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  • 1.
    Anslan, Sten
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Hiiesalu, Indrek
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e234-e240Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable.

  • 2.
    Anslan, Sten
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14A Ravila, EE-50411 Tartu, Estonia..
    Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests2018In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 116, p. 245-252Article in journal (Refereed)
    Abstract [en]

    Soil fauna mediate nutrient cycling through engineering physical properties and altering microbial commtmities in soil. Collembola is one of the most abundant groups of soil fauna, which regulates microbial communities by consumption and dispersal. The spatial structure of associations between Collembola and soil microbes have been described in several studies, but temporal variation of these associations remains unclear. Using high throughput sequencing, we studied the fungal communities on Collembola (Entomobiya nivalis, Orchesella flavescens, Pogonognathellus longicornis) body surface, gut and their immediate habitat (topsoil samples) in four seasons across three years. The soil samples were characterized by fairly uniform relative abundance of saprotrophic and mycorrhizal fungi, whereas collembolans were associated mostly with saprotrophs. The structure of fungal communities from all substrate types exhibited comparable patterns of temporal distance decay of shnilarity. Unlike in soil, fungal richness and composition in Collembola body and gut samples exhibited seasonal and annual variation, with a significant interaction term, indicating low predictability. These results reflect spatial and temporal plasticity of the fungal communities associated with epigeic Collembola, indicating the high adaptability of collembolans to available conditions. We found that the Collembola associations with fungi (including diet) did not vary among the studied epigeic Collembola species. The detected high diversity of fungi associated with Collembola suggests that dispersal by arthropod vectors may represent a powerful alternative to aerial dispersal of fungal propagules.

  • 3. Anslan, Sten
    et al.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Temporal changes in fungal communities associated with guts and appendages of Collembola as based on culturing and high-throughput sequencing2016In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 96, p. 152-159Article in journal (Refereed)
    Abstract [en]

    Due to high abundance and feeding habits, invertebrates are of great importance for shaping microbial communities at the fine scale. Springtails (Collembola) that feed on fungal spores and mycelia may contribute to dispersal through carrying fungal propagules in their guts or on their appendages. The Collembola–fungal associations are mainly investigated by microscopy or culturing techniques, which allow identify only fungi that have distinctive morphological characteristics or that can be cultured in vitro. Here we identified the Collembola-associated fungi on the body surface and in the gut content using both culturing and high-throughput sequencing (HTS) methods. We studied three epigeic Collembola species found on the Norway spruce dominated forest stands throughout the vegetation period – Entomobrya nivalisOrchesella flavescens andPogonognathellus longicornis. We discovered over 1200 fungal operational taxonomic units (OTUs), i.e. the proxies for species, based on 97% sequence similarity of the ITS2 subregion of ribosomal DNA. Most of the fungi were saprotrophs, but we detected also mycorrhizal, parasitic and lichenized fungi. Season was the most important factor affecting fungal richness and composition, especially on body surface. Although the data matrix revealed significant effect of substrate, we were unable to detect the significant fungal community differences between body surface and gut samples of conspecifics. There were no significant differences among studied epigeic Collembola species in the preference for fungal diet. Our study demonstrates that collembolans associate with a broader range of fungi than previously observed and thus potentially play an important role in enhancing fungal colonization through dispersal activities.

  • 4.
    Anslan, Sten
    et al.
    Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg Global Biodivers Ctr, Box 461, S-40530 Gothenburg, Sweden.
    Wurzbacher, Christian
    Tech Univ Munich, Coulombwall 3, D-85748 Garching, Germany.
    Baldrian, Petr
    Czech Acad Sci, Inst Microbiol, Videnska 1083, Prague 14220 4, Czech Republic.
    Tedersoo, Leho
    Tartu Univ, Nat Hist Museum, 14a Ravila, Tartu 50411, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Tartu Univ, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Ulls Vag 16, S-75651 Uppsala, Sweden.
    Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 39, p. 29-40Article in journal (Refereed)
    Abstract [en]

    Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

  • 5.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Ulls Vag 16, S-75651 Uppsala, Sweden.
    Anslan, Sten
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, Tartu, Estonia;Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
    Hildebrand, Falk
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
    Bork, Peer
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany;Max Delbruck Ctr Mol Med, Berlin, Germany;Univ Wurzburg, Bioctr, Dept Bioinformat, Wurzburg, Germany.
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14A Ravila, EE-50411 Tartu, Estonia.
    Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment2019In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 11, no 4, p. 487-494Article in journal (Refereed)
    Abstract [en]

    High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately.

  • 6.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hildebrand, Falk
    Forslund, Sofia K
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Soudzilovskaia, Nadejda A
    Bodegom, Peter M
    Bengtsson-Palme, Johan
    Anslan, Sten
    Coelho, Luis Pedro
    Harend, Helery
    Huerta-Cepas, Jaime
    Medema, Marnix H
    Maltz, Mia R
    Mundra, Sunil
    Olsson, Pål Axel
    Pent, Mari
    Põlme, Sergei
    Sunagawa, Shinichi
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Bork, Peer
    Structure and function of the global topsoil microbiome.2018In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 560, no 7717, p. 233-237Article in journal (Refereed)
    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.

  • 7.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 40 Lai St, EE-50411 Tartu, Estonia.
    Kohout, Petr
    Anslan, Sten
    Harend, Helery
    Abarenkov, Kessy
    Tedersoo, Leho
    Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, p. 885-896Article in journal (Refereed)
    Abstract [en]

    A central challenge in ecology is to understand the relative importance of processes that shape diversity patterns. Compared with aboveground biota, little is known about spatial patterns and processes in soil organisms. Here we examine the spatial structure of communities of small soil eukaryotes to elucidate the underlying stochastic and deterministic processes in the absence of environmental gradients at a local scale. Specifically, we focus on the fine-scale spatial autocorrelation of prominent taxonomic and functional groups of eukaryotic microbes. We collected 123 soil samples in a nested design at distances ranging from 0.01 to 64 m from three boreal forest sites and used 454 pyrosequencing analysis of Internal Transcribed Spacer for detecting Operational Taxonomic Units of major eukaryotic groups simultaneously. Among the main taxonomic groups, we found significant but weak spatial variability only in the communities of Fungi and Rhizaria. Within Fungi, ectomycorrhizas and pathogens exhibited stronger spatial structure compared with saprotrophs and corresponded to vegetation. For the groups with significant spatial structure, autocorrelation occurred at a very fine scale (<2 m). Both dispersal limitation and environmental selection had a weak effect on communities as reflected in negative or null deviation of communities, which was also supported by multivariate analysis, that is, environment, spatial processes and their shared effects explained on average <10% of variance. Taken together, these results indicate a random distribution of soil eukaryotes with respect to space and environment in the absence of environmental gradients at the local scale, reflecting the dominant role of drift and homogenizing dispersal.

  • 8. Bahram, Mohammad
    et al.
    Kõljalg, Urmas
    Courty, Pierre-Emmanuel
    Diédhiou, Abdala G.
    Kjøller, Rasmus
    Põlme, Sergei
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Veldre, Vilmar
    Tedersoo, Leho
    The distance decay of similarity in communities of ectomycorrhizal fungi in different ecosystems and scales2013In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 101, no 5, p. 1335-1344Article in journal (Refereed)
    Abstract [en]

    Despite recent advances in understanding community ecology of ectomycorrhizal fungi, little is known about their spatial patterning and the underlying mechanisms driving these patterns across different ecosystems. * This meta-study aimed to elucidate the scale, rate and causes of spatial structure of ectomycorrhizal fungal communities in different ecosystems by analysing 16 and 55 sites at the local and global scales, respectively. We examined the distance decay of similarity relationship in species- and phylogenetic lineage-based communities in relation to sampling and environmental variables. * Tropical ectomycorrhizal fungal communities exhibited stronger distance-decay patterns compared to non-tropical communities. Distance from the equator and sampling area were the main determinants of the extent of distance decay in fungal communities. The rate of distance decay was negatively related to host density at the local scale. At the global scale, lineage-level community similarity decayed faster with latitude than with longitude. * Synthesis. Spatial processes play a stronger role and over a greater scale in structuring local communities of ectomycorrhizal fungi than previously anticipated, particularly in ecosystems with greater vegetation age and closer to the equator. Greater rate of distance decay occurs in ecosystems with lower host density that may stem from increasing dispersal and establishment limitation. The relatively strong latitude effect on distance decay of lineage-level community similarity suggests that climate affects large-scale spatial processes and may cause phylogenetic clustering of ectomycorrhizal fungi at the global scale.

  • 9.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden.
    Vanderpool, Dan
    Univ Montana, Div Biol Sci, 32 Campus Dr, Missoula, MT 59812 USA.
    Pent, Mari
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Hiltunen, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics2018In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 2, p. 155-166Article in journal (Refereed)
    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.

  • 10.
    Bedarf, J. R.
    et al.
    Univ Bonn, Dept Neurol, Bonn, Germany.;German Ctr Neurodegenerat Dis Res DZNE, Bonn, Germany..
    Hildebrand, F.
    EMBL, Heidelberg, Germany..
    Coelho, L. P.
    EMBL, Heidelberg, Germany..
    Sunagawa, S.
    EMBL, Heidelberg, Germany.;Swiss Fed Inst Technol, Inst Microbiol, Vladimir Prelog 1-5-10, CH-8093 Zurich, Switzerland..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth, 40 Lai St, EE-51005 Tartu, Estonia..
    Goeser, F.
    Univ Bonn, Dept Internal Med 1, Bonn, Germany.;German Ctr Infect Res DZIF, Bonn, Germany..
    Bork, P.
    EMBL, Heidelberg, Germany.;Heidelberg Univ, MMPU, Heidelberg, Germany.;European Mol Biol Lab, Heidelberg, Germany.;Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany.;Univ Wurzburg, Dept Bioinformat, D-97074 Wurzburg, Germany.;Meyerhofstr 1, D-69117 Heidelberg, Germany..
    Wüllner, U.
    Univ Bonn, Dept Neurol, Bonn, Germany.;German Ctr Neurodegenerat Dis Res DZNE, Bonn, Germany.;Sigmund Freud Str 25, D-53127 Bonn, Germany..
    Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients2017In: Genome Medicine, ISSN 1756-994X, E-ISSN 1756-994X, Vol. 9, article id 39Article in journal (Refereed)
    Abstract [en]

    Background: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naive PD patients might also serve as a biomarker.

    Methods: We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naive PD patients to 28 age-matched controls.

    Results: We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the beta-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions.

    Conclusions: Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.

  • 11.
    Bálint, Miklós
    et al.
    Senckenberg Biodivers & Climate Res Ctr, Senckenberganlage 25, D-60325 Frankfurt, Germany.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Eren, A. Murat
    Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA; Univ Chicago, Dept Med, 5841 S Maryland Ave, Chicago, IL 60637 USA.
    Faust, Karoline
    Katholieke Univ Leuven, Rega Inst, Ctr Biol Dis, B-3000 Leuven, Belgium.
    Fuhrman, Jed
    Univ Southern Calif, Dept Biol Sci, MC0371, Los Angeles, CA 90089 USA.
    Lindahl, Björn
    Swedish Univ Agr Sci, Dept Soil & Environm, Box 7014, SE-75007 Uppsala, Sweden.
    O'Hara, Robert B.
    Senckenberg Biodivers & Climate Res Ctr, Senckenberganlage 25, D-60325 Frankfurt, Germany.
    Öpik, Maarja
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Sogin, Mitchell L.
    Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA.
    Untersehe, Martin
    Ernst Moritz Arndt Univ Greifswald, Inst Bot & Landscape Ecol, Soldmannstr 15, D-17487 Greifswald, Germany.
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14a Ravila St, EE-50411 Tartu, Estonia.
    Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes2016In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 40, no 5, p. 686-700Article in journal (Refereed)
    Abstract [en]

    With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.

  • 12.
    Crous, P. W.
    et al.
    Westerdijk Fungal Biodivers Inst, POB 85167, NL-3508 AD Utrecht, Netherlands;Univ Pretoria, FABI, Dept Genet Biochem & Microbiol, P Bag X20, ZA-0028 Pretoria, South Africa.
    Luangsa-ard, J. J.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Microbe Interact & Ecol Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Wingfield, M. J.
    Univ Pretoria, FABI, ZA-0002 Pretoria, South Africa.
    Carnegie, A. J.
    NSW Dept Primary Ind Forestry, Forest Hlth & Biosecur, Level 12,10 Valentine Ave, Parramatta, NSW 2124, Australia.
    Hernandez-Restrepo, M.
    Westerdijk Fungal Biodivers Inst, POB 85167, NL-3508 AD Utrecht, Netherlands.
    Lombard, L.
    Westerdijk Fungal Biodivers Inst, POB 85167, NL-3508 AD Utrecht, Netherlands.
    Roux, J.
    Univ Pretoria, FABI, ZA-0002 Pretoria, South Africa.
    Barreto, R. W.
    Univ Fed Vicosa, Dept Fitopatol, BR-36570900 Vicosa, MG, Brazil.
    Baseia, I. G.
    Univ Fed Rio Grande do Norte, Ctr Biociencias, Dept Botan & Zool, Campus Univ, BR-59072970 Natal, RN, Brazil.
    Cano-Lira, J. F.
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain.
    Martin, M. P.
    CSIC, RJB, Dept Mycol, Plaza Murillo 2, E-28014 Madrid, Spain.
    Morozova, O. V.
    Russian Acad Sci, Komarov Bot Inst, 2 Prof Popov Str, St Petersburg 197376, Russia.
    Stchigel, A. M.
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain.
    Summerell, B. A.
    Royal Bot Gardens & Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia.
    Brandrud, T. E.
    Norwegian Inst Nat Res, Gaustadalleen 21, NO-0349 Oslo, Norway.
    Dima, B.
    Eotvos Lorand Univ, Inst Biol, Dept Plant Anat, Pazmany Peter Setany 1-C, H-1117 Budapest, Hungary.
    Garcia, D.
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain.
    Giraldo, A.
    Westerdijk Fungal Biodivers Inst, POB 85167, NL-3508 AD Utrecht, Netherlands;Univ Free State, Dept Plant Sci, Fac Nat & Agr Sci, POB 339, ZA-9300 Bloemfontein, South Africa.
    Guarro, J.
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain.
    Gusmao, L. F. P.
    Univ Estadual Feira de Santana, Av Transnordestina S-N Novo Horizonte, BR-44036900 Feira De Santana, BA, Brazil.
    Khamsuntorn, P.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Microbe Interact & Ecol Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Noordeloos, M. E.
    Naturalis Biodivers Ctr, Sect Bot, POB 9517, NL-2300 RA Leiden, Netherlands.
    Nuankaew, S.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Fungal Biodivers Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Pinruan, U.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Microbe Interact & Ecol Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Rodriguez-Andrade, E.
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain.
    Souza-Motta, C. M.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Thangavel, R.
    Minist Primary Ind, Plant Hlth & Environm Lab, POB 2095, Auckland 1140, New Zealand.
    van Iperen, A. L.
    Westerdijk Fungal Biodivers Inst, POB 85167, NL-3508 AD Utrecht, Netherlands.
    Abreu, V. P.
    Univ Fed Vicosa, Dept Microbiol, BR-36570000 Vicosa, MG, Brazil.
    Accioly, T.
    Univ Fed Rio Grande do Norte, Programa Posgrad Sistemat & Evolucao, Natal, RN, Brazil.
    Alves, J. L.
    Univ Fed Vicosa, Dept Fitopatol, BR-36570900 Vicosa, MG, Brazil.
    Andrade, J. P.
    Univ Estadual Feira de Santana, Av Transnordestina S-N Novo Horizonte, BR-44036900 Feira De Santana, BA, Brazil.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Baral, H. -O
    Barbier, E.
    Univ Fed Pernambuco, Dept Zool, Recife, PE, Brazil.
    Barnes, C. W.
    Inst Nacl Invest Agr, Estac Expt Santa Catalina, Panamer Km 1,Sect Cutuglahua, Pichincha, Ecuador.
    Bendiksen, E.
    Norwegian Inst Nat Res, Gaustadalleen 21, NO-0349 Oslo, Norway.
    Bernard, E.
    Univ Fed Pernambuco, Dept Zool, Recife, PE, Brazil.
    Bezerra, J. D. P.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Bezerra, J. L.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Bizio, Enrico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. Soc Veneziana Micol, S Croce 1730, I-30135 Venice, Italy.
    Blair, J. E.
    Franklin & Marshall Coll, Dept Biol, 415 Harrisburg Ave, Lancaster, PA 17603 USA.
    Bulyonkova, T. M.
    Russian Acad Sci, Siberian Branch, AP Ershov Inst Informat Syst, 6 Acad Lavrentieva Pr, Novosibirsk 630090, Russia.
    Cabral, T. S.
    Univ Fed Rio Grande do Norte, Dept Biol Celular & Genet, Natal, RN, Brazil.
    Caiafa, M. V.
    Dept Plant Pathol, 2527 Fifield Hall, Gainesville, FL 32611 USA;Florida Museum Nat Hist, 2527 Fifield Hall, Gainesville, FL 32611 USA.
    Cantillo, T.
    Univ Estadual Feira de Santana, Av Transnordestina S-N Novo Horizonte, BR-44036900 Feira De Santana, BA, Brazil.
    Colman, A. A.
    Univ Fed Vicosa, Dept Fitopatol, BR-36570900 Vicosa, MG, Brazil.
    Conceicao, L. B.
    Univ Estadual Feira de Santana, Av Transnordestina S-N Novo Horizonte, BR-44036900 Feira De Santana, BA, Brazil.
    Cruz, S.
    Dept Plant Pathol, 2527 Fifield Hall, Gainesville, FL 32611 USA;Florida Museum Nat Hist, 2527 Fifield Hall, Gainesville, FL 32611 USA.
    Cunha, A. O. B.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Darveaux, B. A.
    Mycosynthetix Inc, 505 Meadowlands Dr,Suite 103, Hillsborough, NC 27278 USA.
    da Silva, A. L.
    Univ Fed Vicosa, Dept Fitopatol, BR-36570900 Vicosa, MG, Brazil.
    da Silva, G. A.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    da Silva, G. M.
    Univ Fed Rio Grande do Norte, Ctr Biociencias, Dept Botan & Zool, Campus Univ, BR-59072970 Natal, RN, Brazil.
    da Silva, R. M. F.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    de Oliveira, R. J. V.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Oliveira, R. L.
    Univ Fed Rio Grande do Norte, Programa Posgrad Sistemat & Evolucao, Natal, RN, Brazil.
    De Souza, J. T.
    Univ Fed Lavras, Lavras, MG, Brazil.
    Duenas, M.
    CSIC, RJB, Dept Mycol, Plaza Murillo 2, E-28014 Madrid, Spain.
    Evans, H. C.
    CAB Int, Bakeham Lane, Egham TW20 9TY, Surrey, England.
    Epifani, F.
    CNR, Inst Sci Food Prod, Via Amendola 122-O, I-70126 Bari, Italy.
    Felipe, M. T. C.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Fernandez-Lopez, J.
    CSIC, RJB, Dept Mycol, Plaza Murillo 2, E-28014 Madrid, Spain.
    Ferreira, B. W.
    Univ Fed Vicosa, Dept Fitopatol, BR-36570900 Vicosa, MG, Brazil.
    Figueiredo, C. N.
    Reconcavo Bahia Fed Univ, Itabuna, BA, Brazil.
    Filippova, N. V.
    Yugra State Univ, 16 Chekhova Str, Khanty Mansiysk 628012, Russia.
    Flores, J. A.
    Pontificia Univ Catolica Ecuador, Escuela Ciencias Biol, Av 12 Octubre 1076 & Roca, Quito, Ecuador.
    Gene, J.
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain.
    Ghorbani, G.
    Univ Tehran, Coll Agr & Nat Resources, Dept Plant Protect, Karaj 3158777871, Iran.
    Gibertoni, T. B.
    Univ Fed Pernambuco, Dept Micol, Ave Engn S-N Cidade Univ, Recife, PE, Brazil.
    Glushakova, A. M.
    Lomonosov Moscow State Univ, RAS, Moscow All Russian Collect Microorganisms, GK Skryabin Inst Biochem & Physiol Microorganisms, Pushchino, Russia.
    Healy, R.
    Dept Plant Pathol, 2527 Fifield Hall, Gainesville, FL 32611 USA;Florida Museum Nat Hist, 2527 Fifield Hall, Gainesville, FL 32611 USA.
    Huhndorf, S. M.
    Field Museum, Dept Bot, 1400 South Lake Shore Dr, Chicago, IL 60605 USA.
    Iturrieta-Gonzalez, I.
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain.
    Javan-Nikkhah, M.
    Univ Tehran, Coll Agr & Nat Resources, Dept Plant Protect, Karaj 3158777871, Iran.
    Juciano, R. F.
    Univ Fed Pernambuco, Dept Micol, Programa Posgrad Biol Fungos, BR-50670420 Recife, PE, Brazil.
    Jurjevic, Z.
    EMSL Analyt Inc, 200 Route 130 North, Cinnaminson, NJ 08077 USA.
    Kachalkin, A. V.
    Lomonosov Moscow State Univ, RAS, Moscow All Russian Collect Microorganisms, GK Skryabin Inst Biochem & Physiol Microorganisms, Pushchino, Russia.
    Keochanpheng, K.
    Biotechnol & Ecol Inst, Viangchan, Laos.
    Krisai-Greilhuber, I.
    Univ Vienna, Dept Bot & Biodivers Res, Rennweg 14, A-1030 Vienna, Austria.
    Li, Y. -C
    Lima, A. A.
    Univ Fed Rio Grande do Norte, Programa Posgrad Sistemat & Evolucao, Natal, RN, Brazil.
    Machado, A. R.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Madrid, H.
    Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Camino Piramide 5750, Santiago, Chile.
    Magalhaes, O. M. C.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Marbach, P. A. S.
    Reconcavo Bahia Fed Univ, Itabuna, BA, Brazil.
    Melanda, G. C. S.
    Field Museum, Dept Bot, 1400 South Lake Shore Dr, Chicago, IL 60605 USA.
    Miller, A. N.
    Univ Illinois, Illinois Nat Hist Survey, 1816 South Oak St, Champaign, IL 61820 USA.
    Mongkolsamrit, S.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Microbe Interact & Ecol Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Nascimento, R. P.
    Rio De Janeiro Fed Univ, Rio De Janeiro, Brazil.
    Oliveira, T. G. L.
    Univ Fed Pernambuco, Dept Micol Prof Chaves Batista, Recife, PE, Brazil.
    Ordonez, M. E.
    Pontificia Univ Catolica Ecuador, Escuela Ciencias Biol, Av 12 Octubre 1076 & Roca, Quito, Ecuador.
    Orzes, R.
    Grp Micol Bresadola Belluno, Via Bries 25, I-32021 Agordo, Italy.
    Palma, M. A.
    Serv Agr & Ganadero, Lab Reg Valparaiso, Unidad Fitopatol, Valparaiso 2360451, Chile.
    Pearce, C. J.
    Mycosynthetix Inc, 505 Meadowlands Dr,Suite 103, Hillsborough, NC 27278 USA.
    Pereira, O. L.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Microbe Interact & Ecol Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Perrone, G.
    CNR, Inst Sci Food Prod, Via Amendola 122-O, I-70126 Bari, Italy.
    Peterson, S. W.
    ARS, Mycotoxin Prevent & Appl Microbiol Res Unit, USDA, 1815 North Univ St, Peoria, IL 61604 USA.
    Pham, T. H. G.
    St Petersburg State Forestry Univ, 194021,5U Inst Str, St Petersburg, Russia;Joint Russian Vietnamese Trop Res & Technol Ctr, 194021,5U Inst Str, Hanoi, Vietnam.
    Piontelli, E.
    Univ Valparaiso, Facultad Medicina, Prof Emerito Catedra Micol, Hontaneda 2653, Valparaiso 2341369, Chile.
    Pordel, A.
    Univ Tehran, Coll Agr & Nat Resources, Dept Plant Protect, Karaj 3158777871, Iran.
    Quijada, L.
    Harvard Univ, Dept Organism & Evolutionary Biol, Farlow Reference Lib, 22 Divin Ave, Cambridge, MA 02138 USA;Harvard Univ, Herbarium Cryptogam Bot, 22 Divin Ave, Cambridge, MA 02138 USA.
    Raja, H. A.
    Univ N Carolina, Dept Chem & Biochem, 435 Sullivan Sci Bldg,POB 26170, Greensboro, NC 27402 USA.
    de Paz, E. Rosas
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain;IPN, ENCB, Microbiol Dept, Lab Med Bacteriol, Prolongac Manuel Carpio & Plan Ayala S-N, Ciudad De Mexico 11350, DF, Mexico.
    Ryvarden, L.
    Univ Oslo, Dept Bot, POB 1045, N-0316 Oslo, Norway.
    Saitta, A.
    Univ Palermo, Dept Agr Food & Forest Sci, Viale Sci, I-90128 Palermo, Italy.
    Salcedo, S. S.
    Univ Fed Vicosa, Dept Fitopatol, BR-36570900 Vicosa, MG, Brazil.
    Sandoval-Denis, M.
    Westerdijk Fungal Biodivers Inst, POB 85167, NL-3508 AD Utrecht, Netherlands;Univ Free State, Dept Plant Sci, Fac Nat & Agr Sci, POB 339, ZA-9300 Bloemfontein, South Africa.
    Santos, T. A. B.
    Univ Estadual Feira de Santana, Av Transnordestina S-N Novo Horizonte, BR-44036900 Feira De Santana, BA, Brazil.
    Seifert, K. A.
    Agr & Agri Food Canada, Biodivers Mycol, Ottawa, ON K1A 0C6, Canada;Univ Ottawa, Dept Biol, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada.
    Silva, B. D. B.
    Univ Fed Bahia Salvador, Inst Biol, Salvador, BA, Brazil.
    Smith, M. E.
    Dept Plant Pathol, 2527 Fifield Hall, Gainesville, FL 32611 USA;Florida Museum Nat Hist, 2527 Fifield Hall, Gainesville, FL 32611 USA.
    Soares, A. M.
    Univ Fed Pernambuco, Dept Micol, Ave Engn S-N Cidade Univ, Recife, PE, Brazil.
    Sommai, S.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Microbe Interact & Ecol Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Sousa, J. O.
    Univ Fed Rio Grande do Norte, Programa Posgrad Sistemat & Evolucao, Natal, RN, Brazil.
    Suetrong, S.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Fungal Biodivers Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Susca, A.
    CNR, Inst Sci Food Prod, Via Amendola 122-O, I-70126 Bari, Italy.
    Tedersoo, L.
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Telleria, M. T.
    CSIC, RJB, Dept Mycol, Plaza Murillo 2, E-28014 Madrid, Spain.
    Thanakitpipattana, D.
    Natl Ctr Genet Engn & Biotechnol BIOTEC, Microbe Interact & Ecol Lab, 113 Thailand Sci Pk,Phahonyothin Rd, Khlong Luang 12120, Pathum Thani, Thailand.
    Valenzuela-Lopez, N.
    URV, Med Sch, Mycol Unit, St Llorenc 21, Tarragona, Spain;URV, IISPV, St Llorenc 21, Tarragona, Spain;Univ Antofagasta, Fac Hlth Sci, Med Technol Dept, Microbiol Unit, Av Univ Antofagasta S-N, Antofagasta 02800, Chile.
    Visagie, C. M.
    Agr Res Council Plant Hlth & Protect, Biosystemat Div, Private Bag X134, ZA-0121 Pretoria, South Africa.
    Zapata, M.
    Serv Agr & Ganadero, Lab Reg Chillan, Unidad Fitopatol, Claudio Arrau 738, Chillan 3800773, Chile.
    Groenewald, J. Z.
    Westerdijk Fungal Biodivers Inst, POB 85167, NL-3508 AD Utrecht, Netherlands.
    Fungal Planet description sheets: 785-8672018In: Persoonia, ISSN 0031-5850, E-ISSN 1878-9080, Vol. 41, p. 238-417Article in journal (Refereed)
    Abstract [en]

    Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora cotymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia cotymbiicola on Corymbia maculata, Neocelosporium eucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniefia eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora. Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderhenia coussapoae on Coussapoa floccosa. Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis, Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis. Chile, Colletotrichum arboricola on Fuchsia magellanica. Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomyces nerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander. Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus brassiana, Rachicladosporium corymbiae on Corymbia citriodora. Hungary, Entoloma silvae-frondosae in Carpinus betulus-Pinus sylvestris mixed forest. Iran, Pseudopyricularia persiana on Cyperus sp. Italy, lnocybe roseascens on soil in mixed forest. Laos, Ophiocordyceps houaynhangensis on Coleoptera larva. Malaysia, Monilochaetes melastomae on Melastoma sp. Mexico, Absidia terrestris from soil. Netherlands, Acaulium pannemaniae, Conioscypha boutwelliae, Fusicolla septimanifiniscientiae, Gibellulopsis simonii, Lasionectria hilhorstii, Lectera nordwiniana, Leptodiscella rintelii, Parasarocladium debruynii and Sarocladium dejongiae (incl. Sarocladiaceae fam. nov.) from soil. New Zealand, Gnomoniopsis rosae on Rosa sp. and Neodevriesia metrosideri on Metrosideros sp. Puerto Rico, Neodevriesia coccolobae on Coccoloba uvifera, Neodevriesia tabebuiae and Alfaria tabebuiae on Tabebuia chrysantha. Russia, Amanita paludosa on bogged soil in mixed deciduous forest, Entoloma tiliae in forest of Tilia x europaea, Kwoniella endophytica on Pyrus communis. South Africa, Coniella diospyri on Diospyros mespiliformis, Neomelanconiella combreti (incl. Neomelanconiellaceae fam. nov. and Neomelanconiella gen. nov.) on Combretum sp., Polyphialoseptoria natalensis on unidentified plant host, Pseudorobillarda bolusanthi on Bolusanthus speciosus, Thelonectria pelargonii on Pelargonium sp. Spain, Vermiculariopsiella lauracearum and Anungitopsis lauri on Laurus novocanariensis, Geosmithia xerotolerans from a darkened wall of a house, Pseudopenidiella gallaica on leaf litter. Thailand, Corynespora thailandica on wood, Lareunionomyces loeiensis on leaf litter, Neocochlearomyces chromolaenae (incl. Neocochlearomyces gen. nov.) on Chromolaena odorata, Neomyrmecridium septatum (incl. Neomyrmecridium gen. nov.), Pararamichloridium caricicola on Carex sp., Xenodactylaria thailandica (incl. Xenodactylariaceae fam. nov. and Xenodactylaria gen. nov.), Neomyrmecridium asiaticum and Cymostachys thailandica from unidentified vine. USA, Carolinigaster bonitoi (incl. Carolinigaster gen. nov.) from soil, Penicillium fortuitum from house dust, Phaeotheca shathenatiana (incl. Phaeothecaceae fam. nov.) from twig and cone litter, Pythium wohlseniorum from stream water, Superstratomyces tardicrescens from human eye, Talaromyces iowaense from office air. Vietnam, Fistulinella olivaceoalba on soil. Morphological and culture characteristics along with DNA barcodes are provided.

  • 13.
    Hiiesalu, Indrek
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    Plant species richness and productivity determine the diversity of soil fungal guilds in temperate coniferous forest and bog habitats2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 18, p. 4846-4858Article in journal (Refereed)
    Abstract [en]

    Fungi have important roles as decomposers, mycorrhizal root symbionts and pathogens in forest ecosystems, but there is limited information about their diversity and composition at the landscape scale. This work aimed to disentangle the factors underlying fungal richness and composition along the landscape-scale moisture, organic matter and productivity gradients. Using high-throughput sequencing, we identified soil fungi from 54 low-productivity Pinus sylvestris-dominated plots across three study areas in Estonia and determined the main predictors of fungal richness based on edaphic, floristic and spatial variables. Fungal richness displayed unimodal relationship with organic matter and deduced soil moisture. Plant richness and productivity constituted the key predictors for taxonomic richness of functional guilds. Composition of fungi and the main ectomycorrhizal fungal lineages and hyphal exploration types was segregated by moisture availability and soil nitrogen. We conclude that plant productivity and diversity determine the richness and proportion of most functional groups of soil fungi in low-productive pine forests on a landscape scale. Adjacent stands of pine forest may differ greatly in the dominance of functional guilds that have marked effects on soil carbon and nitrogen cycling in these forest ecosystems.

  • 14.
    Johansson, V. A.
    et al.
    Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. Univ Tartu, Inst Ecol & Earth Sci, EE-51005 Tartu, Estonia..
    Tedersoo, L.
    Univ Tartu, Inst Ecol & Earth Sci, EE-51005 Tartu, Estonia..
    Koljalg, U.
    Univ Tartu, Inst Ecol & Earth Sci, EE-51005 Tartu, Estonia..
    Eriksson, O.
    Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Specificity of fungal associations of Pyroleae and Monotropa hypopitys during germination and seedling development2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 9, p. 2591-2604Article in journal (Refereed)
    Abstract [en]

    Mycoheterotrophic plants obtain organic carbon from associated mycorrhizal fungi, fully or partially. Angiosperms with this form of nutrition possess exceptionally small 'dust seeds' which after germination develop 'seedlings' that remain subterranean for several years, fully dependent on fungi for supply of carbon. Mycoheterotrophs which as adults have photosynthesis thus develop from full to partial mycoheterotrophy, or autotrophy, during ontogeny. Mycoheterotrophic plants may represent a gradient of variation in a parasitism-mutualism continuum, both among and within species. Previous studies on plant-fungal associations in mycoheterotrophs have focused on either germination or the adult life stages of the plant. Much less is known about the fungal associations during development of the subterranean seedlings. We investigated germination and seedling development and the diversity of fungi associated with germinating seeds and subterranean seedlings (juveniles) in five Monotropoideae (Ericaceae) species, the full mycoheterotroph Monotropa hypopitys and the putatively partial mycoheterotrophs Pyrola chlorantha, P. rotundifolia, Moneses uniflora and Chimaphila umbellata. Seedlings retrieved from seed sowing experiments in the field were used to examine diversity of fungal associates, using pyrosequencing analysis of ITS2 region for fungal identification. The investigated species varied with regard to germination, seedling development and diversity of associated fungi during juvenile ontogeny. Results suggest that fungal host specificity increases during juvenile ontogeny, most pronounced in the fully mycoheterotrophic species, but a narrowing of fungal associates was found also in two partially mycoheterotrophic species. We suggest that variation in specificity of associated fungi during seedling ontogeny in mycoheterotrophs represents ongoing evolution along a parasitism-mutualism continuum.

  • 15.
    Kleinteich, Julia
    et al.
    Univ Tubingen, Ctr Appl Geosci, Tubingen, Germany.
    Hildebrand, Falk
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia.
    Voigt, Anita Y.
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany;Jackson Lab Genom Med, Farmington, CT USA.
    Wood, Susanna A.
    Cawthron Inst, Coastal & Freshwater, Nelson, New Zealand;Univ Waikato, Environm Res Inst, Hamilton, New Zealand.
    Jungblut, Anne D.
    London Nat Hist Museum, London, England.
    Kupper, Frithjof C.
    Scottish Assoc Marine Sci, Oban, Argyll, Scotland;Univ Aberdeen, Oceanlab, Aberdeen, Scotland.
    Quesada, Antonio
    Autonomous Univ Madrid, Dept Biol, Madrid, Spain.
    Camacho, Antonio
    Univ Valencia, Cavanilles Inst Biodivers & Evolutionary Biol, Valencia, Spain.
    Pearce, David A.
    Univ Northumbria Newcastle, Fac Hlth & Life Sci, Dept Appl Sci, Newcastle Upon Tyne, Tyne & Wear, England;British Antarct Survey, Cambridge, England.
    Convey, Peter
    British Antarct Survey, Cambridge, England.
    Vincent, Warwick F.
    Univ Laval, Dept Biol, Quebec City, PQ, Canada;Univ Laval, Ctr Northern Studies, Quebec City, PQ, Canada.
    Zarfl, Christiane
    Univ Tubingen, Ctr Appl Geosci, Tubingen, Germany.
    Bork, Peer
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany;Max Delbruck Ctr Mol Med, Berlin, Germany;Univ Wurzburg, Dept Bioinformat, Wurzburg, Germany.
    Dietrich, Daniel R.
    Univ Konstanz, Human & Environm Toxicol, Constance, Germany.
    Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change2017In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 5, article id 137Article in journal (Refereed)
    Abstract [en]

    The global biogeography of microorganisms remains poorly resolved, which limits the current understanding of microbial resilience toward environmental changes. Using high-throughput 16S rRNA gene amplicon sequencing, we characterized the microbial diversity of terrestrial and lacustrine biofilms from the Arctic, Antarctic and temperate regions. Our analyses suggest that bacterial community compositions at the poles are more similar to each other than they are to geographically closer temperate habitats, with 32% of all operational taxonomic units (OTUs) co-occurring in both polar regions. While specific microbial taxa were confined to distinct regions, representing potentially endemic populations, the percentage of cosmopolitan taxa was higher in Arctic (43%) than in Antarctic samples (36%). The overlap in polar microbial OTUs may be explained by natural or anthropogenically-mediated dispersal in combination with environmental filtering. Current and future changing environmental conditions may enhance microbial invasion, establishment of cosmopolitan genotypes and loss of endemic taxa.

  • 16.
    Kohout, Petr
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, EE-50411 Tartu, Estonia.;Acad Sci Czech Republ, Inst Bot, CZ-25243 Pruhonice, Czech Republic.;Charles Univ Prague, Fac Sci, Dept Expt Plant Biol, CZ-12801 Prague 2, Czech Republic..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, EE-50411 Tartu, Estonia.
    Polme, Sergei
    Univ Tartu, Inst Ecol & Earth Sci, EE-50411 Tartu, Estonia..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, EE-50411 Tartu, Estonia..
    Elevation, space and host plant species structure Ericaceae root-associated fungal communities in Papua New Guinea2017In: Fungal ecology, ISSN 1754-5048, E-ISSN 1878-0083, Vol. 30, p. 112-121Article in journal (Refereed)
    Abstract [en]

    Our study aimed to identify significant predictors (spatial distance, elevation, host plant taxonomy) which shape the structure of endophytic fungal (ENDF) and putative ericoid mycorrhizal (ErMF) communities associated with roots of Ericaceae in Papua New Guinea. Roots of five Ericaceae together with one non-Ericaceae species were sampled at an experimental site and one common Ericaceae species was chosen for sampling along an elevation gradient. ENDF and putative ErMF communities were determined using the 454-sequencing approach. ENDF as well as putative ErMF communities were affected by interacting host plant. While the putative ErMF community was structured by host plants at the genus level, the ENDF community was affected by host plant subfamily level. Composition of ENDF as well as putative ErMF communities were affected by elevation. Non-Ericaceae plant species (Hypericum sp.) harbored similar communities of ENDF as well as putative ErMF as Ericaceae plants. Our study provides a first insight into ErMF and ENDF community ecology of Ericaceae in Papua New Guinea.

  • 17. Kohout, Petr
    et al.
    Doubková, Pavla
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Suda, Jan
    Tedersoo, Leho
    Voříšková, Jana
    Sudová, Radka
    Niche partitioning in arbuscular mycorrhizal communities in temperate grasslands: a lesson from adjacent serpentine and nonserpentine habitats2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 8, p. 1831-1843Article in journal (Refereed)
    Abstract [en]

    Arbuscular mycorrhizal fungi (AMF) represent an important soil microbial group playing a fundamental role in many terrestrial ecosystems. We explored the effects of deterministic (soil characteristics, host plant life stage, neighbouring plant communities) and stochastic processes on AMF colonization, richness and community composition in roots of Knautia arvensis(Dipsacaceae) plants from three serpentine grasslands and adjacent nonserpentine sites. Methodically, the study was based on 454-sequencing of the ITS region of rDNA. In total, we detected 81 molecular taxonomical operational units (MOTUs) belonging to the Glomeromycota. Serpentine character of the site negatively influenced AMF root colonization, similarly as higher Fe concentration. AMF MOTUs richness linearly increased along a pH gradient from 3.5 to 5.8. Contrary, K and Cr soil concentration had a negative influence on AMF MOTUs richness. We also detected a strong relation between neighbouring plant community composition and AMF MOTUs richness. Although spatial distance between the sampled sites (c. 0.3–3 km) contributed to structuring AMF communities in K. arvensis roots, environmental parameters were key factors in this respect. In particular, the composition of AMF communities was shaped by the complex of serpentine conditions, pH and available soil Ni concentration. The composition of AMF communities was also dependent on host plant life stage (vegetative vs. generative). Our study supports the dominance of deterministic factors in structuring AMF communities in heterogeneous environment composed of an edaphic mosaic of serpentine and nonserpentine soils.

  • 18. Kohout, Petr
    et al.
    Sýkorová, Zuzana
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Hadincová, Věroslava
    Albrechtová, Jana
    Tedersoo, Leho
    Vohník, Martin
    Ericaceous dwarf shrubs affect ectomycorrhizal fungal community of the invasive Pinus strobus and native Pinus sylvestris in a pot experiment.2011In: Mycorrhiza, ISSN 0940-6360, E-ISSN 1432-1890, Vol. 21, no 5, p. 403-12Article in journal (Refereed)
    Abstract [en]

    This study aimed to elucidate the relationship between ericaceous understorey shrubs and the diversity and abundance of ectomycorrhizal fungi (EcMF) associated with the invasive Pinus strobus and native Pinus sylvestris. Seedlings of both pines were grown in mesocosms and subjected to three treatments simulating different forest microhabitats: (a) grown in isolation and grown with (b) Vaccinium myrtillus or (c) Vaccinium vitis-idaea. Ericaceous plants did not act as a species pool of pine mycobionts and inhibited the ability of the potentially shared species Meliniomyces bicolor to form ectomycorrhizae. Similarly, Ericaceae significantly reduced the formation of Thelephora terrestris ectomycorrhizae in P. sylvestris. EcMF species composition in the mesocosms was strongly affected by both the host species and the presence of an ericaceous neighbour. When grown in isolation, P. strobus root tips were predominantly colonised by Wilcoxina mikolae, whereas those of P. sylvestris were more commonly colonised by Suillus and Rhizopogon spp. Interestingly, these differences were less evident (Suillus + Rhizopogon spp.) or absent (W. mikolae) when the pines were grown with Ericaceae. P. strobus exclusively associated with Rhizopogon salebrosus s.l., suggesting the presence of host specificity at the intrageneric level. Ericaceous plants had a positive effect on colonisation of P. strobus root tips by R. salebrosus s.l. This study demonstrates that the interaction of selective factors such as host species and presence of ericaceous plants may affect the realised niche of the ectomycorrhizal fungi.

  • 19.
    Mirmajlessi, S. M.
    et al.
    Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Field Crops & Grassland Husb, EE-51014 Tartu, Estonia;Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Plant Protect, EE-51014 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, EE-51005 Tartu, Estonia.
    Mänd, M.
    Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Plant Protect, EE-51014 Tartu, Estonia.
    Najdabbasi, N.
    Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Plant Protect, EE-51014 Tartu, Estonia.
    Mansouripour, S.
    North Dakota State Univ, Dept Plant Pathol, Fargo, ND 58102 USA.
    Loit, E.
    Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Field Crops & Grassland Husb, EE-51014 Tartu, Estonia.
    Survey of Soil Fungal Communities in Strawberry Fields by Illumina Amplicon Sequencing2018In: Eurasian Soil Science, ISSN 1064-2293, E-ISSN 1556-195X, Vol. 51, no 6, p. 682-691Article in journal (Refereed)
    Abstract [en]

    Soil fungal pathogens are the most common cause of diseases in commercial strawberry crops worldwide. Since simultaneous infections by different pathogens can severely damage the crop, understanding the associated fungal communities can be helpful to mitigate crop loss. Herein, we used Illumina metabarcoding to assess the structure of fungal communities in five strawberry production areas in Estonia. Our analysis revealed 990 to 1430 operational taxonomic units (OTUs) per soil sample (pools of eight soil samples per production area). Based on our analyses, Ascomycota (55.5%) and Basidiomycota (25.0%) were the most OTUs-rich. Amongst the 24 most abundant OTUs, Geomyces, Rhodotorula, Verticillium and Microdochium were the most abundant genera, which were found across nearly all the soil samples. The OTUs were also clustered into three distinct groups, corresponding to different functional guilds of fungi. In addition, Fusarium solani, V. dahliae, Rhizoctonia solani and Colletotrichum truncatum were enormously abundant in the fields with disease symptoms, whereas arbuscular mycorrhizal fungi especially Rhizophagus irregularis were considerably more abundant in the fields with healthy plants. These findings provide support that mycorrhizal fungi may play an important role in suppressing pathogens. Our study for the first time shows the usefulness of Illumina technology in surveying the communities of soil fungi in strawberry fields effectively, which may improve available disease management strategies against strawberry diseases.

  • 20.
    Mundra, Sunil
    et al.
    Univ Ctr Svalbard, POB 156, NO-9171 Longyearbyen, Norway; Univ Oslo, Sect Genet & Evolutionary Biol, Dept Biosci, POB 1066, NO-0316 Oslo, Norway.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Eidesen, Pernille
    Univ Ctr Svalbard, POB 156, NO-9171 Longyearbyen, Norway.
    Alpine bistort (Bistorta vivipara) in edge habitat associates with fewer but distinct ectomycorrhizal fungal species: a comparative study of three contrasting soil environments in Svalbard2016In: Mycorrhiza, ISSN 0940-6360, E-ISSN 1432-1890, Vol. 26, no 8, p. 809-818Article in journal (Refereed)
    Abstract [en]

    Bistorta vivipara is a widespread arctic-alpine ectomycorrhizal (ECM) plant species. Recent findings suggest that fungal communities associated with B. vivipara roots appear random over short distances, but at larger scales, environmental filtering structure fungal communities. Habitats in highly stressful environments where specialist species with narrower niches may have an advantage represent unique opportunity to test the effect of environmental filtering. We utilised high-throughput amplicon sequencing to identify ECM communities associated with B. vivipara in Svalbard. We compared ECM communities in a core habitat where B. vivipara is frequent (Dryas-heath) with edge habitats representing extremes in terms of nutrient availability where B. vivipara is less frequent (bird-manured meadow and a nutrient-depleted mine tilling). Our analysis revealed that soil conditions in edge habitats favour less diverse but more distinct ECM fungal communities with functional traits adapted to local conditions. ECM richness was overall lower in both edge habitats, and the taxonomic compositions of ECM fungi were in line with our functional expectations. Stress-tolerant genera such as Laccaria and Hebeloma were abundant in nutrient-poor mine site whereas functional competitors genera such as Lactarius and Russula were dominant in the nutrient-rich bird-cliff site. Our results suggest that ECM communities in rare edge habitats are most likely not subsets of the larger pool of ECM fungi found in natural tundra, and they may represent a significant contribution to the overall diversity of ECM fungi in the Arctic.

  • 21. Mundra, Sunil
    et al.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Kauserud, Havard
    Halvorsen, Rune
    Eidensen, Pernille
    Temporal variation of Bistorta vivipara-associated ectomycorrhizal fungal communities in the High Arctic2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 24, p. 6289-6302Article in journal (Refereed)
    Abstract [en]

    Ectomycorrhizal (ECM) fungi are important for efficient nutrient uptake of several widespread arctic plant species. Knowledge of temporal variation of ECM fungi, and the relationship of these patterns to environmental variables, is essential to understand energy and nutrient cycling in Arctic ecosystems. We sampled roots of Bistorta vivipara ten times over two years; three times during the growing-season (June, July and September) and twice during winter (November and April) of both years. We found 668 ECM OTUs belonging to 25 different ECM lineages, whereof 157 OTUs persisted throughout all sampling time-points. Overall, ECM fungal richness peaked in winter and species belonging to Cortinarius, Serendipita and Sebacina were more frequent in winter than during summer. Structure of ECM fungal communities was primarily affected by spatial factors. However, after accounting for spatial effects, significant seasonal variation was evident revealing correspondence with seasonal changes in environmental conditions. We demonstrate that arctic ECM richness and community structure differ between summer (growing-season) and winter, possibly due to reduced activity of the core community, and addition of fungi adapted for winter conditions forming a winter-active fungal community. Significant month 3 year interactions were observed both for fungal richness and community composition, indicating unpredictable between-year variation. Our study indicates that addressing seasonal changes requires replication over several years.

  • 22. Mundra, Sunil
    et al.
    Halvorsen, Rune
    Kauserud, Håvard
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Institute of Ecology and Earth Sciences, Tartu University, Tartu, Estonia.
    Tedersoo, Leho
    Elberling, Bo
    Cooper, Elisabeth J.
    Eidesen, Pernille Bronken
    Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic2016In: MicrobiologyOpen, ISSN 2045-8827, E-ISSN 2045-8827, Vol. 5, no 5, p. 856-869Article in journal (Refereed)
    Abstract [en]

    Changing climate is expected to alter precipitation patterns in the Arctic, with consequences for subsurface temperature and moisture conditions, community structure, and nutrient mobilization through microbial belowground processes. Here, we address the effect of increased snow depth on the variation in species richness and community structure of ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected weekly from mid-July to mid-September in both control and deep snow plots. Richness of ECM fungi was higher, while saprotrophic fungi was lower in increased snow depth plots relative to controls. ECM fungal richness was related to soil NO3-N, NH4-N, and K; and saprotrophic fungi to NO3-N and pH. Small but significant changes in the composition of saprotrophic fungi could be attributed to snow treatment and sampling time, but not so for the ECM fungi. Delayed snow melt did not influence the temporal variation in fungal communities between the treatments. Results suggest that some fungal species are favored, while others are disfavored resulting in their local extinction due to long-term changes in snow amount. Shifts in species composition of fungal functional groups are likely to affect nutrient cycling, ecosystem respiration, and stored permafrost carbon.

  • 23. Nilsson, R. Henrik
    et al.
    Hyde, Kevin D.
    Pawlowska, Julia
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Aas, Anders Bjornsgard
    Alias, Siti A.
    Alves, Artur
    Anderson, Cajsa Lisa
    Antonelli, Alexandre
    Arnold, A. Elizabeth
    Bahnmann, Barbara
    Bahram, Mohammad
    Bengtsson-Palme, Johan
    Berlin, Anna
    Branco, Sara
    Chomnunti, Putarak
    Dissanayake, Asha
    Drenkhan, Rein
    Friberg, Hanna
    Froslev, Tobias Guldberg
    Halwachs, Bettina
    Hartmann, Martin
    Henricot, Beatrice
    Jayawardena, Ruvishika
    Jumpponen, Ari
    Kauserud, Havard
    Koskela, Sonja
    Kulik, Tomasz
    Liimatainen, Kare
    Lindahl, Bjorn D.
    Lindner, Daniel
    Liu, Jian-Kui
    Maharachchikumbura, Sajeewa
    Manamgoda, Dimuthu
    Martinsson, Svante
    Neves, Maria Alice
    Niskanen, Tuula
    Nylinder, Stephan
    Pereira, Olinto Liparini
    Pinho, Danilo Batista
    Porter, Teresita M.
    Queloz, Valentin
    Riit, Taavi
    Sanchez-Garcia, Marisol
    de Sousa, Filipe
    Stefanczyk, Emil
    Tadych, Mariusz
    Takamatsu, Susumu
    Tian, Qing
    Udayanga, Dhanushka
    Unterseher, Martin
    Wang, Zheng
    Wikee, Saowanee
    Yan, Jiye
    Larsson, Ellen
    Larsson, Karl-Henrik
    Koljalg, Urmas
    Abarenkov, Kessy
    Improving ITS sequence data for identification of plant pathogenic fungi2014In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 67, no 1, p. 11-19Article in journal (Refereed)
    Abstract [en]

    Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results - a total of 31,954 changes - are incorporated in and made available through the UNITE database for molecular identification of fungi (including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.

  • 24.
    Nilsson, R. Henrik
    et al.
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Ulikooli 18, EE-50090 Tartu, Estonia..
    Coimbra, Victor R. M.
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden.;Univ Fed Pernambuco UFPE, Ctr Ciencias Biol CCB, Dept Micol, Av Prof Nelson Chaves S-N, BR-50760901 Recife, PE, Brazil..
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Tedersoo, Leho
    Univ Tartu, Inst Ecol & Earth Sci, Ulikooli 18, EE-50090 Tartu, Estonia..
    Eriksson, Jonna
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Ritter, Camila Duarte
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Svantesson, Sten
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Sanchez-Garcia, Marisol
    Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN 37996 USA..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kristiansson, Erik
    Univ Gothenburg, Chalmers Univ Technol, Dept Math Sci, S-41296 Gothenburg, Sweden..
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Top 50 most wanted fungi2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 12, p. 29-40Article in journal (Refereed)
    Abstract [en]

    Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond "Fungi". There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.

  • 25.
    Oja, Jane
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Vahtra, Johanna
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia.
    Kohout, Petr
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia; Acad Sci Czech Republ, Inst Bot, CS-25243 Pruhonice, Czech Republic.
    Kull, Tiiu
    Univ Life Sci, Inst Agr & Environm Sci Estonian, 5 Kreutzwaldi, EE-51014 Tartu, Estonia.
    Rannap, Riinu
    Univ Tartu, Inst Ecol & Earth Sci, 46 Vanemuise, EE-51014 Tartu, Estonia.
    Kõljalg, Urmas
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Tedersoo, Leho
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands2017In: Mycorrhiza, ISSN 0940-6360, E-ISSN 1432-1890, Vol. 27, no 4, p. 355-367Article in journal (Refereed)
    Abstract [en]

    Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.

  • 26.
    Pent, Mari
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Hiltunen, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Poldmaa, Kadri
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Furneaux, Brendan R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hildebrand, Falk
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies2018In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 20, no 5, p. 1641-1650Article in journal (Refereed)
    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.

  • 27.
    Pent, Mari
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia..
    Poldmaa, Kadri
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia.
    Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 836Article in journal (Refereed)
    Abstract [en]

    Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales-the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.

  • 28.
    Polme, Sergei
    et al.
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia.;Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Jacquemyn, Hans
    Katholieke Univ Leuven, Dept Biol Plant Conservat & Populat Biol, Kasteelpk Arenberg 31, B-3001 Heverlee, Belgium..
    Kennedy, Peter
    Univ Minnesota, Dept Plant Biol, 1445 Gortner Ave, St Paul, MN 55108 USA..
    Kohout, Petr
    Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.;Acad Sci Czech Republ, Inst Bot, CZ-25243 Pruhonice, Czech Republic.;Charles Univ Prague, Fac Sci, CZ-12844 Prague 2, Czech Republic..
    Moora, Mari
    Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia..
    Oja, Jane
    Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia..
    Opik, Maarja
    Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia..
    Pecoraro, Lorenzo
    Natl Orchid Conservat Ctr China, Shenzhen Key Lab Orchid Conservat & Utilizat, Shenzhen 518114, Peoples R China.;Orchid Conservat & Res Ctr Shenzhen, Shenzhen 518114, Peoples R China.;Tsinghua Univ, Grad Sch Shenzhen, Ctr Biotechnol & BioMed, Shenzhen 518055, Peoples R China.;Tsinghua Univ, Grad Sch Shenzhen, Div Life & Hlth Sci, Shenzhen 518055, Peoples R China.;Chinese Acad Sci, Inst Microbiol, State Key Lab Mycol, Beijing 100101, Peoples R China..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia..
    Host preference and network properties in biotrophic plant-fungal associations2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 3, p. 1230-1239Article in journal (Refereed)
    Abstract [en]

    Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks.

    We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds. We also assessed how plant-fungal network structure was related to host phylogeny, environmental and sampling properties.

    Orchid mycorrhizal fungal communities responded most strongly to host identity, but the effect of host was similar among all other fungal guilds. Community nestedness, which did not differ among fungal guilds, declined significantly with increasing mean annual precipitation on a global scale. Orchid and ericoid mycorrhizal fungal communities were more modular than ectomycorrhizal and root endophytic communities, with arbuscular mycorrhizal fungi in an intermediate position.

    Network properties among a broad suite of plant-associated fungi were largely comparable and generally unrelated to phylogenetic distance among hosts. Instead, network metrics were predominantly affected by sampling and matrix properties, indicating the importance of study design in properly inferring ecological patterns.

  • 29.
    Pölme, Sergei
    et al.
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia.;Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Jacquemyn, Hans
    Katholieke Univ Leuven, Dept Biol Plant Conservat & Populat Biol, Kasteelpk Arenberg 31, B-3001 Heverlee, Belgium..
    Kennedy, Peter
    Univ Minnesota, Dept Plant Biol, 1445 Gortner Ave, St Paul, MN 55108 USA..
    Kohout, Petr
    Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.;Acad Sci Czech Republ, Inst Bot, CZ-25243 Pruhonice, Czech Republic.;Charles Univ Prague, Fac Sci, CZ-12844 Prague 2, Czech Republic..
    Moora, Mari
    Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia..
    Oja, Jane
    Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia..
    Öpik, Maarja
    Univ Tartu, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia..
    Pecoraro, Lorenzo
    Natl Orchid Conservat Ctr China, Shenzhen Key Lab Orchid Conservat & Utilizat, Shenzhen 518114, Peoples R China.;Orchid Conservat & Res Ctr Shenzhen, Shenzhen 518114, Peoples R China.;Tsinghua Univ, Grad Sch Shenzhen, Ctr Biotechnol & BioMed, Shenzhen 518055, Peoples R China.;Tsinghua Univ, Grad Sch Shenzhen, Div Life & Hlth Sci, Shenzhen 518055, Peoples R China.;Chinese Acad Sci, Inst Microbiol, State Key Lab Mycol, Beijing 100101, Peoples R China..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia..
    Host preference and network properties in biotrophic plant-fungal associations2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 3, p. 1230-1239Article in journal (Refereed)
    Abstract [en]

    Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks. We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds. We also assessed how plant-fungal network structure was related to host phylogeny, environmental and sampling properties. Orchid mycorrhizal fungal communities responded most strongly to host identity, but the effect of host was similar among all other fungal guilds. Community nestedness, which did not differ among fungal guilds, declined significantly with increasing mean annual precipitation on a global scale. Orchid and ericoid mycorrhizal fungal communities were more modular than ectomycorrhizal and root endophytic communities, with arbuscular mycorrhizal fungi in an intermediate position. Network properties among a broad suite of plant-associated fungi were largely comparable and generally unrelated to phylogenetic distance among hosts. Instead, network metrics were predominantly affected by sampling and matrix properties, indicating the importance of study design in properly inferring ecological patterns.

  • 30.
    Saitta, Alessandro
    et al.
    Univ Palermo, Dept Agr Food & Forest Sci, Palermo, Italy.
    Anslan, Sten
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia.
    Brocca, Luca
    CNR, Res Inst Geohydrol Protect, Perugia, Italy.
    Tedersoo, Leho
    Univ Tartu, Natl Hist Museum, Tartu, Estonia.
    Tree species identity and diversity drive fungal richness and community composition along an elevational gradient in a Mediterranean ecosystem2018In: Mycorrhiza, ISSN 0940-6360, E-ISSN 1432-1890, Vol. 28, no 1, p. 39-47Article in journal (Refereed)
    Abstract [en]

    Ecological and taxonomic knowledge is important for conservation and utilization of biodiversity. Biodiversity and ecology of fungi in Mediterranean ecosystems is poorly understood. Here, we examined the diversity and spatial distribution of fungi along an elevational gradient in a Mediterranean ecosystem, using DNA metabarcoding. This study provides novel information about diversity of all ecological and taxonomic groups of fungi along an elevational gradient in a Mediterranean ecosystem. Our analyses revealed that among all biotic and abiotic variables tested, host species identity is the main driver of the fungal richness and fungal community composition. Fungal richness was strongly associated with tree richness and peaked in Quercus-dominated habitats and Cistus-dominated habitats. The highest taxonomic richness of ectomycorrhizal fungi was observed under Quercus ilex, whereas the highest taxonomic richness of saprotrophs was found under Pinus. Our results suggest that the effect of plant diversity on fungal richness and community composition may override that of abiotic variables across environmental gradients.

  • 31. Sorahinobar, Mona
    et al.
    Niknam, Vahid
    Ebrahimzadeh, Hassan
    Soltanloo, Hassan
    Moradi, Babak
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lack of association between Fusarium graminearum resistance in spike and crude extract tolerance in seedling of wheat2016In: European journal of plant pathology, ISSN 0929-1873, E-ISSN 1573-8469, Vol. 144, no 3, p. 525-538Article in journal (Refereed)
    Abstract [en]

    Fusarium graminearum is a hemibiotrophic plant fungal pathogen that causes head and seedling blight in wheat and other cereals; however little is known about the mechanisms involved in its pathogenicity. To examine the role of pathogen metabolites in pathogenecity, we studied the effects of F. graminearum crude extract on physiological and morphological responses of Falat and Sumai3, as respectively susceptible and resistant wheat cultivars to Fusarium head blight (FHB). Our results showed that seed germination, seedling growth and coleoptile cell development were highly affected by the pathogen crude extract in both cultivars, with Sumai3 growth being more affected than Falat. These results show little correspondence between wheat seedling tolerance to F. graminearumcrude extract and resistance to FHB. Crude extract treatment resulted in significant increase of hydrogen peroxide (H2O2) and malondialdehyde (MDA) content in both cultivars which indicated an oxidative stress. Differential antioxidative responses to crude extract was observed; as activity of polyphenol oxidase (PPO), superoxide dismutase (SOD) and ascorbate peroxidases (APX) increased in Falat and decreased in Sumai3. In addition, a greater phenylalanine ammonia-lyase (PAL) activity was observed in treated seedlings of both cultivars. Quantitative Real- time PCR analysis showed that PAL gene expression in Falat was induced about 4 folds higher than Sumai3 under treatment. Taken together, our data suggest that a better employment of enzymatic and none enzymatic antioxidative systems in Falat could explain its higher degree of tolerance compared with Sumai3.

  • 32.
    Sorahinobar, Mona
    et al.
    University of Tehran, School of Biology, College of Science, Department of Plant Biology; University of Tehran, School of Biology, College of Science, Center of Excellence in Phylogeny of Living Organisms in Iran.
    Soltanloo, Hassan
    Gorgan University of Agricultural Science and Natural Resource, Department of Plant Breeding and Biotechnology.
    Niknam, Vahid
    University of Tehran, School of Biology, College of Science, Department of Plant Biology; University of Tehran, School of Biology, College of Science, Center of Excellence in Phylogeny of Living Organisms in Iran.
    Ebrahimzadeh, Hassan
    University of Tehran, School of Biology, College of Science, Department of Plant Biology; University of Tehran, School of Biology, College of Science, Center of Excellence in Phylogeny of Living Organisms in Iran.
    Moradi, Babak
    Tarbiat Modares University, Faculty of Biological Sciences, Department of Plant Science.
    Safaie, Naser
    Tarbiat Modares University, Faculty of Agriculture, Department of Plant Pathology.
    Behmanesh, Mehrdad
    Tarbiat Modares University, Faculty of Biological Sciences, Department of Genetic.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. University of Tartu, Institute of Ecology and Earth Sciences.
    Physiological and molecular responses of resistant and susceptible wheat cultivars to Fusarium graminearum mycotoxin extract2017In: Canadian journal of plant pathology, ISSN 0706-0661, E-ISSN 1715-2992, Vol. 39, no 4, p. 444-453Article in journal (Refereed)
    Abstract [en]

    Fusarium graminearum, causing Fusarium head blight (FHB), is one of the most important diseases on cereals worldwide leading to a reduction in both grain yield and quality. Currently, there is limited knowledge about the physiological and molecular mechanisms involved in wheat resistance against F. graminearum mycotoxins. Crude culture extract of F. graminearum was used to determine the physiological and molecular responses of wheat cultivars ‘Falat’ and ‘Sumai3‘, susceptible and resistant to FHB, respectively. Point inoculation of crude extract in the wheat spikelets resulted in significant increases in hydrogen peroxide (H2O2) and malondialdehyde (MDA) content in both cultivars, most likely due to oxidative stress. A greater induction level and activity of H2O2, MDA, peroxidase (POX), phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO) was observed in the resistant versus the susceptible cultivar. In addition, quantitative real-time PCR indicated earlier and greater induction of PAL, pleiotropic drug resistance (PDR) and cytochrome P450 (CYP) gene expression in ‘Sumai3‘ compared with ‘Falat’. Responses associated with the resistant interaction in ‘Sumai3‘ were higher induction of superoxide dismutase (SOD) and POX and decreased activity of catalase, while decreased SOD activity was observed in ‘Falat’. Our data suggest that these responses could explain the higher degree of tolerance of ‘Sumai3‘ against F. graminearum.

  • 33. Tedersoo, Leho
    et al.
    Anslan, Sten
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Polme, Sergei
    Riit, Taavi
    Liiv, Ingrid
    Koljalg, Urmas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kisand, Veljo
    Nilsson, R. Henrik
    Hildebrand, Falk
    Bork, Peer
    Abarenkov, Kessy
    Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi2015In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 10, p. 1-43Article in journal (Refereed)
    Abstract [en]

    Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6-38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.

  • 34. Tedersoo, Leho
    et al.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Polme, Sergei
    Anslan, Sten
    Riit, Taavi
    Koljalg, Urmas
    Nilsson, R. Henrik
    Hildebrand, Falk
    Abarenkov, Kessy
    Response to Comment on “Global diversity and geography of soil fungi”2015In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 349, no 6251, p. 936-Article in journal (Refereed)
    Abstract [en]

    Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)-free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.

  • 35.
    Tedersoo, Leho
    et al.
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia..
    Puusepp, Rasmus
    Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia..
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463405 30, Gothenburg, Sweden..
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA..
    Novel soil-inhabiting clades fill gaps in the fungal tree of life2017In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, no 42Article in journal (Refereed)
    Abstract [en]

    Background: Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results: We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions: This study uncovers the great phylogenetic richness of previously unrecognized order- to phylumlevel fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.

  • 36. Tedersoo, Leho
    et al.
    Bahram, Mohammad
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Otsing, Eveli
    Koljalg, Urmas
    Abarenkov, Kessy
    Global biogeography of the ectomycorrhizal/sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 16, p. 4168-4183Article in journal (Refereed)
    Abstract [en]

    Compared with plants and animals, large-scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45-57Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.

  • 37. Tedersoo, Leho
    et al.
    Bahram, Mohammad
    Toots, Märt
    Diédhiou, Abdala G
    Henkel, Terry W
    Kjøller, Rasmus
    Morris, Melissa H
    Nara, Kazuhide
    Nouhra, Eduardo
    Peay, Kabir G
    Põlme, Sergei
    Ryberg, Martin
    Smith, Matthew E
    Kõljalg, Urmas
    Towards global patterns in the diversity and community structure of ectomycorrhizal fungi.2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 17, p. 4160-70Article in journal (Refereed)
    Abstract [en]

    Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next-generation sequencing techniques and relevant soil metadata.

  • 38.
    Tedersoo, Leho
    et al.
    Univ Tartu, Nat Hist Museum, 14A Ravila, EE-51005 Tartu, Estonia.
    Liiv, Ingrid
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-51005 Tartu, Estonia.
    Kivistik, Paula
    Univ Tartu, Estonian Genome Ctr, Riia 23b, EE-51010 Tartu, Estonia.
    Anslan, Sten
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-51005 Tartu, Estonia.
    Kõljalg, Urmas
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-51005 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 13, p. 1-20Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing (HTS) has become a standard technique for genomics, metagenomics and taxonomy, but these analyses typically require large amounts of high-quality DNA that is difficult to obtain from uncultivable organisms including fungi with no living culture or fruit-body representatives. By using 1 ng DNA and low coverage Illumina HiSeqHTS, we evaluated the usefulness of genomics and metagenomics tools to recover fungal barcoding genes from old and problematic specimens of fruit-bodies and ectomycorrhizal (EcM) root tips. Ribosomal DNA and single-copy genes were successfully recovered from both fruit-body and EcM specimens typically <10 years old (maximum, 17 years). Samples with maximum obtained DNA concentration <0.2 ng µl-1 were sequenced poorly. Fungal rDNA molecules assembled from complex mock community and soil revealed a large proportion of chimeras and artefactual consensus sequences of closely related taxa. Genomics and metagenomics tools enable recovery of fungal genomes from very low initial amounts of DNA from fruit-bodies and ectomycorrhizas, but these genomes include a large proportion of prokaryote and other eukaryote DNA. Nonetheless, the recovered scaffolds provide an important source for phylogenetic and phylogenomic analyses and mining of functional genes.

  • 39.
    Tedersoo, Leho
    et al.
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia;Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia;Estonian Young Acad Sci, 6 Kohtu, Tallinn, Estonia.
    Sanchez-Ramirez, Santiago
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M5S 3B2, Canada.
    Koljalg, Urmas
    Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Estonian Young Acad Sci, 6 Kohtu, Tallinn, Estonia.
    Doring, Markus
    Global Biodivers Informat Facil, Copenhagen, Denmark.
    Schigel, Dmitry
    Global Biodivers Informat Facil, Copenhagen, Denmark;Univ Helsinki, Dept Biosci, Helsinki, Finland.
    May, Tom
    Royal Bot Gardens Victoria, Birdwood Ave, Melbourne, Vic 3004, Australia.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia.
    High-level classification of the Fungi and a tool for evolutionary ecological analyses2018In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 90, no 1, p. 135-159Article in journal (Refereed)
    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.

  • 40.
    Vowles, Tage
    et al.
    Univ Gothenburg, Dept Earth Sci, Gothenburg, Sweden; Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Lindwall, Frida
    Univ Copenhagen, Terr Ecol, Dept Biol, Copenhagen, Denmark; Univ Copenhagen, Ctr Permafrost, Dept Geosci & Nat Resource Management, Copenhagen, Denmark.
    Ekblad, Alf
    Örebro Univ, Sch Sci & Technol, Örebro, Sweden.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Dept Bot, Inst Ecol & Earth Sci, Tartu, Estonia.
    Furneaux, Brendan R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Björk, Robert G.
    Univ Gothenburg, Dept Earth Sci, Gothenburg, Sweden; Gothenburg Global Biodivers Ctr, Gothenburg, Sweden.
    Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone2018In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, no 2, p. 1019-1030Article in journal (Refereed)
    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.

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