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Lanfranco L, Bonfante P. Lessons from arbuscular mycorrhizal fungal genomes. Curr Opin Microbiol 2023; 75:102357. [PMID: 37419003 DOI: 10.1016/j.mib.2023.102357] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/09/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) have accompanied the majority of land plants since their evolution in the Devonian period with a symbiotic alliance centered on nutrient exchanges. The exploration of AMF genomes is providing clues to explain major questions about their biology, evolution, and ecology. The dynamics of nuclei across the fungal life cycle, the abundance of transposable elements, and the epigenome landscape are emerging as sources of intraspecific variability, which can be especially important in organisms with no or rare sexual reproduction such as AMF. These features have been hypothesized to support AMF adaptability to a wide host range and to environmental changes. New insights on plant-fungus communication and on the iconic function of phosphate transport were also recently obtained that overall contribute to a better understanding of this ancient and fascinating symbiosis.
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Affiliation(s)
- Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy.
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
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2
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Groten K, Yon F, Baldwin IT. Arbuscular mycorrhizal fungi influence the intraspecific competitive ability of plants under field and glasshouse conditions. PLANTA 2023; 258:60. [PMID: 37535207 PMCID: PMC10400695 DOI: 10.1007/s00425-023-04214-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
MAIN CONCLUSION Nicotiana attenuata's capacity to interact with arbuscular mycorrhizal fungi influences its intraspecific competitive ability under field and glasshouse conditions, but not its overall community productivity. Arbuscular mycorrhizal (AM) fungi can alter the nutrient status and growth of plants, and they can also affect plant-plant, plant-herbivore, and plant-pathogen interactions. These AM effects are rarely studied in populations under natural conditions due to the limitation of non-mycorrhizal controls. Here we used a genetic approach, establishing field and glasshouse communities of AM-harboring Nicotiana attenuata empty vector (EV) plants and isogenic plants silenced in calcium- and calmodulin-dependent protein kinase expression (irCCaMK), and unable to establish AM symbioses. Performance and growth were quantified in communities of the same (monocultures) or different genotypes (mixed cultures) and both field and glasshouse experiments returned similar responses. In mixed cultures, AM-harboring EV plants attained greater stalk lengths, shoot and root biomasses, clearly out-competing the AM fungal-deficient irCCaMK plants, while in monocultures, both genotypes grew similarly. Competitive ability was also reflected in reproductive traits: EV plants in mixed cultures outperformed irCCaMK plants. When grown in monocultures, the two genotypes did not differ in reproductive performance, though total leaf N and P contents were significantly lower independent of the community type. Plant productivity in terms of growth and seed production at the community level did not differ, while leaf nutrient content of phosphorus and nitrogen depended on the community type. We infer that AM symbioses drastically increase N. attenuata's competitive ability in mixed communities resulting in increased fitness for the individuals harboring AM without a net gain for the community.
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Affiliation(s)
- Karin Groten
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany.
| | - Felipe Yon
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ian T Baldwin
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
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Gao Y, Huang S, Wang Y, Lin H, Pan Z, Zhang S, Zhang J, Wang W, Cheng S, Chen Y. Analysis of the molecular and biochemical mechanisms involved in the symbiotic relationship between Arbuscular mycorrhiza fungi and Manihot esculenta Crantz. FRONTIERS IN PLANT SCIENCE 2023; 14:1130924. [PMID: 36959933 PMCID: PMC10028151 DOI: 10.3389/fpls.2023.1130924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/22/2023] [Indexed: 05/27/2023]
Abstract
INTRODUCTION Plants and arbuscular mycorrhizal fungi (AMF) mutualistic interactions are essential for sustainable agriculture production. Although it is shown that AMF inoculation improves cassava physiological performances and yield traits, the molecular mechanisms involved in AM symbiosis remain largely unknown. Herein, we integrated metabolomics and transcriptomics analyses of symbiotic (Ri) and asymbiotic (CK) cassava roots and explored AM-induced biochemical and transcriptional changes. RESULTS Three weeks (3w) after AMF inoculations, proliferating fungal hyphae were observable, and plant height and root length were significantly increased. In total, we identified 1,016 metabolites, of which 25 were differentially accumulated (DAMs) at 3w. The most highly induced metabolites were 5-aminolevulinic acid, L-glutamic acid, and lysoPC 18:2. Transcriptome analysis identified 693 and 6,481 differentially expressed genes (DEGs) in the comparison between CK (3w) against Ri at 3w and 6w, respectively. Functional enrichment analyses of DAMs and DEGs unveiled transport, amino acids and sugar metabolisms, biosynthesis of secondary metabolites, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interactions as the most differentially regulated pathways. Potential candidate genes, including nitrogen and phosphate transporters, transcription factors, phytohormone, sugar metabolism-related, and SYM (symbiosis) signaling pathway-related, were identified for future functional studies. DISCUSSION Our results provide molecular insights into AM symbiosis and valuable resources for improving cassava production.
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Affiliation(s)
- Yu Gao
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
| | - Siyuan Huang
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Yujie Wang
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
| | - Hongxin Lin
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Zhiyong Pan
- College of Horticulture and Forestry of Huazhong Agricultural University, Wuhan, China
| | - Shubao Zhang
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
| | - Jie Zhang
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Wenquan Wang
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Shanhan Cheng
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
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McGale E, Sanders IR. Integrating plant and fungal quantitative genetics to improve the ecological and agricultural applications of mycorrhizal symbioses. Curr Opin Microbiol 2022; 70:102205. [PMID: 36201974 DOI: 10.1016/j.mib.2022.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 01/25/2023]
Abstract
Finding and targeting genes that quantitatively contribute to agricultural and ecological processes progresses food production and conservation efforts. Typically, quantitative genetic approaches link variants in a single organism's genome with a trait of interest. Recently, genome-to-genome mapping has found genome variants interacting between species to produce the result of a multiorganism (including multikingdom) interaction. These were plant and bacterial pathogen genome interactions; plant-fungal coquantitative genetics have not yet been applied. Plant-mycorrhizae symbioses exist across most biomes, for a majority of land plants, including crop plants, and manipulate many traits from single organisms to ecosystems for which knowing the genetic basis would be useful. The availability of Rhizophagus irregularis mycorrhizal isolates, with genomic information, makes dual-genome methods with beneficial mutualists accessible and imminent.
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Affiliation(s)
- Erica McGale
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland.
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Bennett AE, Groten K. The Costs and Benefits of Plant-Arbuscular Mycorrhizal Fungal Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:649-672. [PMID: 35216519 DOI: 10.1146/annurev-arplant-102820-124504] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi is often perceived as beneficial for both partners, though a large ecological literature highlights the context dependency of this interaction. Changes in abiotic variables, such as nutrient availability, can drive the interaction along the mutualism-parasitism continuum with variable outcomes for plant growth and fitness. However, AM fungi can benefit plants in more ways than improved phosphorus nutrition and plant growth. For example, AM fungi can promote abiotic and biotic stress tolerance even when considered parasitic from a nutrient provision perspective. Other than being obligate biotrophs, very little is known about the benefits AM fungi gain from plants. In this review, we utilize both molecular biology and ecological approaches to expand our understanding of the plant-AM fungal interaction across disciplines.
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Affiliation(s)
- Alison E Bennett
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio, USA;
| | - Karin Groten
- Max Planck Institute for Chemical Ecology, Jena, Germany;
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Robbins C, Cruz Corella J, Aletti C, Seiler R, Mateus ID, Lee S, Masclaux FG, Sanders IR. Generation of unequal nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription. THE NEW PHYTOLOGIST 2021; 231:1984-2001. [PMID: 34085297 PMCID: PMC8457141 DOI: 10.1111/nph.17530] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/25/2021] [Indexed: 05/05/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form mutualisms with most plant species. The model AMF Rhizophagus irregularis is common in many ecosystems and naturally forms homokaryons and dikaryons. Quantitative variation in allele frequencies in clonally dikaryon offspring suggests they disproportionately inherit two distinct nuclear genotypes from their parent. This is interesting, because such progeny strongly and differentially affect plant growth. Neither the frequency and magnitude of this occurrence nor its effect on gene transcription are known. Using reduced representation genome sequencing, transcriptomics, and quantitative analysis tools, we show that progeny of homokaryons and dikaryons are qualitatively genetically identical to the parent. However, dikaryon progeny differ quantitatively due to unequal inheritance of nuclear genotypes. Allele frequencies of actively transcribed biallelic genes resembled the frequencies of the two nuclear genotypes. More biallelic genes showed transcription of both alleles than monoallelic transcription, but biallelic transcription was less likely with greater allelic divergence. Monoallelic transcription levels of biallelic genes were reduced compared with biallelic gene transcription, a finding consistent with genomic conflict. Given that genetic variation in R. irregularis is associated with plant growth, our results establish quantitative genetic variation as a future consideration when selecting AMF lines to improve plant production.
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Affiliation(s)
- Chanz Robbins
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Joaquim Cruz Corella
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Consolée Aletti
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Réjane Seiler
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Ivan D. Mateus
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Soon‐Jae Lee
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Frédéric G. Masclaux
- Group of Genetic MedicineGeneva University HospitalBuilding DGeneva1205Switzerland
| | - Ian R. Sanders
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
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7
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Plett KL, Kohler A, Lebel T, Singan VR, Bauer D, He G, Ng V, Grigoriev IV, Martin F, Plett JM, Anderson IC. Intra-species genetic variability drives carbon metabolism and symbiotic host interactions in the ectomycorrhizal fungus Pisolithus microcarpus. Environ Microbiol 2020; 23:2004-2020. [PMID: 33185936 DOI: 10.1111/1462-2920.15320] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning and nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages and the impacts of genetic variation across species, and especially within a given ECM species, on function and interactions with the environment is not well understood. Here, we explore the extent of intra-species variation between four isolates of the ECM fungus Pisolithus microcarpus, in terms of gene regulation, carbon metabolism and growth, and interactions with a host, Eucalyptus grandis. We demonstrate that, while a core response to the host is maintained by all of the isolates tested, they have distinct patterns of gene expression and carbon metabolism, resulting in the differential expression of isolate-specific response pathways in the host plant. Together, these results highlight the importance of using a wider range of individuals within a species to understand the broader ecological roles of ECM fungi and their host interactions.
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Affiliation(s)
- Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE GrandEst-Nancy, Champenoux, 54280, France
| | - Teresa Lebel
- Royal Botanic Gardens Victoria, Melbourne, VIC, 3004, Australia.,Botanic Gardens and State Herbarium of South Australia, Adelaide, SA, 5000, Australia
| | - Vasanth R Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE GrandEst-Nancy, Champenoux, 54280, France
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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