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Duan S, Feng G, Limpens E, Bonfante P, Xie X, Zhang L. Cross-kingdom nutrient exchange in the plant-arbuscular mycorrhizal fungus-bacterium continuum. Nat Rev Microbiol 2024:10.1038/s41579-024-01073-7. [PMID: 39014094 DOI: 10.1038/s41579-024-01073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2024] [Indexed: 07/18/2024]
Abstract
The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF-plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant-AMF-bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF-bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture.
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Affiliation(s)
- Shilong Duan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Gu Feng
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Erik Limpens
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
| | - Lin Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
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2
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Choreño-Parra EM, Treseder KK. Mycorrhizal fungi modify decomposition: a meta-analysis. THE NEW PHYTOLOGIST 2024; 242:2763-2774. [PMID: 38605488 DOI: 10.1111/nph.19748] [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: 02/10/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024]
Abstract
It has been proposed that ectomycorrhizal fungi can reduce decomposition while arbuscular mycorrhizal fungi may enhance it. These phenomena are known as the 'Gadgil effect' and 'priming effect', respectively. However, it is unclear which one predominates globally. We evaluated whether mycorrhizal fungi decrease or increase decomposition, and identified conditions that mediate this effect. We obtained decomposition data from 43 studies (97 trials) conducted in field or laboratory settings that controlled the access of mycorrhizal fungi to substrates colonized by saprotrophs. Across studies, mycorrhizal fungi promoted decomposition of different substrates by 6.7% overall by favoring the priming effect over the Gadgil effect. However, we observed significant variation among studies. The substrate C : N ratio and absolute latitude influenced the effect of mycorrhizal fungi on decomposition and contributed to the variation. Specifically, mycorrhizal fungi increased decomposition at low substrate C : N and absolute latitude, but there was no discernable effect at high values. Unexpectedly, the effect of mycorrhizal fungi was not influenced by the mycorrhizal type. Our findings challenge previous assumptions about the universality of the Gadgil effect but highlight the potential of mycorrhizal fungi to negatively influence soil carbon storage by promoting the priming effect.
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Affiliation(s)
- Eduardo M Choreño-Parra
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
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3
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Rosling A, Eshghi Sahraei S, Kalsoom Khan F, Desirò A, Bryson AE, Mondo SJ, Grigoriev IV, Bonito G, Sánchez-García M. Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis. BMC Genomics 2024; 25:529. [PMID: 38811885 PMCID: PMC11134847 DOI: 10.1186/s12864-024-10391-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid. RESULTS In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89. CONCLUSION Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.
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Affiliation(s)
- Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | | | | | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Abigail E Bryson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Stephen J Mondo
- Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
- Department of Forest Mycology and Plant Pathology, Uppsala Biocentre, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Barua D, Płecha M, Muszewska A. A minimal Fanconi Anemia complex in early diverging fungi. Sci Rep 2024; 14:9922. [PMID: 38688950 PMCID: PMC11061109 DOI: 10.1038/s41598-024-60318-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fanconi Anemia (FA) pathway resolves DNA interstrand cross links (ICL). The FA pathway was initially recognized in vertebrates, but was later confirmed in other animals and speculated in fungi. FA proteins FANCM, FANCL and FANCJ are present in Saccharomyces cerevisiae but, their mechanism of interaction to resolve ICL is still unclear. Unlike Dikarya, early diverging fungi (EDF) possess more traits shared with animals. We traced the evolutionary history of the FA pathway across Opisthokonta. We scanned complete proteomes for FA-related homologs to establish their taxonomic distribution and analyzed their phylogenetic trees. We checked transcription profiles of FA genes to test if they respond to environmental conditions and their genomic localizations for potential co-localization. We identified fungal homologs of the activation and ID complexes, 5 out of 8 core proteins, all of the endonucleases, and deubiquitination proteins. All fungi lack FANCC, FANCF and FANCG proteins responsible for post-replication repair and chromosome stability in animals. The observed taxonomic distribution can be attributed to a gradual degradation of the FA pathway from EDF to Dikarya. One of the key differences is that EDF have the ID complex recruiting endonucleases to the site of ICL. Moreover, 21 out of 32 identified FA genes are upregulated in response to different growth conditions. Several FA genes are co-localized in fungal genomes which also could facilitate co-expression. Our results indicate that a minimal FA pathway might still be functional in Mucoromycota with a gradual loss of components in Dikarya ancestors.
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Affiliation(s)
- Drishtee Barua
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Magdalena Płecha
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
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Slimani A, Ait-El-Mokhtar M, Ben-Laouane R, Boutasknit A, Anli M, Abouraicha EF, Oufdou K, Meddich A, Baslam M. Molecular and Systems Biology Approaches for Harnessing the Symbiotic Interaction in Mycorrhizal Symbiosis for Grain and Oil Crop Cultivation. Int J Mol Sci 2024; 25:912. [PMID: 38255984 PMCID: PMC10815302 DOI: 10.3390/ijms25020912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Mycorrhizal symbiosis, the mutually beneficial association between plants and fungi, has gained significant attention in recent years due to its widespread significance in agricultural productivity. Specifically, arbuscular mycorrhizal fungi (AMF) provide a range of benefits to grain and oil crops, including improved nutrient uptake, growth, and resistance to (a)biotic stressors. Harnessing this symbiotic interaction using molecular and systems biology approaches presents promising opportunities for sustainable and economically-viable agricultural practices. Research in this area aims to identify and manipulate specific genes and pathways involved in the symbiotic interaction, leading to improved cereal and oilseed crop yields and nutrient acquisition. This review provides an overview of the research frontier on utilizing molecular and systems biology approaches for harnessing the symbiotic interaction in mycorrhizal symbiosis for grain and oil crop cultivation. Moreover, we address the mechanistic insights and molecular determinants underpinning this exchange. We conclude with an overview of current efforts to harness mycorrhizal diversity to improve cereal and oilseed health through systems biology.
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Affiliation(s)
- Aiman Slimani
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Microbial Biotechnologies, Agrosciences, and Environment, Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Mohamed Ait-El-Mokhtar
- Laboratory Biochemistry, Environment & Agri-Food URAC 36, Department of Biology, Faculty of Science and Techniques—Mohammedia, Hassan II University of Casablanca, Mohammedia 28800, Morocco
| | - Raja Ben-Laouane
- Laboratory of Environment and Health, Department of Biology, Faculty of Science and Techniques, Errachidia 52000, Morocco
| | - Abderrahim Boutasknit
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- Department of Biology, Multidisciplinary Faculty of Nador, Mohamed First University, Nador 62700, Morocco
| | - Mohamed Anli
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- Department of Life, Earth and Environmental Sciences, University of Comoros, Patsy University Center, Moroni 269, Comoros
| | - El Faiza Abouraicha
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- Higher Institute of Nursing and Health Techniques (ISPITS), Essaouira 44000, Morocco
| | - Khalid Oufdou
- Laboratory of Microbial Biotechnologies, Agrosciences, and Environment, Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Abdelilah Meddich
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Marouane Baslam
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- GrowSmart, Seoul 03129, Republic of Korea
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Sokołowska B, Orłowska M, Okrasińska A, Piłsyk S, Pawłowska J, Muszewska A. What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota. IMA Fungus 2023; 14:22. [PMID: 37932857 PMCID: PMC10629195 DOI: 10.1186/s43008-023-00127-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid metabolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the question on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation components common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metabolism currently being explored by biotechnological studies.
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Affiliation(s)
- Blanka Sokołowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Małgorzata Orłowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Alicja Okrasińska
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Julia Pawłowska
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
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Liu X, Feng Z, Zhang W, Yao Q, Zhu H. Exogenous myristate promotes the colonization of arbuscular mycorrhizal fungi in tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1250684. [PMID: 38023845 PMCID: PMC10652774 DOI: 10.3389/fpls.2023.1250684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) can establish symbiotic associations with the roots of most terrestrial plants, thereby improving the tolerance of the host plants to biotic and abiotic stresses. Although AMF cannot synthesize lipids de novo, they can obtain lipids from the root cells for their growth and development. A recent study reveals that AMF can directly take up myristate (C14:0 lipid) from the environment and produce a large amount of hyphae in asymbiotic status; however, the effect of environmental lipids on AM symbiosis is still unclear. In this study, we inoculated tomato (Solanum lycopersicum) with AMF in an in vitro dual culture system and a sand culture system, and then applied exogenous myristate to the substrate, in order to explore the effect of exogenous lipids on the mycorrhizal colonization of AMF. We investigated the hyphae growth, development, and colonization of AMF, and examined the gene expression involved in phosphate transport, lipid biosynthesis, and transport. Results indicate that exogenous lipids significantly stimulated the growth and branching of hyphae, and significantly increased the number of hyphopodia and mycorrhizal colonization of AMF, with arbuscular abundance and intraradical spores or vesicles being the most promoted. In contrast, exogenous myristate decreased the growth range and host tropism of the germ tubes, and largely inhibited the exchange of nutrition between symbionts. As a result, exogenous myristate did not affect the plant growth. This study suggests that lipids promote mycorrhizal colonization by enhancing the growth and development of AMF hyphae and increasing their contact opportunities with plant roots. To the best of our knowledge, this is the first report that shows that lipids promote the colonization of AMF. Our study highlights the importance of better understanding the roles of environmental lipids in the establishment and maintenance of AM symbiosis and, thus, in agricultural production.
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Affiliation(s)
- Xiaodi Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zengwei Feng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Wei Zhang
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou, China
| | - Qing Yao
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Gryganskyi AP, Golan J, Muszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith ME, Reynolds N, James TY, Grigoriev IV, Spatafora JW, Stajich JE. Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms 2023; 11:1830. [PMID: 37513002 PMCID: PMC10386755 DOI: 10.3390/microorganisms11071830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.
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Affiliation(s)
- Andrii P. Gryganskyi
- Division of Biological & Nanoscale Technologies, UES, Inc., Dayton, OH 45432, USA
| | - Jacob Golan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Anna Muszewska
- Institute of Biochemistry & Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Somayeh Dolatabadi
- Biology Department, Hakim Sabzevari University, Sabzevar 96179-76487, Iran;
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
| | - Vira B. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | - Volodymyr O. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | | | - Iryna M. Anishchenko
- MG Kholodny Institute of Botany, National Academy of Sciences, 01030 Kyiv, Ukraine;
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological & Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland;
| | - Ngoc Vinh Tran
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Ingo Ebersberger
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Ying Chang
- Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore;
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Joseph Heitman
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, NC 27708, USA;
| | - Gregory Bonito
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA;
| | - Gerald L. Benny
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Matthew E. Smith
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Nicole Reynolds
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Joseph W. Spatafora
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 93106, USA;
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Aparicio Chacón MV, Van Dingenen J, Goormachtig S. Characterization of Arbuscular Mycorrhizal Effector Proteins. Int J Mol Sci 2023; 24:9125. [PMID: 37298075 PMCID: PMC10252856 DOI: 10.3390/ijms24119125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Plants are colonized by various fungi with both pathogenic and beneficial lifestyles. One type of colonization strategy is through the secretion of effector proteins that alter the plant's physiology to accommodate the fungus. The oldest plant symbionts, the arbuscular mycorrhizal fungi (AMF), may exploit effectors to their benefit. Genome analysis coupled with transcriptomic studies in different AMFs has intensified research on the effector function, evolution, and diversification of AMF. However, of the current 338 predicted effector proteins from the AM fungus Rhizophagus irregularis, only five have been characterized, of which merely two have been studied in detail to understand which plant proteins they associate with to affect the host physiology. Here, we review the most recent findings in AMF effector research and discuss the techniques used for the functional characterization of effector proteins, from their in silico prediction to their mode of action, with an emphasis on high-throughput approaches for the identification of plant targets of the effectors through which they manipulate their hosts.
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Affiliation(s)
- María V. Aparicio Chacón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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10
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Arévalo-Granda V, Hickey-Darquea A, Prado-Vivar B, Zapata S, Duchicela J, van ‘t Hof P. Exploring the mycobiome and arbuscular mycorrhizal fungi associated with the rizosphere of the genus Inga in the pristine Ecuadorian Amazon. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1086194. [PMID: 37746118 PMCID: PMC10512398 DOI: 10.3389/ffunb.2023.1086194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/20/2023] [Indexed: 09/26/2023]
Abstract
This study explored the composition of the mycobiome in the rhizosphere of Inga seedlings in two different but neighboring forest ecosystems in the undisturbed tropical Amazon rainforest at the Tiputini Biodiversity Station in Ecuador. In terra firme plots, which were situated higher up and therefore typically outside of the influence of river floods, and in várzea plots, the lower part of the forest located near the riverbanks and therefore seasonally flooded, tree seedlings of the genus Inga were randomly collected and measured, and the rhizosphere soils surrounding the root systems was collected. Members of the Fabaceae family and the genus Inga were highly abundant in both forest ecosystems. Inga sp. seedlings collected in terra firme showed a lower shoot to root ratio compared to seedlings that were collected in várzea, suggesting that Inga seedlings which germinated in várzea soils could invest more resources in vegetative growth with shorter roots. Results of the physical-chemical properties of soil samples indicated higher proportions of N, Mo, and V in terra firme soils, whereas várzea soils present higher concentrations of all other macro- and micronutrients, which confirmed the nutrient deposition effect of seasonal flooding by the nearby river. ITS metabarcoding was used to explore the mycobiome associated with roots of the genus Inga. Bioinformatic analysis was performed using Qiime 2 to calculate the alpha and beta diversity, species taxonomy and the differential abundance of fungi and arbuscular mycorrhizal fungi. The fungal community represented 75% of the total ITS ASVs, and although present in all samples, the subphylum Glomeromycotina represented 1.42% of all ITS ASVs with annotations to 13 distinct families, including Glomeraceae (72,23%), Gigasporaceae (0,57%), Acaulosporaceae (0,49%). AMF spores of these three AMF families were morphologically identified by microscopy. Results of this study indicate that AMF surround the rhizosphere of Inga seedlings in relatively low proportions compared to other fungal groups but present in both terra firme and várzea Neotropical ecosystems.
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Affiliation(s)
- Valentina Arévalo-Granda
- Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Institute of Microbiology, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
| | - Aileen Hickey-Darquea
- Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
| | - Belén Prado-Vivar
- Institute of Microbiology, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
| | - Sonia Zapata
- Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Institute of Microbiology, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Tiputini Biodiversity Station, Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
| | - Jéssica Duchicela
- Department of Life Sciences and Agriculture, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Pieter van ‘t Hof
- Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Institute of Microbiology, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Tiputini Biodiversity Station, Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
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11
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Zhang S, Nie Y, Fan X, Wei W, Chen H, Xie X, Tang M. A transcriptional activator from Rhizophagus irregularis regulates phosphate uptake and homeostasis in AM symbiosis during phosphorous starvation. Front Microbiol 2023; 13:1114089. [PMID: 36741887 PMCID: PMC9895418 DOI: 10.3389/fmicb.2022.1114089] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/28/2022] [Indexed: 01/22/2023] Open
Abstract
Introduction Phosphorus (P) is one of the most important nutrient elements for plant growth and development. Under P starvation, arbuscular mycorrhizal (AM) fungi can promote phosphate (Pi) uptake and homeostasis within host plants. However, the underlying mechanisms by which AM fungal symbiont regulates the AM symbiotic Pi acquisition from soil under P starvation are largely unknown. Here, we identify a HLH domain containing transcription factor RiPho4 from Rhizophagus irregularis. Methods To investigate the biological functions of the RiPho4, we combined the subcellular localization and Yeast One-Hybrid (Y1H) experiments in yeasts with gene expression and virus-induced gene silencing approach during AM symbiosis. Results The approach during AM symbiosis. The results indicated that RiPho4 encodes a conserved transcription factor among different fungi and is induced during the in planta phase. The transcription of RiPho4 is significantly up-regulated by P starvation. The subcellular localization analysis revealed that RiPho4 is located in the nuclei of yeast cells during P starvation. Moreover, knock-down of RiPho4 inhibits the arbuscule development and mycorrhizal Pi uptake under low Pi conditions. Importantly, RiPho4 can positively regulate the downstream components of the phosphate (PHO) pathway in R. irregularis. Discussion In summary, these new findings reveal that RiPho4 acts as a transcriptional activator in AM fungus to maintain arbuscule development and regulate Pi uptake and homeostasis in the AM symbiosis during Pi starvation.
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Affiliation(s)
| | | | | | | | | | - Xianan Xie
- *Correspondence: Xianan Xie, ; Ming Tang,
| | - Ming Tang
- *Correspondence: Xianan Xie, ; Ming Tang,
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12
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Liu H, Pausch J, Wu Y, Xu H, Liu G, Ma L, Xue S. Implications of plant N/P stoichiometry influenced by arbuscular mycorrhizal fungi for stability of plant species and community in response to nutrient limitation. OIKOS 2022. [DOI: 10.1111/oik.09649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hongfei Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F Univ. Yangling PR China
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), Univ. of Bayreuth Bayreuth Germany
- Chinese Academy of Sciences and Ministry Water Resources, Inst. of Soil and Water Conservation Yangling PR China
| | - Johanna Pausch
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), Univ. of Bayreuth Bayreuth Germany
| | - Yang Wu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F Univ. Yangling PR China
- Chinese Academy of Sciences and Ministry Water Resources, Inst. of Soil and Water Conservation Yangling PR China
| | - Hongwei Xu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F Univ. Yangling PR China
- Chinese Academy of Sciences and Ministry Water Resources, Inst. of Soil and Water Conservation Yangling PR China
| | - Guobin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F Univ. Yangling PR China
- Chinese Academy of Sciences and Ministry Water Resources, Inst. of Soil and Water Conservation Yangling PR China
| | - LiHui Ma
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F Univ. Yangling PR China
- Chinese Academy of Sciences and Ministry Water Resources, Inst. of Soil and Water Conservation Yangling PR China
| | - Sha Xue
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F Univ. Yangling PR China
- Chinese Academy of Sciences and Ministry Water Resources, Inst. of Soil and Water Conservation Yangling PR China
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13
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Gámez-Arjona FM, Vitale S, Voxeur A, Dora S, Müller S, Sancho-Andrés G, Montesinos JC, Di Pietro A, Sánchez-Rodríguez C. Impairment of the cellulose degradation machinery enhances Fusarium oxysporum virulence but limits its reproductive fitness. SCIENCE ADVANCES 2022; 8:eabl9734. [PMID: 35442735 PMCID: PMC9020665 DOI: 10.1126/sciadv.abl9734] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fungal pathogens grow in the apoplastic space, in constant contact with the plant cell wall (CW) that hinders microbe progression while representing a source of nutrients. Although numerous fungal CW modifying proteins have been identified, their role during host colonization remains underexplored. Here, we show that the root-infecting plant pathogen Fusarium oxysporum (Fo) does not require its complete arsenal of cellulases to infect the host plant. Quite the opposite: Fo mutants impaired in cellulose degradation become hypervirulent by enhancing the secretion of virulence factors. On the other hand, the reduction in cellulase activity had a severe negative effect on saprophytic growth and microconidia production during the final stages of the Fo infection cycle. These findings enhance our understanding of the function of plant CW degradation on the outcome of host-microbe interactions and reveal an unexpected role of cellulose degradation in a pathogen's reproductive success.
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Affiliation(s)
| | - Stefania Vitale
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14014 Córdoba, Spain
| | - Aline Voxeur
- Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Susanne Dora
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Sascha Müller
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | | | | | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14014 Córdoba, Spain
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14
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Xie X, Lai W, Che X, Wang S, Ren Y, Hu W, Chen H, Tang M. A SPX domain-containing phosphate transporter from Rhizophagus irregularis handles phosphate homeostasis at symbiotic interface of arbuscular mycorrhizas. THE NEW PHYTOLOGIST 2022; 234:650-671. [PMID: 35037255 DOI: 10.1111/nph.17973] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 12/22/2021] [Indexed: 05/28/2023]
Abstract
Reciprocal symbiosis of > 70% of terrestrial vascular plants with arbuscular mycorrhizal (AM) fungi provides the fungi with fatty acids and sugars. In return, AM fungi facilitate plant phosphate (Pi) uptake from soil. However, how AM fungi handle Pi transport and homeostasis at the symbiotic interface of AM symbiosis is poorly understood. Here, we identify an SPX (SYG1/Pho81/XPR1) domain-containing phosphate transporter, RiPT7 from Rhizophagus irregularis. To characterize the RiPT7 transporter, we combined subcellular localization and heterologous expression studies in yeasts with reverse genetics approaches during the in planta phase. The results show that RiPT7 is conserved across fungal species and expressed in the intraradical mycelia. It is expressed in the arbuscules, intraradical hyphae and vesicles, independently of Pi availability. The plasma membrane-localized RiPT7 facilitates bidirectional Pi transport, depending on Pi gradient across the plasma membrane, whereas the SPX domain of RiPT7 inhibits Pi transport activity and mediates the vacuolar targeting of RiPT7 in yeast in response to Pi starvation. Importantly, RiPT7 silencing hampers arbuscule development of R. irregularis and symbiotic Pi delivery under medium- to low-Pi conditions. Collectively, our findings reveal a role for RiPT7 in fine-tuning of Pi homeostasis across the fungal membrane to maintain the AM development.
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Affiliation(s)
- Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Wenzhen Lai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Che
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Sijia Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Ren
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Wentao Hu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
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15
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Zhang L, Zhou J, George TS, Limpens E, Feng G. Arbuscular mycorrhizal fungi conducting the hyphosphere bacterial orchestra. TRENDS IN PLANT SCIENCE 2022; 27:402-411. [PMID: 34782247 DOI: 10.1016/j.tplants.2021.10.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 05/22/2023]
Abstract
More than two-thirds of terrestrial plants acquire nutrients by forming a symbiosis with arbuscular mycorrhizal (AM) fungi. AM fungal hyphae recruit distinct microbes into their hyphosphere, the narrow region of soil influenced by hyphal exudates. They thereby shape this so-called second genome of AM fungi, which significantly contributes to nutrient mobilization and turnover. We summarize current insights into characteristics of the hyphosphere microbiome and the role of hyphal exudates on orchestrating its composition. The hyphal exudates not only contain carbon-rich compounds but also promote bacterial growth and activity and influence the microbial community structure. These effects lead to shifts in function and cause changes in organic nutrient cycling, making the hyphosphere a unique and largely overlooked functional zone in ecosystems.
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Affiliation(s)
- Lin Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Jiachao Zhou
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | | | - Erik Limpens
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen 6708, PB, The Netherlands
| | - Gu Feng
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China.
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16
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Liu YN, Liu CC, Zhu AQ, Niu KX, Guo R, Tian L, Wu YN, Sun B, Wang B. OsRAM2 Function in Lipid Biosynthesis Is Required for Arbuscular Mycorrhizal Symbiosis in Rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:187-199. [PMID: 34077267 DOI: 10.1094/mpmi-04-21-0097-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Arbuscular mycorrhiza (AM) is a mutualistic symbiosis formed between most land plants and Glomeromycotina fungi. During symbiosis, plants provide organic carbon to fungi in exchange for mineral nutrients. Previous legume studies showed that the required for arbuscular mycorrhization2 (RAM2) gene is necessary for transferring lipids from plants to AM fungi (AMF) and is also likely to play a "signaling" role at the root surface. To further explore RAM2 functions in other plant lineages, in this study, two rice (Oryza sativa) genes, OsRAM2 and OsRAM2L, were identified as orthologs of legume RAM2. Examining their expression patterns during symbiosis revealed that only OsRAM2 was strongly upregulated upon AMF inoculation. CRISPR/Cas9 mutagenesis was then performed to obtain three Osram2 mutant lines (-1, -2, and -3). After inoculation by AMF Rhizophagus irregularis or Funneliformis mosseae, all of the mutant lines showed extremely low colonization rates and the rarely observed arbuscules were all defective, thus supporting a conserved "nutritional" role of RAM2 between monocot and dicot lineages. As for the signaling role, although the hyphopodia numbers formed by both AMF on Osram2 mutants were indeed reduced, their morphology showed no abnormality, with fungal hyphae invading roots successfully. Promoter activities further indicated that OsRAM2 was not expressed in epidermal cells below hyphopodia or outer cortical cells enclosing fungal hyphae but instead expressed exclusively in cortical cells containing arbuscules. Therefore, this suggested an indirect role of RAM2 rather than a direct involvement in determining the symbiosis signals at the root surface.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Ying-Na Liu
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Cheng-Chen Liu
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - An-Qi Zhu
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ke-Xin Niu
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Rui Guo
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Li Tian
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ya-Nan Wu
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bo Sun
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bin Wang
- School of Life Sciences, Nanjing University, Nanjing 210023, China
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17
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Tanaka S, Hashimoto K, Kobayashi Y, Yano K, Maeda T, Kameoka H, Ezawa T, Saito K, Akiyama K, Kawaguchi M. Asymbiotic mass production of the arbuscular mycorrhizal fungus Rhizophagus clarus. Commun Biol 2022; 5:43. [PMID: 35022540 PMCID: PMC8755765 DOI: 10.1038/s42003-021-02967-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
Arbuscular mycorrhizal (AM) symbiosis is a mutually beneficial interaction between fungi and land plants and promotes global phosphate cycling in terrestrial ecosystems. AM fungi are recognised as obligate symbionts that require root colonisation to complete a life cycle involving the production of propagules, asexual spores. Recently, it has been shown that Rhizophagus irregularis can produce infection-competent secondary spores asymbiotically by adding a fatty acid, palmitoleic acid. Furthermore, asymbiotic growth can be supported using myristate as a carbon and energy source for their asymbiotic growth to increase fungal biomass. However, the spore production and the ability of these spores to colonise host roots were still limited compared to the co-culture of the fungus with plant roots. Here we show that a combination of two plant hormones, strigolactone and jasmonate, induces the production of a large number of infection-competent spores in asymbiotic cultures of Rhizophagus clarus HR1 in the presence of myristate and organic nitrogen. Inoculation of asymbiotically-generated spores promoted the growth of host plants, as observed for spores produced by symbiotic culture system. Our findings provide a foundation for the elucidation of hormonal control of the fungal life cycle and the development of inoculum production schemes.
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Affiliation(s)
- Sachiko Tanaka
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Kayo Hashimoto
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Yuuki Kobayashi
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Institute for Advanced Biosciences, Keio University, Kakuganji 246-2 Mizukami, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka, 599-8531, Japan
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Tatsuhiro Ezawa
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Katsuharu Saito
- Faculty of Agriculture, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan
| | - Kohki Akiyama
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka, 599-8531, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
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18
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Singh PP, Srivastava D, Shukla S, Varsha. Rhizophagus proliferus genome sequence reiterates conservation of genetic traits in AM fungi, but predicts higher saprotrophic activity. Arch Microbiol 2021; 204:105. [DOI: 10.1007/s00203-021-02651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/24/2022]
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19
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Kuga Y, Wu TD, Sakamoto N, Katsuyama C, Yurimoto H. Allocation of Carbon from an Arbuscular Mycorrhizal Fungus, Gigaspora margarita, to Its Gram-Negative and Positive Endobacteria Revealed by High-Resolution Secondary Ion Mass Spectrometry. Microorganisms 2021; 9:microorganisms9122597. [PMID: 34946198 PMCID: PMC8705746 DOI: 10.3390/microorganisms9122597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Arbuscular mycorrhizal fungi are obligate symbionts of land plants; furthermore, some of the species harbor endobacteria. Although the molecular approach increased our knowledge of the diversity and origin of the endosymbiosis and its metabolic possibilities, experiments to address the functions of the fungal host have been limited. In this study, a C flow of the fungus to the bacteria was investigated. Onion seedlings colonized with Gigaspora margarita, possessing Candidatus Glomeribacter gigasporarum (CaGg, Gram-negative, resides in vacuole) and Candidatus Moeniiplasma glomeromycotorum (CaMg, Gram-positive, resides in the cytoplasm,) were labelled with 13CO2. The 13C localization within the mycorrhiza was analyzed using high-resolution secondary ion mass spectrometry (SIMS). Correlative TEM-SIMS analysis of the fungal cells revealed that the 13C/12C ratio of CaGg was the lowest among CaMg and mitochondria and was the highest in the cytoplasm. By contrast, the plant cells, mitochondria, plastids, and fungal cytoplasm, which are contributors to the host, showed significantly higher 13C enrichment than the host cytoplasm. The C allocation patterns implied that CaMg has a greater impact than CaGg on G. margarita, but both seemed to be less burdensome to the host fungus in terms of C cost.
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Affiliation(s)
- Yukari Kuga
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Hiroshima, Japan;
- Correspondence:
| | - Ting-Di Wu
- Institut Curie, Université PSL, CNRS UMS2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France;
| | - Naoya Sakamoto
- Isotope Imaging Laboratory, Creative Research Institution, Hokkaido University, Kita-21 Nishi-11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan;
| | - Chie Katsuyama
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Hiroshima, Japan;
| | - Hisayoshi Yurimoto
- Department of Natural History Sciences, Hokkaido University, Kita-21 Nishi-11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan;
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20
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Banasiak J, Jamruszka T, Murray JD, Jasiński M. A roadmap of plant membrane transporters in arbuscular mycorrhizal and legume-rhizobium symbioses. PLANT PHYSIOLOGY 2021; 187:2071-2091. [PMID: 34618047 PMCID: PMC8644718 DOI: 10.1093/plphys/kiab280] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/24/2021] [Indexed: 05/20/2023]
Abstract
Most land plants live in close contact with beneficial soil microbes: the majority of land plant species establish symbiosis with arbuscular mycorrhizal fungi, while most legumes, the third largest plant family, can form a symbiosis with nitrogen-fixing rhizobia. These microbes contribute to plant nutrition via endosymbiotic processes that require modulating the expression and function of plant transporter systems. The efficient contribution of these symbionts involves precisely controlled integration of transport, which is enabled by the adaptability and plasticity of their transporters. Advances in our understanding of these systems, driven by functional genomics research, are rapidly filling the gap in knowledge about plant membrane transport involved in these plant-microbe interactions. In this review, we synthesize recent findings associated with different stages of these symbioses, from the pre-symbiotic stage to nutrient exchange, and describe the role of host transport systems in both mycorrhizal and legume-rhizobia symbioses.
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Affiliation(s)
- Joanna Banasiak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań 61-704, Poland
| | - Tomasz Jamruszka
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań 61-704, Poland
| | - Jeremy D Murray
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań 61-704, Poland
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Poznań 60-632, Poland
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21
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Venice F, Chialva M, Domingo G, Novero M, Carpentieri A, Salvioli di Fossalunga A, Ghignone S, Amoresano A, Vannini C, Lanfranco L, Bonfante P. Symbiotic responses of Lotus japonicus to two isogenic lines of a mycorrhizal fungus differing in the presence/absence of an endobacterium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1547-1564. [PMID: 34767660 PMCID: PMC9300078 DOI: 10.1111/tpj.15578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 05/05/2023]
Abstract
As other arbuscular mycorrhizal fungi, Gigaspora margarita contains unculturable endobacteria in its cytoplasm. A cured fungal line has been obtained and showed it was capable of establishing a successful mycorrhizal colonization. However, previous OMICs and physiological analyses have demonstrated that the cured fungus is impaired in some functions during the pre-symbiotic phase, leading to a lower respiration activity, lower ATP, and antioxidant production. Here, by combining deep dual-mRNA sequencing and proteomics applied to Lotus japonicus roots colonized by the fungal line with bacteria (B+) and by the cured line (B-), we tested the hypothesis that L. japonicus (i) activates its symbiotic pathways irrespective of the presence or absence of the endobacterium, but (ii) perceives the two fungal lines as different physiological entities. Morphological observations confirmed the absence of clear endobacteria-dependent changes in the mycorrhizal phenotype of L. japonicus, while transcript and proteomic datasets revealed activation of the most important symbiotic pathways. They included the iconic nutrient transport and some less-investigated pathways, such as phenylpropanoid biosynthesis. However, significant differences between the mycorrhizal B+/B- plants emerged in the respiratory pathways and lipid biosynthesis. In both cases, the roots colonized by the cured line revealed a reduced capacity to activate genes involved in antioxidant metabolism, as well as the early biosynthetic steps of the symbiotic lipids, which are directed towards the fungus. Similar to its pre-symbiotic phase, the intraradical fungus revealed transcripts related to mitochondrial activity, which were downregulated in the cured line, as well as perturbation in lipid biosynthesis.
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Affiliation(s)
- Francesco Venice
- Department of Life Sciences and Systems BiologyUniversity of TurinTurinItaly
| | - Matteo Chialva
- Department of Life Sciences and Systems BiologyUniversity of TurinTurinItaly
| | - Guido Domingo
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Mara Novero
- Department of Life Sciences and Systems BiologyUniversity of TurinTurinItaly
| | - Andrea Carpentieri
- Department of Chemical SciencesUniversity of Naples Federico IINapoliItaly
| | | | - Stefano Ghignone
- National Research Council (CNR)Institute for Sustainable Plant Protection (IPSP)TurinItaly
| | - Angela Amoresano
- Department of Chemical SciencesUniversity of Naples Federico IINapoliItaly
| | - Candida Vannini
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Luisa Lanfranco
- Department of Life Sciences and Systems BiologyUniversity of TurinTurinItaly
| | - Paola Bonfante
- Department of Life Sciences and Systems BiologyUniversity of TurinTurinItaly
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22
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Fasusi OA, Amoo AE, Babalola OO. Propagation and characterization of viable arbuscular mycorrhizal fungal spores within maize plant (Zea mays L.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:5834-5841. [PMID: 33788958 DOI: 10.1002/jsfa.11235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/18/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The harmful effect of chemical fertilizer application on human health and the environment as a modern method of meeting the food demand of the increasing world population demands an urgent alternative that is environmentally friendly, which will pose no harm to human health and the environment. Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms that provide various ecological functions in increasing soil fertility and enhancing plant growth. This present study aimed to propagate, characterize and examine the effect of viable arbuscular mycorrhizal fungal spores on maize (Zea mays L) hosts using molecular methods. The propagation of AMF in the host plant using sterile soil and vermiculite was conducted in the greenhouse. RESULT The effect of AMF inoculation revealed a significant difference (P > 0.05) in maize growth, root colonization and AMF spore count when compared with the control. In all the parameters measured in this study, all the AMF spores propagated had a positive effect on the maize plant over the control, with the highest value mostly recorded in Rhizophagus irregularis AOB1. The molecular characterization of the spore using a specific universal primer for Glomeromycota established the success of the propagation process, which enhanced the classification of the AMF species into Rhizophagus irregularis OAB1, Glomus mosseae OAB2 and Paraglomus occultum OAB3. CONCLUSION This finding will be a starting point in producing arbuscular mycorrhizal inoculum as a biofertilizer to enhance plant growth promotion. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Oluwaseun Adeyinka Fasusi
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
| | - Adenike Eunice Amoo
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
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23
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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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24
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Montoliu-Nerin M, Sánchez-García M, Bergin C, Kutschera VE, Johannesson H, Bever JD, Rosling A. In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:716385. [PMID: 37744125 PMCID: PMC10512289 DOI: 10.3389/ffunb.2021.716385] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/06/2021] [Indexed: 09/26/2023]
Abstract
Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.
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Affiliation(s)
- Merce Montoliu-Nerin
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
- Department of Forest Mycology and Plant Pathology, Uppsala Biocentre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Claudia Bergin
- Microbial Single Cell Genomics Facility, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Verena Esther Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden
| | - James D. Bever
- Department of Ecology and Evolutionary Biology, and Kansas Biological Survey, University of Kansas, Lawrence, KS, United States
| | - Anna Rosling
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
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25
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Zhou X, Li J, Tang N, Xie H, Fan X, Chen H, Tang M, Xie X. Genome-Wide Analysis of Nutrient Signaling Pathways Conserved in Arbuscular Mycorrhizal Fungi. Microorganisms 2021; 9:1557. [PMID: 34442636 PMCID: PMC8401276 DOI: 10.3390/microorganisms9081557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with a majority of terrestrial vascular plants. To achieve an efficient nutrient trade with their hosts, AM fungi sense external and internal nutrients, and integrate different hierarchic regulations to optimize nutrient acquisition and homeostasis during mycorrhization. However, the underlying molecular networks in AM fungi orchestrating the nutrient sensing and signaling remain elusive. Based on homology search, we here found that at least 72 gene components involved in four nutrient sensing and signaling pathways, including cAMP-dependent protein kinase A (cAMP-PKA), sucrose non-fermenting 1 (SNF1) protein kinase, target of rapamycin kinase (TOR) and phosphate (PHO) signaling cascades, are well conserved in AM fungi. Based on the knowledge known in model yeast and filamentous fungi, we outlined the possible gene networks functioning in AM fungi. These pathways may regulate the expression of downstream genes involved in nutrient transport, lipid metabolism, trehalase activity, stress resistance and autophagy. The RNA-seq analysis and qRT-PCR results of some core genes further indicate that these pathways may play important roles in spore germination, appressorium formation, arbuscule longevity and sporulation of AM fungi. We hope to inspire further studies on the roles of these candidate genes involved in these nutrient sensing and signaling pathways in AM fungi and AM symbiosis.
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Affiliation(s)
- Xiaoqin Zhou
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Jiangyong Li
- Institute for Environmental and Climate Research, Jinan University, Guangzhou 511443, China;
| | - Nianwu Tang
- UMR Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280 Champenoux, France;
| | - Hongyun Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xiaoning Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
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26
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Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree. Sci Rep 2021; 11:8576. [PMID: 33883599 PMCID: PMC8060265 DOI: 10.1038/s41598-021-87886-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/06/2021] [Indexed: 02/02/2023] Open
Abstract
Mycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungus Pisolithus tinctorius were compared with non-colonized roots. Results show that compounds putatively corresponding to carbohydrates, organic acids, tannins, long-chain fatty acids and monoacylglycerols, were depleted in ectomycorrhizal cork oak colonized roots. Conversely, non-proteogenic amino acids, such as gamma-aminobutyric acid (GABA), and several putative defense-related compounds, including oxylipin-family compounds, terpenoids and B6 vitamers were induced in mycorrhizal roots. Transcriptomic analysis suggests the involvement of GABA in ectomycorrhizal symbiosis through increased synthesis and inhibition of degradation in mycorrhizal roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such as P. tinctorius benefit their host plants.
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27
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Chen M, Bruisson S, Bapaume L, Darbon G, Glauser G, Schorderet M, Reinhardt D. VAPYRIN attenuates defence by repressing PR gene induction and localized lignin accumulation during arbuscular mycorrhizal symbiosis of Petunia hybrida. THE NEW PHYTOLOGIST 2021; 229:3481-3496. [PMID: 33231304 PMCID: PMC7986166 DOI: 10.1111/nph.17109] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/16/2020] [Indexed: 05/08/2023]
Abstract
The intimate association of host and fungus in arbuscular mycorrhizal (AM) symbiosis can potentially trigger induction of host defence mechanisms against the fungus, implying that successful symbiosis requires suppression of defence. We addressed this phenomenon by using AM-defective vapyrin (vpy) mutants in Petunia hybrida, including a new allele (vpy-3) with a transposon insertion close to the ATG start codon. We explore whether abortion of fungal infection in vpy mutants is associated with the induction of defence markers, such as cell wall alterations, accumulation of reactive oxygen species (ROS), defence hormones and induction of pathogenesis-related (PR) genes. We show that vpy mutants exhibit a strong resistance against intracellular colonization, which is associated with the generation of cell wall appositions (papillae) with lignin impregnation at fungal entry sites, while no accumulation of defence hormones, ROS or callose was observed. Systematic analysis of PR gene expression revealed that several PR genes are induced in mycorrhizal roots of the wild-type, and even more in vpy plants. Some PR genes are induced exclusively in vpy mutants. Our results suggest that VPY is involved in avoiding or suppressing the induction of a cellular defence syndrome that involves localized lignin deposition and PR gene induction.
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Affiliation(s)
- Min Chen
- Department of BiologyUniversity of FribourgFribourgCH‐1700Switzerland
| | | | - Laure Bapaume
- Department of BiologyUniversity of FribourgFribourgCH‐1700Switzerland
| | - Geoffrey Darbon
- Department of BiologyUniversity of FribourgFribourgCH‐1700Switzerland
| | - Gaëtan Glauser
- Neuchâtel Platform of Analytical ChemistryUniversity of NeuchâtelNeuchâtel2000Switzerland
| | | | - Didier Reinhardt
- Department of BiologyUniversity of FribourgFribourgCH‐1700Switzerland
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28
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Reinhardt D, Roux C, Corradi N, Di Pietro A. Lineage-Specific Genes and Cryptic Sex: Parallels and Differences between Arbuscular Mycorrhizal Fungi and Fungal Pathogens. TRENDS IN PLANT SCIENCE 2021; 26:111-123. [PMID: 33011084 DOI: 10.1016/j.tplants.2020.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/29/2020] [Accepted: 09/08/2020] [Indexed: 05/25/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) live as obligate root symbionts on almost all land plants. They have long been regarded as ancient asexuals that have propagated clonally for millions of years. However, genomic studies in Rhizophagus irregularis and other AMF revealed many features indicative of sex. Surprisingly, comparative genomics of conspecific isolates of R. irregularis revealed an unexpected interstrain diversity, suggesting that AMF carry a high number of lineage-specific (LS) genes. Intriguingly, cryptic sex and LS genomic regions have previously been reported in a number of fungal pathogens of plants and humans. Here, we discuss these genomic similarities and highlight their potential relevance for AMF adaptation to the environment and for symbiotic functioning.
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Affiliation(s)
- Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan 31326, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Antonio Di Pietro
- Departamento de Genética, Universidad de Cordoba, 14071 Cordoba, Spain
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29
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Sugiura Y, Akiyama R, Tanaka S, Yano K, Kameoka H, Marui S, Saito M, Kawaguchi M, Akiyama K, Saito K. Myristate can be used as a carbon and energy source for the asymbiotic growth of arbuscular mycorrhizal fungi. Proc Natl Acad Sci U S A 2020; 117:25779-25788. [PMID: 32999061 PMCID: PMC7568319 DOI: 10.1073/pnas.2006948117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi, forming symbiotic associations with land plants, are obligate symbionts that cannot complete their natural life cycle without a host. The fatty acid auxotrophy of AM fungi is supported by recent studies showing that lipids synthesized by the host plants are transferred to the fungi, and that the latter lack genes encoding cytosolic fatty acid synthases. Therefore, to establish an asymbiotic cultivation system for AM fungi, we tried to identify the fatty acids that could promote biomass production. To determine whether AM fungi can grow on medium supplied with fatty acids or lipids under asymbiotic conditions, we tested eight saturated or unsaturated fatty acids (C12 to C18) and two β-monoacylglycerols. Only myristate (C14:0) led to an increase in the biomass of Rhizophagus irregularis, inducing extensive hyphal growth and formation of infection-competent secondary spores. However, such spores were smaller than those generated symbiotically. Furthermore, we demonstrated that R. irregularis can take up fatty acids in its branched hyphae and use myristate as a carbon and energy source. Myristate also promoted the growth of Rhizophagus clarus and Gigaspora margarita Finally, mixtures of myristate and palmitate accelerated fungal growth and induced a substantial change in fatty acid composition of triacylglycerol compared with single myristate application, although palmitate was not used as a carbon source for cell wall biosynthesis in this culture system. Our findings demonstrate that myristate boosts the asymbiotic growth of AM fungi and can also serve as a carbon and energy source.
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Affiliation(s)
- Yuta Sugiura
- Graduate School of Science and Technology, Shinshu University, Minamiminowa, 399-4598 Nagano, Japan
| | - Rei Akiyama
- Graduate School of Science and Technology, Shinshu University, Minamiminowa, 399-4598 Nagano, Japan
| | - Sachiko Tanaka
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, 444-0867 Aichi, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, 444-0867 Aichi, Japan
| | - Hiromu Kameoka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531 Osaka, Japan
| | - Shiori Marui
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531 Osaka, Japan
| | - Masanori Saito
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Miyagi, 989-6711 Osaki, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, 444-0867 Aichi, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, 444-0867 Aichi, Japan
| | - Kohki Akiyama
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531 Osaka, Japan
| | - Katsuharu Saito
- Faculty of Agriculture, Shinshu University, Minamiminowa, 399-4598 Nagano, Japan
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de Leeuw M, Baron M, Ben David O, Kushmaro A. Molecular Insights into Bacteriophage Evolution toward Its Host. Viruses 2020; 12:E1132. [PMID: 33036277 PMCID: PMC7599783 DOI: 10.3390/v12101132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages), viruses that infect bacteria, are considered to be highly host-specific. To add to the knowledge about the evolution and development of bacteriophage speciation toward its host, we conducted a 21-day experiment with the broad host-range bacteriophage Aquamicrobium phage P14. We incubated the phage, which was previously isolated and enriched with the Alphaproteobacteria Aquamicrobium H14, with the Betaproteobacteria Alcaligenaceae H5. During the experiment, we observed an increase in the phage's predation efficacy towards Alcaligenaceae H5. Furthermore, genome analysis and the comparison of the bacteriophage's whole genome indicated that rather than being scattered evenly along the genome, mutations occur in specific regions. In total, 67% of the mutations with a frequency higher than 30% were located in genes that encode tail proteins, which are essential for host recognition and attachment. As control, we incubated the phage with the Alphaproteobacteria Aquamicrobium H8. In both experiments, most of the mutations appeared in the gene encoding the tail fiber protein. However, mutations in the gene encoding the tail tubular protein B were only observed when the phage was incubated with Alcaligenaceae H5. This highlights the phage's tail as a key player in its adaptation to different hosts. We conclude that mutations in the phage's genome were mainly located in tail-related regions. Further investigation is needed to fully characterize the adaptation mechanisms of the Aquamicrobium phage P14.
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Affiliation(s)
- Marina de Leeuw
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Maayan Baron
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
| | - Oshrit Ben David
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er Sheva 8410501, Israel
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31
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 2020; 95:1198-1232. [PMID: 32301582 PMCID: PMC7539958 DOI: 10.1111/brv.12605] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental Sciences, Universitat Pompeu Fabra (UPF)Dr. Aiguader 88, 08003BarcelonaSpain
- ICREAPg. Lluís Companys 23, 08010BarcelonaSpain
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Savary R, Dupuis C, Masclaux FG, Mateus ID, Rojas EC, Sanders IR. Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava. THE ISME JOURNAL 2020; 14:1333-1344. [PMID: 32066875 PMCID: PMC7242447 DOI: 10.1038/s41396-020-0606-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 12/19/2022]
Abstract
Most land plants form symbioses with arbuscular mycorrhizal fungi (AMF). Diversity of AMF increases plant community productivity and plant diversity. For decades, it was known that plants trade carbohydrates for phosphate with their fungal symbionts. However, recent studies show that plant-derived lipids probably represent the most essential currency of exchange. Understanding the regulation of plant genes involved in the currency of exchange is crucial to understanding stability of this mutualism. Plants encounter many different AMF genotypes that vary greatly in the benefit they confer to plants. Yet the role that fungal genetic variation plays in the regulation of this currency has not received much attention. We used a high-resolution phylogeny of one AMF species (Rhizophagus irregularis) to show that fungal genetic variation drives the regulation of the plant fatty acid pathway in cassava (Manihot esculenta); a pathway regulating one of the essential currencies of trade in the symbiosis. The regulation of this pathway was explained by clearly defined patterns of fungal genome-wide variation representing the precise fungal evolutionary history. This represents the first demonstrated link between the genetics of AMF and reprogramming of an essential plant pathway regulating the currency of exchange in the symbiosis. The transcription factor RAM1 was also revealed as the dominant gene in the fatty acid plant gene co-expression network. Our study highlights the crucial role of variation in fungal genomes in the trade of resources in this important symbiosis and also opens the door to discovering characteristics of AMF genomes responsible for interactions between AMF and cassava that will lead to optimal cassava growth.
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Affiliation(s)
- Romain Savary
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Cindy Dupuis
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Ivan D Mateus
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Edward C Rojas
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
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Vangelisti A, Turrini A, Sbrana C, Avio L, Giordani T, Natali L, Giovannetti M, Cavallini A. Gene expression in Rhizoglomus irregulare at two different time points of mycorrhiza establishment in Helianthus annuus roots, as revealed by RNA-seq analysis. MYCORRHIZA 2020; 30:373-387. [PMID: 32227272 DOI: 10.1007/s00572-020-00950-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) play a fundamental role in plant growth and nutrition in natural and agricultural ecosystems. Despite the importance of such symbionts, the different developmental changes occurring during the AMF life cycle have not been fully elucidated at the molecular level. Here, the RNA-seq approach was used to investigate Rhizoglomus irregulare specific and common transcripts at two different time points of mycorrhizal establishment in Helianthus annuus in vivo. Four days after inoculation, transcripts related to cellular remodeling (actin and tubulin), cellular signaling (calmodulin, serine/threonine protein kinase, 14-3-3 protein, and calcium transporting ATPase), lipid metabolism (fatty acid desaturation, steroid hormone, and glycerophospholipid biosynthesis), and biosynthetic processes were detected. In addition to such transcripts, 16 days after inoculation, expressed genes linked to binding and catalytic activities; ion (K+, Ca2+, Fe2+, Zn2+, Mn2+, Pi, ammonia), sugar, and lipid transport; and those involved in vacuolar polyphosphate accumulation were found. Knowledge of transcriptomic changes required for symbiosis establishment and performance is of great importance to understand the functional role of AMF symbionts in food crop nutrition and health, and in plant diversity in natural ecosystems.
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Affiliation(s)
- Alberto Vangelisti
- Department of Agriculture, Food, and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food, and Environment, University of Pisa, Pisa, Italy.
| | - Cristiana Sbrana
- CNR, Institute of Agricultural Biology and Biotechnology UOS Pisa, Pisa, Italy
| | - Luciano Avio
- Department of Agriculture, Food, and Environment, University of Pisa, Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food, and Environment, University of Pisa, Pisa, Italy
| | - Lucia Natali
- Department of Agriculture, Food, and Environment, University of Pisa, Pisa, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food, and Environment, University of Pisa, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food, and Environment, University of Pisa, Pisa, Italy
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Roy R, Reinders A, Ward JM, McDonald TR. Understanding transport processes in lichen, Azolla-cyanobacteria, ectomycorrhiza, endomycorrhiza, and rhizobia-legume symbiotic interactions. F1000Res 2020; 9. [PMID: 32047609 PMCID: PMC6979478 DOI: 10.12688/f1000research.19740.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
Intimate interactions between photosynthetic and non-photosynthetic organisms require the orchestrated transfer of ions and metabolites between species. We review recent progress in identifying and characterizing the transport proteins involved in five mutualistic symbiotic interactions: lichens,
Azolla–cyanobacteria, ectomycorrhiza, endomycorrhiza, and rhizobia–legumes. This review focuses on transporters for nitrogen and carbon and other solutes exchanged in the interactions. Their predicted functions are evaluated on the basis of their transport mechanism and prevailing transmembrane gradients of H
+ and transported substrates. The symbiotic interactions are presented in the assumed order from oldest to most recently evolved.
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Affiliation(s)
- Rahul Roy
- Department of Plant and Microbial Biology, University of Minnesota, Minnesota, USA
| | - Anke Reinders
- College of Continuing and Professional Studies, University of Minnesota, Minnesota, USA
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota, Minnesota, USA
| | - Tami R McDonald
- Biology Department, St. Catherine University, Minnesota, USA
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Zeng T, Rodriguez‐Moreno L, Mansurkhodzaev A, Wang P, van den Berg W, Gasciolli V, Cottaz S, Fort S, Thomma BPHJ, Bono J, Bisseling T, Limpens E. A lysin motif effector subverts chitin-triggered immunity to facilitate arbuscular mycorrhizal symbiosis. THE NEW PHYTOLOGIST 2020; 225:448-460. [PMID: 31596956 PMCID: PMC6916333 DOI: 10.1111/nph.16245] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/24/2019] [Indexed: 05/13/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi greatly improve mineral uptake by host plants in nutrient-depleted soil and can intracellularly colonize root cortex cells in the vast majority of higher plants. However, AM fungi possess common fungal cell wall components such as chitin that can be recognized by plant chitin receptors to trigger immune responses, raising the question as to how AM fungi effectively evade chitin-triggered immune responses during symbiosis. In this study, we characterize a secreted lysin motif (LysM) effector identified from the model AM fungal species Rhizophagus irregularis, called RiSLM. RiSLM is one of the highest expressed effector proteins in intraradical mycelium during the symbiosis. In vitro binding assays show that RiSLM binds chitin-oligosaccharides and can protect fungal cell walls from chitinases. Moreover, RiSLM efficiently interferes with chitin-triggered immune responses, such as defence gene induction and reactive oxygen species production in Medicago truncatula. Although RiSLM also binds to symbiotic (lipo)chitooligosaccharides it does not interfere significantly with symbiotic signalling in Medicago. Host-induced gene silencing of RiSLM greatly reduces fungal colonization levels. Taken together, our results reveal a key role for AM fungal LysM effectors to subvert chitin-triggered immunity in symbiosis, pointing to a common role for LysM effectors in both symbiotic and pathogenic fungi.
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Affiliation(s)
- Tian Zeng
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Luis Rodriguez‐Moreno
- Department of Plant SciencesLaboratory of PhytopathologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Artem Mansurkhodzaev
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Peng Wang
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Willy van den Berg
- Laboratory of BiochemistryWageningen University & Research6708 WEWageningenthe Netherlands
| | | | - Sylvain Cottaz
- CNRSCERMAVUniversity Grenoble AlpesUPR 530138041GrenobleFrance
| | - Sébastien Fort
- CNRSCERMAVUniversity Grenoble AlpesUPR 530138041GrenobleFrance
| | - Bart P. H. J. Thomma
- Department of Plant SciencesLaboratory of PhytopathologyWageningen University & Research6708 PBWageningenthe Netherlands
| | | | - Ton Bisseling
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Erik Limpens
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
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36
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Calabrese S, Cusant L, Sarazin A, Niehl A, Erban A, Brulé D, Recorbet G, Wipf D, Roux C, Kopka J, Boller T, Courty PE. Imbalanced Regulation of Fungal Nutrient Transports According to Phosphate Availability in a Symbiocosm Formed by Poplar, Sorghum, and Rhizophagus irregularis. FRONTIERS IN PLANT SCIENCE 2019; 10:1617. [PMID: 31921260 PMCID: PMC6920215 DOI: 10.3389/fpls.2019.01617] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/18/2019] [Indexed: 05/05/2023]
Abstract
In arbuscular mycorrhizal (AM) symbiosis, key components of nutrient uptake and exchange are specialized transporters that facilitate nutrient transport across membranes. As phosphate is a nutrient and a regulator of nutrient exchanges, we investigated the effect of P availability to extraradical mycelium (ERM) on both plant and fungus transcriptomes and metabolomes in a symbiocosm system. By perturbing nutrient exchanges under the control of P, our objectives were to identify new fungal genes involved in nutrient transports, and to characterize in which extent the fungus differentially modulates its metabolism when interacting with two different plant species. We performed transportome analysis on the ERM and intraradical mycelium of the AM fungus Rhizophagus irregularis associated to Populus trichocarpa and Sorghum bicolor under high and low P availability in ERM, using quantitative RT-PCR and Illumina mRNA-sequencing. We observed that mycorrhizal symbiosis induces expression of specific phosphate and ammonium transporters in both plants. Furthermore, we identified new AM-inducible transporters and showed that a subset of phosphate transporters is regulated independently of symbiotic nutrient exchange. mRNA-Sequencing revealed that the fungal transportome was not similarly regulated in the two host plant species according to P availability. Mirroring this effect, many plant carbohydrate transporters were down-regulated in P. trichocarpa mycorrhizal root tissue. Metabolome analysis revealed further that AM root colonization led to a modification of root primary metabolism under low and high P availability and to a decrease of primary metabolite pools in general. Moreover, the down regulation of the sucrose transporters suggests that the plant limits carbohydrate long distance transport (i.e. from shoot to the mycorrhizal roots). By simultaneous uptake/reuptake of nutrients from the apoplast at the biotrophic interface, plant and fungus are both able to control reciprocal nutrient fluxes.
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Affiliation(s)
- Silvia Calabrese
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Loic Cusant
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, Castanet-Tolosan, France
| | - Alexis Sarazin
- Department of Biology at the Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
| | - Annette Niehl
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Daphnée Brulé
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Ghislaine Recorbet
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, Castanet-Tolosan, France
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Thomas Boller
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Pierre-Emmanuel Courty
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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Frey SD. Mycorrhizal Fungi as Mediators of Soil Organic Matter Dynamics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110617-062331] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Inhabiting the interface between plant roots and soil, mycorrhizal fungi play a unique but underappreciated role in soil organic matter (SOM) dynamics. Their hyphae provide an efficient mechanism for distributing plant carbon throughout the soil, facilitating its deposition into soil pores and onto mineral surfaces, where it can be protected from microbial attack. Mycorrhizal exudates and dead tissues contribute to the microbial necromass pool now known to play a dominant role in SOM formation and stabilization. While mycorrhizal fungi lack the genetic capacity to act as saprotrophs, they use several strategies to access nutrients locked in SOM and thereby promote its decay, including direct enzymatic breakdown, oxidation via Fenton chemistry, and stimulation of heterotrophic microorganisms through carbon provision to the rhizosphere. An additional mechanism, competition with free-living saprotrophs, potentially suppresses SOM decomposition, leading to its accumulation. How these various nutrient acquisition strategies differentially influence SOM formation, stabilization, and loss is an area of critical research need.
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Affiliation(s)
- Serita D. Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire 03824, USA
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Kameoka H, Maeda T, Okuma N, Kawaguchi M. Structure-Specific Regulation of Nutrient Transport and Metabolism in Arbuscular Mycorrhizal Fungi. PLANT & CELL PHYSIOLOGY 2019; 60:2272-2281. [PMID: 31241164 DOI: 10.1093/pcp/pcz122] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with most land plants, mainly for the purpose of nutrient exchange. Many studies have revealed the regulation of processes in AMF, such as nutrient absorption from soil, metabolism and exchange with host plants, and the genes involved. However, the spatial regulation of the genes within the structures comprising each developmental stage is not well understood. Here, we demonstrate the structure-specific transcriptome of the model AMF species, Rhizophagus irregularis. We performed an ultra-low input RNA-seq analysis, SMART-seq2, comparing five extraradical structures, germ tubes, runner hyphae, branched absorbing structures (BAS), immature spores and mature spores. In addition, we reanalyzed the recently reported RNA-seq data comparing intraradical mycelium and arbuscule. Our analyses captured the distinct features of each structure and revealed the structure-specific expression patterns of genes related to nutrient transport and metabolism. Of note, the transcriptional profiles suggest distinct functions of BAS in nutrient absorption. These findings provide a comprehensive dataset to advance our understanding of the transcriptional dynamics of fungal nutrition in this symbiotic system.
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Affiliation(s)
- Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, Japan
| | - Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, Japan
| | - Nao Okuma
- The Graduate University for Advanced Studies, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, Japan
- The Graduate University for Advanced Studies, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, Japan
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39
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Prasad Singh P, Srivastava D, Jaiswar A, Adholeya A. Effector proteins of Rhizophagus proliferus: conserved protein domains may play a role in host-specific interaction with different plant species. Braz J Microbiol 2019; 50:593-601. [PMID: 31250404 PMCID: PMC6863257 DOI: 10.1007/s42770-019-00099-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/29/2019] [Indexed: 12/27/2022] Open
Abstract
Arbuscular mycorrhizal (AM) fungi show high promiscuity in terms of host. Effector proteins expressed by AM fungi are found important in establishing interaction with host. However, the mechanistic underlying host-specific interactions of the fungi remain unknown. The present study aimed (i) to identify effectors encoded by Rhizophagus proliferus and (ii) to understand molecular specificity encoded in effectors for interaction with specific plant species. The effectors predicted from the whole genome sequence were annotated by homology search in NCBI non-redundant protein, Interproscan, and pathogen-host interaction (PHI) databases. In total, 416 small secreted peptides (SSPs) were predicted, which were effector peptides with presence of nuclear localization signal, small cysteine-rich, and repeat-containing proteins domains. Similar to the functionally validated SP7 effectors in Rhizophagus irregularis, two proteins (RP8598 and RP23081) were identified in R. proliferus. To understand whether interaction between SP7 and the plant target protein, ERF19, is specific in nature, we examined protein-peptide interaction using in silico molecular docking. Pairwise interaction of RP8598 and RP23081 with the ethylene-responsive factors (ERF19) coded by five different plant species (Lotus japonicus, Solanum lycopersicum, Ocimum tenuiflorum, Medicago truncatula, Diospyros kaki) was investigated. Prediction of high-quality interaction of SP7 effector with ERF19 protein expressed only by specific plant species was observed in in silico molecular docking, which may reiterate the role of effectors in host specificity. The outcomes from our study indicated that sequence precision encoded in the effector peptides of AM fungi and immunomodulatory proteins of host may regulate host specificity in these fungi.
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Affiliation(s)
- Pushplata Prasad Singh
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gwal Pahari, Gurgaon Faridabad Road, Gurugram, Haryana, 122001, India.
| | - Divya Srivastava
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gwal Pahari, Gurgaon Faridabad Road, Gurugram, Haryana, 122001, India
| | - Akanksha Jaiswar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gwal Pahari, Gurgaon Faridabad Road, Gurugram, Haryana, 122001, India
| | - Alok Adholeya
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gwal Pahari, Gurgaon Faridabad Road, Gurugram, Haryana, 122001, India
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40
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Abstract
Phosphorous is important for life but often limiting for plants. The symbiotic pathway of phosphate uptake via arbuscular mycorrhizal fungi (AMF) is evolutionarily ancient and today occurs in natural and agricultural ecosystems alike. Plants capable of this symbiosis can obtain up to all of the phosphate from symbiotic fungi, and this offers potential means to develop crops less dependent on unsustainable P fertilizers. Here, we review the mechanisms and insights gleaned from the fine-tuned signal exchanges that orchestrate the intimate mutualistic symbiosis between plants and AMF. As the currency of trade, nutrients have signaling functions beyond being the nutritional goal of mutualism. We propose that such signaling roles and metabolic reprogramming may represent commitments for a mutualistic symbiosis that act across the stages of symbiosis development.
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Affiliation(s)
- Chai Hao Chiu
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Uta Paszkowski
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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41
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Morin E, Miyauchi S, San Clemente H, Chen ECH, Pelin A, de la Providencia I, Ndikumana S, Beaudet D, Hainaut M, Drula E, Kuo A, Tang N, Roy S, Viala J, Henrissat B, Grigoriev IV, Corradi N, Roux C, Martin FM. Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina. THE NEW PHYTOLOGIST 2019; 222:1584-1598. [PMID: 30636349 DOI: 10.1111/nph.15687] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/28/2018] [Indexed: 05/21/2023]
Abstract
Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology. We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation. The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.
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Affiliation(s)
- Emmanuelle Morin
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
| | - Shingo Miyauchi
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Adrian Pelin
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | | | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Mathieu Hainaut
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
| | - Elodie Drula
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Nianwu Tang
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Sébastien Roy
- Agronutrition- rue Pierre et Marie Curie, Immeuble BIOSTEP, 31670, Labège, France
| | - Julie Viala
- Agronutrition- rue Pierre et Marie Curie, Immeuble BIOSTEP, 31670, Labège, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13007, Marseille, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Francis M Martin
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forest University, 100080, Beijing, China
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Le Marquer M, Bécard G, Frei Dit Frey N. Arbuscular mycorrhizal fungi possess a CLAVATA3/embryo surrounding region-related gene that positively regulates symbiosis. THE NEW PHYTOLOGIST 2019; 222:1030-1042. [PMID: 30554405 DOI: 10.1111/nph.15643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/07/2018] [Indexed: 05/03/2023]
Abstract
The arbuscular mycorrhizal (AM) symbiosis is a beneficial association established between land plants and the members of a subphylum of fungi, the Glomeromycotina. How the two symbiotic partners regulate their association is still enigmatic. Secreted fungal peptides are candidates for regulating this interaction. We searched for fungal peptides with similarities with known plant signalling peptides. We identified CLAVATA (CLV)/EMBRYO SURROUNDING REGION (ESR)-RELATED PROTEIN (CLE) genes in phylogenetically distant AM fungi: four Rhizophagus species and one Gigaspora species. These CLE genes encode a signal peptide for secretion and the conserved CLE C-terminal motif. They seem to be absent in the other fungal clades. Rhizophagus irregularis and Gigaspora rosea CLE genes (RiCLE1 and GrCLE1) are transcriptionally induced in symbiotic vs asymbiotic conditions. Exogenous application of synthetic RiCLE1 peptide on Medicago truncatula affects root architecture, by slowing the apical growth of primary roots and stimulating the formation of lateral roots. In addition, pretreatment of seedlings with RiCLE1 peptide stimulates mycorrhization. Our findings demonstrate for the first time that in addition to plants and nematodes, AM fungi also possess CLE genes. These results pave the way for deciphering new mechanisms by which AM fungi modulate plant cellular responses during the establishment of AM symbiosis.
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Affiliation(s)
- Morgane Le Marquer
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France
| | - Guillaume Bécard
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France
| | - Nicolas Frei Dit Frey
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France
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Schmitz AM, Pawlowska TE, Harrison MJ. A short LysM protein with high molecular diversity from an arbuscular mycorrhizal fungus, Rhizophagus irregularis. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2018.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M, Marton T, Ropars J, Grigoriev IV, Hainaut M, Henrissat B, Roux C, Martin F, Corradi N. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. THE NEW PHYTOLOGIST 2018; 220:1161-1171. [PMID: 29355972 DOI: 10.1111/nph.14989] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/03/2017] [Indexed: 05/20/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.
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Affiliation(s)
- Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jessica Noel
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Philippe Charron
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Camille St-Onge
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - John Giorgi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Manuela Krüger
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Timea Marton
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jeanne Ropars
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Francis Martin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
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Strullu-Derrien C, Selosse MA, Kenrick P, Martin FM. The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. THE NEW PHYTOLOGIST 2018; 220:1012-1030. [PMID: 29573278 DOI: 10.1111/nph.15076] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/14/2018] [Indexed: 05/05/2023]
Abstract
Contents Summary 1012 I. Introduction 1013 II. The mycorrhizal symbiosis at the dawn and rise of the land flora 1014 III. From early land plants to early trees: the origin of roots and true mycorrhizas 1016 IV. The diversification of the AM symbiosis 1019 V. The ECM symbiosis 1021 VI. The recently evolved ericoid and orchid mycorrhizas 1023 VII. Limits of paleontological vs genetic approaches and perspectives 1023 Acknowledgements 1025 References 1025 SUMMARY: The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The occurrence of mycorrhizas is now well established in c. 85% of extant plants, yet the geological record of these associations is sparse. Fossils preserved under exceptional conditions provide tantalizing glimpses into the evolutionary history of mycorrhizas, showing the extent of their occurrence and aspects of their evolution in extinct plants. The fossil record has important roles to play in establishing a chronology of when key fungal associations evolved and in understanding their importance in ecosystems through time. Together with calibrated phylogenetic trees, these approaches extend our understanding of when and how groups evolved in the context of major environmental change on a global scale. Phylogenomics furthers this understanding into the evolution of different types of mycorrhizal associations, and genomic studies of both plants and fungi are shedding light on how the complex set of symbiotic traits evolved. Here we present a review of the main phases of the evolution of mycorrhizal interactions from palaeontological, phylogenetic and genomic perspectives, with the aim of highlighting the potential of fossil material and a geological perspective in a cross-disciplinary approach.
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Affiliation(s)
- Christine Strullu-Derrien
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Interactions Arbres/Microorganismes, Laboratoire d'excellence ARBRE, Centre INRA-Lorraine, Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, 54280, Champenoux, France
| | - Marc-André Selosse
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, 75005, Paris, France
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Francis M Martin
- Interactions Arbres/Microorganismes, Laboratoire d'excellence ARBRE, Centre INRA-Lorraine, Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, 54280, Champenoux, France
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Lanfranco L, Fiorilli V, Gutjahr C. Partner communication and role of nutrients in the arbuscular mycorrhizal symbiosis. THE NEW PHYTOLOGIST 2018; 220:1031-1046. [PMID: 29806959 DOI: 10.1111/nph.15230] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/11/2018] [Indexed: 05/20/2023]
Abstract
Contents Summary 1031 I. Introduction 1031 II. Interkingdom communication enabling symbiosis 1032 III. Nutritional and regulatory roles for key metabolites in the AM symbiosis 1035 IV. The plant-fungus genotype combination determines the outcome of the symbiosis 1039 V. Perspectives 1039 Acknowledgements 1041 References 1041 SUMMARY: The evolutionary and ecological success of the arbuscular mycorrhizal (AM) symbiosis relies on an efficient and multifactorial communication system for partner recognition, and on a fine-tuned and reciprocal metabolic regulation of each symbiont to reach an optimal functional integration. Besides strigolactones, N-acetylglucosamine-derivatives released by the plant were recently suggested to trigger fungal reprogramming at the pre-contact stage. Remarkably, N-acetylglucosamine-based diffusible molecules also are symbiotic signals produced by AM fungi (AMF) and clues on the mechanisms of their perception by the plant are emerging. AMF genomes and transcriptomes contain a battery of putative effector genes that may have conserved and AMF- or host plant-specific functions. Nutrient exchange is the key feature of AM symbiosis. A mechanism of phosphate transport inside fungal hyphae has been suggested, and first insights into the regulatory mechanisms of root colonization in accordance with nutrient transfer and status were obtained. The recent discovery of the dependency of AMF on fatty acid transfer from the host has offered a convincing explanation for their obligate biotrophism. Novel studies highlighted the importance of plant and fungal genotypes for the outcome of the symbiosis. These findings open new perspectives for fundamental research and application of AMF in agriculture.
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Affiliation(s)
- Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125, Torino, Italy
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125, Torino, Italy
| | - Caroline Gutjahr
- Plant Genetics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Emil Ramann Str. 4, D-85354, Freising, Germany
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Beaudet D, Chen ECH, Mathieu S, Yildirir G, Ndikumana S, Dalpé Y, Séguin S, Farinelli L, Stajich JE, Corradi N. Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi. DNA Res 2018; 25:217-227. [PMID: 29211832 PMCID: PMC5909441 DOI: 10.1093/dnares/dsx051] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/09/2017] [Indexed: 11/24/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish symbioses with the vast majority of land plants. To date, generation of AMF coding information has been limited to model genera that grow well axenically; Rhizoglomus and Gigaspora. Meanwhile, data on the functional gene repertoire of most AMF families is non-existent. Here, we provide primary large-scale transcriptome data from eight poorly studied AMF species (Acaulospora morrowiae, Diversispora versiforme, Scutellospora calospora, Racocetra castanea, Paraglomus brasilianum, Ambispora leptoticha, Claroideoglomus claroideum and Funneliformis mosseae) using ultra-low input ribonucleic acid (RNA)-seq approaches. Our analyses reveals that quiescent spores of many AMF species harbour a diverse functional diversity and solidify known evolutionary relationships within the group. Our findings demonstrate that RNA-seq data obtained from low-input RNA are reliable in comparison to conventional RNA-seq experiments. Thus, our methodology can potentially be used to deepen our understanding of fungal microbial function and phylogeny using minute amounts of RNA material.
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Affiliation(s)
- Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Stephanie Mathieu
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada
| | - Sylvie Séguin
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada
| | - Laurent Farinelli
- Fasteris SA, Chemin du Pont-du-Centenaire 109, Geneva 1228, Switzerland
| | - Jason E Stajich
- Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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Chen M, Arato M, Borghi L, Nouri E, Reinhardt D. Beneficial Services of Arbuscular Mycorrhizal Fungi - From Ecology to Application. FRONTIERS IN PLANT SCIENCE 2018; 9:1270. [PMID: 30233616 PMCID: PMC6132195 DOI: 10.3389/fpls.2018.01270] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/10/2018] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhiza (AM) is the most common symbiotic association of plants with microbes. AM fungi occur in the majority of natural habitats and they provide a range of important ecological services, in particular by improving plant nutrition, stress resistance and tolerance, soil structure and fertility. AM fungi also interact with most crop plants including cereals, vegetables, and fruit trees, therefore, they receive increasing attention for their potential use in sustainable agriculture. Basic research of the past decade has revealed the existence of a dedicated recognition and signaling pathway that is required for AM. Furthermore, recent evidence provided new insight into the exchange of nutritional benefits between the symbiotic partners. The great potential for application of AM has given rise to a thriving industry for AM-related products for agriculture, horticulture, and landscaping. Here, we discuss new developments in these fields, and we highlight future potential and limits toward the use of AM fungi for plant production.
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Affiliation(s)
- Min Chen
- Department of Biology, Rte Albert Gockel, University of Fribourg, Fribourg, Switzerland
| | | | - Lorenzo Borghi
- Institute of Plant and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Eva Nouri
- Department of Biology, Rte Albert Gockel, University of Fribourg, Fribourg, Switzerland
| | - Didier Reinhardt
- Department of Biology, Rte Albert Gockel, University of Fribourg, Fribourg, Switzerland
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Pawlowska TE, Gaspar ML, Lastovetsky OA, Mondo SJ, Real-Ramirez I, Shakya E, Bonfante P. Biology of Fungi and Their Bacterial Endosymbionts. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:289-309. [PMID: 30149793 DOI: 10.1146/annurev-phyto-080417-045914] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Heritable symbioses, in which endosymbiotic bacteria (EB) are transmitted vertically between host generations, are an important source of evolutionary novelties. A primary example of such symbioses is the eukaryotic cell with its EB-derived organelles. Recent discoveries suggest that endosymbiosis-related innovations can be also found in associations formed by early divergent fungi in the phylum Mucoromycota with heritable EB from two classes, Betaproteobacteria and Mollicutes. These symbioses exemplify novel types of host-symbiont interactions. Studies of these partnerships fuel theoretical models describing mechanisms that stabilize heritable symbioses, control the rate of molecular evolution, and enable the establishment of mutualisms. Lastly, by altering host phenotypes and metabolism, these associations represent an important instrument for probing the basic biology of the Mucoromycota hosts, which remain one of the least explored filamentous fungi.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, New York 14853, USA;
| | - Maria L Gaspar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Olga A Lastovetsky
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Evaniya Shakya
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, New York 14853, USA;
| | - Paola Bonfante
- Department of Life Sciences & Systems Biology, University of Torino, 10125 Torino, Italy
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50
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Choi J, Summers W, Paszkowski U. Mechanisms Underlying Establishment of Arbuscular Mycorrhizal Symbioses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:135-160. [PMID: 29856935 DOI: 10.1146/annurev-phyto-080516-035521] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Most land plants engage in mutually beneficial interactions with arbuscular mycorrhizal (AM) fungi, the fungus providing phosphate and nitrogen in exchange for fixed carbon. During presymbiosis, both organisms communicate via oligosaccharides and butenolides. The requirement for a rice chitin receptor in symbiosis-induced lateral root development suggests that cell division programs operate in inner root tissues during both AM and nodule symbioses. Furthermore, the identification of transcription factors underpinning arbuscule development and degeneration reemphasized the plant's regulatory dominance in AM symbiosis. Finally, the finding that AM fungi, as lipid auxotrophs, depend on plant fatty acids (FAs) to complete their asexual life cycle revealed the basis for fungal biotrophy. Intriguingly, lipid metabolism is also central for asexual reproduction and interaction of the fungal sister clade, the Mucoromycotina, with endobacteria, indicative of an evolutionarily ancient role for lipids in fungal mutualism.
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Affiliation(s)
- Jeongmin Choi
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
| | - William Summers
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
| | - Uta Paszkowski
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
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