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Niezgoda P, Błaszkowski J, Błaszkowski T, Stanisławczyk A, Zubek S, Milczarski P, Malinowski R, Meller E, Malicka M, Goto BT, Uszok S, Casieri L, Magurno F. Three new species of arbuscular mycorrhizal fungi (Glomeromycota) and Acaulospora gedanensis revised. Front Microbiol 2024; 15:1320014. [PMID: 38410392 PMCID: PMC10896085 DOI: 10.3389/fmicb.2024.1320014] [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: 10/11/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024] Open
Abstract
Studies of the morphology and the 45S nuc rDNA phylogeny of three potentially undescribed arbuscular mycorrhizal fungi (phylum Glomeromycota) grown in cultures showed that one of these fungi is a new species of the genus Diversispora in the family Diversisporaceae; the other two fungi are new Scutellospora species in Scutellosporaceae. Diversispora vistulana sp. nov. came from maritime sand dunes of the Vistula Spit in northern Poland, and S. graeca sp. nov. and S. intraundulata sp. nov. originally inhabited the Mediterranean dunes of the Peloponnese Peninsula, Greece. In addition, the morphological description of spores of Acaulospora gedanensis, originally described in 1988, was emended based on newly found specimens, and the so far unknown phylogeny of this species was determined. The phylogenetic analyses of 45S sequences placed this species among Acaulospora species with atypical phenotypic and histochemical features of components of the two inner germinal walls.
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Affiliation(s)
- Piotr Niezgoda
- Department of Environmental Management, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Janusz Błaszkowski
- Department of Environmental Management, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Tomasz Błaszkowski
- Department of General and Oncological Surgery, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Anna Stanisławczyk
- Department of Genetics, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Szymon Zubek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Paweł Milczarski
- Department of Genetic, Plant Breeding & Biotechnology, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Ryszard Malinowski
- Department of Environmental Management, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Edward Meller
- Department of Environmental Management, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Monika Malicka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bruno Tomio Goto
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Sylwia Uszok
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Leonardo Casieri
- Mycorrhizal Applications LLC at Bio-Research & Development Growth Park, St. Louis, MO, United States
| | - Franco Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Uwaremwe C, Bao W, Daoura BG, Mishra S, Zhang X, Shen L, Xia S, Yang X. Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species. Int Microbiol 2023:10.1007/s10123-023-00470-x. [PMID: 38158469 DOI: 10.1007/s10123-023-00470-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/14/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss. METHODS In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection. RESULTS Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification. CONCLUSIONS Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.
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Affiliation(s)
- Constantine Uwaremwe
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
| | - Wenjie Bao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bachir Goudia Daoura
- Department of Biology, Faculty of Sciences and Technology, Dan Dicko Dankoulodo University, POBox, 465, Maradi, Niger
| | - Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China
| | - Xianxian Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingjie Shen
- College of Biology and Chemistry, Pu'er University, Pu'er, 665000, China
| | - Shangwen Xia
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China.
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Błaszkowski J, Sánchez-García M, Niezgoda P, Zubek S, Fernández F, Vila A, Al-Yahya’ei MN, Symanczik S, Milczarski P, Malinowski R, Cabello M, Goto BT, Casieri L, Malicka M, Bierza W, Magurno F. A new order, Entrophosporales, and three new Entrophospora species in Glomeromycota. Front Microbiol 2022; 13:962856. [PMID: 36643412 PMCID: PMC9835108 DOI: 10.3389/fmicb.2022.962856] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/31/2022] [Indexed: 11/30/2022] Open
Abstract
As a result of phylogenomic, phylogenetic, and morphological analyses of members of the genus Claroideoglomus, four potential new glomoid spore-producing species and Entrophospora infrequens, a new order, Entrophosporales, with one family, Entrophosporaceae (=Claroideoglomeraceae), was erected in the phylum Glomeromycota. The phylogenomic analyses recovered the Entrophosporales as sister to a clade formed by Diversisporales and Glomeraceae. The strongly conserved entrophosporoid morph of E. infrequens, provided with a newly designated epitype, was shown to represent a group of cryptic species with the potential to produce different glomoid morphs. Of the four potential new species, three enriched the Entrophosporales as new Entrophospora species, E. argentinensis, E. glacialis, and E. furrazolae, which originated from Argentina, Sweden, Oman, and Poland. The fourth fungus appeared to be a glomoid morph of the E. infrequens epitype. The physical association of the E. infrequens entrophosporoid and glomoid morphs was reported and illustrated here for the first time. The phylogenetic analyses, using nuc rDNA and rpb1 concatenated sequences, confirmed the previous conclusion that the genus Albahypha in the family Entrophosporaceae sensu Oehl et al. is an unsupported taxon. Finally, the descriptions of the Glomerales, Entrophosporaceae, and Entrophospora were emended and new nomenclatural combinations were introduced.
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Affiliation(s)
- Janusz Błaszkowski
- Department of Environmental Management, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Marisol Sánchez-García
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Piotr Niezgoda
- Department of Environmental Management, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Szymon Zubek
- Faculty of Biology, Institute of Botany, Jagiellonian University, Kraków, Poland
| | | | - Ana Vila
- R&D Department, Symborg SL, Murcia, Spain
| | | | - Sarah Symanczik
- Zurich-Basel Plant Science Center, Institute of Botany, University of Basel, Basel, Switzerland
| | - Paweł Milczarski
- Department of Genetic, Plant Breeding and Biotechnology, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Ryszard Malinowski
- Department of Environmental Management, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Marta Cabello
- Instituto Spegazzini, Comisión de Investigaciones Científicas de La Provincia de Buenos Aires (CIC-PBA), La Plata, Argentina
| | - Bruno Tomio Goto
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal, RN, Brazil,*Correspondence: Bruno Tomio Goto,
| | - Leonardo Casieri
- Mycorrhizal Applications LLC at Bio-Research and Development Growth Park, St. Louis, MO, United States
| | - Monika Malicka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Wojciech Bierza
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Franco Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Chen K, Huang G, Li Y, Zhang X, Lei Y, Li Y, Xiong J, Sun Y. Illumina MiSeq Sequencing Reveals Correlations among Fruit Ingredients, Environmental Factors, and AMF Communities in Three Lycium Barbarum Producing Regions of China. Microbiol Spectr 2022; 10:e0229321. [PMID: 35234495 PMCID: PMC8941938 DOI: 10.1128/spectrum.02293-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
The symbiotic relationship of arbuscular mycorrhizal fungi (AMF) is important for Lycium barbarum, a highly nutritious and medicinal crop. However, the influence of environmental factors on AMF communities remains largely elusive. Based on MiSeq sequencing, we analyzed AMF communities in rhizosphere soils of L. barbarum with growth synchronization in three typical L. barbarum cultivation sites in China. The Zhongning region has poor soils with a high richness of AMF communities. Geographical environmental variances lead to differences in AMF communities which in turn affects the active ingredients of L. barbarum fruit. Furthermore, different genera of AMF showed significant correlations with environmental factors and fruit ingredients. The three genera, Claroideoglomus, Dominikia, and Funneliformis correlated to environmental factors and fruits ingredients in a similar manner affecting the whole sugar (TS) and flavonoids (FLA) contents in the fruits of L. barbarum. Also, these showed a significantly positive correlation with soil pH. This fact was unknown so far due to different soil acidity/alkalinity in different studies. IMPORTANCE The climatic and ecological environment is a complex phenomenon, involving various environmental factors that regulate the diversity and population distribution structure of AMF communities affecting plant growth, crop composition, and yield. Current studies on the effects of environmental factors on AMF communities have mainly focused on soil conditions and host plants. Fewer studies have been conducted on the correlation between temperature, enzyme activity, plant fruiting, and AMF communities. The present study investigated the diversity of AMF communities and the influence of environmental factors on their distribution patterns, which showed similar effects on some AMF species. The results suggest that screening AMF fungicides that meet the target may significantly help soil restoration reducing the use of chemical fertilizers and a large amount of human and material resources.
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Affiliation(s)
- Kaili Chen
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Gang Huang
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Yuekun Li
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Xinrui Zhang
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Yonghui Lei
- Department of Plant Protection, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Yang Li
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Jie Xiong
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Yanfei Sun
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
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Błaszkowski J, Niezgoda P, Zubek S, Meller E, Milczarski P, Malinowski R, Malicka M, Uszok S, Goto BT, Bierza W, Casieri L, Magurno F. Three new species of arbuscular mycorrhizal fungi of the genus Diversispora from maritime dunes of Poland. Mycologia 2022; 114:453-466. [PMID: 35358026 DOI: 10.1080/00275514.2022.2030081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Three new species of arbuscular mycorrhizal fungi of the genus Diversispora (phylum Glomeromycota) were described based on their morphology and molecular phylogeny. The phylogeny was inferred from the analyses of the partial 45S rDNA sequences (18S-ITS-28S) and the largest subunit of RNA polymerase II (rpb1) gene. These species were associated in the field with plants colonizing maritime sand dunes of the Baltic Sea in Poland and formed mycorrhiza in single-species cultures.
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Affiliation(s)
- Janusz Błaszkowski
- Department of Protection and Shaping of Environment, West Pomeranian University of Technology in Szczecin, 71-434, Szczecin, Poland
| | - Piotr Niezgoda
- Department of Protection and Shaping of Environment, West Pomeranian University of Technology in Szczecin, 71-434, Szczecin, Poland
| | - Szymon Zubek
- Institute of Botany, Faculty of Biology, Jagiellonian University, 30-387, Kraków, Poland
| | - Edward Meller
- Laboratory of Soil Science and Environmental Chemistry, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, 71-434, Szczecin, Poland
| | - Paweł Milczarski
- Department of Genetics, Plant Breeding & Biotechnology, West Pomeranian University of Technology in Szczecin, 71-434, Szczecin, Poland
| | - Ryszard Malinowski
- Laboratory of Soil Science and Environmental Chemistry, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, 71-434, Szczecin, Poland
| | - Monika Malicka
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032, Katowice, Poland
| | - Sylwia Uszok
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032, Katowice, Poland
| | - Bruno Tomio Goto
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, Brazil
| | - Wojciech Bierza
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032, Katowice, Poland
| | - Leonardo Casieri
- Mycorrhizal Applications LLC at Bio-Research & Development Growth Park, St. Louis, Missouri 63132, USA
| | - Franco Magurno
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032, Katowice, Poland
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Yu F, Goto BT, Magurno F, Błaszkowski J, Wang J, Ma W, Feng H, Liu Y. Glomus chinense and Dominikia gansuensis, two new Glomeraceae species of arbuscular mycorrhizal fungi from high altitude in the Tibetan Plateau. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01799-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sportes A, Hériché M, Boussageon R, Noceto PA, van Tuinen D, Wipf D, Courty PE. A historical perspective on mycorrhizal mutualism emphasizing arbuscular mycorrhizas and their emerging challenges. MYCORRHIZA 2021; 31:637-653. [PMID: 34657204 DOI: 10.1007/s00572-021-01053-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Arbuscular mycorrhiza, one of the oldest interactions on earth (~ 450 million years old) and a first-class partner for plants to colonize emerged land, is considered one of the most pervasive ecological relationships on the globe. Despite how important and old this interaction is, its discovery was very recent compared to the long story of land plant evolution. The story of the arbuscular mycorrhiza cannot be addressed apart from the history, controversies, and speculations about mycorrhiza in its broad sense. The chronicle of mycorrhizal research is marked by multiple key milestones such as the initial description of a "persistent epiderm and pellicular wall structure" by Hartig; the introduction of the "Symbiotismus" and "Mycorrhiza" concepts by Frank; the description of diverse root-fungal morphologies; the first description of arbuscules by Gallaud; Mosse's pivotal statement of the beneficial nature of the arbuscular mycorrhizal symbiosis; the impact of molecular tools on the taxonomy of mycorrhizal fungi as well as the development of in vitro root organ cultures for producing axenic arbuscular mycorrhizal fungi (AMF). An appreciation of the story - full of twists and turns - of the arbuscular mycorrhiza, going from the roots of mycorrhiza history, along with the discovery of different mycorrhiza types such as ectomycorrhiza, can improve research to help face our days' challenge of developing sustainable agriculture that integrates the arbuscular mycorrhiza and its ecosystem services.
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Affiliation(s)
- Antoine Sportes
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Mathilde Hériché
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Raphaël Boussageon
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Antoine Noceto
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Diederik van Tuinen
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Pierre Emmanuel Courty
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France.
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Błaszkowski J, Niezgoda P, Meller E, Milczarski P, Zubek S, Malicka M, Uszok S, Casieri L, Goto BT, Magurno F. New taxa in Glomeromycota: Polonosporaceae fam. nov., Polonospora gen. nov., and P. polonica comb. nov. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01726-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractPhylogenetic analyses of sequences of the nuc rDNA small subunit (18S), internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), and large subunit (28S) region (= 18S-ITS-28S), as well as sequences of this region concatenated with sequences of the largest subunit of RNA polymerase II (RPB1) gene, proved that the species originally described as Acaulospora polonica (phylum Glomeromycota) represents a new genus and a new family of the ancient order Archaeosporales, here introduced into the Glomeromycota under the names Polonospora and Polonosporaceae, respectively. The phylogenetic analyses and BLASTn queries also indicated that the Polonosporaceae with P. polonica comb. nov. still contains several morphologically undescribed taxa at the ranks of genus and species, which have a worldwide distribution.
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Błaszkowski J, Jobim K, Niezgoda P, Meller E, Malinowski R, Milczarski P, Zubek S, Magurno F, Casieri L, Bierza W, Błaszkowski T, Crossay T, Goto BT. New Glomeromycotan Taxa, Dominikia glomerocarpica sp. nov. and Epigeocarpum crypticum gen. nov. et sp. nov. From Brazil, and Silvaspora gen. nov. From New Caledonia. Front Microbiol 2021; 12:655910. [PMID: 33967994 PMCID: PMC8102679 DOI: 10.3389/fmicb.2021.655910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
Examination of fungal specimens collected in the Atlantic rain forest ecosystems of Northeast Brazil revealed many potentially new epigeous and semihypogeous glomerocarp-producing species of the phylum Glomeromycota. Among them were two fungi that formed unorganized epigeous glomerocarps with glomoid spores of almost identical morphology. The sole structure that distinguished the two fungi was the laminate layer 2 of their three-layered spore wall, which in spores of the second fungus crushed in PVLG-based mountants contracted and, consequently, transferred into a crown-like structure. Surprisingly, phylogenetic analyses of sequences of the 18S-ITS-28S nuc rDNA and the rpb1 gene indicated that these glomerocarps represent two strongly divergent undescribed species in the family Glomeraceae. The analyses placed the first in the genus Dominikia, and the second in a sister clade to the monospecific generic clade Kamienskia with Kamienskia bistrata. The first species was described here as Dominikia glomerocarpica sp. nov. Because D. glomerocarpica is the first glomerocarp-forming species in Dominikia, the generic description of this genus was emended. The very large phylogenetic distance and the fundamental morphological differences between the second species and K. bistrata suggested us to introduce a new genus, here named as Epigeocarpum gen. nov., and name the new species Epigeocarpum crypticum sp. nov. In addition, our analyses also focused on an arbuscular mycorrhizal fungus originally described as Rhizophagus neocaledonicus, later transferred to the genus Rhizoglomus. The analyses indicated that this species does not belong to any of these two genera but represents a new clade at the rank of genus in the Glomeraceae, here described as Silvaspora gen. nov.
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Affiliation(s)
- Janusz Błaszkowski
- Laboratory of Plant Protection, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Khadija Jobim
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Piotr Niezgoda
- Laboratory of Plant Protection, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Edward Meller
- Laboratory of Soil Science and Environmental Chemistry, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Ryszard Malinowski
- Laboratory of Soil Science and Environmental Chemistry, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Paweł Milczarski
- Department of Genetics, Plant Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Szymon Zubek
- Faculty of Biology, Institute of Botany, Jagiellonian University, Kraków, Poland
| | - Franco Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Leonardo Casieri
- Mycorrhizal Applications LLC at Bio-Research & Development Growth Park, St. Louis, MO, United States
| | - Wojciech Bierza
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Tomasz Błaszkowski
- Department of General and Oncological Surgery, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Thomas Crossay
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de la Nouvelle Calédonie, Nouméa, New Caledonia
| | - Bruno Tomio Goto
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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Kryukov AA, Gorbunova AO, Machs EM, Mikhaylova YV, Rodionov AV, Zhurbenko PM, Yurkov AP. Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi. Vavilovskii Zhurnal Genet Selektsii 2021; 24:158-167. [PMID: 33659795 PMCID: PMC7716513 DOI: 10.18699/vj19.38-o] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Arbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land
plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply.
The search for the most effective AMF strains for symbiosis and the creation of microbial preparations on that basis
is an important task for modern biology. Owing to the difficulties of cultivation without a host plant and their
high genetic polymorphism, identifying AMF is very difficult. A high number of cryptic species often makes morphological
identification unreliable. Recent years have seen a growth in the number of AMF biodiversity studies
performed by modern NGS-based methods, Illumina MiSeq in particular. Currently, there are still many questions
that remain for the identification of AМF. The most important are whether conservative or variable sequences
should be used to select a marker for barcoding and whether universal primers or those specific to AMF should be
used. In our work, we have successfully used universal primers ITS3 and ITS4 for the sequencing in Illumina MiSeq
of the 5.8S rDNA – ITS2 region of the 35S rRNA genes, which contain both a conservative and variable regions. The
molecular genetic approach for AMF identification was quite effective and allowed us to reliably identify eight of
nine isolates to the species level: five isolates of Rhizophagus irregularis, and one isolate of R. invermaius, Paraglomus
laccatum, and Claroideoglomus etunicatum, respectively. For all five R. irregularis isolates, high variability in
the ITS region and the absence of ecotopic-related molecular characters in the ITS2 region were demonstrated.
The NCBI data is still insufficient for accurate AMF identification of Acaulospora sp. isolates from the genus to the
species level.
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Affiliation(s)
- A A Kryukov
- All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - A O Gorbunova
- All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Russia Saint Petersburg State University, Biological Faculty, St. Petersburg, Russia
| | - E M Machs
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Y V Mikhaylova
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A V Rodionov
- Saint Petersburg State University, Biological Faculty, St. Petersburg, Russia Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - P M Zhurbenko
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A P Yurkov
- All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Russia
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11
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Dominikia bonfanteae and Glomus atlanticum, two new species in the Glomeraceae (phylum Glomeromycota) with molecular phylogenies reconstructed from two unlinked loci. Mycol Prog 2021. [DOI: 10.1007/s11557-020-01659-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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12
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López-Legarda X, Arboleda-Echavarría C, Parra-Saldívar R, Rostro-Alanis M, Alzate JF, Villa-Pulgarín JA, Segura-Sánchez F. Biotechnological production, characterization and in vitro antitumor activity of polysaccharides from a native strain of Lentinus crinitus. Int J Biol Macromol 2020; 164:3133-3144. [DOI: 10.1016/j.ijbiomac.2020.08.191] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
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13
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Vandepol N, Liber J, Desirò A, Na H, Kennedy M, Barry K, Grigoriev IV, Miller AN, O'Donnell K, Stajich JE, Bonito G. Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. FUNGAL DIVERS 2020; 104:267-289. [PMID: 33364917 PMCID: PMC7751987 DOI: 10.1007/s13225-020-00455-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022]
Abstract
Early efforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic groups led to the definition of 14 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a well-resolved phylogeny. The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach, but was unable to resolve higher-level organization of groups. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity, biology, and evolution.
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Affiliation(s)
- Natalie Vandepol
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI 48824, USA
| | - Julian Liber
- Department of Plant Biology, Michigan State University, East Lansing MI 48824, USA
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Hyunsoo Na
- Joint Genome Institute, Berkeley, CA 94720, USA
| | | | | | | | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Kerry O'Donnell
- United States Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology & Institute for Integrative Genome Biology, University of California-Riverside, Riverside CA 92521, USA
| | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI 48824, USA
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
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14
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Abstract
Biomass of arbuscular mycorrhizal fungi (AMF, Glomeromycota) is often only available in small quantities as these fungi are obligate biotrophs and many species are difficult to cultivate under controlled conditions. Here, I describe a simple, efficient approach to produce crude extracts from single or a small number of spores that can be used for genotyping AMF.
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15
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Błaszkowski J, Niezgoda P, de Paiva JN, da Silva KJG, Theodoro RC, Jobim K, Orfanoudakis M, Goto BT. Sieverdingia gen. nov., S. tortuosa comb. nov., and Diversispora peloponnesiaca sp. nov. in the Diversisporaceae (Glomeromycota). Mycol Prog 2019. [DOI: 10.1007/s11557-019-01534-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractPhylogenetic analyses of 18S–ITS–28S nuc rDNA sequences indicated that the arbuscular mycorrhizal fungus originally described asGlomus tortuosumand later transferred to the genusCorymbiglomusrepresents a separate, previously unrecognized clade at the rank of genus in the family Diversisporaceae (order Diversisporales, phylum Glomeromycota). The analyses located the clade between clades representing the generaDesertisporaandRedeckera. Consequently, a new genus,Sieverdingia, was erected, withS. tortuosacomb. nov. The unique morphological feature ofS. tortuosais the formation of glomoid-like spores with a single-layered spore wall covered with a hyphal mantle. Importantly, the erection ofSieverdingiaclarified the definition ofCorymbiglomus, which currently consists of three species producing glomoid-like spores with one, three- to four-layered spore wall. The features of the innermost layer, which is hyaline, laminate, flexible to semi-flexible, indicate that it is a synapomorphy ofCorymbiglomus. The definitions ofCorymbiglomusand its species were emended. Moreover, the distribution ofS. tortuosaand the three species ofCorymbiglomuswas discussed based on own studies, literature data, and molecular sequences deposited in public databases. We concluded that the distribution ofS. tortuosaandC. globiferumknown in environmental studies based on their partial 28S nuc rDNA sequences only may be understated because the main molecular characteristics distinguishing these species reside outside the 28S region. Finally, we described a new species in the genusDiversisporaoriginating from Mediterranean dunes of the Peloponnese peninsula, Greece. The same phylogenetic analyses mentioned above indicated that the closest relative of the new species, producing dark-coloured spores, isD. clara, whose spores are creamy white at most.
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16
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Błaszkowski J, Niezgoda P, Piątek M, Magurno F, Malicka M, Zubek S, Mleczko P, Yorou NS, Jobim K, Vista XM, Lima JLR, Goto BT. Rhizoglomus dalpeae, R. maiae, and R. silesianum, new species. Mycologia 2019; 111:965-980. [PMID: 31560606 DOI: 10.1080/00275514.2019.1654637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We examined three arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota) producing glomoid spores. The mode of formation and morphology of these spores suggested that they represent undescribed species in the genus Rhizoglomus of the family Glomeraceae. Subsequent morphological studies of the spores and molecular phylogenetic analyses of sequences of the nuc rDNA small subunit (18S), internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), and large subunit (28S) region (= 18S-ITS-28S) confirmed the suggestion and indicated that the fungi strongly differ from all previously described Rhizoglomus species with known DNA barcodes. Consequently, the fungi were described here as new species: R. dalpeae, R. maiae, and R. silesianum. Two of these species lived hypogeously in the field in habitats subjected to strong environmental stresses. Rhizoglomus dalpeae originated from an inselberg located within Guineo-Sudanian transition savanna zone in Benin, West Africa, where the temperature of the inselberg rock during a 5-mo drought ranges from 40 to 60 C. Rhizoglomus silesianum originated from a coal mine spoil heap in Poland, whose substrate is extremely poor in nutrients, has unfavorable texture, and may heat up to 50 C. By contrast, R. maiae was found in more favorable habitat conditions. It produced an epigeous cluster of spores among shrubs growing in a tropical humid reserve in Brazil. Moreover, the compatibility of phylogenies of species of the family Glomeraceae reconstructed from analyses of sequences of 18S-ITS-28S and the largest subunit of RNA polymerase II (RPB1) gene was discussed.
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Affiliation(s)
- Janusz Błaszkowski
- Department of Ecology, Protection and Shaping of Environment, West Pomeranian University of Technology, Słowackiego 17, PL-71-434 Szczecin, Poland
| | - Piotr Niezgoda
- Department of Ecology, Protection and Shaping of Environment, West Pomeranian University of Technology, Słowackiego 17, PL-71-434 Szczecin, Poland
| | - Marcin Piątek
- Department of Mycology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland
| | - Franco Magurno
- Department of Botany and Nature Protection, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, PL-40-032 Katowice, Poland
| | - Monika Malicka
- Department of Microbiology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, PL-40-032 Katowice, Poland
| | - Szymon Zubek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, PL-30-387 Kraków, Poland
| | - Piotr Mleczko
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, PL-30-387 Kraków, Poland
| | - Nourou S Yorou
- Faculty of Agronomy, University of Parakou, BP 123, Parakou, Benin
| | - Khadija Jobim
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, Rio Grande do Norte, Brazil
| | - Xochtil Margarito Vista
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, Rio Grande do Norte, Brazil
| | - Juliana L R Lima
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, Rio Grande do Norte, Brazil
| | - Bruno Tomio Goto
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, Rio Grande do Norte, Brazil
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17
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Kashyap PL, Kumar S, Tripathi R, Kumar RS, Jasrotia P, Singh DP, Singh GP. Phylogeography and Population Structure Analysis Reveal Diversity by Gene Flow and Mutation in Ustilago segetum (Pers.) Roussel tritici Causing Loose Smut of Wheat. Front Microbiol 2019; 10:1072. [PMID: 31156587 PMCID: PMC6529584 DOI: 10.3389/fmicb.2019.01072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 04/29/2019] [Indexed: 02/02/2023] Open
Abstract
Ustilago segetum (Pers.) Roussel tritici (UST) causes loose smut of wheat account for considerable grain yield losses globally. For effective management, knowledge of its genetic variability and population structure is a prerequisite. In this study, UST isolates sampled from four different wheat growing zones of India were analyzed using the second largest subunit of the RNA polymerase II (RPB2) and a set of sixteen neutral simple sequence repeats (SSRs) markers. Among the 112 UST isolates genotyped, 98 haplotypes were identified. All the isolates were categorized into two groups (K = 2), each consisting of isolates from different sampling sites, on the basis of unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure. The positive and significant index of association (IA = 1.169) and standardized index of association (rBarD = 0.075) indicate population is of non-random mating type. Analysis of molecular variance showed that the highest variance component is among isolates (91%), with significantly low genetic differentiation variation among regions (8%) (Fst = 0.012). Recombination (Rm = 0) was not detected. The results showed that UST isolates have a clonal genetic structure with limited genetic differentiation and human arbitrated gene flow and mutations are the prime evolutionary processes determining its genetic structure. These findings will be helpful in devising management strategy especially for selection and breeding of resistant wheat cultivars.
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Affiliation(s)
- Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Rahul Tripathi
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Ravi Shekhar Kumar
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Poonam Jasrotia
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Devendra Pal Singh
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
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18
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Hartmann RM, Schaepe S, Nübel D, Petersen AC, Bertolini M, Vasilev J, Küster H, Hohnjec N. Insights into the complex role of GRAS transcription factors in the arbuscular mycorrhiza symbiosis. Sci Rep 2019; 9:3360. [PMID: 30833646 PMCID: PMC6399340 DOI: 10.1038/s41598-019-40214-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/12/2019] [Indexed: 12/19/2022] Open
Abstract
To improve access to limiting nutrients, the vast majority of land plants forms arbuscular mycorrhizal (AM) symbioses with Glomeromycota fungi. We show here that AM-related GRAS transcription factors from different subgroups are upregulated during a time course of mycorrhization. Based on expression studies in mutants defective in arbuscule branching (ram1-1, with a deleted MtRam1 GRAS transcription factor gene) or in the formation of functional arbuscules (pt4-2, mutated in the phosphate transporter gene MtPt4), we demonstrate that the five AM-related GRAS transcription factor genes MtGras1, MtGras4, MtGras6, MtGras7, and MtRad1 can be differentiated by their dependency on MtRAM1 and MtPT4, indicating that the network of AM-related GRAS transcription factors consists of at least two regulatory modules. One module involves the MtRAM1- and MtPT4-independent transcription factor MtGRAS4 that activates MtGras7. Another module is controlled by the MtRAM1- and MtPT4-dependent transcription factor MtGRAS1. Genome-wide expression profiles of mycorrhized MtGras1 knockdown and ram1-1 roots differ substantially, indicating different targets. Although an MtGras1 knockdown reduces transcription of AM-related GRAS transcription factor genes including MtRam1 and MtGras7, MtGras1 overexpression alone is not sufficient to activate MtGras genes. MtGras1 knockdown roots display normal fungal colonization, with a trend towards the formation of smaller arbuscules.
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Affiliation(s)
- Rico M Hartmann
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Sieke Schaepe
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Daniel Nübel
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Arne C Petersen
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Martina Bertolini
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.,Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milano, Italy
| | - Jana Vasilev
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Helge Küster
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
| | - Natalija Hohnjec
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany
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19
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Jobim K, Błaszkowski J, Niezgoda P, Kozłowska A, Zubek S, Mleczko P, Chachuła P, Ishikawa NK, Goto BT. New sporocarpic taxa in the phylum Glomeromycota: Sclerocarpum amazonicum gen. et sp. nov. in the family Glomeraceae (Glomerales) and Diversispora sporocarpia sp. nov. in the Diversisporaceae (Diversisporales). Mycol Prog 2019. [DOI: 10.1007/s11557-018-01462-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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20
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Thioye B, van Tuinen D, Kane A, de Faria SM, Ndiaye C, Duponnois R, Sylla SN, Bâ AM. Tracing Rhizophagus irregularis isolate IR27 in Ziziphus mauritiana roots under field conditions. MYCORRHIZA 2019; 29:77-83. [PMID: 30460497 DOI: 10.1007/s00572-018-0875-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) play a major role as biofertilizer for sustainable agriculture. Nevertheless, it is still poorly documented whether inoculated AMF can successfully establish in field soils as exotic AMF and improve plant growth and productivity. Further, the fate of an exogenous inoculum is still poorly understood. Here, we pre-inoculated two cultivars (Tasset and Gola) of the fruit tree Ziziphus mauritiana (jujube) with the exotic AM fungus Rhizophagus irregularis isolate IR27 before transplantation in the field. In two experiments, tracking and quantification of R. irregularis IR27 were assessed in a 13-month-old jujube and an 18-month-old jujube in two fields located in Senegal. Our results showed that the inoculant R. irregularis IR27 was quantitatively traced and discriminated from native R. irregularis isolates in roots by using a qPCR assay targeting a fragment of the RNA polymerase II gene (RPB1), and that the inoculum represented only fractions ranging from 11 to 15% of the Rhizophagus genus in the two plantations 13 and 18 months after transplantation, respectively. This study validates the use of the RPB1 gene as marker for a relative quantification of a mycorrhizal inoculant fungus isolate in the field.
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Affiliation(s)
- Babacar Thioye
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, BP 1386, Dakar, Senegal.
- Laboratoire des Symbioses Tropicales et Méditerranéennes UMR113 INRA/AGRO-M/CIRAD/IRD/UM2-TA10/J, Campus International de Baillarguet, 34398, Montpellier, France.
| | - Diederik van Tuinen
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Aboubacry Kane
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, BP 1386, Dakar, Senegal
| | | | - Cheikh Ndiaye
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, BP 1386, Dakar, Senegal
| | - Robin Duponnois
- Laboratoire des Symbioses Tropicales et Méditerranéennes UMR113 INRA/AGRO-M/CIRAD/IRD/UM2-TA10/J, Campus International de Baillarguet, 34398, Montpellier, France
| | - Samba Ndao Sylla
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, BP 1386, Dakar, Senegal
| | - Amadou Mustapha Bâ
- Laboratoire des Symbioses Tropicales et Méditerranéennes UMR113 INRA/AGRO-M/CIRAD/IRD/UM2-TA10/J, Campus International de Baillarguet, 34398, Montpellier, France
- Laboratoire de Biologie et Physiologie Végétales, Faculté des Sciences Exactes et Naturelles, Université des Antilles, BP 592, 97159, Pointe-à-Pitre, Guadeloupe, France
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Bruns TD, Corradi N, Redecker D, Taylor JW, Öpik M. Glomeromycotina: what is a species and why should we care? THE NEW PHYTOLOGIST 2018; 220:963-967. [PMID: 29165821 DOI: 10.1111/nph.14913] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A workshop at the recent International Conference on Mycorrhiza was focused on species recognition in Glomeromycotina and parts of their basic biology that define species. The workshop was motivated by the paradigm-shifting evidence derived from genomic data for sex and for the lack of heterokaryosis, and by published exchanges in Science that were based on different species concepts and have led to differing views of dispersal and endemism in these fungi. Although a lively discussion ensued, there was general agreement that species recognition in the group is in need of more attention, and that many basic assumptions about the biology of these important fungi including sexual or clonal reproduction, similarity or dissimilarity of nuclei within an individual, and species boundaries need to be re-examined and scrutinized with current techniques.
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Affiliation(s)
- Thomas D Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Dirk Redecker
- Agroécologie, Université de Bourgogne Franche-Comté, INRA, CNRS, AgroSup Dijon, F-21000, Dijon, France
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Maarja Öpik
- University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
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22
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Sommermann L, Geistlinger J, Wibberg D, Deubel A, Zwanzig J, Babin D, Schlüter A, Schellenberg I. Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing. PLoS One 2018; 13:e0195345. [PMID: 29621291 PMCID: PMC5886558 DOI: 10.1371/journal.pone.0195345] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/20/2018] [Indexed: 01/21/2023] Open
Abstract
Fungal communities in agricultural soils are assumed to be affected by soil and crop management. Our intention was to investigate the impact of different tillage and fertilization practices on fungal communities in a long-term crop rotation field trial established in 1992 in Central Germany. Two winter wheat fields in replicated strip-tillage design, comprising conventional vs. conservation tillage, intensive vs. extensive fertilization and different pre-crops (maize vs. rapeseed) were analyzed by a metabarcoding approach applying Illumina paired-end sequencing of amplicons generated by two recently developed primer pairs targeting the two fungal Internal Transcribed Spacer regions (ITS1, ITS2). Analysis of 5.1 million high-quality sequence reads uncovered a diverse fungal community in the two fields, composed of 296 fungal genera including 3,398 Operational Taxonomic Units (OTUs) at the 97% sequence similarity threshold. Both primer pairs detected the same fungal phyla (Basidio-, Asco-, Zygo-, Glomero- and Chytridiomycota), but in different relative abundances. OTU richness was higher in the ITS1 dataset, while ITS2 data were more diverse and of higher evenness. Effects of farming practice on fungal community structures were revealed. Almost two-thirds of the fungal genera were represented in all different soil treatments, whereas the remaining genera clearly responded to farming practice. Principal Component Analysis revealed four distinct clusters according to tillage practice and pre-crop. Analysis of Variance (ANOVA) substantiated the results and proved significant influences of tillage and pre-crop, while fertilization had the smallest and non-significant effect. In-depth analysis of putative phytopathogenic and plant beneficial fungal groups indicated distinct responses; for example Fusarium was significantly enriched in the intensively fertilized conservation tillage variants with the pre-crop maize, while Phoma displayed significant association with conventional tillage and pre-crop rapeseed. Many putative plant beneficial fungi also reacted differentially to farming practice with the most distinct responders identified among the Glomeromycota (arbuscular mycorrhizal fungi, AMF).
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Affiliation(s)
- Loreen Sommermann
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany
- * E-mail:
| | - Joerg Geistlinger
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms (GRIM), Bielefeld University, Bielefeld, North Rhine-Westphalia, Germany
| | - Annette Deubel
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany
| | - Jessica Zwanzig
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany
| | - Doreen Babin
- Institute for Epidemiology and Pathogen Diagnostics, Julius-Kühn-Institut–Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Lower Saxony, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms (GRIM), Bielefeld University, Bielefeld, North Rhine-Westphalia, Germany
| | - Ingo Schellenberg
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany
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23
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A new genus, Desertispora, and a new species, Diversispora sabulosa, in the family Diversisporaceae (order Diversisporales, subphylum Glomeromycotina). Mycol Prog 2018. [DOI: 10.1007/s11557-017-1369-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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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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25
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Reich M, Labes A. How to boost marine fungal research: A first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry. Mar Genomics 2017; 36:57-75. [PMID: 29031541 DOI: 10.1016/j.margen.2017.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/22/2017] [Accepted: 09/23/2017] [Indexed: 12/30/2022]
Abstract
Marine fungi have attracted attention in recent years due to increased appreciation of their functional role in ecosystems and as important sources of new natural products. The concomitant development of various "omic" technologies has boosted fungal research in the fields of biodiversity, physiological ecology and natural product biosynthesis. Each of these research areas has its own research agenda, scientific language and quality standards, which have so far hindered an interdisciplinary exchange. Inter- and transdisciplinary interactions are, however, vital for: (i) a detailed understanding of the ecological role of marine fungi, (ii) unlocking their hidden potential for natural product discovery, and (iii) designing access routes for biotechnological production. In this review and opinion paper, we describe the two different "worlds" of marine fungal natural product chemists and marine fungal molecular ecologists. The individual scientific approaches and tools employed are summarised and explained, and enriched with a first common glossary. We propose a strategy to find a multidisciplinary approach towards a comprehensive view on marine fungi and their chemical potential.
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Affiliation(s)
- Marlis Reich
- University of Bremen, BreMarE, NW2 B3320, Leobener Str. 5, D-28359 Bremen, Germany.
| | - Antje Labes
- Flensburg University of Applied Sciences, Kanzleistr. 91-93, D-24943 Flensburg, Germany.
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26
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Bouffaud ML, Bragalini C, Berruti A, Peyret-Guzzon M, Voyron S, Stockinger H, van Tuinen D, Lumini E, Wipf D, Plassart P, Lemanceau P, Bianciotto V, Redecker D, Girlanda M. Arbuscular mycorrhizal fungal community differences among European long-term observatories. MYCORRHIZA 2017; 27:331-343. [PMID: 27942957 DOI: 10.1007/s00572-016-0753-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/25/2016] [Indexed: 06/06/2023]
Abstract
Arbuscular mycorrhizal fungal (AMF) communities have been demonstrated to respond to a variety of biotic and abiotic factors, including various aspects of land management. Numerous studies have specifically addressed the impact of land use on AMF communities, but usually have been confined to one or a few sites. In this study, soil AMF assemblages were described in four different long-term observatories (LTOs) across Europe, each of which included a site-specific high-intensity and a low-intensity land use. AMF communities were characterized on the basis of 454 sequencing of the internal transcribed spacer 2 (ITS2) rDNA region. The primary goals of this study were (i) to determine the main factors that shape AMF communities in differentially managed sites in Europe and (ii) to identify individual AMF taxa or combinations of taxa suitable for use as biomarkers of land use intensification. AMF communities were distinct among LTOs, and we detected significant effects of management type and soil properties within the sites, but not across all sites. Similarly, indicator species were identified for specific LTOs and land use types but not universally for high- or low-intensity land uses. Different subsets of soil properties, including several chemical and physical variables, were found to be able to explain an important fraction of AMF community variation alone or together with other examined factors in most sites. The important factors were different from those for other microorganisms studied in the same sites, highlighting particularities of AMF biology.
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Affiliation(s)
- M-L Bouffaud
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
- Helmholtz Center for Environmental Research - UFZ, Halle, Germany, German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - C Bragalini
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy
- Université Claude Bernard Lyon1, Lyon, France
| | - A Berruti
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - M Peyret-Guzzon
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - S Voyron
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy
| | - H Stockinger
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - D van Tuinen
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - E Lumini
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - D Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - P Plassart
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - P Lemanceau
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - V Bianciotto
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - D Redecker
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
| | - M Girlanda
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy.
- Université Claude Bernard Lyon1, Lyon, France.
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Krishnamoorthy R, Premalatha N, Karthik M, Anandham R, Senthilkumar M, Gopal NO, Selvakumar G, Sa T. Molecular Markers for the Identification and Diversity Analysis of Arbuscular Mycorrhizal Fungi (AMF). Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Nadimi M, Stefani FOP, Hijri M. The large (134.9 kb) mitochondrial genome of the glomeromycete Funneliformis mosseae. MYCORRHIZA 2016; 26:747-755. [PMID: 27246226 DOI: 10.1007/s00572-016-0710-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 06/05/2023]
Abstract
Funneliformis mosseae is among the most ecologically and economically important glomeromycete species and occurs both in natural and disturbed areas in a wide range of habitats and climates. In this study, we report the sequencing of the complete mitochondrial (mt) genome of F. mosseae isolate FL299 using 454 pyrosequencing and Illumina HiSeq technologies. This mt genome is a full-length circular chromosome of 134,925 bp, placing it among the largest mitochondrial DNAs (mtDNAs) in the fungal kingdom. A comparative analysis with publically available arbuscular mycorrhizal fungal mtDNAs revealed that the mtDNA of F. mosseae FL299 contained a very large number of insertions contributing to its expansion. The gene synteny was completely reshuffled compared to previously published glomeromycotan mtDNAs and several genes were oriented in an anti-sense direction. Furthermore, the presence of different types of introns and insertions in rnl (14 introns) made this gene very distinctive in Glomeromycota. The presence of alternative genetic codes in both initiation (GUG) and termination (UGA) codons was another new feature in this mtDNA compared to previously published glomeromycotan mt genomes. The phylogenetic analysis inferred from the analysis of 14 protein mt genes confirmed the position of the Glomeromycota clade as a sister group of Mortierellomycotina. This mt genome is the largest observed so far in Glomeromycota and the first mt genome within the Funneliformis clade, providing new opportunities to better understand their evolution and to develop molecular markers.
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Affiliation(s)
- Maryam Nadimi
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Franck O P Stefani
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada.
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30
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Thiéry O, Vasar M, Jairus T, Davison J, Roux C, Kivistik PA, Metspalu A, Milani L, Saks Ü, Moora M, Zobel M, Öpik M. Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions ofRhizophagus irregularisandGigaspora margaritais high and isolate-dependent. Mol Ecol 2016; 25:2816-32. [DOI: 10.1111/mec.13655] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/29/2016] [Accepted: 04/14/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Odile Thiéry
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Martti Vasar
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Teele Jairus
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - John Davison
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales; UPS; CNRS 24 chemin de Borde Rouge-Auzeville; BP 42617; Université de Toulouse; 31326 Castanet-Tolosan France
| | - Paula-Ann Kivistik
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Andres Metspalu
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Lili Milani
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Ülle Saks
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Mari Moora
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Martin Zobel
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Maarja Öpik
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
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31
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Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M. Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 2016. [DOI: 10.3897/mycokeys.13.8140] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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32
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Öpik M, Davison J, Moora M, Pärtel M, Zobel M. Response to Comment on "Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism". Science 2016; 351:826. [PMID: 26912890 DOI: 10.1126/science.aad5495] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bruns and Taylor argue that our finding of widespread distribution among Glomeromycota "virtual taxa" is undermined by the species definition applied. Although identifying appropriate species concepts and accessing taxonomically informative traits are challenges for microorganism biogeography, the virtual taxa represent a pragmatic classification that corresponds approximately to the species rank of classical Glomeromycota taxonomy, yet is applicable to environmental DNA.
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Affiliation(s)
- Maarja Öpik
- Department of Botany, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia.
| | - John Davison
- Department of Botany, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia.
| | - Mari Moora
- Department of Botany, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia
| | - Meelis Pärtel
- Department of Botany, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia
| | - Martin Zobel
- Department of Botany, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia
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33
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Albaina A, Aguirre M, Abad D, Santos M, Estonba A. 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species. Ecol Evol 2016; 6:1809-24. [PMID: 27087935 PMCID: PMC4801955 DOI: 10.1002/ece3.1986] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 12/23/2015] [Accepted: 01/03/2016] [Indexed: 01/26/2023] Open
Abstract
The potential of the 18S rRNA V9 metabarcoding approach for diet assessment was explored using MiSeq paired‐end (PE; 2 × 150 bp) technology. To critically evaluate the method′s performance with degraded/digested DNA, the diets of two zooplanktivorous fish species from the Bay of Biscay, European sardine (Sardina pilchardus) and European sprat (Sprattus sprattus), were analysed. The taxonomic resolution and quantitative potential of the 18S V9 metabarcoding was first assessed both in silico and with mock and field plankton samples. Our method was capable of discriminating species within the reference database in a reliable way providing there was at least one variable position in the 18S V9 region. Furthermore, it successfully discriminated diet between both fish species, including habitat and diel differences among sardines, overcoming some of the limitations of traditional visual‐based diet analysis methods. The high sensitivity and semi‐quantitative nature of the 18S V9 metabarcoding approach was supported by both visual microscopy and qPCR‐based results. This molecular approach provides an alternative cost and time effective tool for food‐web analysis.
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Affiliation(s)
- Aitor Albaina
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - Mikel Aguirre
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - David Abad
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - María Santos
- Marine Research Division AZTI Tecnalia Herrera Kaia Portualdea z/g P.O. Box 20110 Pasaia Gipuzkoa Spain
| | - Andone Estonba
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
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34
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Peyret-Guzzon M, Stockinger H, Bouffaud ML, Farcy P, Wipf D, Redecker D. Arbuscular mycorrhizal fungal communities and Rhizophagus irregularis populations shift in response to short-term ploughing and fertilisation in a buffer strip. MYCORRHIZA 2016; 26:33-46. [PMID: 26023005 DOI: 10.1007/s00572-015-0644-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 04/28/2015] [Indexed: 06/04/2023]
Abstract
Short-term effects of soil physical disturbance by ploughing and nitrogen and phosphate fertilisation on arbuscular mycorrhizal fungal (AMF) communities and on intraspecific populations of Rhizophagus irregularis in a buffer strip surrounded by arable fields were studied. Pre-grown Plantago lanceolata plantlets were transplanted into fertilised and/or ploughed experimental plots. After 3 months, the glomeromycotan communities in the roots of these trap plants were analysed using 454 pyrosequencing of a fragment of the RNA polymerase II gene (RPB1). Intraspecific populations of R. irregularis were studied by restriction fragment length polymorphism (RFLP) analysis of the mitochondrial large ribosomal subunit (mtLSU) gene. Soil disturbance significantly increased the diversity of species-level molecular taxa (MTs) and altered community structure, whilst fertilisation alone had no significant effect, unless coupled with ploughing. At the population level, the expected shift from genotypes of R. irregularis typically found in grasslands to those usually found in arable sites was only partially observed. In conclusion, in the short-term, physical soil disturbance, as well as nitrogen fertilisation when coupled with physical soil disturbance, affected AMF community and to a smaller extent population composition.
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Affiliation(s)
- M Peyret-Guzzon
- INRA, UMR 1347 Agroécologie, 17 Rue Sully, BP 86510, 21065, Dijon Cedex, France
| | - H Stockinger
- INRA, UMR 1347 Agroécologie, 17 Rue Sully, BP 86510, 21065, Dijon Cedex, France
| | - M-L Bouffaud
- INRA, UMR 1347 Agroécologie, 17 Rue Sully, BP 86510, 21065, Dijon Cedex, France
| | - P Farcy
- Domaine Expérimental d'Epoisses, UE 0115 INRA, Dijon, 21110, Bretenières, France
| | - D Wipf
- Université de Bourgogne, UMR 1347 Agroécologie, 17 Rue Sully, BP 86510, 21065, Dijon Cedex, France
| | - D Redecker
- Université de Bourgogne, UMR 1347 Agroécologie, 17 Rue Sully, BP 86510, 21065, Dijon Cedex, France.
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Błaszkowski J, Furrazola E, Chwat G, Góralska A, Lukács AF, Kovács GM. Three new arbuscular mycorrhizal Diversispora species in Glomeromycota. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1122-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia - Molecular Phylogeny and Evolution of Fungi 2015; 35:242-63. [PMID: 26823635 PMCID: PMC4713107 DOI: 10.3767/003158515x689135] [Citation(s) in RCA: 304] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/03/2015] [Indexed: 12/03/2022]
Abstract
The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1–D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β -tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5–6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
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37
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Hart MM, Aleklett K, Chagnon PL, Egan C, Ghignone S, Helgason T, Lekberg Y, Öpik M, Pickles BJ, Waller L. Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2015; 207:235-247. [PMID: 25737096 DOI: 10.1111/nph.13340] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/18/2015] [Indexed: 05/02/2023]
Abstract
Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.
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Affiliation(s)
- Miranda M Hart
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Kristin Aleklett
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Pierre-Luc Chagnon
- Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC, Canada
| | - Cameron Egan
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Stefano Ghignone
- Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino, Italy
| | - Thorunn Helgason
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ylva Lekberg
- MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA
| | - Maarja Öpik
- Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Brian J Pickles
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Lauren Waller
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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