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Bahram, Mohammad
Publications (10 of 36) Show all publications
Vowles, T., Lindwall, F., Ekblad, A., Bahram, M., Furneaux, B. R., Ryberg, M. & Björk, R. G. (2018). Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone. Ecology and Evolution, 8(2), 1019-1030
Open this publication in new window or tab >>Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone
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2018 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, no 2, p. 1019-1030Article in journal (Refereed) Published
Abstract [en]

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

Keywords
Betula nana, Betula pubescens subsp, czerepanovii, ectomycorrhiza, extramatrical mycelia, herbivory, mountain birch forest, shrub heath
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-348781 (URN)10.1002/ece3.3657 (DOI)000425822800019 ()29375775 (PubMedID)
Funder
Swedish Research Council Formas, 214-2010-1411
Available from: 2018-04-17 Created: 2018-04-17 Last updated: 2018-04-17Bibliographically approved
Anslan, S., Nilsson, R. H., Wurzbacher, C., Baldrian, P., Tedersoo, L. & Bahram, M. (2018). Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys (39), 29-40
Open this publication in new window or tab >>Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
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2018 (English)In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 39, p. 29-40Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
PENSOFT PUBL, 2018
Keywords
Microbial communities, microbiome, mycobiome, fungal biodiversity, metagenomics, amplicon sequencing
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-364235 (URN)10.3897/mycokeys.39.28109 (DOI)000444106400001 ()30271256 (PubMedID)
Available from: 2018-10-25 Created: 2018-10-25 Last updated: 2018-10-25Bibliographically approved
Tedersoo, L., Sanchez-Ramirez, S., Koljalg, U., Bahram, M., Doring, M., Schigel, D., . . . Abarenkov, K. (2018). High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal diversity, 90(1), 135-159
Open this publication in new window or tab >>High-level classification of the Fungi and a tool for evolutionary ecological analyses
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2018 (English)In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 90, no 1, p. 135-159Article in journal (Refereed) Published
Abstract [en]

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

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

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

Place, publisher, year, edition, pages
WILEY, 2018
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-365992 (URN)10.1111/1462-2920.14069 (DOI)000445161800002 ()29441658 (PubMedID)
Funder
The Royal Swedish Academy of SciencesHelge Ax:son Johnsons stiftelse
Available from: 2018-11-22 Created: 2018-11-22 Last updated: 2018-11-22Bibliographically approved
Pölme, S., Bahram, M., Jacquemyn, H., Kennedy, P., Kohout, P., Moora, M., . . . Tedersoo, L. (2018). Host preference and network properties in biotrophic plant-fungal associations. New Phytologist, 217(3), 1230-1239
Open this publication in new window or tab >>Host preference and network properties in biotrophic plant-fungal associations
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2018 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 3, p. 1230-1239Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
endophytes, host specificity, macroecology, modularity, mycorrhizal fungi, nestedness, network analysis, phylogenetic distance
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-343789 (URN)10.1111/nph.14895 (DOI)000424541600027 ()29165806 (PubMedID)
Available from: 2018-03-06 Created: 2018-03-06 Last updated: 2018-03-06Bibliographically approved
Polme, S., Bahram, M., Jacquemyn, H., Kennedy, P., Kohout, P., Moora, M., . . . Tedersoo, L. (2018). Host preference and network properties in biotrophic plant-fungal associations. New Phytologist, 217(3), 1230-1239
Open this publication in new window or tab >>Host preference and network properties in biotrophic plant-fungal associations
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2018 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 3, p. 1230-1239Article in journal (Refereed) Published
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.

Keywords
endophytes, host specificity, macroecology, modularity, mycorrhizal fungi, nestedness, network analysis, phylogenetic distance
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-343656 (URN)10.1111/nph.14895 (DOI)000419978500027 ()29165806 (PubMedID)
Available from: 2018-05-09 Created: 2018-05-09 Last updated: 2018-05-09Bibliographically approved
Anslan, S., Bahram, M. & Tedersoo, L. (2018). Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests. Soil Biology and Biochemistry, 116, 245-252
Open this publication in new window or tab >>Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests
2018 (English)In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 116, p. 245-252Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
PERGAMON-ELSEVIER SCIENCE LTD, 2018
Keywords
Collembola, High-throughput sequencing, Fungal community, Arthropod-microbial associations, Seasonality, Temporal changes
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-341306 (URN)10.1016/j.soilbio.2017.10.021 (DOI)000419417900028 ()
Available from: 2018-02-07 Created: 2018-02-07 Last updated: 2018-02-07Bibliographically approved
Bahram, M., Hildebrand, F., Forslund, S. K., Anderson, J. L., Soudzilovskaia, N. A., Bodegom, P. M., . . . Bork, P. (2018). Structure and function of the global topsoil microbiome.. Nature, 560(7717), 233-237
Open this publication in new window or tab >>Structure and function of the global topsoil microbiome.
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2018 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 560, no 7717, p. 233-237Article in journal (Refereed) Published
Abstract [en]

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

National Category
Microbiology Evolutionary Biology Ecology Environmental Sciences
Identifiers
urn:nbn:se:uu:diva-360977 (URN)10.1038/s41586-018-0386-6 (DOI)000441115200048 ()30069051 (PubMedID)
Funder
Swedish Research Council, 2017-05019The Royal Swedish Academy of SciencesHelge Ax:son Johnsons stiftelse EU, Horizon 2020, 686070
Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-11-08Bibliographically approved
Mirmajlessi, S. M., Bahram, M., Mänd, M., Najdabbasi, N., Mansouripour, S. & Loit, E. (2018). Survey of Soil Fungal Communities in Strawberry Fields by Illumina Amplicon Sequencing. Eurasian Soil Science, 51(6), 682-691
Open this publication in new window or tab >>Survey of Soil Fungal Communities in Strawberry Fields by Illumina Amplicon Sequencing
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2018 (English)In: Eurasian Soil Science, ISSN 1064-2293, E-ISSN 1556-195X, Vol. 51, no 6, p. 682-691Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
PLEIADES PUBLISHING INC, 2018
Keywords
fungal communities, Illumina technology, soil borne pathogens, strawberry
National Category
Agricultural Science
Identifiers
urn:nbn:se:uu:diva-358533 (URN)10.1134/S106422931806011X (DOI)000435608500009 ()
Available from: 2018-09-03 Created: 2018-09-03 Last updated: 2018-09-03Bibliographically approved
Bahram, M., Vanderpool, D., Pent, M., Hiltunen, M. & Ryberg, M. (2018). The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics. Environmental Microbiology Reports, 10(2), 155-166
Open this publication in new window or tab >>The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics
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2018 (English)In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 2, p. 155-166Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
WILEY, 2018
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-353114 (URN)10.1111/1758-2229.12612 (DOI)000428391900005 ()29327481 (PubMedID)
Available from: 2018-06-11 Created: 2018-06-11 Last updated: 2018-06-11Bibliographically approved
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