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Publications (10 of 31) 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
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., 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
Looney, B. P., Ryberg, M., Hampe, F., Sanchez-Garcia, M. & Matheny, P. B. (2016). Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi. Molecular Ecology, 25(2), 630-647
Open this publication in new window or tab >>Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi
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2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 630-647Article in journal (Refereed) Published
Abstract [en]

Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.

Keywords
fungi, latitudinal diversity gradient, phylogeography, phyloinformatics, Russulaceae
National Category
Biochemistry and Molecular Biology Ecology
Identifiers
urn:nbn:se:uu:diva-279643 (URN)10.1111/mec.13506 (DOI)000369530000014 ()26642189 (PubMedID)
Available from: 2016-03-08 Created: 2016-03-02 Last updated: 2017-11-30Bibliographically approved
Ryberg, M. (2016). Phylommand - a command line software package for phylogenetics [version 1; referees: awaiting peer review]. F1000 Research, 5, Article ID 2903.
Open this publication in new window or tab >>Phylommand - a command line software package for phylogenetics [version 1; referees: awaiting peer review]
2016 (English)In: F1000 Research, ISSN 0106-3324, E-ISSN 2046-1402, Vol. 5, article id 2903Article in journal (Refereed) Published
Abstract [en]

Phylogenetics is an intrinsic part of many analyses in evolutionary biology and ecology, and as the amount of data available for these analyses is increasing rapidly the need for automated pipelines to deal with the data also increases. Phylommand is a package of four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments. It is built to be easily implemented in software workflows, both directly on the command prompt, and executed using scripts. Inputs can be taken from standard input or a file, and the behavior of the programs can be changed through switches. By using standard file formats for phylogenetic analyses, such as newick, nexus, phylip, and fasta, phylommand is widely compatible with other software.

National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-312004 (URN)10.12688/f1000research.10446.1 (DOI)
Available from: 2017-01-04 Created: 2017-01-04 Last updated: 2017-11-29Bibliographically approved
Phukhamsakda, C., Hongsanan, S., Ryberg, M., Ariyawansa, H., Chomnunti, P., Bahkali, A. & Hyde, K. (2016). The evolution of Massarineae with Longipedicellataceae fam. nov.. Mycosphere, 7(11), 1713-1731
Open this publication in new window or tab >>The evolution of Massarineae with Longipedicellataceae fam. nov.
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2016 (English)In: Mycosphere, ISSN 2077-7000, E-ISSN 2077-7019, Vol. 7, no 11, p. 1713-1731Article in journal (Refereed) Published
Abstract [en]

Massarineae is a suborder of Pleosporales, the latter being the largest order in Dothideomycetes. Massarineae comprises 14 families and six taxa of uncertain placement. In this study, we introduce an additional new family, Longipedicellataceae in Massarineae, which accommodates the genera Longipedicellata and Pseudoxylomyces. The family inhabits submerged culms of plants in freshwater habitats. The family can be distinguished by its very long pedicellate asci and chlamydospore-like structures, which are produced in culture. A LSU, SSU, and RPB2 dataset from representative strains used in our phylogenetic analyses shows the separation of Longipedicellataceae from the other families of Massarineae. In addition, divergence times of families in Massarineae were estimated using a molecular clock methodology. We used an Eocene fossil of Margaretbarromyces dictyosporus to estimate dates in Pleosporales with emphasis on Massarineae. In this study, the crown of Pleosporales is dated to the late Triassic (211 Mya), while the suborder Massarineae is dated to the Cretaceous (130 Mya) and family Longipedicellataceae is dated to Eocene (56 Mya).

National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-312005 (URN)10.5943/mycosphere/7/11/7 (DOI)000393043800007 ()
Available from: 2017-01-04 Created: 2017-01-04 Last updated: 2017-11-29Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-6795-4349

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