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Maillard F, Kohler A, Morin E, Hossann C, Miyauchi S, Ziegler-Devin I, Gérant D, Angeli N, Lipzen A, Keymanesh K, Johnson J, Barry K, Grigoriev IV, Martin FM, Buée M. Functional genomics gives new insights into the ectomycorrhizal degradation of chitin. New Phytol 2023; 238:845-858. [PMID: 36702619 DOI: 10.1111/nph.18773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Ectomycorrhizal (EcM) fungi play a crucial role in the mineral nitrogen (N) nutrition of their host trees. While it has been proposed that several EcM species also mobilize organic N, studies reporting the EcM ability to degrade N-containing polymers, such as chitin, remain scarce. Here, we assessed the capacity of a representative collection of 16 EcM species to acquire 15 N from 15 N-chitin. In addition, we combined genomics and transcriptomics to identify pathways involved in exogenous chitin degradation between these fungal strains. Boletus edulis, Imleria badia, Suillus luteus, and Hebeloma cylindrosporum efficiently mobilized N from exogenous chitin. EcM genomes primarily contained genes encoding for the direct hydrolysis of chitin. Further, we found a significant relationship between the capacity of EcM fungi to assimilate organic N from chitin and their genomic and transcriptomic potentials for chitin degradation. These findings demonstrate that certain EcM fungal species depolymerize chitin using hydrolytic mechanisms and that endochitinases, but not exochitinases, represent the enzymatic bottleneck of chitin degradation. Finally, this study shows that the degradation of exogenous chitin by EcM fungi might be a key functional trait of nutrient cycling in forests dominated by EcM fungi.
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Affiliation(s)
- François Maillard
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Christian Hossann
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | | | - Dominique Gérant
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, 54000, Nancy, France
| | - Nicolas Angeli
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
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52
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Liu H, Jacquemyn H, Yu S, Chen W, He X, Huang Y. Mycorrhizal diversity and community composition in co-occurring Cypripedium species. Mycorrhiza 2023; 33:107-118. [PMID: 36396734 DOI: 10.1007/s00572-022-01095-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Orchids commonly rely on mycorrhizal fungi to obtain the necessary resources for seed germination and growth. Whereas most photosynthetic orchids typically associate with so-called rhizoctonia fungi to complete their life cycle, there is increasing evidence that other fungi may be involved as well and that the mycorrhizal communities associated with orchids may be more diverse. Coexisting orchid species also tend to associate with different fungi to reduce competition for similar resources and to increase long-term population viability. However, few studies have related the mycorrhizal communities in the rhizosphere to communities found in the roots of closely related coexisting orchid species. In this study, we used high-throughput sequencing to investigate the diversity and community composition of orchid mycorrhizal fungi in the roots and the rhizosphere of four Cypripedium species growing in forests in Northeast China. The results showed that the investigated Cypripedium species associated with a wide variety of fungi including members of Tulasnellaceae, Psathyrellaceae, and Herpotrichiellaceae, whereas members of Russulaceae, Cortinariaceae, Thelephoraceae, and Herpotrichiellaceae showed high abundance in rhizosphere soils. The diversity of fungi detected in the rhizosphere soil was much higher than that in the roots. The observed variation in fungal communities in Cypripedium roots was not related to forest site or orchid species. On the other hand, variation in mycorrhizal communities of rhizosphere soil was significantly related to sampling site. These results indicate that orchid mycorrhizal communities in the rhizosphere display considerable variation among sites and that orchids use only a subset of the locally available fungi. Future studies focusing on the fine-scale spatial distribution of orchid mycorrhizal fungi and more detailed assessments of local environmental conditions will provide novel insights into the mechanisms explaining variation of fungal communities in both orchid roots and the rhizosphere.
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Affiliation(s)
- Huanchu Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiangxi, 332900, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, B-3001, Belgium
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, B-3001, Belgium
| | - Shuai Yu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Wei Chen
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China.
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China.
- Key Laboratory of Forest Ecology and Management, Chinese Academy of Sciences, Shenyang, 110016, China.
| | - Xingyuan He
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
- Key Laboratory of Forest Ecology and Management, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yanqing Huang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
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53
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Mleczko P, Hilszczańska D, Karpowicz F, Kozak M, Leonardi M, Rosa-Gruszecka A, Tereba A, Pacioni G. Tuber wenchuanense, a holarctic truffle with a wide range of host plants and description of its ectomycorrhiza with spruce. Mycorrhiza 2023; 33:45-58. [PMID: 36637489 PMCID: PMC9938020 DOI: 10.1007/s00572-022-01097-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Tuber wenchuanense ascomata (Ascomycota, Pezizales), a species originally described from Sichuan (China), were found in the Tatra Mountains in southern Poland. The purpose of this work was to (i) report and assess the first case of the holarctic natural distribution of a Tuber species, (ii) amend the original description of the species, (iii) summarize data on its host plants and (iv) describe its ectomycorrhiza. Specimens of Tuber wenchuanense from the Tatra Mountains were studied morphologically and molecularly. The ectomycorrhiza of this truffle with Picea abies was described for the first time. The distribution of T. wenchuanense, which is reconstructed based on sequences deposited in the publicly available nucleotide sequence databases, makes it the first holarctic Tuber species and the one with the northernmost habitat. In fact, its habitat is confined mainly to mountain coniferous forests and alpine and arctic tundra; although, according to known observations, the fruiting bodies of T. wenchuanense can be produced only under conifers. Based on the sequences of the internal transcribed spacer, this species appears to have low genetic variability over the entire distribution range. The phylogenetic tree showed that some of the unidentified phylotypes from the Rufum clade found by other researchers belong to T. wenchuanense. The ecological implications of these findings are discussed.
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Affiliation(s)
- Piotr Mleczko
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
| | - Dorota Hilszczańska
- Department of Forest Ecology, Forest Research Institute, Sękocin Stary, Braci Leśnej 3, 05-090, Raszyn, Poland
| | - Filip Karpowicz
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
| | | | - Marco Leonardi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Aleksandra Rosa-Gruszecka
- Department of Forest Ecology, Forest Research Institute, Sękocin Stary, Braci Leśnej 3, 05-090, Raszyn, Poland.
| | - Anna Tereba
- Department of Forest Ecology, Forest Research Institute, Sękocin Stary, Braci Leśnej 3, 05-090, Raszyn, Poland
| | - Giovanni Pacioni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
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54
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Rich M. Phylogenomics reveal that plants colonized land together with their fungal symbiotic partners. C R Biol 2023; 346:1-11. [PMID: 37254793 DOI: 10.5802/crbiol.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 06/01/2023]
Abstract
Most extant land plants establish a mutually beneficial relationship with soil fungi called mycorrhizal symbiosis. From their partners, plants get access to mineral nutrient and water resources transported via a fungal network that acts like an extension of their root systems. Using genetic and molecular tools, we showed that distant plant species use similar molecular mechanisms during the symbiosis. This similarity suggests that those mechanisms were inherited from their last common ancestor, a lineage that emerged from an aquatic environment 450 million years ago. Thus, this plant fungal interaction could have helped the first land plants without structures adapted to soil exploration to survive and colonize this new environment.
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55
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Zeng Z, Liu Y, Feng XY, Li SX, Jiang XM, Chen JQ, Shao ZQ. The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network. Plant Commun 2023; 4:100429. [PMID: 36071667 PMCID: PMC9860192 DOI: 10.1016/j.xplc.2022.100429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Arbuscular mycorrhizal symbiosis (AMS) is an ancient plant-fungus relationship that is widely distributed in terrestrial plants. The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes. However, the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly understood. In this study, a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato, an emerging AMS model. The annotation of the tomato genome was improved by a multiple-platform sequencing strategy. A total of 3,174 protein-coding genes were upregulated during AMS, 42% of which were alternatively spliced. Comparative-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant angiosperms. Seven additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host plants. However, these orthogroups were absent or not induced in monocots and/or non-AMS hosts, suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory module. Additionally, we detected 587 lncRNAs, ten miRNAs, and 146 circRNAs that responded to AMS, which were incorporated to establish a tomato AMS-responsive, competing RNA-responsive endogenous RNA (ceRNA) network. Finally, a tomato symbiotic transcriptome database (TSTD, https://efg.nju.edu.cn/TSTD) was constructed to serve as a resource for deep deciphering of the AMS regulatory network. These results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.
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Affiliation(s)
- Zhen Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xing-Yu Feng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Sai-Xi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xing-Mei Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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56
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Kalapchieva S, Tringovska I, Bozhinova R, Kosev V, Hristeva T. Population Response of Rhizosphere Microbiota of Garden Pea Genotypes to Inoculation with Arbuscular Mycorrhizal Fungi. Int J Mol Sci 2023; 24:1119. [PMID: 36674632 PMCID: PMC9866347 DOI: 10.3390/ijms24021119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
This study of a legume's rhizosphere in tripartite symbiosis focused on the relationships between the symbionts and less on the overall rhizosphere microbiome. We used an experimental model with different garden pea genotypes inoculated with AM fungi (Rhizophagus irregularis and with a mix of AM species) to study their influence on the population levels of main trophic groups of soil microorganisms as well as their structure and functional relationships in the rhizosphere microbial community. The experiments were carried out at two phenological cycles of the plants. Analyzes were performed according to classical methods: microbial population density defined as CUF/g a.d.s. and root colonization rate with AMF (%). We found a proven dominant effect of AMF on the densities of micromycetes and actinomycetes in the direction of reduction, suggesting antagonism, and on ammonifying, phosphate-solubilizing and free-living diazotrophic Azotobacter bacteria in the direction of stimulation, an indicator of mutualistic relationships. We determined that the genotype was decisive for the formation of populations of bacteria immobilizing mineral NH4+-N and bacteria Rhizobium. We reported significant two-way relationships between trophic groups related associated with soil nitrogen and phosphorus ions availability. The preserved proportions between trophic groups in the microbial communities were indicative of structural and functional stability.
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Affiliation(s)
- Slavka Kalapchieva
- Maritsa Vegetable Crops Research Institute, Agricultural Academy, 4003 Plovdiv, Bulgaria
| | - Ivanka Tringovska
- Maritsa Vegetable Crops Research Institute, Agricultural Academy, 4003 Plovdiv, Bulgaria
| | - Radka Bozhinova
- Tobacco and Tobacco Products Institute, Agricultural Academy, 4108 Plovdiv, Bulgaria
| | - Valentin Kosev
- Institute of Forage Crops, Agricultural Academy, 5800 Pleven, Bulgaria
| | - Tsveta Hristeva
- Tobacco and Tobacco Products Institute, Agricultural Academy, 4108 Plovdiv, Bulgaria
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Suetsugu K, Hirota SK, Hsu TC, Kurogi S, Imamura A, Suyama Y. Monotropastrum kirishimense (Ericaceae), a new mycoheterotrophic plant from Japan based on multifaceted evidence. J Plant Res 2023; 136:3-18. [PMID: 36445504 PMCID: PMC9832082 DOI: 10.1007/s10265-022-01422-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/26/2022] [Indexed: 05/10/2023]
Abstract
Due to their reduced morphology, non-photosynthetic plants have been one of the most challenging groups to delimit to species level. The mycoheterotrophic genus Monotropastrum, with the monotypic species M. humile, has been a particularly taxonomically challenging group, owing to its highly reduced vegetative and root morphology. Using integrative species delimitation, we have focused on Japanese Monotropastrum, with a special focus on an unknown taxon with rosy pink petals and sepals. We investigated its flowering phenology, morphology, molecular identity, and associated fungi. Detailed morphological investigation has indicated that it can be distinguished from M. humile by its rosy pink tepals and sepals that are generally more numerous, elliptic, and constantly appressed to the petals throughout its flowering period, and by its obscure root balls that are unified with the surrounding soil, with root tips that hardly protrude. Based on genome-wide single-nucleotide polymorphisms, molecular data has provided clear genetic differentiation between this unknown taxon and M. humile. Monotropastrum humile and this taxon are associated with different Russula lineages, even when they are sympatric. Based on this multifaceted evidence, we describe this unknown taxon as the new species M. kirishimense. Assortative mating resulting from phenological differences has likely contributed to the persistent sympatry between these two species, with distinct mycorrhizal specificity.
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Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan.
- The Institute for Advanced Research, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Tian-Chuan Hsu
- Botanical Garden Division, Taiwan Forestry Research Institute, No. 53, Nanhai Rd., Taipei, 100, Taiwan
| | - Shuichi Kurogi
- Miyazaki Prefectural Museum of Nature and History, 2-4-4, Jingû, Miyazaki, 880-0053, Japan
| | - Akio Imamura
- Hokkaido University of Education, Sapporo, 002-8501, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
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58
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Tremble K, Hoffman JI, Dentinger BTM. Contrasting continental patterns of adaptive population divergence in the holarctic ectomycorrhizal fungus Boletus edulis. New Phytol 2023; 237:295-309. [PMID: 36200167 DOI: 10.1111/nph.18521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome-wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis, a globally distributed species complex with broad ecological amplitude. By whole-genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome-wide differentiation and to identify the adaptive processes shaping global population structure. We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62-2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene-Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation. Our study uncovers striking patterns of genome-wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.
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Affiliation(s)
- Keaton Tremble
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
- Natural History Museum of Utah, Salt Lake City, UT, 84108, USA
| | - J I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, 33501, Germany
| | - Bryn T M Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
- Natural History Museum of Utah, Salt Lake City, UT, 84108, USA
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59
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Che X, Wang S, Ren Y, Xie X, Hu W, Chen H, Tang M. A Eucalyptus Pht1 Family Gene EgPT8 Is Essential for Arbuscule Elongation of Rhizophagus irregularis. Microbiol Spectr 2022; 10:e0147022. [PMID: 36227088 PMCID: PMC9769952 DOI: 10.1128/spectrum.01470-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
The majority of vascular flowering plants can establish arbuscular mycorrhizal (AM) symbiosis with AM fungi. These associations contribute to plant health and plant growth against various environmental stresses. In the mutualistic endosymbiosis, the AM fungi deliver phosphate (Pi) to the host root through highly branched hyphae called arbuscules. The molecular mechanisms of Pi transfer from AM fungi to the plant have been determined, which are dominated by AM-specific Pi transporters belonging to the PHOSPHATE TRANSPORTER 1 (Pht1) family within the subfamily I. However, it is unknown whether Pht1 family proteins are involved in other regulations in AM symbiosis. Here, we report that the expression of EgPT8 is specifically activated by AM fungus Rhizophagus irregularis and is localized in root cortical cells containing arbuscules. Interestingly, knockdown of EgPT8 function does not affect the Eucalyptus grandis growth, total phosphorous (P) concentration, and arbuscule formation; however, the size of mature arbuscules was significantly suppressed in the RNAi-EgPT8 lines. Heterogeneous expression of EgPT4, EgPT5, and EgPT8 in the Medicago truncatula mutant mtpt4-2 indicates that EgPT4 and EgPT5 can fully complement the defects of mutant mtpt4-2 in mycorrhizal Pi uptake and arbuscule formation, while EgPT8 cannot complement the defective AM phenotype of the mtpt4-2 mutant. Based on our results, we propose that the AM fungi-specific subfamily I transporter EgPT8 has novel functions and is essential to arbuscule elongation. IMPORTANCE Arbuscular mycorrhizal (AM) formation in host root cortical cells is initiated by exchanges of diffusible molecules, among which Pi uptake is known as the important feature of AM fungi on symbiosis functioning. Over the last two decades, it has been repeatedly proven that most vascular plants harbor two or more AM-specific Pht1 proteins; however, there is no direct evidence regarding the potential link among these Pi transporters at the symbiotic interface. This work revealed a novel function of a structurally conserved protein involved in lateral arbuscule development. In total, we confirmed that three AM-specific Pht1 family proteins are nonredundant in Eucalyptus grandis and that EgPT8 is responsible for fungal arbuscule elongation of Rhizophagus irregularis.
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Affiliation(s)
- 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, People’s Republic of 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, People’s Republic of 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, People’s Republic of China
| | - 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, People’s Republic of 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, People’s Republic of 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, People’s Republic of 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, People’s Republic of China
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60
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Sahraei SE, Sánchez-García M, Montoliu-Nerin M, Manyara D, Bergin C, Rosendahl S, Rosling A. Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum. Mycorrhiza 2022; 32:361-371. [PMID: 36161535 PMCID: PMC9560946 DOI: 10.1007/s00572-022-01091-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/13/2022] [Indexed: 06/02/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis of AM fungi has long been restricted to species and strains that can be maintained under controlled conditions that facilitate collection of biological samples. There is some evidence suggesting that AM fungi can adapt to culture resulting in phenotypic and possibly also genotypic changes in the fungi. In this study, we used field isolated spores of AM fungi and identified them as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two representative spores using DNA sequences of 19 and 22 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum than in the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic and comparative genomic analysis and to study genomic variation in natural populations of these important plant symbionts.
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Affiliation(s)
| | - 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
| | - Merce Montoliu-Nerin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - David Manyara
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Claudia Bergin
- Microbial Single Cell Genomics Facility, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Søren Rosendahl
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
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Yamato M, Yamada H, Maeda T, Yamamoto K, Kusakabe R, Orihara T. Clonal spore populations in sporocarps of arbuscular mycorrhizal fungi. Mycorrhiza 2022; 32:373-385. [PMID: 35767052 DOI: 10.1007/s00572-022-01086-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Some arbuscular mycorrhizal (AM) fungal species known to form sporocarps (i.e., aggregations of spores) are polyphyletic in two orders, Glomerales and Diversisporales. Spore clusters (sporocarp-like structures) often formed in pot cultures or in vitro conditions are supposed to be clonal populations, while sporocarps in natural habitats with a fungal peridium are morphologically similar to those of epigeous sexual (zygosporic) sporocarps of Endogone species. Thus, in this study, we explored the genetics of sporocarpic spores of two AM fungi with a view to possibilities of clonal or sexual reproduction during sporocarps formation. To examine these possibilities, we investigated single-nucleotide polymorphisms (SNPs) in reduced genomic libraries of spores isolated from sporocarps molecularly identified as Rhizophagus irregularis and Diversispora epigaea. In addition, partial sequences of the MAT locus HD2 gene of R. irregularis were phylogenetically analyzed to determine the nuclear status of the spores. We found that most SNPs were shared among the spores isolated from each sporocarp in both species. Furthermore, all HD2 sequences from spores isolated from three R. irregularis sporocarps were identical. These results indicate that those sporocarps comprise clonal spores. Therefore, sporocarps with clonal spores may have different functions than sexual reproduction, such as massive spore production or spore dispersal via mycophagy.
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Affiliation(s)
- Masahide Yamato
- Faculty of Education, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
| | - Hiroki Yamada
- Graduate School of Education, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Taro Maeda
- Institute for Advanced Biosciences, Keio University, Kakuganji 246-2, Mizukami, Tsuruoka, Yamagata, 997-0052, Japan
| | - Kohei Yamamoto
- Tochigi Prefectural Museum, 2-2 Mutsumi-cho, Utsunomiya, Tochigi, 320-0865, Japan
| | - Ryota Kusakabe
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Chiba, 271-8510, Japan
| | - Takamichi Orihara
- Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Odawara, Kanagawa, 250-0031, Japan
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Yoo S, Cho Y, Park KH, Lim YW. Exploring fine-scale assembly of ectomycorrhizal fungal communities through phylogenetic and spatial distribution analyses. Mycorrhiza 2022; 32:439-449. [PMID: 35861929 DOI: 10.1007/s00572-022-01088-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Ectomycorrhizal fungi (EMF) form symbiotic relationship with the roots of host plants. EMF communities are composed of highly diverse species; however, how they are assembled has been a long-standing question. In this study, we investigated from a phylogenetic perspective how EMF communities assemble on Pinus densiflora seedlings at different spatial scales (i.e., seedling scale and root tip scale). P. densiflora seedlings were collected from different habitats (i.e., disturbed areas and mature forests), and their EMF communities were investigated by morphotype sequencing and next-generation sequencing (NGS). To infer assembly mechanisms, phylogenetic relatedness within the community (i.e., phylogenetic structure) was estimated and spatial distribution of EMF root tips was analyzed. The EMF communities on pine seedlings were largely different between the two habitats. Phylogenetically restricted lineages (Amphinema, /suillus-rhizopogon) were abundant in the disturbed areas, whereas species from diverse lineages were abundant in the mature forests (Russula, Sebacina, /tomentella-thelephora, etc.). In the disturbed areas, phylogenetically similar EMF species were aggregated at the seedling scale, suggesting that disturbance acts as a powerful abiotic filter. However, phylogenetically similar species were spatially segregated from each other at the root tip scale, indicating limiting similarity. In the mature forest seedlings, no distinct phylogenetic signals were detected at both seedling and root tip scale. Collectively, our results suggest that limiting similarity may be an important assembly mechanism at the root tip scale and that assembly mechanisms can vary across habitats and spatial scales.
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Affiliation(s)
- Shinnam Yoo
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, South Korea
| | - Yoonhee Cho
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, South Korea
| | - Ki Hyeong Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, South Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, South Korea.
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Huang R, Li Z, Shen X, Choi J, Cao Y. The Perspective of Arbuscular Mycorrhizal Symbiosis in Rice Domestication and Breeding. Int J Mol Sci 2022; 23:ijms232012383. [PMID: 36293238 PMCID: PMC9604486 DOI: 10.3390/ijms232012383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/21/2022] Open
Abstract
In nature, symbiosis with arbuscular mycorrhizal (AM) fungi contributes to sustainable acquisition of phosphorus and other elements in over 80% of plant species; improving interactions with AM symbionts may mitigate some of the environmental problems associated with fertilizer application in grain crops such as rice. Recent developments of high-throughput genome sequencing projects of thousands of rice cultivars and the discovery of the molecular mechanisms underlying AM symbiosis suggest that interactions with AM fungi might have been an overlooked critical trait in rice domestication and breeding. In this review, we discuss genetic variation in the ability of rice to form AM symbioses and how this might have affected rice domestication. Finally, we discuss potential applications of AM symbiosis in rice breeding for more sustainable agriculture.
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Affiliation(s)
- Renliang Huang
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang 330200, China
| | - Zheng Li
- State Key Laboratory of Agriculture Microbiology, Hubei Hongshan Laboratory, Huazhong Agriculture University, Wuhan 430000, China
| | - Xianhua Shen
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang 330200, China
| | - Jeongmin Choi
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | - Yangrong Cao
- State Key Laboratory of Agriculture Microbiology, Hubei Hongshan Laboratory, Huazhong Agriculture University, Wuhan 430000, China
- Correspondence:
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64
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Řezáčová V, Michalová T, Řezáč M, Gryndler M, Duell EB, Wilson GWT, Heneberg P. The root-associated arbuscular mycorrhizal fungal assemblages of exotic alien plants are simplified in invaded distribution ranges, but dominant species are retained: A trans-continental perspective. Environ Microbiol Rep 2022; 14:732-741. [PMID: 35924424 DOI: 10.1111/1758-2229.13108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 05/09/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) provide crucial support for the establishment of plants in novel environments. We hypothesized that the OTU/genus richness and diversity of soil- and root-associated AMF associated with alien plant species in their exotic ranges are lower than those in their native ranges. We examined the root-associated and soil-dwelling AMF of 11 invasive plant species in their native and exotic ranges in the United States and Europe by DNA sequencing of the ITS2 locus. Examined root-associated AMF assemblages were simplified, which manifested as the loss of several AMF genera in the exotic ranges of the plants. These fungal assemblages were also characterized by greater dominance and simplification of the fungal assemblages. The dominant fungal genera were present regardless of whether their host plants were in their native or exotic ranges. Interestingly, both the native and invaded soils hosted diverse local AMF assemblages. Therefore, alien plant invasions were not limited to soils with low AMF diversity. Some AMF taxa could be context-dependent passengers rather than drivers of alien plant invasions. Further studies should identify functions of AMF missing or less abundant in roots of plants growing in exotic ranges.
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Affiliation(s)
- Veronika Řezáčová
- Crop Research Institute, Prague, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Milan Řezáč
- Crop Research Institute, Prague, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Milan Gryndler
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ústí nad Labem, Ústí nad Labem, Czech Republic
| | - Eric B Duell
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, Oklahoma, USA
- Kansas Biological Survey and Center for Ecological Research, Lawrence, Kansas, USA
| | - Gail W T Wilson
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Petr Heneberg
- Third Faculty of Medicine, Charles University, Prague, Czech Republic
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65
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Alguacil MDM, Schlaeppi K, López-García Á, van der Heijden MGA, Querejeta JI. Contrasting Responses of Arbuscular Mycorrhizal Fungal Families to Simulated Climate Warming and Drying in a Semiarid Shrubland. Microb Ecol 2022; 84:941-944. [PMID: 34608508 DOI: 10.1007/s00248-021-01886-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
We carried out a 4-year manipulative field experiment in a semiarid shrubland in southeastern Spain to assess the impacts of experimental warming (W), rainfall reduction (RR), and their combination (W + RR) on the composition and diversity of arbuscular mycorrhizal fungal (AMF) communities in rhizosphere soil of H. syriacum and G. struthium shrubs using single-molecule real-time (SMRT) DNA sequencing. Across climate treatments, we encountered 109 AMF operational taxonomic units (OTUs) that were assigned to four families: Glomeraceae (93.94%), Gigasporaceae (2.19%), Claroideoglomeraceae (1.95%), and Diversisporaceae (1.92%). AMF community composition and diversity at OTU level were unaffected by the climate manipulation treatments, except for a significant decrease in AMF OTU richness in the W treatment relative to the control. However, we found a significant decrease of AMF family richness in all climate manipulation treatments relative to the control treatment. Members of the Gigasporaceae and Diversisporaceae families appeared to be highly vulnerable to intensification of heat and drought stress, as their abundances decreased by 67% and 77%, respectively, in the W + RR treatment relative to current ambient conditions. In contrast, the relative abundance and dominance of the Glomeraceae family within the AMF community increased significantly under the W + RR treatment, with Glomeraceae being the indicator family for the W + RR treatment. The interaction between warming and rainfall reduction had a significant effect on AMF community structure at family level. These findings provide new insights to help in the conservation of the soil biodiversity facing climate change in dryland ecosystems.
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Affiliation(s)
- María Del Mar Alguacil
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain.
| | - Klaus Schlaeppi
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Álvaro López-García
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508TB, Utrecht, The Netherlands
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - José Ignacio Querejeta
- Department of Soil and Water Conservation, CSIC-Centro de Edafología Y Biología Aplicada del Segura, Campus de Espinardo, P.O. Box 164, 30100, Murcia, Spain
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Hackel J, Henkel TW, Moreau P, De Crop E, Verbeken A, Sà M, Buyck B, Neves M, Vasco‐Palacios A, Wartchow F, Schimann H, Carriconde F, Garnica S, Courtecuisse R, Gardes M, Manzi S, Louisanna E, Roy M. Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions. New Phytol 2022; 236:698-713. [PMID: 35811430 PMCID: PMC9795906 DOI: 10.1111/nph.18365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae. We inferred a supertree of 3285 operational taxonomic units, representing worldwide internal transcribed spacer sequences. We reconstructed biogeographic history and diversification and identified lineages in the Neotropics and adjacent Patagonia. The ectomycorrhizal Russulaceae have a tropical African origin. The oldest lineages in tropical South America, most with African sister groups, date to the mid-Eocene, possibly coinciding with a boreotropical migration corridor. There were several transatlantic dispersal events from Africa more recently. Andean and Central American lineages mostly have north-temperate origins and are associated with North Andean uplift and the general north-south biotic interchange across the Panama isthmus, respectively. Patagonian lineages have Australasian affinities. Diversification rates in tropical South America and other tropical areas are lower than in temperate areas. Neotropical Russulaceae have multiple biogeographic origins since the mid-Eocene involving dispersal and co-migration. Discontinuous distributions of host plants may explain low diversification rates of tropical lowland ectomycorrhizal fungi. Deeply diverging neotropical fungal lineages need to be better documented.
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Affiliation(s)
- Jan Hackel
- Royal Botanic Gardens, KewRichmond‐upon‐ThamesTW9 3AEUK
- Laboratoire Evolution et Diversité Biologique (UMR 5174)Université Toulouse III – Paul Sabatier/CNRS/IRD31062Toulouse cedex 9France
| | - Terry W. Henkel
- Department of Biological SciencesCalifornia State Polytechnic University, HumboldtArcataCA95521USA
| | - Pierre‐Arthur Moreau
- Faculté de Pharmacie, Laboratoire des Sciences Végétales et Fongiques (LGCgE, ER4)Université de Lille59006LilleFrance
| | - Eske De Crop
- Department of BiologyGhent University9000GentBelgium
| | | | - Mariana Sà
- Centro Universitário de João PessoaPB 58053‐000João PessoaBrazil
| | - Bart Buyck
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRSSorbonne Université, EPHE, Université des Antilles75231Paris cedex 05France
| | - Maria‐Alice Neves
- Departamento de BotânicaUniversidade Federal de Santa CatarinaSC 88040‐900FlorianópolisBrazil
| | - Aída Vasco‐Palacios
- Microbiología Ambiental–School of Microbiology, Laboratory of Taxonomy and Ecology of Fungi–Institute of BiologyUniversity of Antioquia050010MedellínColombia
| | - Felipe Wartchow
- Departamento de Sistemática e EcologiaUniversidade Federal da ParaíbaPB 58051‐970João PessoaBrazil
| | - Heidy Schimann
- UMR Ecologie des Forêts de GuyaneAgroParisTech/CIRAD/CNRS/Université des Antilles/Université de la Guyane/INRA97379Kourou cedexFrench Guiana
| | - Fabian Carriconde
- Institut Agronomique néo‐Calédonien (IAC), Equipe Sol & Végétations (SolVeg)BP1823998848NouméaNew Caledonia
| | - Sigisfredo Garnica
- Instituto de Bioquímica y MicrobiologíaUniversidad Austral de Chile5049000ValdiviaChile
| | - Régis Courtecuisse
- Faculté de Pharmacie, Laboratoire des Sciences Végétales et Fongiques (LGCgE, ER4)Université de Lille59006LilleFrance
| | - Monique Gardes
- Laboratoire Evolution et Diversité Biologique (UMR 5174)Université Toulouse III – Paul Sabatier/CNRS/IRD31062Toulouse cedex 9France
| | - Sophie Manzi
- Laboratoire Evolution et Diversité Biologique (UMR 5174)Université Toulouse III – Paul Sabatier/CNRS/IRD31062Toulouse cedex 9France
| | - Eliane Louisanna
- UMR Ecologie des Forêts de GuyaneAgroParisTech/CIRAD/CNRS/Université des Antilles/Université de la Guyane/INRA97379Kourou cedexFrench Guiana
| | - Mélanie Roy
- Laboratoire Evolution et Diversité Biologique (UMR 5174)Université Toulouse III – Paul Sabatier/CNRS/IRD31062Toulouse cedex 9France
- Instituto Franco‐Argentino para el Estudio del Clima y sus Impactos (UMI IFAECI/CNRS‐CONICET‐UBA‐IRD)Universidad de Buenos AiresC1428EGACiudad Autonoma de Buenos AiresArgentina
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Rasmussen PU, Abrego N, Roslin T, Öpik M, Sepp S, Blanchet FG, Huotari T, Hugerth LW, Tack AJM. Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic. New Phytol 2022; 236:671-683. [PMID: 35751540 PMCID: PMC9796444 DOI: 10.1111/nph.18342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change.
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Affiliation(s)
- Pil U. Rasmussen
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
- The National Research Centre for the Working Environment105 Lersø ParkalléDK‐2100CopenhagenDenmark
| | - Nerea Abrego
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
| | - Tomas Roslin
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
- Department of EcologySwedish University of Agricultural SciencesBox 7044UppsalaSE‐750 07Sweden
| | - Maarja Öpik
- Department of BotanyUniversity of Tartu40 Lai StreetTartu51005Estonia
| | - Siim‐Kaarel Sepp
- Department of BotanyUniversity of Tartu40 Lai StreetTartu51005Estonia
| | - F. Guillaume Blanchet
- Département de Biologie, Faculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
- Département de Mathématiques, Faculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
- Département des Sciences de la Santé Communautaire, Faculté de Médecine et des Sciences de la SantéUniversité de Sherbrooke3001 12 Avenue NordSherbrookeQCJ1H 5N4Canada
| | - Tea Huotari
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
| | - Luisa W. Hugerth
- Department of Molecular, Tumor and Cell Biology, Science for Life Laboratory, Center for Translational Microbiome ResearchKarolinska InstitutetSE‐171 65SolnaSweden
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
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Puginier C, Keller J, Delaux PM. Plant-microbe interactions that have impacted plant terrestrializations. Plant Physiol 2022; 190:72-84. [PMID: 35642902 PMCID: PMC9434271 DOI: 10.1093/plphys/kiac258] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/09/2022] [Indexed: 05/30/2023]
Abstract
Plants display a tremendous diversity of developmental and physiological features, resulting from gains and losses of functional innovations across the plant phylogeny. Among those, the most impactful have been undoubtedly the ones that allowed plant terrestrializations, the transitions from an aquatic to a terrestrial environment. Although the embryophyte terrestrialization has been particularly scrutinized, others occurred across the plant phylogeny with the involvement of mutualistic symbioses as a common theme. Here, we review the current pieces of evidence supporting that the repeated colonization of land by plants has been facilitated by interactions with mutualistic symbionts. In that context, we detail two of these mutualistic symbioses: the arbuscular mycorrhizal symbiosis in embryophytes and the lichen symbiosis in chlorophyte algae. We suggest that associations with bacteria should be revisited in that context, and we propose that overlooked symbioses might have facilitated the emergence of other land plant clades.
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Affiliation(s)
- Camille Puginier
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
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Guo Y, Zhang H, Bao Y, Tan H, Liu X, Rahman ZU. Distribution characteristics of soil AM fungi community in soft sandstone area. J Environ Manage 2022; 316:115193. [PMID: 35550954 DOI: 10.1016/j.jenvman.2022.115193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/22/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
To explore the diversity and distribution characteristics of soil arbuscular mycorrhizae fungi (AMF) communities in the soft sandstone area, thirteen arsenic sandstone rock samples were collected from three planting plots (SI, SII and SIII) and one bare control plot (CK), separately. The sampling locations are as follows: the top of the slope (denoted by the number 1), sunny slope (2), shady slope (3) and gully bottom (4). These samples were then tested with an Illumina HiSeq PE250 high-throughput sequencing platform. Experimental results show that the SIII4 sample (from the gully bottom of the SIII plot) has the highest moisture content of 9.1%, while the CK sample in the control plot has lowest moisture content. SI2 has the highest pH of 9.58 and CK has the lowest pH of 8.73. SII1 has the highest available phosphorus (AP) content of 9.61 mg/kg, while SII3 has the lowest AP content of 2.29 mg/kg. Furthermore, SI2 has the highest NH4-N content of 11.24 mg/kg, while SII1 has the lowest NH4-N of 4.09 mg/kg. SII1 has the highest available potassium (AK) content of 48.92 mg/kg and CK has the lowest AK content of 1.82 mg/kg. In the observed-species index reflecting AMF genetic diversity, SI1 differences significantly from SII4 and SIII3 (P < 0.05). In the Shannon index, SI1 is significantly different from SI2, SI3, SI4; SII2 is significantly different from SII3; SI2, SI4, SII1 and SII3 are quite different from CK (P < 0.05). The dominant genera of AMF in these plots include Glomus (17.24%-65.53%), Scutellospora (0.04%-67.38%), Septoglomus (2.83%-43.03%) and Kamienskia (0.64%-46.38%). The dominant genera of AMF vary significantly between sunny slope and shady slope. Positive correlation exists between soil NH4-N and the AM fungal community structure. There are prominent positive correlations exist among genetic diversity index chao1, observed-species, pH and AP (P < 0.05), and obviously negative correlation between observed species and AK (P < 0.05). The research findings on the distribution characteristics of AM fungus community in the arsenic sandstone plot and their relationship with environmental factors can help with arsenic sandstone management in other similar areas.
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Affiliation(s)
- Yangnan Guo
- MOE Key Laboratory of Thermo-Fluid Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Life Sciences, Inner Mongolia University, Hohhot, 010018, China; State Key Laboratory of Water Resource Protection and Utilization in Coal Mining, Beijing, 100000, China; China Energy Group, Shendong Coal Group Technology Research Institute, Ordos, 017200, China
| | - Huandi Zhang
- School of Life Sciences, Inner Mongolia University, Hohhot, 010018, China
| | - Yuying Bao
- School of Life Sciences, Inner Mongolia University, Hohhot, 010018, China; State Key Laboratory of Water Resource Protection and Utilization in Coal Mining, Beijing, 100000, China.
| | - Houzhang Tan
- MOE Key Laboratory of Thermo-Fluid Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xianghong Liu
- China Coal Research Institute, Beijing, 100013, China
| | - Zia Ur Rahman
- MOE Key Laboratory of Thermo-Fluid Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
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Suetsugu K, Okada H, Hirota SK, Suyama Y. Evolutionary history of mycorrhizal associations between Japanese Oxygyne (Thismiaceae) species and Glomeraceae fungi. New Phytol 2022; 235:836-841. [PMID: 35445414 DOI: 10.1111/nph.18163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Hyogo, Japan
| | - Hidehito Okada
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Hyogo, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
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71
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Kodama K, Rich MK, Yoda A, Shimazaki S, Xie X, Akiyama K, Mizuno Y, Komatsu A, Luo Y, Suzuki H, Kameoka H, Libourel C, Keller J, Sakakibara K, Nishiyama T, Nakagawa T, Mashiguchi K, Uchida K, Yoneyama K, Tanaka Y, Yamaguchi S, Shimamura M, Delaux PM, Nomura T, Kyozuka J. An ancestral function of strigolactones as symbiotic rhizosphere signals. Nat Commun 2022. [PMID: 35803942 DOI: 10.1101/2021.08.20.457034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
In flowering plants, strigolactones (SLs) have dual functions as hormones that regulate growth and development, and as rhizosphere signaling molecules that induce symbiosis with arbuscular mycorrhizal (AM) fungi. Here, we report the identification of bryosymbiol (BSB), an SL from the bryophyte Marchantia paleacea. BSB is also found in vascular plants, indicating its origin in the common ancestor of land plants. BSB synthesis is enhanced at AM symbiosis permissive conditions and BSB deficient mutants are impaired in AM symbiosis. In contrast, the absence of BSB synthesis has little effect on the growth and gene expression. We show that the introduction of the SL receptor of Arabidopsis renders M. paleacea cells BSB-responsive. These results suggest that BSB is not perceived by M. paleacea cells due to the lack of cognate SL receptors. We propose that SLs originated as AM symbiosis-inducing rhizosphere signaling molecules and were later recruited as plant hormone.
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Affiliation(s)
- Kyoichi Kodama
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Mélanie K Rich
- LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Akiyoshi Yoda
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Shota Shimazaki
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Xiaonan Xie
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Kohki Akiyama
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Yohei Mizuno
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Aino Komatsu
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yi Luo
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hidemasa Suzuki
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hiromu Kameoka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Cyril Libourel
- LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | | | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | | | | | - Kenichi Uchida
- Department of Biosciences, Teikyo University, Tochigi, Japan
| | - Kaori Yoneyama
- Graduate School of Agriculture, Ehime University, Ehime, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Pierre-Marc Delaux
- LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France.
| | - Takahito Nomura
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan.
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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72
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Lebreton A, Tang N, Kuo A, LaButti K, Andreopoulos W, Drula E, Miyauchi S, Barry K, Clum A, Lipzen A, Mousain D, Ng V, Wang R, Dai Y, Henrissat B, Grigoriev IV, Guerin-Laguette A, Yu F, Martin FM. Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk-cap (Lactarius) mushrooms. New Phytol 2022; 235:306-319. [PMID: 35383395 DOI: 10.1111/nph.18143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved symbiosis-related traits among ectomycorrhizal fungal species, but the molecular mechanisms underlying host specificity remain poorly known. We sequenced and compared the genomes of seven species of milk-cap fungi (Lactarius, Russulales) with contrasting host specificity. We also compared these genomes with those of symbiotic and saprotrophic Russulales species, aiming to identify genes involved in their ecology and host specificity. The size of Lactarius genomes is significantly larger than other Russulales species, owing to a massive accumulation of transposable elements and duplication of dispensable genes. As expected, their repertoire of genes coding for plant cell wall-degrading enzymes is restricted, but they retained a substantial set of genes involved in microbial cell wall degradation. Notably, Lactarius species showed a striking expansion of genes encoding proteases, such as secreted ectomycorrhiza-induced sedolisins. A high copy number of genes coding for small secreted LysM proteins and Lactarius-specific lectins were detected, which may be linked to host specificity. This study revealed a large diversity in the genome landscapes and gene repertoires within Russulaceae. The known host specificity of Lactarius symbionts may be related to mycorrhiza-induced species-specific genes, including secreted sedolisins.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
| | - Nianwu Tang
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Elodie Drula
- CNRS, Aix-Marseille Université, Marseille, 13288, France
- USC1408 AFMB, INRAE, Marseille, 13288, France
| | - Shingo Miyauchi
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Alicia Clum
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | | | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Ran Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alexis Guerin-Laguette
- Mycotree C/- Southern Woods Nursery, 1002 Robinsons Road, RD8, Christchurch, 7678, New Zealand
| | - Fuqiang Yu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Francis M Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
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Chen K, Huang G, Li Y, Zhang X, Lei Y, Li Y, Xiong J, Sun Y. Illumina MiSeq Sequencing Reveals Correlations among Fruit Ingredients, Environmental Factors, and AMF Communities in Three Lycium Barbarum Producing Regions of China. Microbiol Spectr 2022; 10:e0229321. [PMID: 35234495 PMCID: PMC8941938 DOI: 10.1128/spectrum.02293-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
The symbiotic relationship of arbuscular mycorrhizal fungi (AMF) is important for Lycium barbarum, a highly nutritious and medicinal crop. However, the influence of environmental factors on AMF communities remains largely elusive. Based on MiSeq sequencing, we analyzed AMF communities in rhizosphere soils of L. barbarum with growth synchronization in three typical L. barbarum cultivation sites in China. The Zhongning region has poor soils with a high richness of AMF communities. Geographical environmental variances lead to differences in AMF communities which in turn affects the active ingredients of L. barbarum fruit. Furthermore, different genera of AMF showed significant correlations with environmental factors and fruit ingredients. The three genera, Claroideoglomus, Dominikia, and Funneliformis correlated to environmental factors and fruits ingredients in a similar manner affecting the whole sugar (TS) and flavonoids (FLA) contents in the fruits of L. barbarum. Also, these showed a significantly positive correlation with soil pH. This fact was unknown so far due to different soil acidity/alkalinity in different studies. IMPORTANCE The climatic and ecological environment is a complex phenomenon, involving various environmental factors that regulate the diversity and population distribution structure of AMF communities affecting plant growth, crop composition, and yield. Current studies on the effects of environmental factors on AMF communities have mainly focused on soil conditions and host plants. Fewer studies have been conducted on the correlation between temperature, enzyme activity, plant fruiting, and AMF communities. The present study investigated the diversity of AMF communities and the influence of environmental factors on their distribution patterns, which showed similar effects on some AMF species. The results suggest that screening AMF fungicides that meet the target may significantly help soil restoration reducing the use of chemical fertilizers and a large amount of human and material resources.
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Affiliation(s)
- Kaili Chen
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Gang Huang
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Yuekun Li
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Xinrui Zhang
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Yonghui Lei
- Department of Plant Protection, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Yang Li
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Jie Xiong
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
| | - Yanfei Sun
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, Xinjiang, China
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Jiang Y, Hu X, Yuan Y, Guo X, Chase MW, Ge S, Li J, Fu J, Li K, Hao M, Wang Y, Jiao Y, Jiang W, Jin X. The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions. BMC Plant Biol 2022; 22:179. [PMID: 35392808 PMCID: PMC8988336 DOI: 10.1186/s12870-022-03573-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/01/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND To illustrate the molecular mechanism of mycoheterotrophic interactions between orchids and fungi, we assembled chromosome-level reference genome of Gastrodia menghaiensis (Orchidaceae) and analyzed the genomes of two species of Gastrodia. RESULTS Our analyses indicated that the genomes of Gastrodia are globally diminished in comparison to autotrophic orchids, even compared to Cuscuta (a plant parasite). Genes involved in arbuscular mycorrhizae colonization were found in genomes of Gastrodia, and many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids. The highly expressed genes for fatty acid and ammonium root transporters suggest that fungi receive material from orchids, although most raw materials flow from the fungi. Many nuclear genes (e.g. biosynthesis of aromatic amino acid L-tryptophan) supporting plastid functions are expanded compared to photosynthetic orchids, an indication of the importance of plastids even in totally mycoheterotrophic species. CONCLUSION Gastrodia menghaiensis has the smallest proteome thus far among angiosperms. Many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids.
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Affiliation(s)
- Yan Jiang
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China
| | - Xiaodi Hu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Yuan Yuan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, Chaoyang, Beijing, 100700, China
| | - Xuelian Guo
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China
| | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, Surrey, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Song Ge
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China
| | - Jianwu Li
- Xishuanbanan Tropical Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Jinlong Fu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Kui Li
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Meng Hao
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Yiming Wang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Yuannian Jiao
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China.
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75
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Li MH, Liu KW, Li Z, Lu HC, Ye QL, Zhang D, Wang JY, Li YF, Zhong ZM, Liu X, Yu X, Liu DK, Tu XD, Liu B, Hao Y, Liao XY, Jiang YT, Sun WH, Chen J, Chen YQ, Ai Y, Zhai JW, Wu SS, Zhou Z, Hsiao YY, Wu WL, Chen YY, Lin YF, Hsu JL, Li CY, Wang ZW, Zhao X, Zhong WY, Ma XK, Ma L, Huang J, Chen GZ, Huang MZ, Huang L, Peng DH, Luo YB, Zou SQ, Chen SP, Lan S, Tsai WC, Van de Peer Y, Liu ZJ. Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy. Nat Plants 2022; 8:373-388. [PMID: 35449401 PMCID: PMC9023349 DOI: 10.1038/s41477-022-01127-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 03/09/2022] [Indexed: 05/12/2023]
Abstract
To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.
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Affiliation(s)
- Ming-He Li
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hsiang-Chia Lu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Qin-Liang Ye
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Diyang Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie-Yu Wang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yu-Feng Li
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Zhi-Ming Zhong
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Xuedie Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xia Yu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiong-De Tu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bin Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Hao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing-Yu Liao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Ting Jiang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Hong Sun
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinliao Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan-Qiong Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Ai
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun-Wen Zhai
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sha-Sha Wu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhuang Zhou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Lin Wu
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Fu Lin
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jui-Ling Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Ying Li
- Department of Applied Chemistry, National Pingtung University, Pingtung, Taiwan
| | | | | | | | - Xiao-Kai Ma
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liang Ma
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Huang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gui-Zhen Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ming-Zhong Huang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Laiqiang Huang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Dong-Hui Peng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shuang-Quan Zou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shi-Pin Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan.
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, China.
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76
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Alarcón S, Tereucán G, Cornejo P, Contreras B, Ruiz A. Metabolic and antioxidant effects of inoculation with arbuscular mycorrhizal fungi in crops of flesh-coloured Solanum tuberosum treated with fungicides. J Sci Food Agric 2022; 102:2270-2280. [PMID: 34625964 DOI: 10.1002/jsfa.11565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 09/15/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Solanum tuberosum tubers have higher content of phenolic compounds such as hydroxycinnamic acid derivatives (HCAD) and anthocyanins in coloured genotypes. The use of fungicides for crops is common, but there are few studies regarding the interaction of fungicides and arbuscular mycorrhizal fungi (AMF). Here, the AMF-plant interactions and the metabolic responses of three potato genotypes with different tuber colorations (VR808, CB2011-509 and CB2011-104) inoculated with Claroideoglomus claroideum (CC), Claroideoglomus lamellosum (HMC26) or Funneliformis mosseae (HMC7) were studied together with the use of the fungicides MONCUT (M) and ReflectXtra (R). Mycorrhizal traits, phenolic compound profiles and antioxidant activity (AA) were evaluated. RESULTS Despite only two HCADs being identified, with 5-caffeolquinic acid the most abundant, four anthocyanins were detected only in purple potato genotypes. The anthocyanin and HCAD profiles, as well as AA, showed that the CB2011-104 genotype had better characteristics than the other genotypes, while VR808 and CB509 showed similar responses. The responses were dependent on the specific combinations of genotype, fungicide and the AMF strain, and generally showed better responses when colonized by AMFs. CONCLUSION The three potato genotypes had differential responses depending on the inoculated AMFs and the fungicide applied before sowing, where the optimal combinations for antioxidant response, mycorrhization degree and performance were HMC26/R for VR808, HMC7/M for CB2011-509 and HMC26/M for CB2011-104. Our results suggest the existence of functional compatibility that can be registered as beneficial effects even at the genotypic level of the host regarding a specific AMF strain. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Sebastián Alarcón
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental, CIMYSA, Universidad de La Frontera, Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Technological Bioresource Nucleus BIOREN-UFRO, Universidad de La Frontera, Temuco, Chile
| | - Gonzalo Tereucán
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental, CIMYSA, Universidad de La Frontera, Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Technological Bioresource Nucleus BIOREN-UFRO, Universidad de La Frontera, Temuco, Chile
| | - Pablo Cornejo
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental, CIMYSA, Universidad de La Frontera, Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Technological Bioresource Nucleus BIOREN-UFRO, Universidad de La Frontera, Temuco, Chile
| | - Boris Contreras
- Novaseed Ltda. and Papas Arcoiris Ltda., Puerto Varas, Chile
| | - Antonieta Ruiz
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental, CIMYSA, Universidad de La Frontera, Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Technological Bioresource Nucleus BIOREN-UFRO, Universidad de La Frontera, Temuco, Chile
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77
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Looney B, Miyauchi S, Morin E, Drula E, Courty PE, Kohler A, Kuo A, LaButti K, Pangilinan J, Lipzen A, Riley R, Andreopoulos W, He G, Johnson J, Nolan M, Tritt A, Barry KW, Grigoriev IV, Nagy LG, Hibbett D, Henrissat B, Matheny PB, Labbé J, Martin FM. Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom-forming fungi. New Phytol 2022; 233:2294-2309. [PMID: 34861049 DOI: 10.1111/nph.17892] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyperdiverse Russulaceae. We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales, of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae, Gloeopeniophorella convolvens. The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell wall-degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE 'nests', or dense aggregations of TEs. Some PCWDEs have been retained or even expanded, mostly in a species-specific manner. The genome of G. convolvens possesses some characteristics of ECM genomes (e.g. loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters). Functional specialization in ECM decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch.
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Affiliation(s)
- Brian Looney
- Department of Biology, Clark University, Worcester, MA, 01610, USA
| | - Shingo Miyauchi
- UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54000, France
| | - Emmanuelle Morin
- UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54000, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Univ., Marseille, 13009, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), INRAE, Marseille, 13009, France
| | - Pierre Emmanuel Courty
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Université de Bourgogne, Université de Bourgogne Franche- Comté, Dijon, 25000, France
| | - Annegret Kohler
- UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54000, France
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Robert Riley
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Guifen He
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Matt Nolan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Andrew Tritt
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kerrie W Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, 6726, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1053, Hungary
| | - David Hibbett
- Department of Biology, Clark University, Worcester, MA, 01610, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Univ., Marseille, 13009, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, TN, 37830, USA
| | - Francis M Martin
- UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54000, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
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78
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Heller WP, Carrara JE. Multiplex qPCR assays to distinguish individual species of arbuscular mycorrhizal fungi from roots and soil. Mycorrhiza 2022; 32:155-164. [PMID: 35133475 DOI: 10.1007/s00572-022-01069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Currently, root colonization measurements of arbuscular mycorrhizal fungi (AMF) require staining and microscopy, and species-level identification of the fungi by such observations is not possible. Here, we present novel multiplex real-time PCR assays targeting the glomalin genes of 11 different species of AMF commonly found in temperate agricultural soils, which independently detect and measure the abundance of these fungi using DNA extracts from soil and or root tissue. The availability of these tools will not only increase throughput in determining levels of root colonization but can provide species-specific levels of root colonization from a single sample. This will help to establish which AMF species, or combinations of different species, provide the most benefits to crops, and will aid in the development of AMF for use as biofertilizers.
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Affiliation(s)
- Wade P Heller
- USDA Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA, USA.
| | - Joseph E Carrara
- USDA Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA, USA
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79
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Minasiewicz J, Krawczyk E, Znaniecka J, Vincenot L, Zheleznaya E, Korybut-Orlowska J, Kull T, Selosse MA. Weak population spatial genetic structure and low infraspecific specificity for fungal partners in the rare mycoheterotrophic orchid Epipogium aphyllum. J Plant Res 2022; 135:275-293. [PMID: 34993702 PMCID: PMC8894228 DOI: 10.1007/s10265-021-01364-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 12/19/2021] [Indexed: 06/02/2023]
Abstract
Some plants abandoned photosynthesis and developed full dependency on fungi for nutrition. Most of the so-called mycoheterotrophic plants exhibit high specificity towards their fungal partners. We tested whether natural rarity of mycoheterotrophic plants and usual small and fluctuating population size make their populations more prone to genetic differentiation caused by restricted gene flow and/or genetic drift. We also tested whether these genetic characteristics might in turn shape divergent fungal preferences. We studied the mycoheterotrophic orchid Epipogium aphyllum, addressing the joint issues of genetic structure of its populations over Europe and possible consequences for mycorrhizal specificity within the associated fungal taxa. Out of 27 sampled E. aphyllum populations, nine were included for genetic diversity assessment using nine nuclear microsatellites and plastid DNA. Population genetic structure was inferred based on the total number of populations. Individuals from 17 locations were included into analysis of genetic identity of mycorrhizal fungi of E. aphyllum based on barcoding by nuclear ribosomal DNA. Epipogium aphyllum populations revealed high genetic diversity (uHe = 0.562) and low genetic differentiation over vast distances (FST = 0.106 for nuclear microsatellites and FST = 0.156 for plastid DNA). Bayesian clustering analyses identified only two genetic clusters, with a high degree of admixture. Epipogium aphyllum genets arise from panmixia and display locally variable, but relatively high production of ramets, as shown by a low value of rarefied genotypic richness (Rr = 0.265). Epipogium aphyllum genotype control over partner selection was negligible as (1) we found ramets from a single genetic individual associated with up to 68% of the known Inocybe spp. associating with the plant species, (2) and partner identity did not show any geographic structure. The absence of mosaicism in the mycorrhizal specificity over Europe may be linked to preferential allogamous habit of E. aphyllum and significant gene flow, which tend to promote host generalism.
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Affiliation(s)
- Julita Minasiewicz
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Emilia Krawczyk
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Joanna Znaniecka
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307, Gdansk, Poland
| | - Lucie Vincenot
- Normandie University, UNIROUEN, INRAE, ECODIV, 76000, Rouen, France
| | - Ekaterina Zheleznaya
- Peoples' Friendship University of Russia, Podolskoye shosse 8/5, 115093, Moscow, Russia
- Timiryazev State Biological Museum, Malaya Gruzinskaya, 15, 123242, Moscow, Russia
| | - Joanna Korybut-Orlowska
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Tiiu Kull
- Estonian University of Life Sciences, Tartu, Estonia
| | - Marc-André Selosse
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308, Gdańsk, Poland
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 39 75005, Paris, France
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80
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Delavaux CS, Ramos RJ, Sturmer SL, Bever JD. Environmental identification of arbuscular mycorrhizal fungi using the LSU rDNA gene region: an expanded database and improved pipeline. Mycorrhiza 2022; 32:145-153. [PMID: 35099622 PMCID: PMC8907093 DOI: 10.1007/s00572-022-01068-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/18/2022] [Indexed: 05/02/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF; Glomeromycota) are difficult to culture; therefore, establishing a robust amplicon-based approach to taxa identification is imperative to describe AMF diversity. Further, due to low and biased sampling of AMF taxa, molecular databases do not represent the breadth of AMF diversity, making database matching approaches suboptimal. Therefore, a full description of AMF diversity requires a tool to determine sequence-based placement in the Glomeromycota clade. Nonetheless, commonly used gene regions, including the SSU and ITS, do not enable reliable phylogenetic placement. Here, we present an improved database and pipeline for the phylogenetic determination of AMF using amplicons from the large subunit (LSU) rRNA gene. We improve our database and backbone tree by including additional outgroup sequences. We also improve an existing bioinformatics pipeline by aligning forward and reverse reads separately, using a universal alignment for all tree building, and implementing a BLAST screening prior to tree building to remove non-homologous sequences. Finally, we present a script to extract AMF belonging to 11 major families as well as an amplicon sequencing variant (ASV) version of our pipeline. We test the utility of the pipeline by testing the placement of known AMF, known non-AMF, and Acaulospora sp. spore sequences. This work represents the most comprehensive database and pipeline for phylogenetic placement of AMF LSU amplicon sequences within the Glomeromycota clade.
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Affiliation(s)
- Camille S Delavaux
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA.
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092, Zurich, Switzerland.
| | - Robert J Ramos
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - Sidney L Sturmer
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, R. Antônio da Veiga 140Santa Catarina, Blumenau, 89030-903, Brazil
| | - James D Bever
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
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81
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Vasar M, Davison J, Sepp SK, Oja J, Al-Quraishy S, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Fraser L, Hiiesalu I, Hozzein WN, Koorem K, Moora M, Mucina L, Onipchenko V, Öpik M, Pärtel M, Phosri C, Vahter T, Tedersoo L, Zobel M. Global taxonomic and phylogenetic assembly of AM fungi. Mycorrhiza 2022; 32:135-144. [PMID: 35138435 DOI: 10.1007/s00572-022-01072-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly - in particular the roles of dispersal limitation and historical drivers - remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small-subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities - occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil.
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Affiliation(s)
- Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia.
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Siim-Kaarel Sepp
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Jane Oja
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - C Guillermo Bueno
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Juan José Cantero
- CONICET, Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía Y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés, Jules Verne University of Picardie, Amiens, France
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Inga Hiiesalu
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Kadri Koorem
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, Australia
- Department of Geography and Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonosov State University, Moscow, Russia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Meelis Pärtel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Tanel Vahter
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, Estonia
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Rivera Pérez CA, Janz D, Schneider D, Daniel R, Polle A. Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provides Insight into N Uptake from Forest Soil. mSystems 2022; 7:e0095721. [PMID: 35089084 PMCID: PMC8725588 DOI: 10.1128/msystems.00957-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/29/2021] [Indexed: 01/05/2023] Open
Abstract
Mineral nitrogen (N) is a major nutrient showing strong fluctuations in the environment due to anthropogenic activities. The acquisition and translocation of N to forest trees are achieved mainly by highly diverse ectomycorrhizal fungi (EMF) living in symbioses with their host roots. Here, we examined colonized root tips to characterize the entire root-associated fungal community by DNA metabarcoding-Illumina sequencing of the fungal internal transcribed spacer 2 (ITS2) molecular marker and used RNA sequencing to target metabolically active fungi and the plant transcriptome after N application. The study was conducted with beech (Fagus sylvatica L.), a dominant tree species in central Europe, grown in native forest soil. We demonstrate strong enrichment of 15N from nitrate or ammonium in the ectomycorrhizal roots by stable-isotope labeling. The relative abundance of the EMF members in the fungal community was correlated with their transcriptional abundances. The fungal metatranscriptome covered Kyoto Encyclopedia of Genes and Genomes (KEGG) and Eukaryotic Orthologous Groups (KOG) categories similar to those of model fungi and did not reveal significant changes related to N metabolization but revealed species-specific transcription patterns, supporting trait stability. In contrast to the resistance of the fungal metatranscriptome, the transcriptome of the host exhibited dedicated nitrate- or ammonium-responsive changes with the upregulation of transporters and enzymes required for nitrate reduction and a drastic enhancement of glutamine synthetase transcript levels, indicating the channeling of ammonium into the pathway for plant protein biosynthesis. Our results support that naturally assembled fungal communities living in association with the tree roots buffer nutritional signals in their own metabolism but do not shield plants from high environmental N levels. IMPORTANCE Although EMF are well known for their role in supporting tree N nutrition, the molecular mechanisms underlying N flux from the soil solution into the host through the ectomycorrhizal pathway remain widely unknown. Furthermore, ammonium and nitrate availability in the soil solution is subject to frequent oscillations that create a dynamic environment for the tree roots and associated microbes during N acquisition. Therefore, it is important to understand how root-associated mycobiomes and the tree roots handle these fluctuations. We studied the responses of the symbiotic partners by screening their transcriptomes after a sudden environmental flux of nitrate or ammonium. We show that the fungi and the host respond asynchronously, with the fungi displaying resistance to increased nitrate or ammonium and the host dynamically metabolizing the supplied N sources. This study provides insights into the molecular mechanisms of the symbiotic partners operating under N enrichment in a multidimensional symbiotic system.
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Affiliation(s)
- Carmen Alicia Rivera Pérez
- Forest Botany and Tree Physiology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Dennis Janz
- Forest Botany and Tree Physiology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
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83
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McDonald TR, Rizvi MF, Ruiter BL, Roy R, Reinders A, Ward JM. Posttranslational regulation of transporters important for symbiotic interactions. Plant Physiol 2022; 188:941-954. [PMID: 34850211 PMCID: PMC8825328 DOI: 10.1093/plphys/kiab544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/27/2021] [Indexed: 05/20/2023]
Abstract
Coordinated sharing of nutritional resources is a central feature of symbiotic interactions, and, despite the importance of this topic, many questions remain concerning the identification, activity, and regulation of transporter proteins involved. Recent progress in obtaining genome and transcriptome sequences for symbiotic organisms provides a wealth of information on plant, fungal, and bacterial transporters that can be applied to these questions. In this update, we focus on legume-rhizobia and mycorrhizal symbioses and how transporters at the symbiotic interfaces can be regulated at the protein level. We point out areas where more research is needed and ways that an understanding of transporter mechanism and energetics can focus hypotheses. Protein phosphorylation is a predominant mechanism of posttranslational regulation of transporters in general and at the symbiotic interface specifically. Other mechanisms of transporter regulation, such as protein-protein interaction, including transporter multimerization, polar localization, and regulation by pH and membrane potential are also important at the symbiotic interface. Most of the transporters that function in the symbiotic interface are members of transporter families; we bring in relevant information on posttranslational regulation within transporter families to help generate hypotheses for transporter regulation at the symbiotic interface.
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Affiliation(s)
- Tami R McDonald
- Department of Biology, St Catherine University, St Paul, Minnesota, USA
| | - Madeeha F Rizvi
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Bretton L Ruiter
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Rahul Roy
- Department of Biology, St Catherine University, St Paul, Minnesota, USA
| | - Anke Reinders
- College of Continuing and Professional Studies, University of Minnesota, St. Paul, Minnesota, USA
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- Author for communication:
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84
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Liu B, Dong P, Zhang X, Feng Z, Wen Z, Shi L, Xia Y, Chen C, Shen Z, Lian C, Chen Y. Identification and characterization of eight metallothionein genes involved in heavy metal tolerance from the ectomycorrhizal fungus Laccaria bicolor. Environ Sci Pollut Res Int 2022; 29:14430-14442. [PMID: 34617232 DOI: 10.1007/s11356-021-16776-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Metallothioneins (MTs) are small, cysteine-rich, heavy metal-binding proteins involved in metal homeostasis and detoxification. The increasing numbers of available genomic sequences of ectomycorrhizal (ECM) fungi enable deeper insights into the characteristics of MT genes in these fungi that form the most important symbiosis with the host trees in forest ecosystems. The aim of this study was to establish a comprehensive, genome-wide inventory of MT genes from the ECM fungus Laccaria bicolor. Eight MT genes in L. bicolor were cloned, and the expression patterns of their transcripts at various developmental stages based on expressed sequence tag (EST) counts were analyzed. The expression levels of four MTs were significantly increased during symbiosis stages. Quantitative real-time PCR (qRT-PCR) analysis revealed that transcripts of LbMT1 were dominant in free-living mycelia and strongly induced by excessive copper (Cu), cadmium (Cd), and hydrogen peroxide (H2O2). To determine whether these eight MTs functioned as metal chelators, we expressed them in the Cu- and Cd-sensitive yeast mutants, cup1∆ and yap1∆, respectively. All LbMT proteins provided similar levels of Cu(II) or Cd(II) tolerance, but did not affect by H2O2. Our findings provide novel data on the evolution and diversification of fungal MT gene duplicates, a valuable resource for understanding the vast array of biological processes in which these proteins are involved.
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Affiliation(s)
- Binhao Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pengcheng Dong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinzhe Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihang Feng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhugui Wen
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng, 224002, Jiangsu, China
| | - Liang Shi
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Xia
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunlan Lian
- Asian Natural Environmental Science Center, The University of Tokyo, 1-1-8 Midoricho, Nishitokyo, Tokyo, 188-0002, Japan
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China.
- Asian Natural Environmental Science Center, The University of Tokyo, 1-1-8 Midoricho, Nishitokyo, Tokyo, 188-0002, Japan.
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85
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Wu G, Miyauchi S, Morin E, Kuo A, Drula E, Varga T, Kohler A, Feng B, Cao Y, Lipzen A, Daum C, Hundley H, Pangilinan J, Johnson J, Barry K, LaButti K, Ng V, Ahrendt S, Min B, Choi IG, Park H, Plett JM, Magnuson J, Spatafora JW, Nagy LG, Henrissat B, Grigoriev IV, Yang ZL, Xu J, Martin FM. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales. New Phytol 2022; 233:1383-1400. [PMID: 34767630 DOI: 10.1111/nph.17858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.
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Affiliation(s)
- Gang Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (USC1408), INRAE, Marseille, 13009, France
| | - Torda Varga
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Bang Feng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Yang Cao
- Yunnan Institute of Tropic Crops, Jinghong, Yunnan, 666100, China
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Christopher Daum
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Hope Hundley
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Steven Ahrendt
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Byoungnam Min
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 02841, Seoul, Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 02841, Seoul, Korea
| | - Hongjae Park
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Jon Magnuson
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (USC1408), INRAE, Marseille, 13009, France
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13009, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Zhu-Liang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
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86
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Vohník M, Figura T, Réblová M. Hyaloscypha gabretae and Hyaloscypha gryndleri spp. nov. (Hyaloscyphaceae, Helotiales), two new mycobionts colonizing conifer, ericaceous and orchid roots. Mycorrhiza 2022; 32:105-122. [PMID: 35028741 DOI: 10.1007/s00572-021-01064-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/23/2021] [Indexed: 05/21/2023]
Abstract
Historically, Hyaloscypha s. lat. (Hyaloscyphaceae, Helotiales) included various saprobes with small apothecia formed on decaying plant matter, usually wood, that were defined by chemical and (ultra)structural aspects. However, recent molecular phylogenetic and resynthesis studies have narrowed the concept of the genus and shown that it contains several widely distributed species with unknown sexual morphs that form ectomycorrhizae, ericoid mycorrhizae, and mycothalli and also grow endophytically in plant roots and hypogeous ectomycorrhizal (EcM) fruitbodies (i.e., the historical Hymenoscyphus ericae aggregate). Hence, some of the sexually reproducing saprobic Hyaloscypha s. lat. and the symbionts belong to the monophyletic Hyaloscypha s. str. Here, we introduce two new root-symbiotic Hyaloscypha s. str. species, i.e., H. gabretae and H. gryndleri spp. nov. While the former was isolated only from ericaceous hosts (Vaccinium myrtillus from Southern Bohemia, Czechia and Calluna vulgaris from England, UK), the latter was obtained from a basidiomycetous EcM root tip of Picea abies (Pinaceae), roots of Pseudorchis albida (Orchidaceae), and hair roots of V. myrtillus from Southern Bohemia and C. vulgaris from England. Hyaloscypha gryndleri comprises two closely related lineages, suggesting ongoing speciation, possibly connected with the root-symbiotic life-style. Fungal isolates from ericaceous roots with sequences similar to H. gabretae and H. gryndleri have been obtained in Japan and in Canada and Norway, respectively, suggesting a wide and scattered distribution across the Northern Hemisphere. In a series of in vitro experiments, both new species failed to form orchid mycorrhizal structures in roots of P. albida and H. gryndleri repeatedly formed what morphologically corresponds to the ericoid mycorrhizal (ErM) symbiosis in hair roots of V. myrtillus, whereas the ErM potential of H. gabretae remained unresolved. Our results highlight the symbiotic plasticity of root-associated hyaloscyphoid mycobionts as well as our limited knowledge of their diversity and distribution, warranting further ecophysiological and taxonomic research of these important and widespread fungi.
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Affiliation(s)
- Martin Vohník
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Lesní 322, 25243, Průhonice, Czechia.
| | - Tomáš Figura
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 - CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, 75005, Paris, France
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12844, Prague, Czechia
| | - Martina Réblová
- Department of Taxonomy, Institute of Botany, Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czechia
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87
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Bai HY, Zhang AY, Mei Y, Xu M, Lu XL, Dai CC, Jia Y. Effects of ectomycorrhizal fungus bolete identity on the community assemblages of endofungal bacteria. Environ Microbiol Rep 2021; 13:852-861. [PMID: 34494716 DOI: 10.1111/1758-2229.13007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Ectomycorrhiza-associated bacteria, especially endofungal bacterial microbiota (EBM) in the fruiting body, play important roles in driving the establishment and function of ectomycorrhizae. However, the influence of ectomycorrhizal fungus bolete identity on their EBM is still unclear. We analysed the EBM of three different bolete fruiting body species on Thousand Island Lake, including Tylopilus felleus, Tylopilus areolatus and Boletus queletii, and compared them with their corresponding mycosphere soil bacterial microbiota by high-throughput sequencing. The EBM was classified into Bacillus, Pseudomonas, Burkholderia and Stenotrophomonas genera. Proteobacteria, Bacteroidetes and Acidobacteria were predominant in the EBM of bolete fruiting bodies as well as their mycosphere soil, while Firmicutes was significantly higher in the EBM. Moreover, the core microbiome (342 operational taxonomic units) of the EBM was shared among the three bolete fungal species. The relative abundances of gene families related to cell cycle control and nucleotide, coenzyme and lipid metabolism were significantly higher in the EBM than in the corresponding mycosphere soil bacterial microbiota, but there was no difference among the three different boletes. The results suggested that the host identity of ectomycorrhizal fungus boletes could affect the EBM, which might be mainly due to the selection of host fungi for the different functional EBM needed.
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Affiliation(s)
- Hong-Yan Bai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yan Mei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Man Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xiao-Lin Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yong Jia
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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88
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Cornell C, Kokkoris V, Turcu B, Dettman J, Stefani F, Corradi N. The arbuscular mycorrhizal fungus Rhizophagus irregularis harmonizes nuclear dynamics in the presence of distinct abiotic factors. Fungal Genet Biol 2021; 158:103639. [PMID: 34800644 DOI: 10.1016/j.fgb.2021.103639] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are widespread obligate root symbionts that assist plants in obtaining nutrients and protection against environmental stresses. In the model species Rhizophagus irregularis, heterokaryotic strains (AMF dikaryons) carry thousands of nuclei originating from two parental strains whose frequency varies depending on strains and host identity. Here, using digital droplet PCR, we demonstrate that surrounding abiotic factors (temperature, phosphorus, and pH) also change the nuclear dynamics of such strains in root organ cultures. Furthermore, when spatially separated portions of the AMF mycelium grow under different abiotic conditions, all the produced spores carry highly similar nuclear ratios. Overall, these findings demonstrate that abiotic stressors impact the nuclear organization of a widespread group of multinucleate plant symbionts, and reveal remarkable mechanisms of nuclear ratio harmonization across the mycelium in these prominent symbionts.
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Affiliation(s)
- Calvin Cornell
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, ON K1A 0C6, Canada
| | - Bianca Turcu
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Jeremy Dettman
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, ON K1A 0C6, Canada
| | - Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, ON K1A 0C6, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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Seasonal variations of arbuscular mycorrhizal fungal community in greenhouse soil under different rotation systems. Ying Yong Sheng Tai Xue Bao 2021; 32:4095-106. [PMID: 34898126 DOI: 10.13287/j.1001-9332.202111.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Soil samples were collected at the fallow period, flowering stage, and fruiting stage of tomato under tomato-melon (TM) and tomato-bean (TB) systems. Illumina MiSeq high-throughput pyrosequencing was performed to analyze the differences in AM fungal community between the two rotation systems. We further analyzed the key factors driving the changes in AM fungal diversity and community composition. Results showed that rotation with legume significantly altered the α-diversity of AM fungi. Shannon diversity and Pielou evenness of AM fungi under the TB system were 24.9% and 24.0% lower than that under TM system, respectively. Compared to the fallow period, richness, Shannon diversity, and phylogenetic diversity of AM fungi at the tomato flowering and fruiting stages decreased significantly by 55.6%-67.5%, 49.6%-51.5%, and 21.4%-23.7%, respectively. Rotation with legume (the TB system) promoted the relative abundance of Glomus in all the three sampling times, but reduced the relative abundance of Paraglomus and Archaeospora at the flowering and fruiting stages. Claroideoglomus was more abundant in soils under the TM system than that under the TB system at the fallow period, but the pattern was the opposite at the flowering stage. Ambispora, Diversispora, and Scutellospora were detected only in soil under the TB system. Results of permutational multivariate analysis of variance (PERMANOVA) and non-metric multidimensional scaling (NMDS) analysis showed that both rotation system and growing stage significantly affected the structure of AM fungal community. Soil moisture, pH, and Olsen-P were the predominant factors controlling the variations in the diversity and composition of AM fungal community. Results of structural equation modeling (SEM) further indicated that rotation system and growing stage affected the variations in AM fungal diversity and community structure indirectly via changing soil pH.
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90
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Van Geel M, Aavik T, Ceulemans T, Träger S, Mergeay J, Peeters G, van Acker K, Zobel M, Koorem K, Honnay O. The role of genetic diversity and arbuscular mycorrhizal fungal diversity in population recovery of the semi-natural grassland plant species Succisa pratensis. BMC Ecol Evol 2021; 21:200. [PMID: 34740329 PMCID: PMC8570031 DOI: 10.1186/s12862-021-01928-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Ecosystem restoration is as a critical tool to counteract the decline of biodiversity and recover vital ecosystem services. Restoration efforts, however, often fall short of meeting their goals. Although functionally important levels of biodiversity can significantly contribute to the outcome of ecosystem restoration, they are often overlooked. One such important facet of biodiversity is within-species genetic diversity, which is fundamental to population fitness and adaptation to environmental change. Also the diversity of arbuscular mycorrhizal fungi (AMF), obligate root symbionts that regulate nutrient and carbon cycles, potentially plays a vital role in mediating ecosystem restoration outcome. In this study, we investigated the relative contribution of intraspecific population genetic diversity, AMF diversity, and their interaction, to population recovery of Succisa pratensis, a key species of nutrient poor semi natural grasslands. We genotyped 180 individuals from 12 populations of S. pratensis and characterized AMF composition in their roots, using microsatellite markers and next generation amplicon sequencing, respectively. We also investigated whether the genetic makeup of the host plant species can structure the composition of root-inhabiting AMF communities. RESULTS Our analysis revealed that population allelic richness was strongly positively correlated to relative population growth, whereas AMF richness and its interaction with population genetic diversity did not significantly contribute. The variation partitioning analysis showed that, after accounting for soil and spatial variables, the plant genetic makeup explained a small but significant part of the unique variation in AMF communities. CONCLUSIONS Our results confirm that population genetic diversity can contribute to population recovery, highlighting the importance of within-species genetic diversity for the success of restoration. We could not find evidence, however, that population recovery benefits from the presence of more diverse AMF communities. Our analysis also showed that the genetic makeup of the host plant structured root-inhabiting AMF communities, suggesting that the plant genetic makeup may be linked to genes that control symbiosis development.
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Affiliation(s)
- Maarten Van Geel
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001, Heverlee, Belgium.
| | - Tsipe Aavik
- Institute of Ecology and Earth Sciences, University of Tartu, 51005, Tartu, Estonia
| | - Tobias Ceulemans
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001, Heverlee, Belgium
| | - Sabrina Träger
- Institute of Ecology and Earth Sciences, University of Tartu, 51005, Tartu, Estonia
- Institute of Biology, Geobotany and Botanical Garden, Martin-Luther-University Halle-Wittenberg, Große Steinstr. 79/80, 06108, Halle (Saale), Germany
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium
- Evolution and Biodiversity Conservation, Ecology, KU Leuven, Charles Deberiotstraat 32, Box 2439, 3000, Leuven, Belgium
| | - Gerrit Peeters
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001, Heverlee, Belgium
| | - Kasper van Acker
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001, Heverlee, Belgium
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, 51005, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, 51005, Tartu, Estonia
| | - Olivier Honnay
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001, Heverlee, Belgium
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91
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Kemppainen M, Pardo A. Nucleus-directed fluorescent reporter system for promoter studies in the ectomycorrhizal fungus Laccaria bicolor. J Microbiol Methods 2021; 190:106341. [PMID: 34610385 DOI: 10.1016/j.mimet.2021.106341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022]
Abstract
Currently ectomycorrhizal research suffers from a lack of molecular tools specifically adapted to study gene expression in fungal symbionts. Considering that, we designed pReNuK, a cloning vector for transcriptional promoter studies in the ectomycorrhizal basidiomycete Laccaria bicolor. The pReNuK vector offers the use of a nuclear localizing and chromatin incorporating histone H2B-mCherry fluorescent reporter protein and it is specifically optimized for efficient transgene expression in Laccaria. Moreover, pReNuK is designed to work in concert with Agrobacterium-mediated transformation under hygromycin B resistance selection. The functionality of the pReNuK reporter system was tested with the constitutive Laccaria glyceraldehyde 3-phosphate dehydrogenase gene promoter and further validated with the nitrogen source regulated nitrate reductase gene promoter. The expression of the nucleus-directed H2B-mCherry reporter is highly stable in time. Moreover, the transformation of Laccaria with pReNuK and the expression of the reporter do not have negative effects on the growth of the fungus. The pReNuK offers a novel tool for studying in vivo gene expression regulation in Laccaria, the leading fungal model for ectomycorrhizal research.
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Affiliation(s)
- Minna Kemppainen
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, National University of Quilmes and CONICET, Bernal, Province of Buenos Aires, Argentina.
| | - Alejandro Pardo
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, National University of Quilmes and CONICET, Bernal, Province of Buenos Aires, Argentina
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92
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Ceola G, Goss-Souza D, Alves J, Alves da Silva A, Stürmer SL, Baretta D, Sousa JP, Klauberg-Filho O. Biogeographic Patterns of Arbuscular Mycorrhizal Fungal Communities Along a Land-Use Intensification Gradient in the Subtropical Atlantic Forest Biome. Microb Ecol 2021; 82:942-960. [PMID: 33656687 DOI: 10.1007/s00248-021-01721-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
Information concerning arbuscular mycorrhizal (AM) fungal geographical distribution in tropical and subtropical soils from the Atlantic Forest (a global hotspot of biodiversity) are scarce and often restricted to the evaluation of richness and abundance of AM fungal species at specific ecosystems or local landscapes. In this study, we hypothesized that AM fungal diversity and community composition in subtropical soils would display fundamental differences in their geographical patterns, shaped by spatial distance and land-use change, at local and regional scales. AM fungal community composition was examined by spore-based taxonomic analysis, using soil trap cultures. Acaulospora koskei and Glomus were found as generalists, regardless of mesoregions and land uses. Other Acaulospora species were also found generalists within mesoregions. Land-use change and intensification did not influence AM fungal composition, partially rejecting our first hypothesis. We then calculated the distance-decay of similarities among pairs of AM fungal communities and the distance-decay relationship within and over mesoregions. We also performed the Mantel test and redundancy analysis to discriminate the main environmental drivers of AM fungal diversity and composition turnover. Overall, we found significant distance-decays for all land uses. We also observed a distance-decay relationship within the mesoregion scale (< 104 km) and these changes were correlated mainly to soil type (not land use), with the secondary influence of both total organic carbon and clay contents. AM fungal species distribution presented significant distance-decays, regardless of land uses, which was indicative of dispersal limitation, a stochastic neutral process. Although, we found evidence that, coupled with dispersal limitation, niche differentiation also played a role in structuring AM fungal communities, driven by long-term historical contingencies, as represented by soil type, resulting from different soil origin and mineralogy across mesoregions.
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Affiliation(s)
- Gessiane Ceola
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, SC, 88520-000, Brazil
| | - Dennis Goss-Souza
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, SC, 88520-000, Brazil
| | - Joana Alves
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, 3000-456, Portugal
| | - António Alves da Silva
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, 3000-456, Portugal
| | - Sidney Luiz Stürmer
- Departament of Natural Sciences, Regional University of Blumenau, Blumenau, SC, 89030-903, Brazil
| | - Dilmar Baretta
- Department of Soils and Sustainability, Santa Catarina State University, Chapecó, SC, 89815-630, Brazil
| | - José Paulo Sousa
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, 3000-456, Portugal
| | - Osmar Klauberg-Filho
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, SC, 88520-000, Brazil.
- Agroveterinary Centre, Santa Catarina State University, Av. Luis de Camões, 2090, Lages, SC, 88520-000, Brazil.
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93
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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.). J Sci Food Agric 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] [What about the content of this article? (0)] [Affiliation(s)] [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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94
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Deepika S, Kothamasi D. Plant hosts may influence arbuscular mycorrhizal fungal community composition in mangrove estuaries. Mycorrhiza 2021; 31:699-711. [PMID: 34477968 DOI: 10.1007/s00572-021-01049-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
We investigated the role of plant host and soil variables in determining arbuscular mycorrhizal fungi (AMF) community composition in plant roots of two spatially separated mangrove estuaries on the rivers Aghanashini (14° 30' 30″ N-74° 22' 44″ E) and Gangavali (14° 35' 26″ N-74° 17' 51″ E) on the west coast of India. Both mangrove estuaries had similar plant species composition but differed in soil chemistries.We amplified a 550-bp portion of 18S small subunit (SSU) rDNA from mangrove plant roots and analysed it by restriction fragment length polymorphism (RFLP). Clones representing unique RFLP patterns were sequenced. A total of 736 clones were obtained from roots of seven and five plant species sampled at Aghanashini and Gangavali, respectively. AMF phylotype numbers in plant roots at Aghanashini (12) were higher than at Gangavali (9) indicating quantitative differences in the AMF community composition in plant roots at the two mangrove estuaries. Because both estuaries had similar plant species composition, the quantitative difference in AMF communities between the estuaries could be an attribute of the differences in rhizospheric chemistry between the two sites.Non-metric multidimensional scaling (NMDS) revealed overlap in the AMF communities of the two sites. Three and two AMF phylotypes had significant indicator value indices with specific hosts at Aghanashini and Gangavali, respectively. Environmental vector fitting to NMDS ordination did not reveal a significant effect of any soil variable on AMF composition at the two sites. However, significant effects of both plant hosts and sites were observed on rhizospheric P. Our results indicate that root AMF community composition may be an outcome of plant response to rhizospheric variables. This suggests that plant identity may have a primary role in shaping AMF communities in mangroves.
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Affiliation(s)
- Sharma Deepika
- Laboratory of Soil Biology and Microbial Ecology, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India.
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Delhi, 110 002, India.
| | - David Kothamasi
- Laboratory of Soil Biology and Microbial Ecology, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India
- Strathclyde Centre for Environmental Law and Governance, University of Strathclyde, Glasgow, G1 1XQ, Scotland
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95
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Shi J, Zhao B, Zheng S, Zhang X, Wang X, Dong W, Xie Q, Wang G, Xiao Y, Chen F, Yu N, Wang E. A phosphate starvation response-centered network regulates mycorrhizal symbiosis. Cell 2021; 184:5527-5540.e18. [PMID: 34644527 DOI: 10.1016/j.cell.2021.09.030] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/06/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022]
Abstract
To secure phosphorus (P) from soil, most land plants use a direct phosphate uptake pathway via root hairs and epidermis and an indirect phosphate uptake pathway via mycorrhizal symbiosis. The interaction between these two pathways is unclear. Here, we mapped a network between transcription factors and mycorrhizal symbiosis-related genes using Y1H. Intriguingly, this gene regulatory network is governed by the conserved P-sensing pathway, centered on phosphate starvation response (PHR) transcription factors. PHRs are required for mycorrhizal symbiosis and regulate symbiosis-related genes via the P1BS motif. SPX-domain proteins suppress OsPHR2-mediated induction of symbiosis-related genes and inhibit mycorrhizal infection. In contrast, plants overexpressing OsPHR2 show improved mycorrhizal infection and are partially resistant to P-mediated inhibition of symbiosis. Functional analyses of network nodes revealed co-regulation of hormonal signaling and mycorrhizal symbiosis. This network deciphers extensive regulation of mycorrhizal symbiosis by endogenous and exogenous signals and highlights co-option of the P-sensing pathway for mycorrhizal symbiosis.
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Affiliation(s)
- Jincai Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Boyu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shuang Zheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wentao Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qiujin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gang Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yunping Xiao
- Shanghai OE Biotech Co., Ltd., Shanghai 201114, China
| | - Fan Chen
- Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Nan Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China.
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96
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Manz C, Adamčík S, Looney BP, Corrales A, Ovrebo C, Adamčíková K, Hofmann TA, Hampe F, Piepenbring M. Four new species of Russula subsection Roseinae from tropical montane forests in western Panama. PLoS One 2021; 16:e0257616. [PMID: 34644307 PMCID: PMC8513850 DOI: 10.1371/journal.pone.0257616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/02/2021] [Indexed: 11/18/2022] Open
Abstract
Species of the genus Russula are key components of ectomycorrhizal ecosystems worldwide. Nevertheless, their diversity in the tropics is still poorly known. This study aims to contribute to the knowledge of the diversity of Russula species classified in subsection Roseinae based on specimens recently collected in tropical montane rainforests in western Panama. A five gene multilocus phylogeny based on the nuclear markers ITS nrDNA, MCM7, RPB1, RPB2 and TEF-1α was constructed to identify the systematic position of 22 collections from Panama. Four new species, Russula cornicolor, Russula cynorhodon, Russula oreomunneae and Russula zephyrovelutipes are formally described and illustrated. None of the four species are sister species and they are more closely related to North American or Asian species. Two of the newly described species were associated with the ectomycorrhizal tree species Oreomunnea mexicana, while the other two species were associated with Quercus species. All four species are so far only known from mountains in western Panama.
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Affiliation(s)
- Cathrin Manz
- Mycology Research Group, Faculty of Biological Sciences, Goethe University Frankfurt am Main, Frankfurtam Main, Germany
| | - Slavomír Adamčík
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Brian P. Looney
- Department of Biology, Clark University, Worcester, MA, United States of America
| | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Clark Ovrebo
- Department of Biology, University of Central Oklahoma, Edmond, OK, United States of America
| | - Katarína Adamčíková
- Department of Plant Pathology and Mycology, Institute of Forest Ecology, Slovak Academy of Sciences Zvolen, Nitra, Slovakia
| | - Tina A. Hofmann
- Mycological Research Center (CIMi), Herbarium UCH, Autonomous University of Chiriquí (UNACHI), David, Chiriquí Province, Panama
| | | | - Meike Piepenbring
- Mycology Research Group, Faculty of Biological Sciences, Goethe University Frankfurt am Main, Frankfurtam Main, Germany
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97
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Ray P, Guo Y, Chi MH, Krom N, Boschiero C, Watson B, Huhman D, Zhao P, Singan VR, Lindquist EA, Yan J, Adam C, Craven KD. Serendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship. Mol Plant Microbe Interact 2021; 34:1128-1142. [PMID: 34260261 DOI: 10.1094/mpmi-04-21-0084-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to Serendipita spp. colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain, S. vermifera, isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells to, finally, the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Furthermore, genes involved in phytohormone metabolism such as gibberellin, jasmonic acid, and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita spp. will inform our efforts to integrate them into forages and row crops for optimal plant-microbe functioning, thus facilitating low-input, sustainable agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Yingqing Guo
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Bonnie Watson
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - David Huhman
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Patrick Zhao
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Vasanth R Singan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Erika A Lindquist
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Juying Yan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Catherine Adam
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
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98
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Park KH, Yoo S, Park MS, Kim CS, Lim YW. Different patterns of belowground fungal diversity along altitudinal gradients with respect to microhabitat and guild types. Environ Microbiol Rep 2021; 13:649-658. [PMID: 34162018 DOI: 10.1111/1758-2229.12976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/12/2021] [Indexed: 06/13/2023]
Abstract
Fungi are key components of belowground ecosystems with various ecological roles in forests. Although the changes in the richness and composition of belowground fungi across altitudinal gradients have been widely reported, only a few studies have focused on the microhabitat types along altitudinal gradients. Here, we analysed the effect of altitude on the ectomycorrhizal and non-ectomycorrhizal fungal communities in belowground microhabitats. We collected root and soil samples from 16 Pinus densiflora forests at various altitudes across Korea, and measured the soil properties as potential factors. Fungal communities were analysed by high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region. We found that altitude negatively affected the species richness of root-inhabiting fungi but did not influence that of soil-inhabiting fungi. In addition, the composition of ectomycorrhizal (ECM) fungi was less influenced by altitude than non-ECM fungi. Most of the soil properties did not show a significant relationship with altitude, but the effect of soil properties was different across microhabitat types and ecological roles of fungi. Our results reveal that microhabitat types and altitudinal gradients differently affect the richness and composition of fungal communities associated with P. densiflora, providing a better understanding of plant-associated fungal communities.
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Affiliation(s)
- Ki Hyeong Park
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Shinnam Yoo
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Myung Soo Park
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Young Woon Lim
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, South Korea
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99
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Robbins C, Cruz Corella J, Aletti C, Seiler R, Mateus ID, Lee S, Masclaux FG, Sanders IR. Generation of unequal nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription. New Phytol 2021; 231:1984-2001. [PMID: 34085297 PMCID: PMC8457141 DOI: 10.1111/nph.17530] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/25/2021] [Indexed: 05/05/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form mutualisms with most plant species. The model AMF Rhizophagus irregularis is common in many ecosystems and naturally forms homokaryons and dikaryons. Quantitative variation in allele frequencies in clonally dikaryon offspring suggests they disproportionately inherit two distinct nuclear genotypes from their parent. This is interesting, because such progeny strongly and differentially affect plant growth. Neither the frequency and magnitude of this occurrence nor its effect on gene transcription are known. Using reduced representation genome sequencing, transcriptomics, and quantitative analysis tools, we show that progeny of homokaryons and dikaryons are qualitatively genetically identical to the parent. However, dikaryon progeny differ quantitatively due to unequal inheritance of nuclear genotypes. Allele frequencies of actively transcribed biallelic genes resembled the frequencies of the two nuclear genotypes. More biallelic genes showed transcription of both alleles than monoallelic transcription, but biallelic transcription was less likely with greater allelic divergence. Monoallelic transcription levels of biallelic genes were reduced compared with biallelic gene transcription, a finding consistent with genomic conflict. Given that genetic variation in R. irregularis is associated with plant growth, our results establish quantitative genetic variation as a future consideration when selecting AMF lines to improve plant production.
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Affiliation(s)
- Chanz Robbins
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Joaquim Cruz Corella
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Consolée Aletti
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Réjane Seiler
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Ivan D. Mateus
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Soon‐Jae Lee
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Frédéric G. Masclaux
- Group of Genetic MedicineGeneva University HospitalBuilding DGeneva1205Switzerland
| | - Ian R. Sanders
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
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100
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Freestone MW, Swarts ND, Reiter N, Tomlinson S, Sussmilch FC, Wright MM, Holmes GD, Phillips RD, Linde CC. Continental-scale distribution and diversity of Ceratobasidium orchid mycorrhizal fungi in Australia. Ann Bot 2021; 128:329-343. [PMID: 34077492 PMCID: PMC8389474 DOI: 10.1093/aob/mcab067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Mycorrhizal fungi are a critical component of the ecological niche of most plants and can potentially constrain their geographical range. Unlike other types of mycorrhizal fungi, the distributions of orchid mycorrhizal fungi (OMF) at large spatial scales are not well understood. Here, we investigate the distribution and diversity of Ceratobasidium OMF in orchids and soils across the Australian continent. METHODS We sampled 217 Ceratobasidium isolates from 111 orchid species across southern Australia and combined these with 311 Ceratobasidium sequences from GenBank. To estimate the taxonomic diversity of Ceratobasidium associating with orchids, phylogenetic analysis of the ITS sequence locus was undertaken. Sequence data from the continent-wide Australian Microbiome Initiative were used to determine the geographical range of operational taxonomic units (OTUs) detected in orchids, with the distribution and climatic correlates of the two most frequently detected OTUs modelled using MaxEnt. KEY RESULTS We identified 23 Ceratobasidium OTUs associating with Australian orchids, primarily from the orchid genera Pterostylis, Prasophyllum, Rhizanthella and Sarcochilus. OTUs isolated from orchids were closely related to, but distinct from, known pathogenic fungi. Data from soils and orchids revealed that ten of these OTUs occur on both east and west sides of the continent, while 13 OTUs were recorded at three locations or fewer. MaxEnt models suggested that the distributions of two widespread OTUs are correlated with temperature and soil moisture of the wettest quarter and far exceeded the distributions of their host orchid species. CONCLUSIONS Ceratobasidium OMF with cross-continental distributions are common in Australian soils and frequently have geographical ranges that exceed that of their host orchid species, suggesting these fungi are not limiting the distributions of their host orchids at large spatial scales. Most OTUs were distributed within southern Australia, although several OTUs had distributions extending into central and northern parts of the continent, illustrating their tolerance of an extraordinarily wide range of environmental conditions.
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Affiliation(s)
- Marc W Freestone
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
- Royal Botanic Gardens Victoria, Cranbourne, VIC 3977, Australia
- Biodiversity and Conservation Division, Department of Agriculture, Water and Environment, Canberra, ACT 2600, Australia
| | - Nigel D Swarts
- Tasmanian Institute of Agriculture, The University of Tasmania, Sandy Bay, TAS 7005, Australia
- Royal Tasmanian Botanical Gardens, Hobart, TAS 7000, Australia
| | - Noushka Reiter
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
- Royal Botanic Gardens Victoria, Cranbourne, VIC 3977, Australia
| | - Sean Tomlinson
- Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, West Perth, WA 6005, Australia
| | - Frances C Sussmilch
- Tasmanian Institute of Agriculture, The University of Tasmania, Sandy Bay, TAS 7005, Australia
| | - Magali M Wright
- Royal Tasmanian Botanical Gardens, Hobart, TAS 7000, Australia
| | - Gareth D Holmes
- Royal Botanic Gardens Victoria, Cranbourne, VIC 3977, Australia
| | - Ryan D Phillips
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
- Royal Botanic Gardens Victoria, Cranbourne, VIC 3977, Australia
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, West Perth, WA 6005, Australia
- Department of Ecology, Environment and Evolution, LaTrobe University, Bundoora, VIC 3086, Australia
| | - Celeste C Linde
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
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