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Tags:
RAD sequencing,
Fungi,
Sopp,
Evolutionary biology,
Population genetics,
Genomics
Publications
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Asplund, Johan; Birkemoe, Tone; Kauserud, Håvard; Maurice, Sundy; Ronold, Eivind Kverme & Nordén, Jenni
(2025).
Functional diversity of dead wood promotes species-rich communities of fungi.
Fungal ecology.
ISSN 1754-5048.
79,
p. 1–9.
doi:
10.1016/j.funeco.2025.101473.
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Dead wood is a vital structural element in boreal forests, supporting diverse fungal and insect communities. Wood-inhabiting fungi, in particular, are influenced by both the volume and characteristics of dead wood. However, forestry practices often reduce dead wood quantity and diversity, impacting these communities. This study investigates how different facets of dead wood functional diversity − richness, evenness, divergence, and dispersion − alongside volume, affect fruiting polyporoid and corticioid fungi in Agaricomycetes. Using a paired design of previously clear-cut and near-natural forests, we assess fungal responses to dead wood traits. Our findings show that near-natural forests host greater fungal species richness due to higher dead wood volume and diversity. A combined measure of volume and functional diversity better predicts fungal richness and composition than either factor alone. Notably, functional divergence and evenness are key indicators of niche variety and distribution. These results emphasize the need to enhance both quantity and structural diversity of dead wood in forest management.
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Lü, Dabao Sun; Methlie, Ine-Susanne Hopland; Sønstebø, Jørn Henrik; Andersen, Anneli; Peris, David & Maurice, Sundy Ursula MaryJanne
[Show all 8 contributors for this article]
(2025).
Postglacial History of a Widespread Wood-Decaying Fungus in Europe Suggests Migration out of Multiple Refugia Followed by Admixture.
Molecular Ecology.
ISSN 0962-1083.
34(22),
p. 1–14.
doi:
10.1111/mec.70053.
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While postglacial migration patterns have been well-studied in plants and animals in Europe, the same is not true for microorganisms such as fungi, and it remains unclear whether fungi have followed the same postglacial migration trajectories. In this study, we infer the postglacial history of the widespread wood-decay fungus Trichaptum abietinum in Europe. We investigate whether this fungus resided in multiple glacial refugia, as observed in many plants and animals, and how it migrated following the retreat of the ice. Population genomic analyses of T. abietinum suggest at least two glacial refugia in Europe: a southern refugium extending from Portugal to the Caucasus (potentially formed by several earlier distinct refugia), an eastern refugium and a potential third western refugium. Expansion from these refugia followed by migration and secondary contact has led to a complex genomic pattern of what we call the Mediterranean, Boreal, Atlantic and Central European admixed groups. From the southern and potential western refugia there have likely been northwards expansions resulting in the Mediterranean and Atlantic groups, while the Boreal group probably expanded westwards from the eastern refugium. A contact zone is present in Central Europe, where the Mediterranean and Boreal groups are admixing. In these admixed individuals, the second half of their largest scaffold is entirely inherited from the Boreal group, indicating either strong selection or genomic incompatibilities. In Scandinavia, the Atlantic and Boreal groups are in close contact but with limited admixture. Tajima's D and analyses of linkage disequilibrium decay support a recent history of contraction and expansion of this fungus in Europe. We conclude that the postglacial migration patterns in T. abietinum resemble those observed in several plants and animals, suggesting multiple glacial refugia followed by admixture during northward and westward expansions.
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Kauserud, Håvard; Sanchez, Pedro Maria Martin; Estensmo, Eva Lena Fjeld; Botnen, Synnøve Smebye; Morgado, Luis & Maurice, Sundy Ursula MaryJanne
[Show all 8 contributors for this article]
(2025).
Yeasts Prefer Daycares and Molds Prefer Private Homes.
Microbial Ecology.
ISSN 0095-3628.
88(1).
doi:
10.1007/s00248-025-02505-4.
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Worldwide, people spend most of their time indoors; in their homes, workplaces, schools, and daycares. Indoor fungi can cause negative health effects due to the production of toxins or volatiles that trigger the immune system of the occupants. To what degree indoor fungi (mycobiomes) differ between buildings with different usage is poorly known. Here, we compare the indoor mycobiomes in 123 children’s daycare centers and 214 private homes throughout Norway, as revealed by metabarcoding of DNA extracted from dust samples collected by community scientists. Although the fungal richness per se was similar in dust samples from daycares and homes, the fungal community composition differed. Yeast fungi, distributed mainly across the orders Saccharomycetales, Filobasidiales, and Tremellales, were proportionally more abundant in the daycares, while filamentous fungi, including spore-producing molds such as Aspergillus, Penicillum, and Cladosporium, were relatively more abundant in homes. Number of occupants, which is considerably higher in daycares, correlated significantly with the fungal community shift. We hypothesize that the density of occupants and their age distribution drive the systematic difference of yeasts and filamentous fungi in the two building types.
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Dirks, Alden C.; Methven, Andrew S.; Miller, Andrew N.; Orozco-Quime, Michelle; Maurice, Sundy Ursula MaryJanne & Bonito, Gregory
[Show all 20 contributors for this article]
(2025).
Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota).
Molecular Phylogenetics and Evolution.
ISSN 1055-7903.
205,
p. 1–19.
doi:
10.1016/j.ympev.2025.108286.
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Lunde, Lisa Fagerli; Birkemoe, Tone; Sverdrup-Thygeson, Anne; Asplund, Johan; Halvorsen, Rune & Kjønaas, O. Janne
[Show all 11 contributors for this article]
(2025).
Towards repeated clear-cutting of boreal forests – a tipping point for biodiversity?
Biological Reviews.
ISSN 1464-7931.
100(3),
p. 1181–1205.
doi:
10.1111/brv.13180.
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Boreal forests are important carbon sinks and host a diverse array of species that provide important ecosystem functions. Boreal forests have a long history of intensive forestry, in which even-aged management with clear-cutting has been the dominant harvesting practice for the past 50–80 years. As a second cycle of clear-cutting is emerging, there is an urgent need to examine the effects of repeated clear-cutting events on biodiversity. Clear-cutting has led to reduced numbers of old and large trees, decreased volumes of dead wood of varied decay stages and diameters, and altered physical and chemical compositions of soils. The old-growth boreal forest has been fragmented and considerably reduced. Here, we review short- and long-term (≥50 years) effects of clear-cutting on boreal forest biodiversity in four key substrates: living trees, dead wood, ground and soil. We then assess landscape-level changes (habitat fragmentation and edge effects) on this biodiversity. There is evidence for long-term community changes after clear-cutting for several taxa: epiphytic lichens; saproxylic fungi, bryophytes and insects; epigeic bryophytes; and soil snails, bacteria, and ectomycorrhizal fungi. Long-term declines in species richness were found for saproxylic fungi, bryophytes and true flies. However, for the majority of taxa, long-term effects of clear-cutting are not well understood. On the landscape level, reduced connectivity to old-growth forests has negative effects on several species of fungi, lichens, bryophytes and insects, notably among Red-Listed species. Furthermore, altered microclimate near clear-cut edges negatively affects epiphytic lichens and epigeic arthropods, implying complex effects of habitat fragmentation. Repeated cycles of clear-cutting might pose even stronger pressures on boreal forest biodiversity due to continued fragmentation of old-growth forests and accumulation of extinction debts. Examining the broad effects of forestry on biodiversity across the boreal biome is crucial: (i) to increase our knowledge of long-term and landscape-level effects of former clear-cutting; and (ii) to gain a better understanding of how forestry will affect biodiversity and, subsequently, ecosystem functioning, with repeated cycles of clear-cutting.
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Zhao, Heng; Wu, Fang; Maurice, Sundy; Pavlov, Igor N.; Krutovsky, Konstantin V. & Liu, Hong-Gao
[Show all 8 contributors for this article]
(2024).
Large-scale phylogenomic insights into the evolution of the Hymenochaetales.
Mycology: An International Journal on Fungal Biology.
ISSN 2150-1203.
doi:
10.1080/21501203.2024.2391527.
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The Hymenochaetales is an order with most species as wood-inhabiting fungi that have high phylogenetic complexity and morphological diversity. Species in this order play important roles in forest ecosystems and include wood decomposers, pathogens, and those that form ectomycorrhizal associations. However, we have limited knowledge of the patterns of large-scale evolutionary history of the order. In this study, using 171 genomes, including 113 newly assembled, we reconstructed the phylogenomic relationships, divergence times, biogeographic patterns, morphological evolution of basidiomata, and patterns of speciation/extinction in the Hymenochaetales. The phylogenomic relationships of 12 families within the Hymenochaetales suggested that 10 families can be accepted, and 2 families rejected. Molecular clock dating analyses suggested that the Hymenochaetales possibly started a rapid family-wide and genus-wide radiation during the early Cretaceous to late Jurassic and Cretaceous, respectively. Reconstruction of the ancestral state implied that Hymenochaetales probably originated from the temperate regions of Asia, with the basidiomata of the common ancestor likely being a corticioid species that rapidly transformed between the early Cretaceous and late Jurassic, coinciding with radiations at the family level. Furthermore, we detected a gradually increasing trend of speciation, extinction, and net diversification rates. We provided large-scale genomes of the Hymenochaetales and revealed evolutionary history patterns, which are key to understanding the evolution of fungi.
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Asplund, Johan; Nordén, Jenni; Kjønaas, O. Janne; Madsen, Rieke Lo; Lunde, Lisa Fagerli & Birkemoe, Tone
[Show all 18 contributors for this article]
(2024).
Long term effects of forest management on forest structure and dead wood in mature boreal forests.
Forest Ecology and Management.
ISSN 0378-1127.
572.
doi:
10.1016/j.foreco.2024.122315.
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The history of forestry in Fennoscandia spans five centuries, with clear-cutting being the dominant practice since the mid-20th century. This has led to a significant transformation of the forest landscape. In this study we investigated long-term effects of clear-cutting on forest structure and dead wood volumes. We established twelve pairs of spruce forest sites in southeastern Norway, each pair constituting of a mature, previously clear-cut stand and its near-natural counterpart with similar edaphic factors. The near-natural stands had 2.8 times higher volumes of dead wood and a larger proportion of dead wood in late stages of decay. The near-natural stands had on average 36.8 ± 9.1 m3 ha− 1 of downed dead wood and 24.1 ± 6.2 m3 ha− 1 of standing dead wood. Corresponding numbers for the previously clear-cut stands were 10.2 ± 2.8 m3 ha− 1 and 11.9 ± 3.7 m3 ha− 1 . Forests with lower volumes of dead wood often also had lower connectivity of old spruce forests, which potentially have further negative effects on biodiversity. Furthermore, near-natural stands displayed greater tree size heterogeneity, resulting in a wider variation in light conditions. While no difference was observed in living tree volume, we found only weak evidence for higher basal area in the previously clear-cut stands, which had a higher stem density with more slender stems and shorter crowns. Our findings suggest that managed forests do not develop structures typical of near-natural forests before they become mature for logging. We stress the importance of a thorough site selection for studies of management effects, as forest management history may be confounded with productivity and other edaphic factors. Experimental designs like ours are vital for testing how differences in structure and deadwood volumes, driven by forest management, translate into variations in biodiversity, carbon sequestration and ecosystem functioning in future studies Coarse woody debris Clear-cutting forestry Norway spruce Structural heterogeneity
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Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; James, Timothy Y.; Rieseberg, Loren H. & Maurice, Sundy
[Show all 9 contributors for this article]
(2024).
Reticulate evolution and rapid development of reproductive barriers upon secondary contact in a forest fungus.
Current Biology.
ISSN 0960-9822.
34(19),
p. 4513–4525.
doi:
10.1016/j.cub.2024.08.046.
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Reproductive barriers between sister species of the mushroom-forming fungi tend to be stronger in sympatry, leading to speculation on whether they are being reinforced by selection against hybrids. We have used population genomic analyses together with in vitro crosses of a global sample of the wood decay fungus Trichaptum abietinum to investigate reproductive barriers within this species complex and the processes that have shaped them. Our phylogeographic analyses show that T. abietinum is delimited into six major genetic groups: one in Asia, two in Europe, and three in North America. The groups present in Europe are interfertile and admixed, whereas our crosses show that the North American groups are reproductively isolated. In Asia, a more complex pattern appears, with partial intersterility between subgroups that likely originated independently and more recently than the reproductive barriers in North America. We found pre-mating barriers in T. abietinum to be moderately correlated with genomic divergence, whereas mean growth reduction of the mated hybrids showed a strong correlation with increasing genomic divergence. Genome-wide association analyses identified candidate genes with programmed cell death annotations, which are known to be involved in intersterility in distantly related fungi, although their link here remains unproven. Our demographic modeling and phylogenetic network analyses fit a scenario where reproductive barriers in Trichaptum abietinum could have been reinforced upon secondary contact between groups that diverged in allopatry during the Pleistocene glacial cycles. Our combination of experimental and genomic approaches demonstrates how T. abietinum is a tractable system for studying speciation mechanisms.
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Zhao, Heng; Dai, Yu-Cheng; Wu, Fang; Liu, Xiao-Yong; Maurice, Sundy & Krutovsky, Konstantin V.
[Show all 10 contributors for this article]
(2023).
Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics with an Emphasis on Coltricia.
Genome Biology and Evolution (GBE).
15(8),
p. 1–15.
doi:
10.1093/gbe/evad136.
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Abstract To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.
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Bonin, Frédéric; Maurice, Sundy & Bastit, Félix
(2023).
Une planification des forêts à adapter face à des défis encore inconnus.
Revue forestière française.
ISSN 0035-2829.
74(2),
p. 293–298.
doi:
10.20870/revforfr.2023.7613.
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Dans le cadre du Forum Jeunes Chercheurs des REGEFOR 2020, trois jeunes chercheurs – aux champs de prédilection divers (respectivement sciences de gestion, mycologie et sciences économiques) – ont réfléchi à une approche croisée des crises que traversent les forêts. Il leur a semblé que la planification forestière était actuellement soumise à de grands défis qui pourront être résolus, d’une part, en améliorant la compréhension des écosystèmes forestiers et leurs interactions avec la société, et d’autre part, en acceptant des régimes de crise encore mal connus et donc en faisant appel à davantage de souplesse et d’agilité pour une “nouvelle” gestion et planification forestière. Messages clésLa planification forestière doit répondre à des nouveaux défis.La compréhension des interactions forêt-société doit être améliorée.Une gestion plus souple doit être mise en place.
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Sønstebø, Jørn Henrik; Trucchi, Emiliano; Nordén, Jenni; Skrede, Inger; Miettinen, Otto & Haridas, Sajeet
[Show all 11 contributors for this article]
(2022).
Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures.
Molecular Ecology.
ISSN 0962-1083.
31(7),
p. 1963–1979.
doi:
10.1111/mec.16369.
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Genome sequencing of spatially distributed individuals sheds light on how evolution structures genetic variation. Populations of Phellopilus nigrolimitatus, a red-listed
wood-inhabiting fungus associated with old-growth coniferous forests, have decreased in size over the last century due to a loss of suitable habitats. We assessed
the population genetic structure and investigated local adaptation in P. nigrolimitatus,
by establishing a reference genome and genotyping 327 individuals sampled from
24 locations in Northern Europe by RAD sequencing. We revealed a shallow population genetic structure, indicating large historical population sizes and high levels of
gene flow. Despite this weak substructuring, two genetic groups were recognized;
a western group distributed mostly in Norway and an eastern group covering most
of Finland, Poland and Russia. This substructuring may reflect coimmigration with
the main host, Norway spruce (Picea abies), into Northern Europe after the last ice
age. We found evidence of low levels of genetic diversity in southwestern Finland,
which has a long history of intensive forestry and urbanization. Numerous loci were
significantly associated with one or more environmental factors, indicating adaptation to specific environments. These loci clustered into two groups with different
associations with temperature and precipitation. Overall, our findings indicate that
the current population genetic structure of P. nigrolimitatus results from a combination
of gene flow, genetic drift and selection. The acquisition of similar knowledge especially over broad geographic scales, linking signatures of adaptive genetic variation to
evolutionary processes and environmental variation, for other fungal species will undoubtedly be useful for assessment of the combined effects of habitat fragmentation
and climate change on fungi strongly bound to old-growth forests.
demography, forest fragmentation, genotype-environment associations, local adaptation, Picea
abies, post-glacial colonization, wood decay fungi
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Estensmo, Eva Lena Fjeld; Botnen, Synnøve Smebye; Maurice, Sundy; Sanchez, Pedro Maria Martin; Morgado, Luis & Engh, Ingeborg Bjorvand
[Show all 9 contributors for this article]
(2022).
The Indoor Mycobiomes of Daycare Centers Are Affected by Occupancy and Climate.
Applied and Environmental Microbiology.
ISSN 0099-2240.
88(6).
doi:
10.1128/aem.02113-21.
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With an alarming increase in chronic diseases like childhood asthma and allergies, there is an increased focus on the exposure of young children to indoor biological and chemical air pollutants. Our study of 125 daycares throughout Norway demonstrates that the indoor mycobiome not only reflects cooccurring outdoor fungi but also includes a high abundance of yeast and mold fungi with an affinity for indoor environments.
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Lunde, Lisa Fagerli; Birkemoe, Tone; Kauserud, Håvard; Boddy, Lynne; Jacobsen, Rannveig Margrete & Morgado, Luis
[Show all 8 contributors for this article]
(2022).
DNA metabarcoding reveals host-specific communities of arthropods residing in fungal fruit bodies.
Proceedings of the Royal Society of London. Biological Sciences.
ISSN 0962-8452.
289(1968).
doi:
10.1098/rspb.2021.2622.
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Biological communities within living organisms are structured by their
host’s traits. How host traits affect biodiversity and community composition
is poorly explored for some associations, such as arthropods within fungal
fruit bodies. Using DNA metabarcoding, we characterized the arthropod
communities in living fruit bodies of 11 wood-decay fungi from boreal
forests and investigated how they were affected by different fungal traits.
Arthropod diversity was higher in fruit bodies with a larger surface
area-to-volume ratio, suggesting that colonization is crucial to maintain
arthropod populations. Diversity was not higher in long-lived fruit bodies,
most likely because these fungi invest in physical or chemical defences
against arthropods. Arthropod community composition was structured by
all measured host traits, namely fruit body size, thickness, surface area,
morphology and toughness. Notably, we identified a community gradient
where soft and short-lived fruit bodies harboured more true flies, while
tougher and long-lived fruit bodies had more oribatid mites and beetles,
which might reflect different development times of the arthropods.
Ultimately, close to 75% of the arthropods were specific to one or two
fungal hosts. Besides revealing surprisingly diverse and host-specific arthropod communities within fungal fruit bodies, our study provided insight into
how host traits structure communities.
host traits, arthropod, DNA metabarcoding,
wood-decay fungi, fruit body, insect–fungus
interactions
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Estensmo, Eva Lena Fjeld; Maurice, Sundy Ursula Mary Jane; Morgado, Luis; Martin-Sanchez, Pedro Maria; Skrede, Inger & Kauserud, Håvard
(2021).
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species.
Molecular Ecology Resources.
ISSN 1755-098X.
doi:
10.1111/1755-0998.13329.
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DNA metabarcoding has become a powerful approach for analysing complex communities from environmental samples, but there are still methodological challenges limiting its full potential. While conserved DNA markers, like 16S and 18S, often are not able to discriminate among closely related species, other more variable markers – like the fungal ITS region, may include considerable intraspecific variation, which can lead to oversplitting of species during DNA metabarcoding analyses. Here we assessed the effects of intraspecific sequence variation in DNA metabarcoding by analysing local populations of eleven fungal species. We investigated the allelic diversity of ITS2 haplotypes using both Sanger sequencing and high throughput sequencing (HTS) coupled with error correction with the software dada2. All the eleven species, except one, included some level of intraspecific variation in the ITS2 region. Overall, we observed a high correspondence between haplotypes generated by Sanger sequencing and HTS, with the exception of a few additional haplotypes detected using either approach. These extra haplotypes, typically occurring in low frequencies, were probably due to PCR and sequencing errors or intragenomic variation in the rDNA region. The presence of intraspecific (and possibly intragenomic) variation in ITS2 suggest that haplotypes (or ASVs) should not be used as basic units in ITS‐based fungal community analyses, but an extra clustering step is needed to approach species‐level resolution.
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Maurice, Sundy Ursula Mary Jane; Arnault, Gontran; Nordén, Jenni; Botnen, Synnøve Smebye; Miettinen, Otto & Kauserud, Håvard
(2021).
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi.
The ISME Journal.
ISSN 1751-7362.
15,
p. 1445–1457.
doi:
10.1038/s41396-020-00862-1.
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porocarps (fruit bodies) are the sexual reproductive stage in the life cycle of many fungi. They are highly nutritious and consequently vulnerable to grazing by birds and small mammals, and invertebrates, and can be infected by microbial and
fungal parasites and pathogens. The complexity of communities thriving inside sporocarps is largely unknown. In this study,
we revealed the diversity, taxonomic composition and host preference of fungicolous fungi (i.e., fungi that feed on other
fungi) in sporocarps. We carried out DNA metabarcoding of the ITS2 region from 176 sporocarps of 11 wood-decay fungal
host species, all collected within a forest in northeast Finland. We assessed the influence of sporocarp traits, such as lifespan,
morphology and size, on the fungicolous fungal community. The level of colonisation by fungicolous fungi, measured as the
proportion of non-host ITS2 reads, varied between 2.8–39.8% across the 11 host species and was largely dominated by
Ascomycota. Host species was the major determinant of the community composition and diversity of fungicolous fungi,
suggesting that host adaptation is important for many fungicolous fungi. Furthermore, the alpha diversity was consistently
higher in short-lived and resupinate sporocarps compared to long-lived and pileate ones, perhaps due to a more hostile
environment for fungal growth in the latter too. The fungicolous fungi represented numerous lineages in the fungal tree of
life, among which a significant portion was poorly represented with reference sequences in databases.
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Skrede, Inger; Murat, Claude; Hess, Jaqueline; Maurice, Sundy Ursula Mary Jane; Sønstebø, Jørn Henrik & Kohler, Annegret
[Show all 11 contributors for this article]
(2021).
Contrasting demographic histories revealed in two invasive populations of the dry rot fungus Serpula lacrymans.
Molecular Ecology.
ISSN 0962-1083.
30(12),
p. 2772–2789.
doi:
10.1111/mec.15934.
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Globalization and international trade have impacted organisms around the world leading to a considerable number of species establishing in new geographic areas. Many organisms have taken advantage of human-made environments, including buildings. One such species is the dry rot fungus Serpula lacrymans, which is the most aggressive wood-decay fungus in indoor environments in temperate regions. Using population genomic analyses of 36 full genome sequenced isolates, we demonstrated that European and Japanese isolates are highly divergent and the populations split 3000–19,000 generations ago, probably predating human influence. Approximately 250 generations ago, the European population went through a tight bottleneck, probably corresponding to the fungus colonization of the built environment in Europe. The demographic history of these populations, probably lead to low adaptive potential. Only two loci under selection were identified using a Fst outlier approach, and selective sweep analyses identified three loci with extended haplotype homozygosity. The selective sweep analyses found signals in genes possibly related to decay of various substrates in Japan and in genes involved DNA replication and protein modification in Europe. Our results suggest that the dry rot fungus independently established in indoor environments in Europe and Japan and that invasive species can potentially establish large populations in new habitats based on a few colonizing individuals.
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Hage, Hayat; Miyauchi, Shingo; Virágh, Máté; Drula, Elodie; Min, Byoungnam & Chaduli, Delphine
[Show all 37 contributors for this article]
(2021).
Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.
Environmental Microbiology.
ISSN 1462-2912.
23(10),
p. 5716–5732.
doi:
10.1111/1462-2920.15423.
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Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.
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Martin-Sanchez, Pedro Maria; Estensmo, Eva Lena Fjeld; Morgado, Luis; Maurice, Sundy Ursula Mary Jane; Engh, Ingeborg Bjorvand & Skrede, Inger
[Show all 7 contributors for this article]
(2021).
Analysing indoor mycobiomes through a large‐scale citizen science study in Norway.
Molecular Ecology.
ISSN 0962-1083.
30,
p. 2689–2705.
doi:
10.1111/mec.15916.
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In the built environment, fungi can cause important deterioration of building materials and adverse health effects on occupants. Increased knowledge about indoor mycobiomes from different regions of the world, and their main environmental determinants, will enable improved indoor air quality management and identification of health risks. This is the first citizen science study about indoor mycobiomes at a large geographical scale in Europe, including 271 houses from Norway and 807 dust samples from three house compartments: outside of the building, living room and bathroom. The fungal community composition determined by DNA metabarcoding was clearly different between indoor and outdoor samples, but there were no significant differences between the two indoor compartments. The 32 selected variables, related to the outdoor environment, building features and occupant characteristics, accounted for 15% of the overall variation in community composition, with the house compartment as the key factor (7.6%). Next, the climate was the main driver of the dust mycobiomes (4.2%), while building and occupant variables had significant but minor influences (1.4% and 1.1%, respectively). The house‐dust mycobiomes were dominated by ascomycetes (⁓70%) with Capnodiales and Eurotiales as the most abundant orders. Compared to the outdoor samples, the indoor mycobiomes showed higher species richness, which is probably due to the mixture of fungi from outdoor and indoor sources. The main indoor indicator fungi belonged to two ecological groups with allergenic potential: xerophilic molds and skin‐associated yeasts. Our results suggest that citizen science is a successful approach for unraveling the built microbiome at large geographical scales.
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Estensmo, Eva Lena F.; Morgado, Luis; Maurice, Sundy; Sanchez, Pedro Maria Martin; Engh, Ingeborg B. & Mattsson, Johan
[Show all 8 contributors for this article]
(2021).
Spatiotemporal variation of the indoor mycobiome in daycare centers.
Microbiome.
9(1),
p. 1–12.
doi:
10.1186/s40168-021-01167-x.
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Background Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and between buildings, depending on occupancy, climate, and season. In order to evaluate indoor air quality, and the effect of usage and seasonality, we investigated the spatiotemporal variation in the indoor mycobiomes of two daycare centers. We collected dust samples from different rooms throughout a year and analyzed their mycobiomes using DNA metabarcoding. Results The fungal community composition in rooms with limited occupancy (auxiliary rooms) was similar to the outdoor samples, and clearly different from the rooms with higher occupancy (main rooms). The main rooms had higher abundance of Ascomycota, while the auxiliary rooms contained comparably more Basidiomycota. We observed a strong seasonal pattern in the mycobiome composition, mainly structured by the outdoor climate. Most markedly, basidiomycetes of the orders Agaricales and Polyporales, mainly reflecting typical outdoor fungi, were more abundant during summer and fall. In contrast, ascomycetes of the orders Saccharomycetales and Capnodiales were dominant during winter and spring. Conclusions Our findings provide clear evidences that the indoor mycobiomes in daycare centers are structured by occupancy as well as outdoor seasonality. We conclude that the temporal variability should be accounted for in indoor mycobiome studies and in the evaluation of indoor air quality of buildings.
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Nordén, Jenni; Abrego, Nerea; Boddy, Lynne; Bässler, Claus; Dahlberg, Anders & Halme, Panu
[Show all 16 contributors for this article]
(2020).
Ten principles for conservation translocations of threatened wood-inhabiting fungi.
Fungal ecology.
ISSN 1754-5048.
44.
doi:
10.1016/j.funeco.2020.100919.
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Unlike for many other organism groups, conservation translocations of fungi are still rare.
Encouraged by recent successful translocations, there is a growing interest in applying this
conservation tool to threatened wood-inhabiting fungi. When combined with other conservation or
restoration measures, translocation can be an effective measure for preventing further population
decline in the short term, and species extinctions in the long term. Translocations can be appropriate
for rare and specialist fungal species that occur as small local populations in isolated patches across
fragmented landscapes, where there is a low likelihood of successful dispersal between distant host
trees that have special qualities and are situated in suitable conditions. As species translocations are
a controversial topic, the pros and cons of translocation as a conservation tool for threatened fungi
need careful consideration. We highlight the uncertainties and risks that are connected to fungal
translocations, and propose ten principles adhering to the precautionary principle.
Cryptic species; dispersal limitation; extinction; forest fragmentation; genetic variation; habitat loss;
population viability; reintroduction; species interactions; species restoration
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Maurice, Sundy Ursula Mary Jane; Montes, Melanie; Nielsen, Bent J.; Bødker, Lars; Martin, Michael David & Jønck, Carina
[Show all 8 contributors for this article]
(2019).
Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity.
Molecular plant pathology.
ISSN 1464-6722.
20(8),
p. 1134–1146.
doi:
10.1111/mpp.12819.
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An outbreak of the potato late blight pathogen Phytophthora infestans in Denmark was characterized in order to resolve the population structure and determine to what extent sexual reproduction was occurring. A standard set of microsatellite simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers generated using restriction site‐associated DNA sequencing (RAD‐seq) were employed in parallel. A total of 83 individuals, isolated from seven different potato fields in 2014, were analysed together with five Danish whole‐genome sequenced isolates, as well as two Mexican individuals used as an outgroup. From a filtered dataset of 55 288 SNPs, population genomics analyses revealed no sign of recombination, implying clonality. In spite of this, multilocus genotypes were unique to individual potato fields, with little evidence of gene flow between fields. Ploidy analysis performed on the SNPs dataset indicated that the majority of isolates were diploid. These contradictory results with clonality and high genotypic diversity may suggest that rare sexual events likely still contribute to the population. Comparison of the results generated by SSRs vs SNPs data indicated that large marker sets, generated by RAD‐seq, may be advised going forward, as it provides a higher level of genetic discrimination than SSRs.
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Maurice, Sundy; Skrede, Inger; LeFloch, Gaetan; Barbier, Georges & Kauserud, Håvard
(2014).
Population structure of Serpula lacrymans in Europe with an outlook to the French population.
Mycologia.
ISSN 0027-5514.
106(5),
p. 889–895.
doi:
10.3852/12-344.
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Skrede, Inger; Hess, Jaqueline; Sønstebø, Jørn Henrik; Maurice, Sundy Ursula Mary Jane; Eastwood, Daniel C. & Kauserud, Håvard
(2018).
How to decompose a house? Comparative and population genomic analyses of the dry rot fungus.
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Ronold, Eivind Kverme; Kauserud, Håvard; Maurice, Sundy & Skrede, Inger
(2025).
Concerning fungi: Community ecology and diversity in natural and managed boreal forests.
Universitetet i Oslo.
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Fungal communities in Norwegian forests are highly diverse and species-rich. Fulfilling roles as mutualists, pathogens, parasites and decomposers, it is hard to imagine how a forest ecosystem would function without fungi. In this thesis I describe fungal communities in Norwegian boreal forests and how they are structured by the environment and the composition of vegetation and how forestry may impact fungal communities following clear-cutting.
In the first paper I use DNA-metabarcoding to describe how soil fungal communities in a forest reserve with negligible human impact are structured and influenced by the vegetation composition, soil edaphic parameters and topographic factors in the landscape. Soil was sampled along several transects representing transition from moist, shaded spruce forests to dry and topographically exposed pine forests, a common landscape characteristic in boreal ecosystem. I show that vegetation composition is the major driver of fungal community structure, more so than either topography or soil parameters. This likely reflects the tight symbiosis between many fungal species and plants, and the fact that vegetation and soil fungi are structured by similar processes over longer time scales.
The next three papers are from the EcoForest project, investigating fungal communities in south-eastern Norwegian spruce forests in the context of clear-cutting and long-term regeneration of community composition. By setting up 12 paired forest sites, with a plot in a five-to-nine-decade old previously clear-cut forest and a nearby plot in a forest that has never been clear-cut, we aim to investigate to what extent fungal communities in soil and deadwood y recover following clear-cutting, using the near-natural sites as reference. Applying DNA-metabarcoding, I found no differences in species richness or species diversity between soil fungal communities in the previous clear-cut and the near-natural forests. Instead, species identity and the relative abundances of species in the community are different. Previously clear-cut plots seemingly have a larger abundance of soil fungi adapted for faster nutrient turnover and more accessible forms of nutrients, while the near-natural forest soil fungal communities supported more slow-growing fungi adapted to accessing organically bound nutrients and slower nutrient turnover.
I also describe a long-term shift in the deadwood-inhabiting fungal communities. Many wood-decomposing fungi in the Polyporales, Hymenochaetales and Helotiales were more abundant in near-natural forest sites. This was not simply due to the forest type but was strongly driven by the diversity and variability of the deadwood on the forest floor. In essence, a previous clear-cut forest with high diversity of deadwood would host higher fungal richness and diversity than a near-natural forest with low deadwood variability. The majority of red-listed fungal species, however, were restricted to the near-natural forests. I found, in addition, a vast diversity of yeasts outnumbering the more conspicuous deadwood decomposing fungi. This community also exhibited compositional shifts in response to deadwood variability among sites.
Finally, I combine the data from soil and deadwood to investigate how certain species in the ectomycorrhizal community may grow and proliferate within deadwood on the forest floor. The few ectomycorrhizal species inhabiting deadwood were consistent across sites and comprised species known to access and mobilize nitrogen bound in complex organic forms. For some species this may represent an important adaptation in boreal forest soils, where soluble nitrogen is generally low and competition with soil saprotrophs is high, additionally, there is competition with other ectomycorrhizal species more specialized for the fast absorption of mineral nutrients. Deadwood on the forest floor may thus act as “nutrient banks” for certain ectomycorrhizal species adapted to this habitat, characterized by low carbon availability, but high concentrations of organic nitrogen and other vital nutrients.
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Lü, Dabao Sun; Peris, David; Skrede, Inger; Kauserud, Håvard; Ravinet, Mark & Sønstebø, Jørn Henrik
[Show all 8 contributors for this article]
(2023).
Fungi contain multitudes: Tempo and modes of evolution in the purplepore bracket fungus Trichaptum.
Universitetet i Oslo.
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Evolution has brought to life an immense diversity of forms, lifestyles and species in the fungi. Yet our knowledge about how this diversity has been generated remains sparse. I have taken a closer look at evolution in a group of wood decay fungi in genus Trichaptum, with the aim of gaining more insight about the speciation process in fungi. Trichaptum species are common, easy to culture, and can be crossed in the lab. Moreover, they have varying degrees of reproductive barriers, and these attributes make them suitable for speciation studies as the development of reproductive barriers is central to the speciation process. I have established a comprehensive culture collection that have been put through crossing experiments and whole genome DNA sequencing to investigate the evolutionary history of different Trichaptum lineages and the genetic causes of their reproductive barriers. Analyses of the sequenced genomes revealed multiple hybridization events, which speaks to the importance of reticulate evolution in these fungi. The studies cover evolution in genus Trichaptum at multiple scales, from the relatively recent changes occurring within Europe in T. abietinum, to changes that have happened between continents and distinctly differentiated species across larger time spans. Altogether this work demonstrates how multiple evolutionary forces across different temporal and genetic scales have interacted to shape the current diversity and genomic landscape in Trichaptum.
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Published
Sep. 12, 2014 1:40 PM
- Last modified
Jan. 4, 2024 10:05 AM
