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  • 1.
    Cheeke, Tanya E.
    et al.
    Swedish Univ Agr Sci, Uppsala Bioctr, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden.;Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA..
    Phillips, Richard P.
    Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA..
    Brzostek, Edward R.
    West Virginia Univ, Dept Biol, 53 Campus Dr, Morgantown, WV 26506 USA..
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bever, James D.
    Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA.;Univ Kansas, Dept Ecol & Evolutionary Biol, 2041 Haworth Hall,1200 Sunnyside Ave, Lawrence, KS 66045 USA..
    Fransson, Petra
    Swedish Univ Agr Sci, Uppsala Bioctr, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden..
    Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, no 1, p. 432-442Article in journal (Refereed)
    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.

  • 2. Clarholm, Marianne
    et al.
    Skyllberg, Ulf
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Organic acid induced release of nutrients from metal-stabilized soil organic matter - The unbutton model2015In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 84, p. 168-176Article, review/survey (Refereed)
    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.

  • 3. Fransson, Petra
    et al.
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Fungal and bacterial community responses to Suillus variegtus extraradical mycelia and soil profile in Scots pine microcosms2014In: Plant and Soil, ISSN 0032-079X, E-ISSN 1573-5036, Vol. 385, no 1-2, p. 255-272Article in journal (Refereed)
    Abstract [en]

    Aims To investigate the importance of ectomycorrhizal (ECM) extraradical mycelia and soil substrate in shaping specific mycorrhizosphere microbial communities. Methods Suillus variagtus inoculated Scots pine seedlings were grown for approximately 5 months in soil microcosms using five soil layer treatments. Fungal and bacterial community composition near roots, in hyphal fronts and 'bulk soil' was studied using T-RFLP, cloning and sequencing. Plant chemistry at harvest and initial chemical properties for the soil layers were analysed. Results Both fungal and bacterial community compositions differed between different soil layers for S. variegatus inoculated seedlings. The mixed soil, corresponding to the interface between organic and mineral layers, supported the highest plant and fungal biomass and the most diverse fungal communities. Environmental variables explained ca. 50 % of the variation in data. In OE mixed layers the main driver shaping communities was plant chemistry, reflecting below-ground C flow, and for O and E layers soil chemistry (nutrients and pH) was the main driver. Fungal communities included 56 identified taxa, and more taxa were found in soil associated with hyphal fronts compared to 'bulk soil' and roots. Bacterial communities changed over time and bacteria associated with hyphal fronts partly differentiated from other sampling sites. Conclusion The experimental microcosm setup allowed establishment of communities reflecting those naturally occurring at the field site. Given that below-ground C flow is sufficient, extraradical mycelial expansion in the substrate has the potential to drive microbial community development.

  • 4. Menkis, Audrius
    et al.
    Urbina, Hector
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    James, Timothy Y.
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Archaeorhizomyces borealis sp nov and a sequence-based classification of related soil fungal species2014In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 118, no 12, p. 943-955Article in journal (Refereed)
    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.

  • 5.
    Rosling, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Midgley, Meghan G.
    Cheeke, Tanya
    Urbina, Hector
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Fransson, Petra
    Phillips, Richard P.
    Phosphorus cycling in deciduous forest soil differs betweenstands dominated by ecto- and arbuscular mycorrhizal trees2016In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 209, no 3, p. 1184-1195Article in journal (Refereed)
    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.

  • 6.
    Rosling, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Timling, Ina
    University of Alaska Fairbanks.
    Taylor, Lee
    University of New Mexico.
    Archaeorhizomycetes: Patterns of Distribution and Abundance in Soil2013In: Genomics of Soil- and Plant-Associated Fungi / [ed] Benjamin A. Horwitz, Prasun K Mukherjee, Mala Mukherjee, Christian P Kubicek, Heidelberg: Springer Berlin/Heidelberg, 2013, p. 333-349Chapter in book (Refereed)
    Abstract [en]

    Soil fungal ecology has developed tremendously with the introduction of environmental sequencing. The soil under our feet harbors great fungal diversity including species and even lineages of unknown identity. Beyond identification we can use environmental sequences to trace distribution patterns of species and lineages to better understand their life strategies and ecological roles. Environmental sequences provide the largest available source of information on the ecology of Archaeorhizomycetes, a class of globally distributed ubiquitous soil fungi for which there are no known fruiting structures and only two of over 250 estimated species have been cultured.

    The class was initially known as the Soil Clone Group 1 (SCG1) (Porter et al. 2008) based on environmental sequences from four diverse ecosystems and twelve published studies. Porter and co-workers highlighted two important features of the class Archaeorhizomycetes: its broad distribution across diverse ecosystems as well as its high species diversity within sites. When the class of Archaeorhizomycetes was formally described by Rosling et al. in 2011, thousands of ITS sequences were available in public databases. Based on meta-data associated with these sequences, ecosystem specificity and geographic distribution patterns emerged among several putative species, i.e. OTUs, within the class. In this chapter we expand upon earlier analyses of distribution by adding complementary datasets including environmental LSU and SSU sequences. Habitat specificity and geographic distribution are further analyzed using public and previously unpublished sequences from ten field studies in Alaska.

  • 7. Schadt, Christopher W.
    et al.
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Comment on "Global diversity and geography of soil fungi"2015In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 348, no 6242Article in journal (Other academic)
    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.

  • 8.
    Urbina, Hector
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Purdue Univ, Dept Bot & Plant Pathol, 915 W State St, W Lafayette, IN 47907 USA.
    Breed, Martin F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Adelaide, Sch Biol Sci, North Terrace, SA 5005, Australia;Univ Adelaide, Environm Inst, North Terrace, SA 5005, Australia.
    Zhao, Weizhou
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Gurrala, Kanaka Lakshmi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere2018In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 122, no 4, p. 231-240Article in journal (Refereed)
    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.

  • 9.
    Urbina, Hector
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala Univ, Dept Informat Technol, Uppsala Multidisciplinary Ctr Adv Computat Sci, Box 137, S-75105 Uppsala, Sweden..
    Cafaro, Matias
    Univ Puerto Rico, Dept Biol, Mayaguez, PR 00681 USA..
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico2016In: Mycoscience, ISSN 1340-3540, E-ISSN 1618-2545, Vol. 57, no 3, p. 217-227Article in journal (Refereed)
    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.

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