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Tedersoo L, Magurno F, Alkahtani S, Mikryukov V. Phylogenetic classification of arbuscular mycorrhizal fungi: new species and higher-ranking taxa in Glomeromycota and Mucoromycota (class Endogonomycetes). MycoKeys 2024; 107:273-325. [PMID: 39169987 PMCID: PMC11336396 DOI: 10.3897/mycokeys.107.125549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/20/2024] [Indexed: 08/23/2024] Open
Abstract
Arbuscular mycorrhizal (AM) fungi - Glomeromycota and Endogonomycetes - comprise multiple species and higher-level taxa that have remained undescribed. We propose a mixed morphology- and DNA-based classification framework to promote taxonomic communication and shed light into the phylogenetic structure of these ecologically essential fungi. Based on eDNA samples and long reads as type materials, we describe 15 new species and corresponding genera (Pseudoentrophosporakesseensis, Hoforsarebekkae, Kahvenarebeccae, Kelottijaerviashannonae, Kungsaengenashadiae, Langduoadianae, Lehetuaindrekii, Lokrumastenii, Moosteastephanieae, Nikkaluoktamahdiehiae, Parniguacraigii, Riederbergasylviae, Ruuacoralieae, Tammsaareavivikae and Unemaeeanathalieae), the genus Parvocarpum as well as 19 families (Pseudoentrophosporaceae, Hoforsaceae, Kahvenaceae, Kelottijaerviaceae, Kungsaengenaceae, Langduoaceae, Lehetuaceae, Lokrumaceae, Moosteaceae, Nikkaluoktaceae, Parniguaceae, Riederbergaceae, Ruuaceae, Tammsaareaceae, Unemaeeaceae, Bifigurataceae, Planticonsortiaceae, Jimgerdemanniaceae and Vinositunicaceae) and 17 orders (Hoforsales, Kahvenales, Kelottijaerviales, Kungsaengenales, Langduoales, Lehetuales, Lokrumales, Moosteales, Nikkaluoktales, Parniguales, Riederbergales, Ruuales, Tammsaareales, Unemaeeales, Bifiguratales and Densosporales), and propose six combinations (Diversisporabareae, Diversisporanevadensis, Fuscutatacerradensis, Fuscutatareticulata, Viscosporadeserticola and Parvocarpumbadium) based on phylogenetic evidence. We highlight further knowledge gaps in the phylogenetic structure of AM fungi and propose an alphanumeric coding system for preliminary communication and reference-based eDNA quality-filtering of the remaining undescribed genus- and family-level groups. Using AM fungi as examples, we hope to offer a sound, mixed framework for classification to boost research in the alpha taxonomy of fungi, especially the "dark matter fungi".
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, 2 Liivi, 50409 Tartu, Estonia
- Department of Zoology, College of Science, King Saud University, 12371 Riyadh, Saudi Arabia
| | - Franco Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, 12371 Riyadh, Saudi Arabia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, 2 Liivi, 50409 Tartu, Estonia
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Montoliu-Nerin M, Sánchez-García M, Bergin C, Kutschera VE, Johannesson H, Bever JD, Rosling A. In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:716385. [PMID: 37744125 PMCID: PMC10512289 DOI: 10.3389/ffunb.2021.716385] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/06/2021] [Indexed: 09/26/2023]
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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Affiliation(s)
- Merce Montoliu-Nerin
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
- Department of Forest Mycology and Plant Pathology, Uppsala Biocentre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Claudia Bergin
- Microbial Single Cell Genomics Facility, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Verena Esther Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden
| | - James D. Bever
- Department of Ecology and Evolutionary Biology, and Kansas Biological Survey, University of Kansas, Lawrence, KS, United States
| | - Anna Rosling
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
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Stürmer SL, Bever JD, Schultz PA, Bentivenga SP. Celebrating INVAM: 35 years of the largest living culture collection of arbuscular mycorrhizal fungi. MYCORRHIZA 2021; 31:117-126. [PMID: 33205230 DOI: 10.1007/s00572-020-01008-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
The International Culture Collection of (Vesicular-) Arbuscular Mycorrhizal Fungi-INVAM-the largest living culture collection of arbuscular mycorrhizal fungi (AMF) celebrated its 35th year in 2020. The authors record here the mission and goals of INVAM, its contribution as a living culture collection, some historical aspects of INVAM, and describe the advances in mycorrhizology and AMF systematics after INVAM moved to West Virginia University. This commentary emphasizes the importance of a living culture collection to preserve germplasm and to educate and assist researchers in mycorrhizal science.
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Affiliation(s)
- Sidney L Stürmer
- Universidade Regional de Blumenau, Departamento de Ciências Naturais, Blumenau, SC, 89030-903, Brazil.
| | - James D Bever
- University of Kansas, Kansas Biological Survey, Department of Ecology and Evolution, Lawrence, KS, 66047, USA
| | - Peggy A Schultz
- University of Kansas, Kansas Biological Survey, Department of Ecology and Evolution, Lawrence, KS, 66047, USA
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Maeda T, Kobayashi Y, Kameoka H, Okuma N, Takeda N, Yamaguchi K, Bino T, Shigenobu S, Kawaguchi M. Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis. Commun Biol 2018; 1:87. [PMID: 30271968 PMCID: PMC6123716 DOI: 10.1038/s42003-018-0094-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/12/2018] [Indexed: 01/21/2023] Open
Abstract
Arbuscular mycorrhizal fungus (AMF) species are some of the most widespread symbionts of land plants. Our much improved reference genome assembly of a model AMF, Rhizophagus irregularis DAOM-181602 (total contigs = 210), facilitated a discovery of repetitive elements with unusual characteristics. R. irregularis has only ten or 11 copies of complete 45S rDNAs, whereas the general eukaryotic genome has tens to thousands of rDNA copies. R. irregularis rDNAs are highly heterogeneous and lack a tandem repeat structure. These findings provide evidence for the hypothesis that rDNA heterogeneity depends on the lack of tandem repeat structures. RNA-Seq analysis confirmed that all rDNA variants are actively transcribed. Observed rDNA/rRNA polymorphisms may modulate translation by using different ribosomes depending on biotic and abiotic interactions. The non-tandem repeat structure and intragenomic heterogeneity of AMF rDNA/rRNA may facilitate successful adaptation to various environmental conditions, increasing host compatibility of these symbiotic fungi.
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Affiliation(s)
- Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Yuuki Kobayashi
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Nao Okuma
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan
| | - Naoya Takeda
- School of Science and Technology, Kwansei Gakuin University, Gakuen, Mita, Hyogo, 669-1337, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Takahiro Bino
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Shuji Shigenobu
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan.
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan.
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan.
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan.
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Crossay T, Antheaume C, Redecker D, Bon L, Chedri N, Richert C, Guentas L, Cavaloc Y, Amir H. New method for the identification of arbuscular mycorrhizal fungi by proteomic-based biotyping of spores using MALDI-TOF-MS. Sci Rep 2017; 7:14306. [PMID: 29084976 PMCID: PMC5662746 DOI: 10.1038/s41598-017-14487-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF, Glomeromycota) are mutualistic symbionts associated with majority of land plants. These fungi play an important role in plant growth, but their taxonomic identification remains a challenge for academic research, culture collections and inoculum producers who need to certify their products. Identification of these fungi was traditionally performed based on their spore morphology. DNA sequence data have successfully been used to study the evolutionary relationships of AMF, develop molecular identification tools and assess their diversity in the environment. However, these methods require considerable expertise and are not well-adapted for "routine" quality control of culture collections and inoculum production. Here, we show that Matrix-Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry proteomic-based biotyping is a highly efficient approach for AMF identification. Nineteen isolates belonging to fourteen species, seven genera and five families were clearly differentiated by MALDI biotyping at the species level, and intraspecific differentiation was achieved for the majority. AMF identification by MALDI biotyping could be highly useful, not only for research but also in agricultural and environmental applications. Fast, accurate and inexpensive molecular mass determination and the possibility of automation make MALDI-TOF-MS a real alternative to conventional morphological and molecular methods for AMF identification.
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Affiliation(s)
- Thomas Crossay
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France
| | - Cyril Antheaume
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France. .,Plate-forme d'Analyse Chimique Strasbourg-Illkirch. Université de Strasbourg, F-67400, Illkirch, France.
| | - Dirk Redecker
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Lucie Bon
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France
| | - Nicolas Chedri
- Institut Pasteur, Bacteriology Research Unit, 98800, Nouméa, Nouvelle-Calédonie, France
| | | | - Linda Guentas
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France
| | - Yvon Cavaloc
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France
| | - Hamid Amir
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France.
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Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota. ISME JOURNAL 2017; 11:1727-1735. [PMID: 28387771 DOI: 10.1038/ismej.2017.21] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 01/07/2023]
Abstract
Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial-fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endosymbionts, which dwell inside fungal cells, provide the most intimate example. Bacterial endosymbionts mostly occur in fungi of the phylum Mucoromycota and include Betaproteobacteria (Burkhoderia-related) and Mollicutes (Mycoplasma-related). Based on phylogenomics and estimations of divergence time, we hypothesized two different scenarios for the origin of these interactions (early vs late bacterial invasion). Sequencing of the genomes of fungal endobacteria revealed a significant reduction in genome size, particularly in endosymbionts of Glomeromycotina, as expected by their uncultivability and host dependency. Similar to endobacteria of insects, the endobacteria of fungi show a range of behaviours from mutualism to antagonism. Emerging results suggest that some benefits given by the endobacteria to their plant-associated fungal host may propagate to the interacting plant, giving rise to a three-level inter-domain interaction.
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8
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Uniting species- and community-oriented approaches to understand arbuscular mycorrhizal fungal diversity. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.07.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering. Appl Environ Microbiol 2016; 82:4921-30. [PMID: 27260357 DOI: 10.1128/aem.00816-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/27/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. IMPORTANCE Arbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account.
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Young JPW. Genome diversity in arbuscular mycorrhizal fungi. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:113-119. [PMID: 26190590 DOI: 10.1016/j.pbi.2015.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/28/2015] [Accepted: 06/06/2015] [Indexed: 06/04/2023]
Abstract
Arbuscular mycorrhizal fungi (Glomeromycota) are the most widespread and important symbionts of plants. They cannot be cultured without plants, are apparently asexual, and have multiple nuclei in a common cytoplasm. There is evidence for genetic variation among nuclei, and for segregation of this variation during growth, but these findings remain contentious. Recently, two papers have reported whole genome sequences for a strain of Rhizophagus irregularis; both suggest that genetic variation among nuclei is low. Genome assembly is very incomplete, though, so significant nuclear diversity cannot be excluded. While the diversity of nuclear genomes remains unresolved, multiple complete mitochondrial genomes are now available; there is virtually no variation within isolates, but significant variation between them.
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Affiliation(s)
- J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
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Bills RJ, Morton JB. A combination of morphology and 28S rRNA gene sequences provide grouping and ranking criteria to merge eight into three Ambispora species (Ambisporaceae, Glomeromycota). MYCORRHIZA 2015; 25:485-498. [PMID: 25638691 DOI: 10.1007/s00572-015-0626-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/14/2015] [Indexed: 06/04/2023]
Abstract
Ambispora, the only genus in Ambisporaceae and one of three deeply rooted families in Archaeosporales, Glomeromycetes, is amended. Analysis of the morphology of specimens from types and living cultures and 28S ribosomal DNA (rDNA; LSU) sequences resulted in two major changes that redefined Ambispora to include only species with the potential for spore dimorphism (acaulosporoid and glomoid). First, species described as producing only glomoid spores (Ambispora leptoticha, Ambispora fecundispora, and Ambispora callosa), only acaulosporoid spores (Ambispora jimgerdemannii), or both spore morphotypes (Ambispora appendicula) were synonymized with a redefined dimorphic species, A. leptoticha. LSU sequences and more conserved SSU gene data indicated little divergence between genotypes formerly classified as separate species. Second, Ambispora fennica was synonymized with Ambispora gerdemannii based on morphological and LSU sequence variation equivalent to that measured in the sister clade A. leptoticha. With this analysis, Ambispora was reduced to three species: A. leptoticha, A. gerdemannii, and Ambispora granatensis. Morphological and molecular characters were given equal treatment in this study, as each data set informed and clarified grouping and ranking decisions. The two inner layers of the acaulosporoid spore wall were the only structural characters uniquely defining each of these three species; all other characters were shared. Phenotypes of glomoid spores were indistinguishable between species, and thus were informative only at the genus level. Distinct subclade structure of the LSU gene tree suggests fixation of discrete variants typical of clonal reproduction and possible retention of polymorphisms in rDNA repeats, so that not all discrete genetic variants are indicative of speciation.
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Affiliation(s)
- Robert J Bills
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506-6108, USA,
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Toomer KH, Chen X, Naito M, Mondo SJ, den Bakker HC, VanKuren NW, Lekberg Y, Morton JB, Pawlowska TE. Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungi. Mol Ecol 2015; 24:3485-500. [DOI: 10.1111/mec.13250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 05/01/2015] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin H. Toomer
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Xiuhua Chen
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan 430070 China
| | - Mizue Naito
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Stephen J. Mondo
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Henk C. den Bakker
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Nicholas W. VanKuren
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Ylva Lekberg
- MPG Ranch; Missoula MT 59802 USA
- Department of Ecosystem and Conservation Sciences; University of Montana; Missoula MT 59812 USA
| | - Joseph B. Morton
- Division of Plant & Soil Sciences; West Virginia University; Morgantown WV 26506 USA
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
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Stockinger H, Peyret-Guzzon M, Koegel S, Bouffaud ML, Redecker D. The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field. PLoS One 2014; 9:e107783. [PMID: 25275381 PMCID: PMC4183475 DOI: 10.1371/journal.pone.0107783] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/14/2014] [Indexed: 11/30/2022] Open
Abstract
Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.
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Affiliation(s)
- Herbert Stockinger
- Université de Bourgogne, UMR1347 Agroécologie, Dijon, France
- INRA, UMR1347 Agroécologie, Dijon, France
| | | | | | | | - Dirk Redecker
- Université de Bourgogne, UMR1347 Agroécologie, Dijon, France
- * E-mail:
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Morton JB, Benedito VA, Panaccione DG, Jenks MA. Potential for Industrial Application of Microbes in Symbioses that Influence Plant Productivity and Sustainability in Agricultural, Natural, or Restored Ecosystems. Ind Biotechnol (New Rochelle N Y) 2014. [DOI: 10.1089/ind.2014.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Joseph B. Morton
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Vagner A. Benedito
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Daniel G. Panaccione
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Matthew A. Jenks
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
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Bik HM, Fournier D, Sung W, Bergeron RD, Thomas WK. Intra-genomic variation in the ribosomal repeats of nematodes. PLoS One 2013; 8:e78230. [PMID: 24147124 PMCID: PMC3795665 DOI: 10.1371/journal.pone.0078230] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 09/18/2013] [Indexed: 12/25/2022] Open
Abstract
Ribosomal loci represent a major tool for investigating environmental diversity and community structure via high-throughput marker gene studies of eukaryotes (e.g. 18S rRNA). Since the estimation of species' abundance is a major goal of environmental studies (by counting numbers of sequences), understanding the patterns of rRNA copy number across species will be critical for informing such high-throughput approaches. Such knowledge is critical, given that ribosomal RNA genes exist within multi-copy repeated arrays in a genome. Here we measured the repeat copy number for six nematode species by mapping the sequences from whole genome shotgun libraries against reference sequences for their rRNA repeat. This revealed a 6-fold variation in repeat copy number amongst taxa investigated, with levels of intragenomic variation ranging from 56 to 323 copies of the rRNA array. By applying the same approach to four C. elegans mutation accumulation lines propagated by repeated bottlenecking for an average of ~400 generations, we find on average a 2-fold increase in repeat copy number (rate of increase in rRNA estimated at 0.0285-0.3414 copies per generation), suggesting that rRNA repeat copy number is subject to selection. Within each Caenorhabditis species, the majority of intragenomic variation found across the rRNA repeat was observed within gene regions (18S, 28S, 5.8S), suggesting that such intragenomic variation is not a product of selection for rRNA coding function. We find that the dramatic variation in repeat copy number among these six nematode genomes would limit the use of rRNA in estimates of organismal abundance. In addition, the unique pattern of variation within a single genome was uncorrelated with patterns of divergence between species, reflecting a strong signature of natural selection for rRNA function. A better understanding of the factors that control or affect copy number in these arrays, as well as their rates and patterns of evolution, will be critical for informing estimates of global biodiversity.
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Affiliation(s)
- Holly M. Bik
- Union Council Davis Genome Center, University of California Davis, Davis, California, United States of America
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
| | - David Fournier
- Department of Computer Science, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Way Sung
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - R. Daniel Bergeron
- Department of Computer Science, University of New Hampshire, Durham, New Hampshire, United States of America
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
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Redecker D, Schüssler A, Stockinger H, Stürmer SL, Morton JB, Walker C. An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota). MYCORRHIZA 2013; 23:515-31. [PMID: 23558516 DOI: 10.1007/s00572-013-0486-y] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/07/2013] [Indexed: 05/03/2023]
Abstract
The publication of a large number of taxon names at all levels within the arbuscular mycorrhizal fungi (Glomeromycota) has resulted in conflicting systematic schemes and generated considerable confusion among biologists working with these important plant symbionts. A group of biologists with more than a century of collective experience in the systematics of Glomeromycota examined all available molecular-phylogenetic evidence within the framework of phylogenetic hypotheses, incorporating morphological characters when they were congruent. This study is the outcome, wherein the classification of Glomeromycota is revised by rejecting some new names on the grounds that they are founded in error and by synonymizing others that, while validly published, are not evidence-based. The proposed "consensus" will provide a framework for additional original research aimed at clarifying the evolutionary history of this important group of symbiotic fungi.
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Affiliation(s)
- Dirk Redecker
- Université de Bourgogne/INRA, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21000, Dijon, France,
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17
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Beaudet D, Nadimi M, Iffis B, Hijri M. Rapid mitochondrial genome evolution through invasion of mobile elements in two closely related species of arbuscular mycorrhizal fungi. PLoS One 2013; 8:e60768. [PMID: 23637766 PMCID: PMC3630166 DOI: 10.1371/journal.pone.0060768] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/02/2013] [Indexed: 11/19/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are common and important plant symbionts. They have coenocytic hyphae and form multinucleated spores. The nuclear genome of AMF is polymorphic and its organization is not well understood, which makes the development of reliable molecular markers challenging. In stark contrast, their mitochondrial genome (mtDNA) is homogeneous. To assess the intra- and inter-specific mitochondrial variability in closely related Glomus species, we performed 454 sequencing on total genomic DNA of Glomus sp. isolate DAOM-229456 and we compared its mtDNA with two G. irregulare isolates. We found that the mtDNA of Glomus sp. is homogeneous, identical in gene order and, with respect to the sequences of coding regions, almost identical to G. irregulare. However, certain genomic regions vary substantially, due to insertions/deletions of elements such as introns, mitochondrial plasmid-like DNA polymerase genes and mobile open reading frames. We found no evidence of mitochondrial or cytoplasmic plasmids in Glomus species, and mobile ORFs in Glomus are responsible for the formation of four gene hybrids in atp6, atp9, cox2, and nad3, which are most probably the result of horizontal gene transfer and are expressed at the mRNA level. We found evidence for substantial sequence variation in defined regions of mtDNA, even among closely related isolates with otherwise identical coding gene sequences. This variation makes it possible to design reliable intra- and inter-specific markers.
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Affiliation(s)
- Denis Beaudet
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Maryam Nadimi
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Bachir Iffis
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
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