in mid-summer and autumn. • Wood-decomposing fungi (WDC) showed two peaks in spring and mid- or late-autumn. • Litter-decomposing fungi (LDC) showed a peak in autumn. • ECM showed more extensive yearly variation in fruiting phenology than WDC. • Precipitation is assumed to affect the fruiting-body production.

Molecular prospecting for cryptic species of the Hypholoma fasciculare complex: toward the effective and practical delimitation of cryptic macrofungal species

Many macrofungal cryptic species remain unidentified. A possible solution is to increase the number of loci analyzed and use rigorous statistics for macrofungal species delimitation. To validate this assumption, cryptic species of the Hypholoma fasciculare complex, a group of common wood-decomposing fungi, were attempted to be delineated. Massively parallel sequencing of mitochondrial ribosomal RNA (mt_rRNA), nuclear ribosomal internal transcribed spacer (ITS) region, and 24 single-copy genes were performed for 96 specimens collected in Japan. Then, the species boundaries were inferred using comparative gene genealogies (mt_rRNA vs. ITS), Bayesian Poisson tree process (bPTP) model for the phylogeny of concatenated nuclear sequences, and analysis of molecular variance (AMOVA) for single nucleotide polymorphisms. In both the mt_rRNA and ITS phylogenies, the H. fasciculare complex was not divided into well-supported clades. Nevertheless, based on the bPTP, two mitochondrial haplotypes were inferred to represent distinct species (H. fasciculare and H. subviride). The results of AMOVA also indicated that the differentiation of nuclear loci can be explained mostly by differences between haplotype. These results suggest that it is necessary to increase the number of target loci to 20 or more and use both phylogeny-based and population genetics-based statistics for the accurate delimitation of macrofungal species.

An agent-based model of the foraging ascomycete hypothesis

Abstract Most trees host hundreds of species of fungi asymptomatically in their internal tissues, known collectively as fungal endophytes. The Foraging Ascomycete (FA) hypothesis proposed that some fungal endophytes inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia during periods of environmental stress. This dispersal strategy has recently been termed viaphytism and is now thought to apply to fungal groups beyond ascomycetes. Viaphytism implies that many fungi may be in continuous and cyclical flux between life stages as endophytes in the forest canopy and as wood-decomposing fungi on the forest floor. This cycle may represent a very common and previously-ignored process in the ecology of forests, with implications for forest health. The ecological consequences of the viaphyte lifestyle are complex, so we constructed an agent-based model to explore it. Our model is intended to serve as both an explicit conceptual explanation of viaphytism, and as an exploration of the conditions in which a strategy of endophytism accompanied by leaf dispersal may be advantageous for fungi. In a scenario of a viaphytic fungal species on a model forest landscape, without fungal competitors, viaphytism is predicted to be a plausible alternative to dispersal to substrates by spores alone, allowing the fungus to persist reliably in the landscape. In a scenario that allows competition from aggressively dispersed non-viaphytic fungi, the model predicts some competitive benefits to fungal dispersal via leaves. However, these benefits are conditional, requiring sufficient retention through time of endophyte infections by host trees, and sufficient host trees in the landscape. In the model, loss of these fungal populations can result from increased local disturbances of forest canopy, and deforestation.

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.”

Humic Acid Transformation by the Fungus Cerrena unicolor Growing on Cellulose and Glucose

Microbial degradation of lignocellulose and soil organic matter is an important process controlling CO2 flow into the atmosphere, which is mostly carried out by fungi. The alkali-soluble fraction, which is represented mostly by the so-called humic acids (HA), dark-colored compounds of phenolic nature, constitute ~30‒70% of soil Corg. This is the first report on efficient degradation of soil HA under cellulolytic conditions; cellobiose dehydrogenase (CDH), an oxidative enzyme of the cellulolytic complex, was shown to play the key role in this process. Growth of a wood-decomposing fungus Cerrena unicolor on cellulose (CDH and laccase production) and glucose (laccase production) resulted in HA decolorization by 60 and 20%, respectively. HA depolymerization in the presence of CDH and its polymerization in the presence of laccase were shown by gel filtration experiments with the culture liquid and pure enzyme preparations. HA degradation in the presence of CDH was inhibited by radical scavengers, indicating the radical nature of this process (probably the Fenton’s reaction). HA depolymerization by CDH decreased in the presence of laccase, while HA polymerization by laccase decreased in the presence of CDH. Thus, the interaction of these enzymes affects HA transformation under cellulolytic conditions. These results improve our understanding of the mechanisms of microbial degradation of the aromatic components of soil humus and of the ecological functions of wood-decomposing fungi grown under cellulolytic conditions.

Fungal communities in decomposing wood along an energy wood harvest gradient

The current requirements to decrease the consumption and greenhouse gas emissions of fossil fuels have increased the demand of renewable energy sources. In forestry, this situation has intensified harvesting practices resulting in a decreased amount of woody debris left on the clear-cut areas. Impacts of energy wood harvest on wood-decomposing fungi were studied in a large-scale experiment in clear-cut stands in three geographical areas in Finland. A sequence of treatments was expected to form a forestry induced soil disturbance gradient: (1) logging residues left at site, no soil preparation; (2) logging residues left at site, patch mounding; (3) 70% logging residue removal, patch mounding; and (4) complete stump and logging residue removal, patch mounding. Pre-weighed wood discs were incubated on the intact soil cover for four years to estimate decomposition rate and fungal decomposer community. A soil sample was taken underneath each disc to evaluate the direct inoculation potential of the soil. The main results were as follows: (1) The differences between the treatments were not significant, while the geographical factors affected the decomposition rate and the fungal communities of the wood discs. (2) The fungal composition in the wood discs did not reflect the underlying soil fungal community, which indicates that a part of the fungal species inhabiting wood discs originated from airborne surrounding sources. (3) The increase in fungal species diversity was associated to the wood decay process, indicated by parallel increase in the wood decomposition rate and the number of white rot and mycorrhizal fungi. Thus our study indicates that in addition to local environment, landscape-level factors control the decomposer fungal community and its activity in wood.

Formerly managed forest reserves complement integrative management for biodiversity conservation in temperate European forests

In Central Europe, the predominant conservation strategy in forests is integrative management, seeking to balance economic interests with conservation goals. This is complemented by unmanaged strict forest reserves, most often small and with a history of forest management. Whether and how such reserves contribute to conservation when the surrounding forest is under progressive integrative management remains unclear.We compared forest structure and biodiversity of several taxa between formerly managed forest reserves and stands under progressive integrative management in beech and beech-oak forests. Alpha diversity was higher in reserves for birds and bats and higher in managed stands for plants and beetles, with no significant differences for fungi. Community composition differed between reserves and managed stands for plants, wood-decomposing fungi, beetles and birds. Reserves had 17 indicator species, including three red-listed species, and managed stands had 34, including one red-listed species. Diversity metrics differed between reserves and managed stands for both beech and beech-oak forests.Our results indicate that progressive integrative management and reserves, even when located in formerly managed stands, are complementary approaches benefitting different taxa and hosting partly different communities. Higher numbers of plants and beetles in managed stands were associated with higher light availability, as reserves in our study were undisturbed mature stands characterized by low light availability and low deadwood volumes. To benefit light and deadwood demanding species, new reserves should include early or late successional stands. If this is not feasible, restoration measures prior to designation or where possible under current protection status should be discussed.

Reference genes for accurate normalization of gene expression in wood-decomposing fungi

Wood-decomposing fungi efficiently decompose plant lignocellulose, and there is increasing interest in characterizing and perhaps harnessing the fungal gene regulation strategies that enable wood decomposition. Proper interpretation of these fungal mechanisms relies on accurate quantification of gene expression, demanding reliable internal control genes (ICGs) as references. Commonly used ICGs such as actin, however, fluctuate among wood-decomposing fungi under defined conditions. In this study, by mining RNA-seq data in silico and validating ICGs in vitro using qRT-PCR, we targeted more reliable ICGs for studying transcriptional responses in wood-decomposing fungi, particularly responses to changing environments (e.g., carbon sources, decomposition stages) in various culture conditions. Using the model brown rot fungus Postia placenta in a first-pass study, our mining efforts yielded 15 constitutively-expressed genes robust in variable carbon sources (e.g., no carbon, glucose, cellobiose, aspen) and cultivation stages (e.g., 15 h, 72 h) in submerged cultures. Of these, we found 7 genes as most suitable ICGs. Expression stabilities of these newly selected ICGs were better than commonly used ICGs, analyzed by NormFinder algorithm and qRT-PCR. In a second-pass, multi-species study in solid wood, our RNA-seq mining efforts revealed hundreds of highly constitutively expressed genes among four wood-decomposing fungi with varying nutritional modes (brown rot, white rot), including a shared core set of ICGs numbering 11 genes. Together, the newly selected ICGs highlighted here will increase reliability when studying gene regulatory mechanisms of wood-decomposing fungi.