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1. Traits related to reproduction and dispersal drive the assembly and dynamics of species communities and can explain and predict how species respond to habitat loss and fragmentation and to the changing climate. For fungi, such links remain poorly known. 2. We examine how spore production rate, a key demographic trait, is influenced by the interaction between environmental conditions and species traits. We monitored the spore production of 97 wood-inhabiting fungal species on 107 decaying logs for two years and analyzed the data with a hierarchical community model. 3. Our analysis demonstrates clear species differences in seasonal patterns, with spring and summer release dominating in perennial species, contrary to the commonly held view of autumn as the primary ?mushroom season?. Many species follow a diurnal pattern with a higher spore release rate during the night. Such patterns in release timing have important implications for dispersal, as shown by recent model simulations. 4. The overall level of spore release was negatively correlated with spore size, providing new evidence that fungi face the classic trade-off of investing either in the number or size of offspring. 5. We found that different species within the functional group of wood-inhabiting fungi display alternative strategies in spore release timing and along the trade-off between offspring size and number. Linking our findings to previously reported correlations between spore size and other traits, we propose a new conceptualization of life history strategies in wood-inhabiting fungi, with implications for species? ability to survive the ongoing biodiversity crisis.

A major goal in ecology is understanding the factors which determine the diversity and distribution of organisms. The outcome of the symbiotic relationship between plants and arbuscular mycorrhizal (AM) fungi is strongly influenced by soil phosphorus (P) availability. Despite this knowledge, there is still much to uncover about how soil P status can shape the taxonomic and phylogenetic assembly of root-colonising AM fungi. Additionally, there is a paucity of understanding about the implications of these changes for the outcome of the AM symbiosis in terms of plant growth, nutrient status and defence traits. We conducted a factorial pot experiment where sorghum (Sorghum bicolor) was grown under three different P treatments (low, medium and high), in the presence or absence of a natural AM fungal community. By analysing the diversity and community structure of the fungal community colonising roots, we aimed to determine if and how soil P influences the relatedness of these communities and whether competitive exclusion or environmental filtering play a more significant role in their assembly. Additionally, we evaluated the concomitant outcomes for plant growth, nutrient acquisition and defensive chemistry (phenolics). Increasing P availability reduced AM fungal richness and increased community evenness. Root-colonising AM fungal communities under the high P treatment had significantly reduced phylogenetic diversity and comparatively lower mean pairwise distances among all treatments. This indicated that AM fungal communities became more closely related (phylogenetically clustered) with increasing soil P. The mycorrhizal growth and mycorrhizal P responses of plants were positive under low and medium P, but this was lost under high P, however, plant phenolics were increased. Our results suggest that under high P conditions, environmental filtering plays an important role in AM fungal community assembly as host plants alter their selectivity of fungal functional groups prioritising those associated with enhancing plant stress resistance and defences, rather than nutrient acquisition. Here we demonstrated how soil P status can shape taxonomic and phylogenetic assembly of AM fungi and the associated functional outcomes for the host. peerReviewed

Adaptation to changing environments often requires meaningful phenotypic modifications to match the current conditions. However, obtaining information about the surroundings during an organism’s own lifetime may only permit accommodating relatively late developmental modifications. Therefore, it may be advantageous to rely on inter-generational or trans-generational cues that provide information about the environment as early as possible to allow development along an optimal trajectory. Transfer of information or resources across generations, known as parental effects, is well documented in animals and plants but not in other eukaryotes, such as fungi. Understanding parental effects and their evolutionary consequences in fungi is of vital importance as they perform crucial ecosystem functions. In this study, we investigated whether parental effects are present in the filamentous fungusNeurospora crassa, how long do they last, are the effects adaptive, and what is their mechanism. We performed a fully factorial match / mismatch experiment for a good and poor quality environment, in which we measured mycelium size of strains that experienced either a matched or mismatched environment in their previous generation. We found a strong silver spoon effect in initial mycelium growth, which lasted for one generation, and increased fitness during competition experiments. By using deletion mutants that lacked key genes in epigenetic processes, we show that epigenetic mechanisms are not involved in this effect. Instead, we show that spore glycogen content, glucose availability and a radical transcription shift in spores are the main mechanisms behind this parental effect.

While mutation rates have been extensively studied, variation in mutation rates throughout the genome is poorly understood. To understand patterns of genetic variation, it is important to understand how mutation rates vary. Chromatin modifications may be an important factor in determining variation in mutation rates in eukaryotic genomes. To study variation in mutation rates, we performed a mutation accumulation experiment in the filamentous fungus Neurospora crassa, and sequenced the genomes of the 40 MA lines that had been propagated asexually for approximately 1015 [1003, 1026] mitoses. We detected 1322 mutations in total, and observed that the mutation rate was higher in regions of low GC, in domains of H3K9 trimethylation, in centromeric regions, and in domains of H3K27 trimethylation. The rate of single nucleotide mutations in euchromatin was 2.46 [2.19, 2.77] × 10-10. In contrast, the mutation rate in H3K9me3 domains was tenfold higher: 2.43 [2.25, 2.62] × 10-9. We also observed that the spectrum of single nucleotide mutations was different between H3K9me3 and euchromatic domains. Our statistical model of mutation rate variation predicted a moderate amount of extant genetic variation, suggesting that the mutation rate is an important factor in determining levels of natural genetic variation. Furthermore, we characterized mutation rates of structural variants, complex mutations, and the effect of local sequence context on the mutation rate. Our study highlights that chromatin modifications are associated with mutation rates, and accurate evolutionary inferences should take variation in mutation rates across the genome into account. peerReviewed

Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms. peerReviewed

Human actions are considered to cause a severe threat to boreal forest systems. Even though some influences are noticed to occur with a remarkable time-lag, long-term studies of this topic are still scarce and partly contradictory. The importance of above-ground and below-ground linkages has also only recently been emphasized. Yet, boreal forests have potential to be resistant and resilient to global change. Understanding the impacts of these pressures on various aspects of forest systems, has scientific and functional value. In this thesis, I have studied natural and altered long-term dynamics of forest understory vegetation (vascular plants, bryophytes and lichens) on nutritionally different boreal forests using resurvey data. I have also studied the development of understory vegetation and soil microbial communities (fungi and bacteria) on a long-term (ca 1500 yrs.) soil primary successional series on land uplift shores. All studied communities changed remarkably in time, partly naturally by succession, partly due to human influence. Interestingly, the development of vegetation and soil microbial communities was related to accumulation of organic matter instead of nutrients on our nutrient limited study system. In herb-rich forests, temporal changes led to increasing homogeneity in forest understorey communities. This study is among the first to show that reindeer grazing can regulate vegetation dynamics in boreal, herb-rich forests by reducing vegetation height and maintaining diversity. Forest management had surprisingly little influence on the understory vegetation of herb-rich and coniferous forests. Forest management reduced the accumulation of coarse woody debris. Importantly, forest management impacts were detectable long time after management, and thus appear as legacy effects in forest plant community structure and woody debris. The results of this thesis emphasize the value of long-term studies and involving above-ground and below-ground linkages. When using larger datasets, taking regional processes into account can be highly useful as can be the use of diverse response variables for detecting ecologically relevant changes of e.g. lighter forest management practices. Tiivistelmä Ihmistoiminnan on arvioitu heikentävän pohjoisia metsiä osan vaikutuksista ilmetessä pitkien aikojen kuluttua. Silti pitkäaikaistutkimusta aiheesta on vähän ja tulokset ovat osin ristiriitaisia. Maaperän ja kasvillisuuden vuorovaikutusten merkitystä metsien toimintaan on vasta alettu ymmärtää syvällisemmin. Toisaalta metsäkasvillisuuden on arvioitu sietävän muutoksia. Tiedolla globaalimuutoksen vaikutuksista metsäyhteisöjen ominaisuuksiin on merkittävää tieteellistä ja käytännön arvoa. Väitöskirjassani tutkin lehtojen ja kangasmetsien aluskasvillisuuden (putkilokasvit, sammalet ja jäkälät) luontaisia ja muuttuneita pitkän ajan kehityskulkuja uudelleenkartoitusaineistoilla. Tutkin myös kasvillisuuden ja maan mikrobiyhteisöjen (bakteerit ja sienet) kehitystä sukkessiosarjalla. Kaikki tutkimani yhteisöt muuttuivat ajassa ja osa muutoksista liittyi luontaiseen kehitykseen, osa ihmisvaikutukseen. Mikrobi- ja kasviyhteisöjen vuorovaikutteinen kehitys kytkeytyi ravinteiden sijaan orgaanisen aineen kertymiseen ravinnerajoitteisissa metsissä. Lehdoissa luontainen kehitys muutti aluskasvillisuuden yhteisöjä ja latvustoa kohti havupuuvaltaisempaa tilaa, mikä onkin yksi lehtoja uhkaava tekijä. Tämä on ensimmäisiä tutkimuksia, joka osoittaa porolaidunnuksen säätelevän kasviyhteisöjä boreaalisissa lehtometsissä ylläpitämällä monimuotoisuutta ja lehdoille tyypillistä lajikoostumusta pitämällä kasvillisuuden matalana. Metsätaloustoimien vaikutukset ilmenivät yllättävän vähän lehtojen ja havumetsien aluskasvillisuudessa. Lahopuun määrää metsätalous vähensi voimakkaasti. Tärkeä havainto oli, että metsänhoitotoimenpiteiden vaikutuksia ilmenee huomattavalla viipeellä. Väitöskirjani tulokset korostavat pitkäaikaistutkimuksen arvoa sekä maanpäällisten ja -alaisten prosessien huomioimista. Työni tulokset osoittavat, että suurilla aineistoilla alueellisten tekijöiden huomioimisesta voi olla hyötyjä samoin kuin monipuolisten ekologisten mittareiden käytöstä ekologisesti merkittävien muutosten havaitsemiseksi esimerkiksi tutkittaessa lievempien metsätaloustoimien vaikutuksia.

Peatlands are carbon dioxide (CO2) sinks that, in parallel, release methane (CH4). The peatland carbon (C) balance depends on the interplay of decomposer and CH4-cycling microbes, vegetation, and environmental conditions. These interactions are susceptible to the changes that occur along a successional gradient from vascular plant-dominated systems to Sphagnum moss-dominated systems. Changes similar to this succession are predicted to occur from climate change. Here, we investigated how microbial and plant communities are interlinked with each other and with ecosystem C cycling along a successional gradient on a boreal land uplift coast. The gradient ranged from shoreline to meadows and fens, and further to bogs. Potential microbial activity (aerobic CO2 production; CH4 production and oxidation) and biomass were greatest in the early successional meadows, although their communities of aerobic decomposers (fungi, actinobacteria), methanogens, and methanotrophs did not differ from the older fens. Instead, the functional microbial communities shifted at the fen–bog transition concurrent with a sudden decrease in C fluxes. The successional patterns of decomposer versus CH4-cycling communities diverged at the bog stage, indicating strong but distinct microbial responses to Sphagnum dominance and acidity. We highlight young meadows as dynamic sites with the greatest microbial potential for C release. These hot spots of C turnover with dense sedge cover may represent a sensitive bottleneck in succession, which is necessary for eventual long-term peat accumulation. The distinctive microbes in bogs could serve as indicators of the C sink function in restoration measures that aim to stabilize the C in the peat.

Animal gut mycobiota, the community of fungi that reside within the gastrointestinal tract, make an important contribution to host health. Accordingly, there is an emerging interest to quantify the gut mycobiota of wild animals. However, many studies of wild animal gut mycobiota do not distinguish between the fungi that likely can reside within animal gastrointestinal tracts from the fungal taxa that are non-residents, such as macrofungi, lichens or plant symbionts/pathogens that can be ingested as part of the host’s diet. Confounding the non-resident and resident gut fungi may obscure attempts to identify processes associated with the authentic, resident gut mycobiota per se. To redress this problem, we propose some strategies to filter the taxa identified within an apparent gut mycobiota based on an assessment of host ecology and fungal traits. Consideration of the different sources and roles of fungi present within the gastrointestinal tract should facilitate a more precise understanding of the causes and consequences of variation in wild animal gut mycobiota composition. peerReviewed

Anthropogenic changes to land use drive concomitant changes in biodiversity, including that of the soil microbiota. However, it is not clear how increasing intensity of human disturbance is reflected in the soil microbial communities. To address this issue, we used amplicon sequencing to quantify the microbiota (bacteria and fungi) in the soil of forests (n=312) experiencing four different land uses, national parks (set aside for nature conservation), managed (for forestry purposes), suburban (on the border of an urban area) and urban (fully within a town or city), which broadly represent a gradient of anthropogenic disturbance. Alpha diversity of bacteria and fungi increased with increasing levels of anthropogenic disturbance, and was thus highest in urban forest soils and lowest in the national parks. The forest soil microbial communities were structured according to the level of anthropogenic disturbance, with a clear urban signature evident in both bacteria and fungi. Despite notable differences in community composition, there was little change in the predicted functional traits of urban bacteria. By contrast, urban soils exhibited a marked loss of ectomycorrhizal fungi. Soil pH was positively correlated with the level of disturbance, and thus was the strongest predictor of variation in alpha and beta diversity of forest soil communities, indicating a role of soil alkalinity in structuring urban soil microbial communities. Hence, our study shows how the properties of urban forest soils promote an increase in microbial diversity and a change in forest soil microbiota composition. peerReviewed

Interactions among fungi and insects involve hundreds of thousands of species. While insect communities on plants have formed some of the classic model systems in ecology, fungus-based communities and the forces structuring them remain poorly studied by comparison. We characterize the arthropod communities associated with fruiting bodies of eight mycorrhizal basidiomycete fungus species from three different orders along a 1200-km latitudinal gradient in northern Europe. We hypothesized that, matching the pattern seen for most insect taxa on plants, we would observe a general decrease in fungal-associated species with latitude. Against this backdrop, we expected local communities to be structured by host identity and phylogeny, with more closely related fungal species sharing more similar communities of associated organisms. As a more unique dimension added by the ephemeral nature of fungal fruiting bodies, we expected further imprints generated by successional change, with younger fruiting bodies harboring communities different from older ones. Using DNA metabarcoding to identify arthropod communities from fungal fruiting bodies, we found that latitude left a clear imprint on fungus-associated arthropod community composition, with host phylogeny and decay stage of fruiting bodies leaving lesser but still-detectable effects. The main latitudinal imprint was on a high arthropod species turnover, with no detectable pattern in overall species richness. Overall, these findings paint a new picture of the drivers of fungus-associated arthropod communities, suggesting that latitude will not affect how many arthropod species inhabit a fruiting body but, rather, what species will occur in it and at what relative abundances (as measured by sequence read counts). These patterns upset simplistic predictions regarding latitudinal gradients in species richness and in the strength of biotic interactions.

The general negative impact of forestry on wood-inhabiting fungal diversity is well recognized, yet the effect of forest naturalness is poorly disentangled among different fungal groups inhabiting dead wood of different tree species. We studied the relationship between forest naturalness, log characteristics and diversity of different fungal morpho-groups inhabiting large decaying logs of similar quality in spruce dominated boreal forests. We sampled all non-lichenized fruitbodies from birch, spruce, pine and aspen in 12 semi-natural forest sites of varying level of naturalness. The overall fungal community composition was mostly determined by host tree species. However, when assessing the relevance of the environmental variables separately for each tree species, the most important variable varied, naturalness being the most important explanatory variable for fungi inhabiting pine and aspen. More strikingly, the overall species richness increased as the forest naturalness increased, both at the site and log levels. At the site scale, the pattern was mostly driven by the discoid and pyrenoid morpho-groups inhabiting pine, whereas at the log scale, it was driven by pileate and resupinate morpho-groups inhabiting spruce. Although our study demonstrates that formerly managed protected forests serve as effective conservation areas for most wood-inhabiting fungal groups, it also shows that conservation planning and management should account for group- or host tree -specific responses.

Earth’s temperature is increasing due to anthropogenic CO2emissions; and organisms need either to adapt to higher temperatures, migrate into colder areas, or face extinction. Temperature affects nearly all aspects of an organism’s physiology via its influence on metabolic rate and protein structure, therefore genetic adaptation to increased temperature may be much harder to achieve compared to other abiotic stresses. There is still much to be learned about the evolutionary potential for adaptation to higher temperatures, therefore we studied the quantitative genetics of growth rates in different temperatures that make up the thermal performance curve of the fungal model systemNeurospora crassa. We studied the amount of genetic variation for thermal performance curves and examined possible genetic constraints by estimating theG-matrix. We observed a substantial amount of genetic variation for growth in different temperatures, and most genetic variation was for performance curve elevation. Contrary to common theoretical assumptions, we did not find strong evidence for genetic trade-offs for growth between hotter and colder temperatures. We also simulated short term evolution of thermal performance curves ofN. crassa, and suggest that they can have versatile responses to selection.

Wood-pastures are threatened anthropogenic biotopes that provide habitat for an extensive group of species. Here we studied the effect of management, grazing intensity, time since abandonment, historical land-use intensity, soil properties and stand conditions on communities of saprotrophic fungi in wood-pastures in Central Finland. We found that the proportion of broadleaved trees and soil pH are the major drivers in the communities of saprotrophic fungi in these boreal wood-pastures. In addition, tree species richness, soil moisture, historical land-use intensity and time since abandonment affected the communities of saprotrophic fungi. Current management or grazing intensity did not have a clear effect on saprotrophic fungal species richness, although dung-inhabiting fungal species richness was highest at intermediate to high grazing intensity. Obviously, there were many more dung-inhabiting fungal species on grazed than on abandoned sites. Our study highlights the conservation value of wood-pastures as hotspots of saprotrophic fungi. peerReviewed

Publisher Copyright: © 2021 The Author The interest in studying wood-inhabiting fungal communities has grown in recent years. This interest has mainly been motivated by the important roles of wood-inhabiting fungi in ecosystem functioning (e.g. nutrient cycling) and conservation biology (e.g. their sensitivity to forest management). In this paper, I argue that another important, but yet largely unexplored motivation for studying wood-inhabiting fungal communities, is their potential to advance fundamental community ecology. One major advantage of wood-inhabiting fungi as model systems is that they are organized as spatially well-defined metacommunities, thus conforming to the assumptions of many theoretical frameworks. Another major advantage is that they allow observations and manipulations over large numbers of local communities (habitat patches). After reviewing recent approaches in theoretical community ecology, I discuss how past empirical studies on wood-inhabiting fungal communities relate to community assembly processes, and provide future research directions on how the still unstudied assembly processes could be tackled using wood-inhabiting fungi as a model system.

During the last few decades, a plethora of sequencing studies provided insight into fungal community composition under various environmental conditions. Still, the mechanisms of species assembly and fungal spread in soil remain largely unknown. While mycelial growth patterns are studied extensively, the abundant formation of asexual spores is often overlooked, though representing a substantial part of the fungal life cycle relevant for survival and dispersal. Here, we explore asexual sporulation (spore abundance, size and shape) in 32 co-occurring soil fungal isolates under varying resource conditions, to answer the question whether resource limitation triggers or inhibits fungal investment into reproduction. We further hypothesized that trade-offs exist in fungal investment towards growth, spore production and size. The results revealed overall increased fungal investment into spore production under resource limitations; however, effect sizes and response types varied strongly among fungal isolates. Such isolate-specific effects were apparent in all measured traits, resulting in unique trait spaces of individual isolates. This comprehensive dataset also elucidated variability in sporulation strategies and trade-offs with fungal growth and reproduction under resource scarcity, as only predicted by theoretical models before. The observed isolate-specific strategies likely underpin mechanisms of co-existence in this diverse group of saprobic soil fungi. peerReviewed

Ectomycorrhizal fungi form a mutualistic symbiosis with plant roots, and are key for nutrient cycling in many ecosystems. Here we study the ectomycorrhizal fungal communities in the Oueme Superieur reserve forest in Benin (West Africa). We use phylogenetic methods to test if the species from the study site are closer to other tropical African species than to species from other regions. The Oueme Superieur community was represented by nine Operational Taxonomic Units in Amanitaceae, one in Boletaceae, one in Cantharellaceae, one in Cortinariaceae, two in Inocybaceae, fourteen in Russulaceae and three in Sclerodermataceae. Of these thirty-one Operational Taxonomic Units, twenty had no record in other areas, and unique Operational Taxonomic Units were found in all families except Boletaceae and Sclerodermataceae. The added phylogenetic diversity from these unique Operational Taxonomic Units tended to be higher than expected by chance in all families but Cantharellaceae. The Operational Taxonomic Units are generally fairly distinct and contribute proportionally to the phylogenetic diversity, reflecting that they do not only represent recently diverging species, but also more divergent lineages. Our analyses of the different families show that the communities of Amanitaceae, Inocybaceae, and Russulaceae are more closely related to the general Afrotropic community than expected by chance, at least measured as the nearest taxon distance. The lack of significant patterns in the other families may be due to lack of power, but the wide distribution of many Operational Taxonomic Units suggests that there are not likely to be strong patterns. It is only for Russulaceae that there is a significant pattern in the Oueme Superieur ectomycorrhizal fungal communities at a regional scale, with the Operational Taxonomic Units being less closely related than expected. At a global scale the patterns seem to reflect the overall distribution of the Afrotropic ectomycorrhizal fungal community. The phylogenetic patterns in the Afrotropic communities differ between families, from clustered to no clear pattern to over-dispersed measured as mean average phylogenetic distance. Each family seems to have its own biogeographic history, and there is no clear pattern for the ectomycorrhizal fungal community at large. Despite the lack of comprehensive taxonomic work to identify fungi in a region, it is still possible to draw some conclusions on their diversity using molecular phylogenetic methods. However, limited success in getting good sequence data from specimens, probably due to preservation issues in the field, and the lack of well annotated molecular data from many regions limit the power of these inferences. peerReviewed

Chemical profiles of arbuscular (AM) and ectomycorrhizal (EM) fungi reveal that differences in decomposability-relevant chemistry are larger between AM and EM fungi than across plant functional groups. The chemical quality of soil carbon (C) inputs is a major factor controlling litter decomposition and soil C dynamics. Mycorrhizal fungi constitute one of the dominant pools of soil microbial C, while their litter quality (chemical proxies of litter decomposability) is understood poorly, leading to major uncertainties in estimating soil C dynamics. We examined litter decomposability of arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungal species using samples obtained from in vitro cultivation. We showed that the chemical composition of AM and EM fungal mycelium differs significantly: EM fungi have higher concentrations of labile (water-soluble, ethanol-soluble) and recalcitrant (non-extractable) chemical components, while AM fungi have higher concentrations of acid-hydrolysable components. Our results imply that differences in decomposability traits among mycorrhizal fungal guilds represent a critically important driver of the soil C cycle, which could be as vital as is recognized for differences among aboveground plant litter. This research was supported by the Vidi grant 016.161.318 (issued to N.A.S. by The Netherlands Organization for Scientific research) and China Scholarship Council (CSC, grant No. 201706040071 issued to W.H.). M.C. was supported by the European Commission’s grant H2020-MSCA-IF-2018 ‘SYMBIO-INC’ (GA 838525). T.V., J.L., and J.H. were supported by the Strategic Research Council at the Academy of Finland (decision 327214, 327342) and the Nessling foundation TWINWIN project. We appreciate the Natural Resources Institute Finland and Prof. Hannu Fritze for supporting chemical analysis. We would like to thank colleagues of the Soil-process group and Chen Li (CML, Leiden University) for discussions. We also thank the anonymous reviewers for their constructive comments and suggestions.

Woodchip bioreactors are being successfully applied to remove nitrate from commercial land-based recirculating aquaculture system (RAS) effluents. In order to understand and optimize the overall function of these bioreactors, knowledge on the microbial communities, especially on the microbes with potential for production or mitigation of harmful substances (e.g. hydrogen sulfide; H2S) is needed. In this study, we quantified and characterized bacterial and fungal communities, including potential H2S producers and consumers, using qPCR and high throughput sequencing of 16S rRNA gene. We took water samples from bioreactors and their inlet and outlet, and sampled biofilms growing on woodchips and on the outlet of the three full-scale woodchip bioreactors treating effluents of three individual RAS. We found that bioreactors hosted a high biomass of both bacteria and fungi. Although the composition of microbial communities of the inlet varied between the bioreactors, the conditions in the bioreactors selected for the same core microbial taxa. The H2S producing sulfate reducing bacteria (SRB) were mainly found in the nitrate-limited outlets of the bioreactors, the main groups being deltaproteobacterial Desulfobulbus and Desulfovibrio. The abundance of H2S consuming sulfate oxidizing bacteria (SOB) was 5–10 times higher than that of SRB, and SOB communities were dominated by Arcobacter and other genera from phylum Epsilonbacteraeota, which are also capable of autotrophic denitrification. Indeed, the relative abundance of potential autotrophic denitrifiers of all denitrifier sequences was even 54% in outlet water samples and 56% in the outlet biofilm samples. Altogether, our results show that the highly abundant bacterial and fungal communities in woodchip bioreactors are shaped through the conditions prevailing within the bioreactor, indicating that the bioreactors with similar design and operational settings should provide similar function even when conditions in the preceding RAS would differ. Furthermore, autotrophic denitrifiers can have a significant role in woodchip biofilters, consuming potentially produced H2S and removing nitrate, lengthening the operational age and thus further improving the overall environmental benefit of these bioreactors.

Traditional rural biotopes such as wood-pastures are species-rich environments that have been created by low-intensity agriculture. Their amount has decreased dramatically during the 20th century in whole Europe due to the intensification of agriculture. Wood-pastures host some fungal species that prefer warm areas and are adapted to semi-open conditions, but still very little is known about fungi in these habitats. We studied how management, historical land-use intensity, present grazing intensity, time since abandonment, and stand conditions affect the species richness and community composition of ectomycorrhizal fungi. We surveyed fruit bodies on three 10 m × 10 m study plots in 36 sites and repeated the surveys three times. Half of the sites were currently unmanaged but had a grazing history. We measured soil pH, soil moisture and the basal area of different tree species, and interviewed landowners about grazing history. We found that the proportion of broadleaved trees, soil pH, and soil moisture are the major drivers of the communities of ectomycorrhizal fungi in boreal wood-pastures. Management or grazing intensity did not have significant effects on fungal species richness, whereas historical land-use intensity seemed to have a negative effect on species richness. To conclude, present stand conditions are the most important factors to evaluate when planning the conservation of ectomycorrhizal fungi living in semi-open forest habitats. peerReviewed

Highlights • We compared fungi, invertebrates and diatoms in model-based stream bioassessment. • Fungal models virtually equaled the overall best model in precision and accuracy. • Fungi were superior in identifying streams degraded by multiple stressors. • Results strongly support the use of microbial communities in stream bioassessment. Degradation of freshwater ecosystems requires efficient tools for assessing the ecological status of freshwater biota and identifying potential cause(s) for their biological degradation. While diatoms and macroinvertebrates are widely used in stream bioassessment, the potential utility of microbial communities has not been fully harnessed. Using data from 113 Finnish streams, we assessed the performance of aquatic leaf-associated fungal decomposers, relative to benthic macroinvertebrates and diatoms, in modelling-based bioassessment. We built multi-taxon niche -type predictive models for fungal assemblages by using genus-based and sequence-based identification levels. We then compared the models’ precision and accuracy in the prediction of reference conditions (number of native taxa) to corresponding models for macroinvertebrates and diatoms. Genus-based fungal model nearly equalled the accuracy and precision of our best model (macroinvertebrates), whereas the sequence-based model was less accurate and tended to overestimate the number of taxa. However, when the models were applied to streams disturbed by anthropogenic stressors (nutrient enrichment, sedimentation and acidification), alone or in combination, the sequence-based fungal assemblages were more sensitive than other taxonomic groups, especially when multiple stressors were present. Microbial leaf decomposition rates were elevated in sediment-stressed streams whereas decomposition attributable to leaf-shredding macroinvertebrates was accelerated by nutrients and decelerated by sedimentation. Comparison of leaf decomposition results to model output suggested that leaf decomposition rates do not detect effectively the presence of multiple simultaneous disturbances. The rapid development of global microbial database may soon enable species-level identification of leaf-associated fungi, facilitating a more precise and accurate modelling of reference conditions in streams using fungal communities. This development, combined with the sensitivity of aquatic fungi in detecting the presence of multiple human disturbances, makes leaf-associated fungal assemblages an indispensable addition in a stream ecologist’s toolbox.

Kirja-arvostelu teoksesta Michael Pollan: Tuntematon mieli, mitä uusi psykedeliatutkimus opettaa (How to Change Your Mind. What the New Science of Psychedelics Teaches Us About Consciousness, Dying, Addiction, Depression, and Transcendence) suom. Mika Pekkola, Like -kustannus, 2021. nonPeerReviewed

According to ecology theory, isolated habitat fragments cannot maintain populations of specialized species. Yet, empirical evidence based on monitoring of the same fragments over time is still limited. We studied the colonization–extinction dynamics of eight wood-decaying fungal species in 16 old-growth forest fragments (Phellinus nigrolimitatusPhellinus ferrugineofuscus

Infections with microsporidian parasites are described in skeletal muscle of burbot Lota lota from Lake Haukivesi, Finland. Infected myocytes contained spores within sporophorous vesicles (SPVs) in contact with host cell cytoplasm, similar to Pleistophora ladogensis in L. lota and smelt Osmerus eperlanus in western Russia and northern Germany. Analysis of small subunit ribosomal RNA (SSU rRNA) gene sequences indicated identity with Myosporidium spraguei in burbot and pike-perch from this lake. The latter is considered a junior synonym of P. ladogensis. Phylogenetic analysis of SSU rRNA sequences resolved the burbot parasite apart from a clade containing the type species P. typicalis, but together with M. merluccius. The parasite is renamed Myosporidium ladogensis (Voronin, 1978) n. comb. Networks of tubular appendages arising from developing meronts and SPVs were associated with degradation of host cell cytoplasm.

Microbes have driven eco-evolutionary adaptations organizing biodiversity from the origin of life. They are ubiquitous and abundant, facilitating the biochemical processes that make Earth habitable and shape ecosystem structures, functions, and services. Recent studies reveal that commensalistic and beneficial microbes associated with wild and domesticated plants may aid in establishing sustainable agriculture for a changing climate. However, developing microbe-based biotechnologies and ecosystem services requires a thorough understanding of the diversity and complexity of microbial interactions with each other and with higher organisms. We discuss the hot and blind spots in contemporary research on plant microbiomes, and how the latest molecular biological techniques and empirical eco-evolutionary approaches could elevate our perception of microbe–plant interactions through multidisciplinary studies. peerReviewed

We contribute to the knowledge on the occurrences and distributions of both aphyllophoroid and heterobasidioid fungi in Finland. We present four species new to Finland, i.e. Helicogloea sebacea, Phanerochaete cremeo-ochracea, Steccherinum cremeoalbum, and Uncobasidium luteolum, as well as 46 new records (locations) of 34 rare or rarely collected species. Additionally, we report on 40 species considered new to a certain subzone of the boreal forest vegetation zone in Finland. These records contain notes on their substrata, and the ecology and distribution of nationally new species are briefly discussed.

Ongoing climate change is increasing the occurrence and intensity of drought episodes worldwide, including in boreal regions not previously regarded as drought prone, and where the impacts of drought remain poorly understood. Ecological connectivity is one factor that might influence community structure and ecosystem functioning post‐drought, by facilitating the recovery of sensitive species via dispersal at both local (e.g. a nearby habitat patch) and regional (from other systems within the same region) scales. In an outdoor mesocosm experiment, we investigated how impacts of drought on boreal stream ecosystems are altered by the spatial arrangement of local habitat patches within stream channels, and variation in ecological connectivity with a regional species pool. We measured basal ecosystem processes underlying carbon and nutrient cycling: (a) algal biomass accrual; (b) microbial respiration; and (c) decomposition of organic matter, and sampled communities of aquatic fungi and benthic invertebrates. An 8‐day drought event had strong impacts on both community structure and ecosystem functioning, including algal accrual, leaf decomposition and microbial respiration, with many of these impacts persisting even after water levels had been restored for 3.5 weeks. Enhanced connectivity with the regional species pool and increased aggregation of habitat patches also affected multiple response variables, especially those associated with microbes, and in some cases reduced the effects of drought to a small extent. This indicates that spatial processes might play a role in the resilience of communities and ecosystem functioning, given enough time. These effects were however insufficient to facilitate significant recovery in algal growth before seasonal dieback began in autumn. The limited resilience of ecosystem functioning in our experiment suggests that even short‐term droughts can have extended consequences for stream ecosystems in the world‘s vast boreal region, and especially on the ecosystem processes and services mediated by algal biofilms.

Increasing evidence suggests that degradation of biodiversity in human populated areas is a threat for the ecosystem processes that are relevant for human well-being. Fungi are a megadiverse kingdom that plays a key role in ecosystem processes and affects human well-being. How urbanization influences fungi has remained poorly understood, partially due to the methodological difficulties in comprehensively surveying fungi. Here we show that both aerial and soil fungal communities are greatly poorer in urban than in natural areas. Strikingly, a fivefold reduction in fungal DNA abundance took place in both air and soil samples already at 1 km scale when crossing the edge from natural to urban habitats. Furthermore, in the air, fungal diversity decreased with urbanization even more than in the soil. This result is counterintuitive as fungal spores are known to disperse over large distances. A large proportion of the fungi detectable in the air are specialized to natural habitats, whereas soil fungal communities comprise a large proportion of habitat generalists. The sensitivity of the aerial fungal community to anthropogenic disturbance makes this method a reliable and efficient bioindicator of ecosystem health in urban areas. peerReviewed

•Primary succession models focus on aboveground vascular plants. However, the prevalence of mosses and lichens, i.e. cryptogams, suggests they play a role in soil successions. Here, we explore whether effects of cryptogams on belowground microbes can facilitate progressive shifts in sand dune succession. •We linked aboveground vegetation, belowground bacterial and fungal communities, and soil chemical properties in six successional stages in Arctic inland sand dunes: bare sand, grass, moss, lichen, ericoid heath and mountain birch forest. •Compared to the bare sand and grass stages, microbial biomass and the proportion of fungi increased in the moss stage, and later stage microbial groups appeared despite the absence of their host plants. Microbial communities of the lichen stage resembled the communities in the vascular plant stages. Bacterial communities correlated better with soil chemical variables than with vegetation and vice versa for fungal communities. The correlation of fungi with vegetation increased with vascular vegetation. •Distinct bacterial and fungal patterns of biomass, richness, and plant‐microbe interactions showed that the aboveground vegetation change structured the bacterial and fungal community differently. The asynchrony of aboveground vs. belowground changes suggests that cryptogams can drive succession towards vascular plant dominance through microbially mediated facilitation in eroded Arctic soil. peerReviewed

Anthropogenic environmental changes have resulted in biodiversity crisis. Although tropical rainforests are one of the global biodiversity hotspots, their biodiversity is still poorly known. Especially fungi are poorly represented in national Red Lists and conservation plans, despite their important role in ecosystem functioning. We studied wood-inhabiting fungi (polypores) in four areas within two Atlantic rainforest fragments in Southeast Brazil. Our aim was to investigate fungal substrate characteristics and community composition. Deadwood amount ranged from 27 to 82 m3/ha among the four study areas and altogether we recorded 53 polypore species. More species were observed in intermediate and late decay stages than in early decay stages, but other deadwood variables did not explain the occurrence of polypores. Similarity in polypore community composition within and among the areas was low. Dissimilarity originated mostly from species turnover from a transect and area to another, and no nestedness in species occurrence pattern was detected. Hence, the observed dissimilarity in community composition was probably a result of heterogeneity in forest composition and structure, instead of environmental gradients or substrate limitations. These results corroborate previous polypore studies from the Atlantic forest in that tropical polypores are specialists toward particular decay stages. To develop ecologically effective conservation program for tropical polypores, more studies are needed on their distribution and abundance globally. peerReviewed

Fungal hyphal growth and branching are essential traits that allow fungi to spread and proliferate in many environments. This sustained growth is essential for a myriad of applications in health, agriculture, and industry. However, comparisons between different fungi are difficult in the absence of standardized metrics. Here, we used a microfluidic device featuring four different maze patterns to compare the growth velocity and branching frequency of fourteen filamentous fungi. These measurements result from the collective work of several labs in the form of a competition named the “Fungus Olympics.” The competing fungi included five ascomycete species (ten strains total), two basidiomycete species, and two zygomycete species. We found that growth velocity within a straight channel varied from 1 to 4 μm/min. We also found that the time to complete mazes when fungal hyphae branched or turned at various angles did not correlate with linear growth velocity. We discovered that fungi in our study used one of two distinct strategies to traverse mazes: high-frequency branching in which all possible paths were explored, and low-frequency branching in which only one or two paths were explored. While the high-frequency branching helped fungi escape mazes with sharp turns faster, the low-frequency turning had a significant advantage in mazes with shallower turns. Future work will more systematically examine these trends.

Generalist species are usually widespread and abundant, and thrive in heterogeneous environments. Specialists, in turn, are generally more restricted in their range, and benefit from more stable conditions. Therefore, increasing human-induced disturbance can have more negative effects on specialist than generalist species. We assessed the specialization of 77 wood-inhabiting fungal species across seven boreal forest types and different substratum qualities. A significantly higher number of specialist species was associated with herb-rich forests and afforested fields than with managed coniferous forests and wood pastures, the number of specialists associated with natural coniferous forests being intermediate. Also, forest type specialists were indicated to be specialists for their substratum tree species as well, but specialization in substratum diameter was not connected with other kinds of specialization. Species with restricted resource or habitat preferences can less readily respond to environmental change, and therefore are more vulnerable to extinction. peerReviewed

The filamentous fungusNeurospora crassa, a model microbial eukaryote, has a life cycle with many features that make it suitable for studying experimental evolution. However, it has lacked a general tool for estimating relative fitness of different strains in competition experiments. To remedy this need, we constructedN. crassastrains that contain a modifiedcsr-1locus and developed an assay for detecting the proportion of the marked strain using a post PCR high resolution melting assay. DNA extraction from spore samples can be performed on 96-well plates, followed by a PCR step, which allows many samples to be processed with ease. Furthermore, we suggest a Bayesian approach for estimating relative fitness from competition experiments that takes into account the uncertainty in measured strain proportions. We show that there is a fitness effect of the mating type locus, as mating typemat ahas a higher competitive fitness thanmat A. Thecsr-1* marker also has a small fitness effect, but is still a suitable marker for competition experiments. As a proof of concept, we estimate the fitness effect of theqde-2mutation, a gene in the RNA interference pathway, and show that its competitive fitness is lower than what would be expected from its mycelial growth rate alone.

Biomass production and decomposition are key processes in ecology, where plants are primarily responsible for production and microbes act in decomposition. Trees harbor foliar microfungi living on and inside leaf tissues, epiphytes, and endophytes, respectively. Early researchers hypothesized that all fungal endophytes are parasites or latent saprophytes, which slowly colonize the leaf tissues for decomposition. While this has been proven for some strains in the terrestrial environment, it is not known whether foliar microfungi from terrestrial origin can survive or perform decomposition in the aquatic environment. On the other hand, aquatic hyphomycetes, fungi which decompose organic material in stream environments, have been suggested to have a plant-associated life phase. Our aim was to study how much the fungal communities of leaves and litter submerged in streams overlap. Ergosterol content on litter, which is an estimator of fungal biomass, was 5–14 times higher in submerged litter than in senescent leaves, indicating active fungal colonization. Leaves generally harbored a different microbiome prior to than after submergence in streams. The Chao1 richness was significantly higher (93.7 vs. 60.7, p = 0.004) and there were more observed operational taxonomic units (OTUs) (78.3 vs. 47.4, p = 0.004) in senescent leaves than in stream-immersed litter. There were more Leotiomycetes (9%, p = 0.014) in the litter. We identified a group of 35 fungi (65%) with both plant- and water-associated lifestyles. Of these, eight taxa had no previous references to water, such as lichenicolous fungi. Six OTUs were classified within Glomeromycota, known as obligate root symbionts with no previous records from leaves. Five members of Basidiomycota, which are rare in aquatic environments, were identified in the stream-immersed litter only. Overall, our study demonstrates that foliar microfungi contribute to fungal diversity in submerged litter.

Keystone microbial species have driven eco-evolutionary processes since the origin of life. However, due to our inability to detect the majority of microbiota, members of diverse microbial communities of fungi, bacteria and viruses have largely been ignored as keystone species in past literature. Here we tested whether heritable Epichloë species of pooidae grasses modulate microbiota of their shared host plant. peerReviewed

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Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.

Phenotypic plasticity is the ability of a genotype to produce different phenotypes under different environmental or developmental conditions. Phenotypic plasticity is a ubiquitous feature of living organisms, and is typically based on variable patterns of gene expression. However, the mechanisms by which gene expression is influenced and regulated during plastic responses are poorly understood in most organisms. While modifications to DNA and histone proteins have been implicated as likely candidates for generating and regulating phenotypic plasticity, specific details of each modification and its mode of operation have remained largely unknown. In this study, we investigated how epigenetic mechanisms affect phenotypic plasticity in the filamentous fungus Neurospora crassa. By measuring reaction norms of strains that are deficient in one of several key physiological processes, we show that epigenetic mechanisms play a role in homeostasis and phenotypic plasticity of the fungus across a range of controlled environments. In general, effects on plasticity are specific to an environment and mechanism, indicating that epigenetic regulation is context dependent and is not governed by general plasticity genes. Specifically, we found that, in Neurospora, histone methylation at H3K36 affected plastic response to high temperatures, H3K4 methylation affected plastic response to pH, but H3K27 methylation had no effect. Similarly, DNA methylation had only a small effect in response to sucrose. Histone deacetylation mainly decreased reaction norm elevation, as did genes involved in histone demethylation and acetylation. In contrast, the RNA interference pathway was involved in plastic responses to multiple environments.

Bioremediation of contaminated soil involves the utilization of innovative technology such as mycoremediation. The capability of fungi to grow in 2,4,6-trinitrotoluene (TNT) contaminated soil, to produce lignin modifying enzymes and to degrade TNT in soil was studied. White-rot fungi, namely Gymnopilus luteofolius, Kuehneromyces mutabilis, and Phanerochaete velutina, were incubated with TNT contaminated non-sterile soil (1000 mg kg−1). All the fungi produced high amounts of manganese peroxidase (MnP) in TNT contaminated soil, but no laccase. The most efficient fungus, P. velutina, degraded 80% of TNT in 2.5 months and was selected for further scale-up experiment with 0.3 t (0.56 m3) of soil and inoculum soil ratio of 1:30. The degradation of TNT was 70% in 49 days, and production of fungal metabolites, namely 4-amino-2,6-diaminotoluene and 2-amino-4,6-diaminotoluene was only 1% of the original TNT concentration. These metabolites were degraded to less than 0.5% during the following 58 days incubation. Fungal remediation process was scaled-up with P. velutina, which tolerated high concentration of TNT and was able to invade the whole mass of soil with only 10 kg of fungal inoculum growing on pine bark. With these parameters the process should be easy to scale-up for soil treatment in field.