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Publications (10 of 34) Show all publications
Vowles, T., Lindwall, F., Ekblad, A., Bahram, M., Furneaux, B. R., Ryberg, M. & Björk, R. G. (2018). Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone. Ecology and Evolution, 8(2), 1019-1030
Open this publication in new window or tab >>Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone
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2018 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, no 2, p. 1019-1030Article in journal (Refereed) Published
Abstract [en]

Mycorrhizal associations are widespread in high‐latitude ecosystems and are potentially of great importance for global carbon dynamics. Although large herbivores play a key part in shaping subarctic plant communities, their impact on mycorrhizal dynamics is largely unknown. We measured extramatrical mycelial (EMM) biomass during one growing season in 16‐year‐old herbivore exclosures and unenclosed control plots (ambient), at three mountain birch forests and two shrub heath sites, in the Scandes forest‐tundra ecotone. We also used high‐throughput amplicon sequencing for taxonomic identification to investigate differences in fungal species composition. At the birch forest sites, EMM biomass was significantly higher in exclosures (1.36 ± 0.43 g C/m2) than in ambient conditions (0.66 ± 0.17 g C/m2) and was positively influenced by soil thawing degree‐days. At the shrub heath sites, there was no significant effect on EMM biomass (exclosures: 0.72 ± 0.09 g C/m2; ambient plots: 1.43 ± 0.94). However, EMM biomass was negatively related to Betula nana abundance, which was greater in exclosures, suggesting that grazing affected EMM biomass positively. We found no significant treatment effects on fungal diversity but the most abundant ectomycorrhizal lineage/cortinarius, showed a near‐significant positive effect of herbivore exclusion (p = .08), indicating that herbivory also affects fungal community composition. These results suggest that herbivory can influence fungal biomass in highly context‐dependent ways in subarctic ecosystems. Considering the importance of root‐associated fungi for ecosystem carbon balance, these findings could have far‐reaching implications.

Keywords
Betula nana, Betula pubescens subsp, czerepanovii, ectomycorrhiza, extramatrical mycelia, herbivory, mountain birch forest, shrub heath
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-348781 (URN)10.1002/ece3.3657 (DOI)000425822800019 ()29375775 (PubMedID)
Funder
Swedish Research Council Formas, 214-2010-1411
Available from: 2018-04-17 Created: 2018-04-17 Last updated: 2018-04-17Bibliographically approved
Tedersoo, L., Sanchez-Ramirez, S., Koljalg, U., Bahram, M., Doring, M., Schigel, D., . . . Abarenkov, K. (2018). High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal diversity, 90(1), 135-159
Open this publication in new window or tab >>High-level classification of the Fungi and a tool for evolutionary ecological analyses
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2018 (English)In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 90, no 1, p. 135-159Article in journal (Refereed) Published
Abstract [en]

High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

Place, publisher, year, edition, pages
SPRINGER, 2018
Keywords
51 new taxa, Species Hypothesis, Taxonomy of fungi, Phylogenetic classification, Subkingdom, Phylum, Nucleariae, Ascomycota, Aphelidiomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Zoopagomycota
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-358556 (URN)10.1007/s13225-018-0401-0 (DOI)000434755000004 ()
Available from: 2018-09-21 Created: 2018-09-21 Last updated: 2018-09-21Bibliographically approved
Pent, M., Hiltunen, M., Poldmaa, K., Furneaux, B. R., Hildebrand, F., Johannesson, H., . . . Bahram, M. (2018). Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies. Environmental Microbiology, 20(5), 1641-1650
Open this publication in new window or tab >>Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies
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2018 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 20, no 5, p. 1641-1650Article in journal (Refereed) Published
Abstract [en]

Despite increasing knowledge on host-associated microbiomes, little is known about mechanisms underlying fungus-microbiome interactions. This study aimed to examine the relative importance of host genetic, geographic and environmental variations in structuring fungus-associated microbiomes. We analyzed the taxonomic composition and function of microbiomes inhabiting fungal fruiting-bodies in relation to host genetic variation, soil pH and geographic distance between samples. For this, we sequenced the metagenomes of 40 fruiting-bodies collected from six fairy rings (i.e., genets) of a sapro-trophic fungus Marasmius oreades. Our analyses revealed that fine genetic variations between host fungi could strongly affect their associated microbiome, explaining, respectively, 25% and 37% of the variation in microbiome structure and function, whereas geographic distance and soil pH remained of secondary importance. These results, together with the smaller genome size of fungi compared to other eukaryotes, suggest that fruiting-bodies are suitable for further genome-centric studies on hostmicrobiome interactions.

Place, publisher, year, edition, pages
WILEY, 2018
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-365992 (URN)10.1111/1462-2920.14069 (DOI)000445161800002 ()29441658 (PubMedID)
Funder
The Royal Swedish Academy of SciencesHelge Ax:son Johnsons stiftelse
Available from: 2018-11-22 Created: 2018-11-22 Last updated: 2018-11-22Bibliographically approved
Ryberg, M. & Nilsson, R. H. (2018). New light on names and naming of dark taxa. MycoKeys (30), 31-39
Open this publication in new window or tab >>New light on names and naming of dark taxa
2018 (English)In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 30, p. 31-39Article in journal (Refereed) Published
Abstract [en]

A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as "dark taxa" or "dark matter fungi". As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.

Place, publisher, year, edition, pages
PENSOFT PUBL, 2018
Keywords
Taxonomy, nomenclature, mycology, biodiversity
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-348986 (URN)10.3897/mycokeys.30.24376 (DOI)000426093600001 ()
Available from: 2018-04-26 Created: 2018-04-26 Last updated: 2018-04-26Bibliographically approved
Bahram, M., Hildebrand, F., Forslund, S. K., Anderson, J. L., Soudzilovskaia, N. A., Bodegom, P. M., . . . Bork, P. (2018). Structure and function of the global topsoil microbiome.. Nature, 560(7717), 233-237
Open this publication in new window or tab >>Structure and function of the global topsoil microbiome.
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2018 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 560, no 7717, p. 233-237Article in journal (Refereed) Published
Abstract [en]

Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

National Category
Microbiology Evolutionary Biology Ecology Environmental Sciences
Identifiers
urn:nbn:se:uu:diva-360977 (URN)10.1038/s41586-018-0386-6 (DOI)000441115200048 ()30069051 (PubMedID)
Funder
Swedish Research Council, 2017-05019The Royal Swedish Academy of SciencesHelge Ax:son Johnsons stiftelse EU, Horizon 2020, 686070
Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-11-08Bibliographically approved
Bahram, M., Vanderpool, D., Pent, M., Hiltunen, M. & Ryberg, M. (2018). The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics. Environmental Microbiology Reports, 10(2), 155-166
Open this publication in new window or tab >>The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics
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2018 (English)In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 2, p. 155-166Article in journal (Refereed) Published
Abstract [en]

Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.

Place, publisher, year, edition, pages
WILEY, 2018
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-353114 (URN)10.1111/1758-2229.12612 (DOI)000428391900005 ()29327481 (PubMedID)
Available from: 2018-06-11 Created: 2018-06-11 Last updated: 2018-06-11Bibliographically approved
Liu, J.-K., Hyde, K. D., Jeewon, R., Phillips, A. J. L., Maharachchikumbura, S. S. N., Ryberg, M., . . . Zhao, Q. (2017). Ranking higher taxa using divergence times: a case study in Dothideomycetes. Fungal diversity, 84(1), 75-99
Open this publication in new window or tab >>Ranking higher taxa using divergence times: a case study in Dothideomycetes
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2017 (English)In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 84, no 1, p. 75-99Article in journal (Refereed) Published
Abstract [en]

The current classification system for the recognition of taxonomic ranks among fungi, especially at high-ranking level, is subjective. With the development of molecular approaches and the availability of fossil calibration data, the use of divergence times as a universally standardized criterion for ranking taxa has now become possible. We can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of Dothideomycetes. We chose Dothideomycetes, the largest class of the phylum Ascomycota, which contains 32 orders, to establish ages at which points orders have split; and Pleosporales, the largest order of Dothideomycetes with 55 families, to establish family divergence times. We have assembled a multi-gene data set (LSU, SSU, TEF1 and RPB2) from 391 taxa representing most family groups of Dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of Dothideomycetes lineages. Two separated datasets were analysed: (i) 272 taxa representing 32 orders of Dothideomycetes were included for the order level analysis, and (ii) 191 taxa representing 55 families of Pleosporales were included for the family level analysis. Our results indicate that divergence times (crown age) for most orders (20 out of 32, or 63%) are between 100 and 220 Mya, while divergence times for most families (39 out of 55, or 71%) are between 20 and 100 Mya. We believe that divergence times can provide additional evidence to support establishment of higher level taxa, such as families, orders and classes. Taking advantage of this added approach, we can strive towards establishing a standardized taxonomic system both within and outside Fungi. In this study we found that molecular dating coupled with phylogenetic inferences provides no support for the taxonomic status of two currently recognized orders, namely Bezerromycetales and Wiesneriomycetales and these are treated as synonyms of Tubeufiales while Asterotexiales is treated as a synonym of Asterinales. In addition, we provide an updated phylogenetic assessment of Dothideomycetes previously published as the Families of Dothideomycetes in 2013 with a further ten orders and 35 families.

Place, publisher, year, edition, pages
SPRINGER, 2017
Keywords
BEAST, Clade age, Classification, Calibration, Family, Order, Phylogeny, Pleosporales
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-329126 (URN)10.1007/s13225-017-0385-1 (DOI)000403785900004 ()
Available from: 2017-10-13 Created: 2017-10-13 Last updated: 2017-10-13Bibliographically approved
Nilsson, R. H., Sánchez-García, M., Ryberg, M., Abarenkov, K., Wurzbacher, C. & Kristiansson, E. (2017). Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys, 26, 13-24
Open this publication in new window or tab >>Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory
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2017 (English)In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, Vol. 26, p. 13-24Article in journal (Refereed) Published
Abstract [en]

DNA sequences are increasingly used for taxonomic and functional assessment of environmental communities. In mycology, the nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen marker for such pursuits. Molecular identification is associated with many challenges, one of which is low read quality of the reference sequences used for inference of taxonomic and functional properties of the newly sequenced community (or single taxon). This study investigates whether public fungal ITS sequences are subjected to sufficient trimming in their distal (5’ and 3’) ends prior to deposition in the public repositories. We examined 86 species (and 10,584 sequences) across the fungal tree of life, and we found that on average 13.1% of the sequences were poorly trimmed in one or both of their 5’ and 3’ ends. Deposition of poorly trimmed entries was found to continue through 2016. Poorly trimmed reference sequences add noise and mask biological signal in sequence similarity searches and phylogenetic analyses, and we provide a set of recommendations on how to manage the sequence trimming problem.

Keywords
Molecular identification, DNA barcoding, database curation, Sanger sequencing, high-throughput sequencing, molecular ecology
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:uu:diva-334539 (URN)10.3897/mycokeys.26.14591 (DOI)000408265600002 ()
Funder
Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 215-2011-498Swedish Research Council FormasSwedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 226-2014-1109Knut and Alice Wallenberg FoundationStiftelsen Olle Engkvist ByggmästareLars Hierta Memorial Foundation
Available from: 2017-11-23 Created: 2017-11-23 Last updated: 2017-11-24Bibliographically approved
Sheedy, E. M., Ryberg, M., Lebel, T., May, T. W., Bougher, N. L. & Matheny, P. B. (2016). Dating the emergence of truffle-like fungi in Australia, by using an augmented meta-analysis. Australian Systematic Botany, 29(5), 284-302
Open this publication in new window or tab >>Dating the emergence of truffle-like fungi in Australia, by using an augmented meta-analysis
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2016 (English)In: Australian Systematic Botany, ISSN 1030-1887, E-ISSN 1446-5701, Vol. 29, no 5, p. 284-302Article in journal (Refereed) Published
Abstract [en]

Australia supports a high diversity of sequestrate (truffle-like) macrofungi. This has long been thought to be related to the predominantly or seasonally dry climate. The present study posits that if aridity were a key factor in the evolution of sequestrate fruit-bodies, most sequestrate species would have emerged in Australia only after it began to aridify, which occurred post-separation with Antarctica (c. 32 million years ago). Focusing on the high phylogenetic diversity of sequestrate taxa in the Agaricomycetes in Australia, dates of sequestrate nodes were compiled directly from published phylogenies (four lineages) or created using sequences available on GenBank that were processed in BEAST using a secondary calibration method (nine lineages). Although the morphologically diverse Hysterangiales was found to be the first group to become sequestrate, c. 83 million years ago, overall sequestration in Australia occurred more recently. Models were created and compared and support was found for an increased rate of sequestration in Australia at some point between 34 and 13 million years ago (during the Oligocene and Miocene). Although the rate of sequestration is shown to have increased in Australia after separation from Antarctica, the timing also overlaps with the radiation of potential mycorrhizal plant associates, and the emergence of specialised mycophagous marsupials. Although aridification is evidently not the sole driver of sequestration, it is still likely to have had a major influence on the diversity of sequestrate fungi in Australia. Comparisons with other regions of high sequestrate diversity will be informative.

Keywords
aridification, Agaricomycetes, sequestrate, Basidiomycota, Cortinariaceae, Russulaceae
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-312003 (URN)10.1071/SB16025 (DOI)000391723300003 ()
Available from: 2017-01-04 Created: 2017-01-04 Last updated: 2017-11-29Bibliographically approved
Rosenblad, M. A., Martin, M. P., Tedersoo, L., Ryberg, M., Larsson, E., Wurzbacher, C., . . . Nilsson, R. H. (2016). Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys (13), 21-33
Open this publication in new window or tab >>Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)
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2016 (English)In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 13, p. 21-33Article in journal (Refereed) Published
Abstract [en]

During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.

Keywords
SRP RNA, non-coding RNA, ribosomal RNA, internal transcribed spacer 1 (ITS1), ectomycorrhizal fungi
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-298708 (URN)10.3897/mycokeys.13.8579 (DOI)000376791100002 ()
Funder
Swedish Research Council Formas, 215-2011-498Stiftelsen Olle Engkvist Byggmästare
Available from: 2016-07-07 Created: 2016-07-06 Last updated: 2017-11-28Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-6795-4349

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