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| 2. |
- Cheeke, Tanya, et al.
(author)
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Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function
- 2017
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 214:1, s. 432-442
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Journal article (peer-reviewed)abstract
- 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.
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| 3. |
- Manyara, David, et al.
(author)
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Purifying Selection and Persistent Polymorphism among Nuclei in the Multinucleate Arbuscular Mycorrhizal Fungi
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Other publication (other academic/artistic)abstract
- Arbuscular mycorrhizal (AM) fungi form an obligate symbiosis with the roots of the majority of land plants and are found in all terrestrial ecosystems. The source and structure of genetic variation in AM fungi has remained an enigma due to difficulties in the axenic cultivation and generation of high-quality genome assemblies from most species. Furthermore, how AM fungi survive long-term without a known single nucleus per cell stage in their life cycle is puzzling. Purifying selection acting at the nuclear level has been hypothesized as a mechanism to purge deleterious mutations. In this study, we aimed to characterize both intra- and inter-organismal genetic variation in AM fungi by analyzing genomic information from individual nuclei of three strains of two species in the genus Claroideoglomus. We observed overall low levels of genetic variation within the strains, most of which represent rare variants and with average dN/dS ratios within nuclei indicating that these are kept at low frequency by purifying selection. We also observed sites that are maintained as polymorphic across both strains and species, and discuss different models to explain this pattern. The results in this study affirm our conceptual understanding that nuclei in AM fungal strains function as populations of asexually reproducing units with strong signals of purifying selection on nuclei within the strains.
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| 4. |
- Montoliu-Nerin, Merce, et al.
(author)
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In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
- 2021
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In: Frontiers in Fungal Biology. - : Frontiers Media S.A.. - 2673-6128. ; 2
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Journal article (peer-reviewed)abstract
- Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.
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| 5. |
- Montoliu-Nerin, Merce, 1991-, et al.
(author)
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In-depth phylogenomic analysis of Glomeromycota based on a comprehensive set of de novogenome assemblies
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Other publication (other academic/artistic)abstract
- Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have been the bases of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the AM fungi phylogeny will depend upon a more extensive ortholog sampling, resulting from a wider range of available whole genome sequences from a large set of taxa. To circumvent the need for axenic culturing of AM fungi we use single nuclei sequencing to generate de novogenome assemblies of AM fungi covering seven families of Glomeromycota. The predicted genes of these assemblies, together with the available protein sequences of AM fungi and sister clades, were used for phylogenomic analysis. We confirm that our novel workflow generates high quality genome assemblies suitable for phylogenomic analysis of AM fungi. Within the monophyletic phylum Glomeromycota, we identify three candidate topologies, in which the family Glomerales is recovered as polyphyletic in two of them. Our results support family level classification from previous phylogenetic studies using sequences of the rDNA operon. Our multi-locus analyses identify alternative evolutionary histories within this diverse phylum.
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| 6. |
- Sánchez-García, Marisol, et al.
(author)
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Single nuclei sequencing reveals low levels of intra-organismal genomic variation across strains in the genus Claroideoglomus
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Other publication (other academic/artistic)abstract
- Arbuscular mycorrhizal (AM) fungi are important plant symbionts that propagate predominantly with multinucleate asexual spores formed below ground. The degree of intra-organismal genetic variation in AM fungi has been a long-standing topic of debate due to difficulties in generating high quality genome assemblies from most species in this phylum in combination with exceptionally high levels of rDNA polymorphism compared to other eukaryotes.In the AM fungi Claroideoglomus etunicatum, visualization of nuclei migration during spore formation has demonstrated that sporogenesis is random or sectorial, firmly rejecting false sporogenesis with one or two founding nuclei (Jany and Pawlowska, 2010). We thus expect the composition of nuclei in a single Claroideoglomusspore to reflect that of the entire organism when we study intra-organismal genetic variation of individual spores from three strains in the genus Claroideoglomus. The three strains are all within the luteum/claroideumspecies complex that cannot be phylogenetically resolved based on rRNA large subunit genes (Vankuren et al., 2013). From each strain we generated 24 single nuclei genome assemblies to identify rRNA gene variants and MAT locus in each nucleus. Then, we map the reads of each individual nucleus to two different reference assemblies and identify SNPs within and between nuclei from single spores using two different softwares for variant calling. We identify the mating type locus and characterized intra-organismal genetic diversity in each strain and explore patterns of recombination and shared variants across strains. Based on earlier studies in the genus Rhizophagus, we expect nuclei to be haploid and within spore allele frequency patterns to be explained by the number of MAT type alleles.
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