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Zamora, J. C., Svensson, M., Kirschner, R., Olariaga, I., Ryman, S., Alberto Parra, L., . . . Ekman, S. (2018). Considerations and consequences of allowing DNA sequence data as types of fungal taxa. IMA Fungus, 9(1), 167-185
Open this publication in new window or tab >>Considerations and consequences of allowing DNA sequence data as types of fungal taxa
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2018 (English)In: IMA Fungus, ISSN 2210-6340, E-ISSN 2210-6359, Vol. 9, no 1, p. 167-185Article in journal (Refereed) Published
Abstract [en]

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Place, publisher, year, edition, pages
INT MYCOLOGICAL ASSOC, 2018
Keywords
IMC11, nomenclature, speciation, taxonomy, typification, voucherless fungi
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-360540 (URN)10.5598/imafungus.2018.09.01.10 (DOI)000438287000033 ()30018877 (PubMedID)
Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-09-20Bibliographically approved
George, T. S., Giles, C. D., Menezes-Blackburn, D., Condron, L. M., Gama-Rodrigues, A. C., Jaisi, D., . . . Haygarth, P. M. (2018). Correction to: Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities. Plant and Soil, 427(1-2), 209-211
Open this publication in new window or tab >>Correction to: Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities
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2018 (English)In: Plant and Soil, ISSN 0032-079X, E-ISSN 1573-5036, Vol. 427, no 1-2, p. 209-211Article in journal (Other academic) Published
National Category
Soil Science
Identifiers
urn:nbn:se:uu:diva-362651 (URN)10.1007/s11104-017-3488-2 (DOI)000434056500015 ()
Note

Correction to: Plant and Soil, vol. 427, issue 1-2, pages 191-208.

DOI: 10.1007/s11104-017-3391-x

Available from: 2018-10-16 Created: 2018-10-16 Last updated: 2018-10-16Bibliographically approved
George, T. S., Giles, C. D., Menezes-Blackburn, D., Condron, L. M., Gama-Rodrigues, A. C., Jaisi, D., . . . Haygarth, P. M. (2018). Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities. Plant and Soil, 427(1-2), 191-208
Open this publication in new window or tab >>Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities
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2018 (English)In: Plant and Soil, ISSN 0032-079X, E-ISSN 1573-5036, Vol. 427, no 1-2, p. 191-208Article in journal (Refereed) Published
Abstract [en]

The dynamics of phosphorus (P) in the environment is important for regulating nutrient cycles in natural and managed ecosystems and an integral part in assessing biological resilience against environmental change. Organic P (P-o) compounds play key roles in biological and ecosystems function in the terrestrial environment being critical to cell function, growth and reproduction. We asked a group of experts to consider the global issues associated with P-o in the terrestrial environment, methodological strengths and weaknesses, benefits to be gained from understanding the P-o cycle, and to set priorities for P-o research. We identified seven key opportunities for P-o research including: the need for integrated, quality controlled and functionally based methodologies; assessment of stoichiometry with other elements in organic matter; understanding the dynamics of P-o in natural and managed systems; the role of microorganisms in controlling P-o cycles; the implications of nanoparticles in the environment and the need for better modelling and communication of the research. Each priority is discussed and a statement of intent for the P-o research community is made that highlights there are key contributions to be made toward understanding biogeochemical cycles, dynamics and function of natural ecosystems and the management of agricultural systems.

Keywords
Ecosystems services, Method development, Microbiome, Modelling, Organic phosphorus, Stoichiometry
National Category
Soil Science
Identifiers
urn:nbn:se:uu:diva-357702 (URN)10.1007/s11104-017-3391-x (DOI)000434056500014 ()
Note

Correction in: Plant and Soil, vol. 427, issue 1-2, pages 209-211.

DOI: 10.1007/s11104-017-3488-2

Available from: 2018-08-21 Created: 2018-08-21 Last updated: 2018-10-16Bibliographically approved
Urbina, H., Breed, M. F., Zhao, W., Gurrala, K. L., Andersson, S. G. .., Ågren, J., . . . Rosling, A. (2018). Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere. Fungal Biology, 122(4), 231-240
Open this publication in new window or tab >>Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere
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2018 (English)In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 122, no 4, p. 231-240Article in journal (Refereed) Published
Abstract [en]

Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endo-sphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.

Keywords
Arabidopsis, Archaeorhizomcyetes, Brassicaceae, Ion Torrent, ITS metabarcoding, Rhizosphere
National Category
Botany
Identifiers
urn:nbn:se:uu:diva-354246 (URN)10.1016/j.funbio.2017.12.013 (DOI)000430773300005 ()29551197 (PubMedID)
Funder
Swedish Research Council, 349-2007-8731Swedish Research Council, 2012-3950Australian Research Council, DE150100542Australian Research Council, DP150103414
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2018-06-19 Created: 2018-06-19 Last updated: 2018-06-19Bibliographically approved
Cheeke, T. E., Phillips, R. P., Brzostek, E. R., Rosling, A., Bever, J. D. & Fransson, P. (2017). Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function. New Phytologist, 214(1), 432-442
Open this publication in new window or tab >>Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function
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2017 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, no 1, p. 432-442Article in journal (Refereed) Published
Abstract [en]

While it is well established that plants associating with arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi cycle carbon (C) and nutrients in distinct ways, we have a limited understanding of whether varying abundance of ECM and AM plants in a stand can provide integrative proxies for key biogeochemical processes. We explored linkages between the relative abundance of AM and ECM trees and microbial functioning in three hardwood forests in southern Indiana, USA. Across each site's 'mycorrhizal gradient', we measured fungal biomass, fungal : bacterial (F : B) ratios, extracellular enzyme activities, soil carbon : nitrogen ratio, and soil pH over a growing season. We show that the percentage of AM or ECM trees in a plot promotes microbial communities that both reflect and determine the C to nutrient balance in soil. Soils dominated by ECM trees had higher F : B ratios and more standing fungal biomass than AM stands. Enzyme stoichiometry in ECM soils shifted to higher investment in extracellular enzymes needed for nitrogen and phosphorus acquisition than in C-acquisition enzymes, relative to AM soils. Our results suggest that knowledge of mycorrhizal dominance at the stand or landscape scale may provide a unifying framework for linking plant and microbial community dynamics, and predicting their effects on ecological function.

Keywords
arbuscular mycorrhizal (AM) fungi, carbon : nitrogen (C : N) ratio, ectomycorrhizal (ECM) fungi, enzyme stoichiometry, ergosterol, extracellular enzymes, fungal : bacterial (F : B) ratio, temperate forest
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-321440 (URN)10.1111/nph.14343 (DOI)000398130300039 ()27918073 (PubMedID)
Available from: 2017-05-09 Created: 2017-05-09 Last updated: 2017-05-31Bibliographically approved
Urbina, H., Scofield, D. G., Cafaro, M. & Rosling, A. (2016). DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico. Mycoscience, 57(3), 217-227
Open this publication in new window or tab >>DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico
2016 (English)In: Mycoscience, ISSN 1340-3540, E-ISSN 1618-2545, Vol. 57, no 3, p. 217-227Article in journal (Refereed) Published
Abstract [en]

Soil fungal communities in tropical regions remain poorly understood. In order to increase the knowledge of diversity of soil-inhabiting fungi, we extracted total DNA from top-organic soil collected in seven localities dominated by four major ecosystems in the tropical island of Puerto Rico. In order to comprehensively characterize the fungal community, we PCR-amplified the internal transcribed spacer 2 (ITS2) fungal barcode using newly designed degenerated primers and varying annealing temperatures to minimize primer bias. Sequencing results, obtained using Ion Torrent technology, comprised a total of 566,613 sequences after quality filtering. These sequences were clustered into 4140 molecular operational taxonomic units (MOTUs) after removing low frequency sequences and rarefaction to account for differences in read depth between samples. Our results demonstrate that soil fungal communities in Puerto Rico are structured by ecosystem. Ascomycota, followed by Basidiomycota, dominates the diversity of fungi in soil. Amongst Ascomycota, the recently described soil-inhabiting class Archaeorhizomycetes was present in all localities, and taxa in Archaeorhizomycetes were among the most commonly observed MOTUs. The Basidiomycota community was dominated by soil decomposers and ectomycorrhizal fungi with a distribution strongly affected by local variation to a greater degree than Ascomycota.

Keywords
Communities, Dikarya, High-throughput sequencing, Internal transcribed spacer, Molecular operational taxonomic unit
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-294653 (URN)10.1016/j.myc.2016.02.001 (DOI)000373377800009 ()
Funder
Swedish Research Council FormasCarl Tryggers foundation
Available from: 2016-06-02 Created: 2016-05-26 Last updated: 2017-11-30Bibliographically approved
Rosling, A., Midgley, M. G., Cheeke, T., Urbina, H., Fransson, P. & Phillips, R. P. (2016). Phosphorus cycling in deciduous forest soil differs betweenstands dominated by ecto- and arbuscular mycorrhizal trees. New Phytologist, 209(3), 1184-1195
Open this publication in new window or tab >>Phosphorus cycling in deciduous forest soil differs betweenstands dominated by ecto- and arbuscular mycorrhizal trees
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2016 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 209, no 3, p. 1184-1195Article in journal (Refereed) Published
Abstract [en]

Although much is known about how trees and their associated microbes influence nitrogen cycling in temperate forest soils, less is known about biotic controls over phosphorus (P) cycling. Given that mycorrhizal fungi are instrumental for P acquisition and that the two dominant associations – arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi – possess different strategies for acquiring P, we hypothesized that P cycling would differ in stands dominated by trees associated with AM vs ECM fungi.We quantified soil solution P, microbial biomass P, and sequentially extracted inorganic and organic P pools from May to November in plots dominated by trees forming either AM or ECM associations in south-central Indiana, USA.Overall, fungal communities in AM and ECM plots were functionally different and soils exhibited fundamental differences in P cycling. Organic forms of P were more available in ECM plots than in AM plots. Yet inorganic P decreased and organic P accumulated over the growing season in both ECM and AM plots, resulting in increasingly P-limited microbial biomass. Collectively, our results suggest that P cycling in hardwood forests is strongly influenced by biotic processes in soil and that these are driven by plant-associated fungal communities.

National Category
Biological Sciences Botany
Identifiers
urn:nbn:se:uu:diva-288648 (URN)10.1111/nph.13720 (DOI)000373378000030 ()26510093 (PubMedID)
Funder
Swedish Research Council Formas, 2008-1410Magnus Bergvall FoundationCarl Tryggers foundation Swedish Research Council
Available from: 2016-04-28 Created: 2016-04-28 Last updated: 2017-11-30Bibliographically approved
Schadt, C. W. & Rosling, A. (2015). Comment on "Global diversity and geography of soil fungi". Science, 348(6242)
Open this publication in new window or tab >>Comment on "Global diversity and geography of soil fungi"
2015 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 348, no 6242Article in journal, Editorial material (Other academic) Published
Abstract [en]

Tedersoo et al. (Research Article, 28 November 2014, p. 1078) present a compelling study regarding patterns of biodiversity of fungi, carried out at a scale unprecedented to date for fungal biogeographical studies. The study demonstrates strong global biogeographic patterns in richness and community composition of soil fungi. What concerns us with the study is what we do not see. Unfortunately, this study underestimates the fungal diversity of one key group of soil fungi due to reliance on a single primer with known flaws.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-259199 (URN)10.1126/science.aaa4269 (DOI)000356869100029 ()
Available from: 2015-07-30 Created: 2015-07-29 Last updated: 2017-12-04Bibliographically approved
Clarholm, M., Skyllberg, U. & Rosling, A. (2015). Organic acid induced release of nutrients from metal-stabilized soil organic matter - The unbutton model. Soil Biology and Biochemistry, 84, 168-176
Open this publication in new window or tab >>Organic acid induced release of nutrients from metal-stabilized soil organic matter - The unbutton model
2015 (English)In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 84, p. 168-176Article, review/survey (Refereed) Published
Abstract [en]

Processes of soil organic matter (SOM) stabilization and the reverse, destabilization of SOM resulting in subsequent release and mobilization of nutrients from SOM, remain largely unresolved. The perception of SOM as supramolecular aggregates built of low molecular mass biomolecules is currently emerging. Polyvalent metal cations contribute to SOM tertiary structure by bridging functional groups of such molecules (Simpson et al., 2002). The strong bond to metals protects high quality organic material from being immediately accessed and decomposed. Here we propose a three-step process by which low molecular mass organic acids (LMMOAs) and hydrolytic enzymes act in series to destabilize SOM supramolecules to release organic nitrogen (N) and phosphorus (P) for local hyphal and root uptake. Complexation of the stabilizing metals by fungal-released LMMOA gives fungal-root consortia direct access to organic substrates of good quality. Because of their small sizes and carboxyl group configuration, citric and oxalic acids are the most effective LMMOAs forming stable complexes with the main SOM bridging metals Ca and Al in SOM. Citrate, forming particularly strong complexes with the trivalent cations Al and Fe, is dominant in soil solutions of low-productive highly acidic boreal forest soils where mycorrhizal associations with roots are formed predominantly by fungi with hydrophobic hyphal surfaces. In these systems mycelia participate in the formation of N-containing SOM with a significant contribution from strong Al bridges. In less acidic soils of temperate forests, including calcareous influenced soils, SOM is stabilized predominantly by Ca bridges. In such systems mycorrhizal fungi with more hydrophilic surfaces dominate, and oxalic acid, forming strong bidentate complexes with Ca, is the most common LMMOA exuded. A plant-fungus driven biotic mechanism at the supramolecular aggregate level (10(3)-10(5) Da) resolves micro-spatial priming of SOM, where the destabilization step is prerequisite for subsequent release of nutrients. (C) 2015 Elsevier Ltd. All rights reserved.

Keywords
Citrate, Hydrophobic mycorrhizae, Organo-metal complexes, Oxalate, Rhizosphere priming, Soil organic matter
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-257114 (URN)10.1016/j.soilbio.2015.02.019 (DOI)000353087600017 ()
Funder
Swedish Research Council, 2012-3950
Available from: 2015-06-30 Created: 2015-06-30 Last updated: 2017-12-04Bibliographically approved
Menkis, A., Urbina, H., James, T. Y. & Rosling, A. (2014). Archaeorhizomyces borealis sp nov and a sequence-based classification of related soil fungal species. Fungal Biology, 118(12), 943-955
Open this publication in new window or tab >>Archaeorhizomyces borealis sp nov and a sequence-based classification of related soil fungal species
2014 (English)In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 118, no 12, p. 943-955Article in journal (Refereed) Published
Abstract [en]

The class Archaeorhizomycetes (Taphrinomycotina, Ascomycota) was introduced to accommodate an ancient lineage of soil-inhabiting fungi found in association with plant roots. Based on environmental sequencing data Archaeorhizomycetes may comprise a significant proportion of the total fungal community in soils. Yet the only species described and cultivated in this class is Archaeorhizomyces finlayi. In this paper, we describe a second species from a pure culture, Archaeorhizomyces borealis NS99-600(T) (=CBS138755(ExT)) based on morphological, physiological, and multi-locus molecular characterization. Archaeorhizomyces borealis was isolated from a root tip of a Pinus sylvestris seedling grown in a forest nursery in Lithuania. Analysis of Archaeorhizomycete species from environmental samples shows that it has a Eurasian distribution and is the most commonly observed species. Archaeorhizomyces borealis shows slow growth in culture and forms yellowish creamy colonies, characteristics that distinguish A. borealis from its closest relative A. finlayi. Here we also propose a sequence-based taxonomic classification of Archaeorhizomycetes and predict that approximately 500 species in this class remain to be isolated and described.

Keywords
Plant roots, Rhizosphere, Soil clone group 1, Soil fungi, Symbiosis
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-243695 (URN)10.1016/j.funbio.2014.08.005 (DOI)000347603500001 ()25457942 (PubMedID)
Available from: 2015-02-16 Created: 2015-02-11 Last updated: 2017-12-04Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7003-5941

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