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Eichfeld R, Mahdi LK, De Quattro C, Armbruster L, Endeshaw AB, Miyauchi S, Hellmann MJ, Cord-Landwehr S, Peterson D, Singan V, Lail K, Savage E, Ng V, Grigoriev IV, Langen G, Moerschbacher BM, Zuccaro A. Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18-CBM5 chitinase to protect their hosts. THE NEW PHYTOLOGIST 2024. [PMID: 39224928 DOI: 10.1111/nph.20080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Effector secretion is crucial for root endophytes to establish and protect their ecological niche. We used time-resolved transcriptomics to monitor effector gene expression dynamics in two closely related Sebacinales, Serendipita indica and Serendipita vermifera, during symbiosis with three plant species, competition with the phytopathogenic fungus Bipolaris sorokiniana, and cooperation with root-associated bacteria. We observed increased effector gene expression in response to biotic interactions, particularly with plants, indicating their importance in host colonization. Some effectors responded to both plants and microbes, suggesting dual roles in intermicrobial competition and plant-microbe interactions. A subset of putative antimicrobial effectors, including a GH18-CBM5 chitinase, was induced exclusively by microbes. Functional analyses of this chitinase revealed its antimicrobial and plant-protective properties. We conclude that dynamic effector gene expression underpins the ability of Sebacinales to thrive in diverse ecological niches with a single fungal chitinase contributing substantially to niche defense.
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Affiliation(s)
- Ruben Eichfeld
- University of Cologne, Institute for Plant Sciences, Cologne, 50674, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, 50674, Germany
| | - Lisa K Mahdi
- University of Cologne, Institute for Plant Sciences, Cologne, 50674, Germany
| | - Concetta De Quattro
- University of Cologne, Institute for Plant Sciences, Cologne, 50674, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, 50674, Germany
| | - Laura Armbruster
- University of Cologne, Institute for Plant Sciences, Cologne, 50674, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, 50674, Germany
| | - Asmamaw B Endeshaw
- University of Cologne, Institute for Plant Sciences, Cologne, 50674, Germany
| | - Shingo Miyauchi
- University of Cologne, Institute for Plant Sciences, Cologne, 50674, Germany
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Margareta J Hellmann
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, 48149, Germany
| | - Stefan Cord-Landwehr
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, 48149, Germany
| | - Daniel Peterson
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kathleen Lail
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Emily Savage
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Gregor Langen
- University of Cologne, Institute for Plant Sciences, Cologne, 50674, Germany
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, 48149, Germany
| | - Alga Zuccaro
- University of Cologne, Institute for Plant Sciences, Cologne, 50674, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, 50674, Germany
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2
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Gajdošová Z, Caboň M, Kolaříková Z, Sudová R, Rydlová J, Turisová I, Turis P, Kučera J, Slovák M. Environmental heterogeneity structures root-associated fungal communities in Daphne arbuscula (Thymelaeaceae), a shrub adapted to extreme rocky habitats. Mol Ecol 2024; 33:e17441. [PMID: 38923648 DOI: 10.1111/mec.17441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/04/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Rocky habitats, globally distributed ecosystems, harbour diverse biota, including numerous endemic and endangered species. Vascular plants thriving in these environments face challenging abiotic conditions, requiring diverse morphological and physiological adaptations. Their engagement with the surrounding microbiomes is, however, equally vital for their adaptation, fitness, and long-term survival. Nevertheless, there remains a lack of understanding surrounding this complex interplay within this fascinating biotic ecosystem. Using microscopic observations and metabarcoding analyses, we examined the fungal abundance and diversity in the root system of the rock-dwelling West Carpathian endemic shrub, Daphne arbuscula (Thymelaeaceae). We explored the diversification of root-associated fungal communities in relation to microclimatic variations across the studied sites. We revealed extensive colonization of the Daphne roots by diverse taxonomic fungal groups attributed to different ecological guilds, predominantly plant pathogens, dark septate endophytes (DSE), and arbuscular mycorrhizal fungi (AMF). Notably, differences in taxonomic composition and ecological guilds emerged between colder and warmer microenvironments. Apart from omnipresent AMF, warmer sites exhibited a prevalence of plant pathogens, while colder sites were characterized by a dominance of DSE. This mycobiome diversification, most likely triggered by the environment, suggests that D. arbuscula populations in warmer areas may be more vulnerable to fungal diseases, particularly in the context of global climate change.
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Affiliation(s)
- Zuzana Gajdošová
- Plant Sciences and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslav Caboň
- Plant Sciences and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Kolaříková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Radka Sudová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Jana Rydlová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Ingrid Turisová
- Department of Biology, Ecology and Environment, Faculty of Natural Sciences, Matej Bel University in Banská Bystrica, Banská Bystrica, Slovakia
| | - Peter Turis
- Department of Biology, Ecology and Environment, Faculty of Natural Sciences, Matej Bel University in Banská Bystrica, Banská Bystrica, Slovakia
| | - Jaromír Kučera
- Plant Sciences and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marek Slovák
- Plant Sciences and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Praha, Czech Republic
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3
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Pujasatria GC, Miura C, Yamaguchi K, Shigenobu S, Kaminaka H. Colonization by orchid mycorrhizal fungi primes induced systemic resistance against necrotrophic pathogen. FRONTIERS IN PLANT SCIENCE 2024; 15:1447050. [PMID: 39145195 PMCID: PMC11322130 DOI: 10.3389/fpls.2024.1447050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
Orchids and arbuscular mycorrhiza (AM) plants evolved independently and have different structures and fungal partners, but they both facilitate nutrient uptake. Orchid mycorrhiza (OM) supports orchid seed germination, but unlike AM, its role in disease resistance of mature plants is largely unknown. Here, we examined whether OM induces systemic disease resistance against a necrotrophic pathogen in a similar fashion to AM. We investigated the priming effect of mycorrhizal fungi inoculation on resistance of a terrestrial orchid, Bletilla striata, to soft rot caused by Dickeya fangzhongdai. We found that root colonization by a compatible OM fungus primed B. striata seedlings and induced systemic resistance against the infection. Transcriptome analysis showed that priming was mediated by the downregulation of jasmonate and ethylene pathways and that these pathways are upregulated once infection occurs. Comparison with the reported transcriptome of AM fungus-colonized rice leaves revealed similar mechanisms in B. striata and in rice. These findings highlight a novel aspect of commonality between OM and AM plants in terms of induced systemic resistance.
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Affiliation(s)
| | - Chihiro Miura
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology Core Research Facilities, Okazaki, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology Core Research Facilities, Okazaki, Japan
| | - Hironori Kaminaka
- Faculty of Agriculture, Tottori University, Tottori, Japan
- Unused Bioresource Utilization Center, Tottori University, Tottori, Japan
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Perdikopanis N, Giannakakis A, Kavakiotis I, Hatzigeorgiou AG. D-sORF: Accurate Ab Initio Classification of Experimentally Detected Small Open Reading Frames (sORFs) Associated with Translational Machinery. BIOLOGY 2024; 13:563. [PMID: 39194501 DOI: 10.3390/biology13080563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024]
Abstract
Small open reading frames (sORFs; <300 nucleotides or <100 amino acids) are widespread across all genomes, and an increasing variety of them appear to be translating from non-genic regions. Over the past few decades, peptides produced from sORFs have been identified as functional in various organisms, from bacteria to humans. Despite recent advances in next-generation sequencing and proteomics, accurate annotation and classification of sORFs remain a rate-limiting step toward reliable and high-throughput detection of small proteins from non-genic regions. Additionally, the cost of computational methods utilizing machine learning is lower than that of biological experiments, and they can be employed to detect sORFs, laying the groundwork for biological experiments. We present D-sORF, a machine-learning framework that integrates the statistical nucleotide context and motif information around the start codon to predict coding sORFs. D-sORF scores directly for coding identity and requires only the underlying genomic sequence, without incorporating parameters such as the conservation, which, in the case of sORFs, may increase the dispersion of scores within the significantly less conserved non-genic regions. D-sORF achieves 94.74% precision and 92.37% accuracy for small ORFs (using the 99 nt medium length window). When D-sORF is applied to sORFs associated with ribosomes, the identification of transcripts producing peptides (annotated by the Ensembl IDs) is similar to or superior to experimental methodologies based on ribosome-sequencing (Ribo-Seq) profiling. In parallel, the recognition of putative negative data, such as the intron-containing transcripts that associate with ribosomes, remains remarkably low, indicating that D-sORF could be efficiently applied to filter out false-positive sORFs from Ribo-Seq data because of the non-productive ribosomal binding or noise inherent in these protocols.
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Affiliation(s)
- Nikos Perdikopanis
- Department of Electrical and Computer Engineering, University of Thessaly, 38221 Volos, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 38221 Volos, Greece
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Ioannis Kavakiotis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 38221 Volos, Greece
| | - Artemis G Hatzigeorgiou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 38221 Volos, Greece
- Hellenic Pasteur Institute, 11521 Athens, Greece
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5
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Shi L, Wang Z, Chen JH, Qiu H, Liu WD, Zhang XY, Martin FM, Zhao MW. LbSakA-mediated phosphorylation of the scaffolding protein LbNoxR in the ectomycorrhizal basidiomycete Laccaria bicolor regulates NADPH oxidase activity, ROS accumulation and symbiosis development. THE NEW PHYTOLOGIST 2024; 243:381-397. [PMID: 38741469 DOI: 10.1111/nph.19813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Ectomycorrhizal symbiosis, which involves mutually beneficial interactions between soil fungi and tree roots, is essential for promoting tree growth. To establish this symbiotic relationship, fungal symbionts must initiate and sustain mutualistic interactions with host plants while avoiding host defense responses. This study investigated the role of reactive oxygen species (ROS) generated by fungal NADPH oxidase (Nox) in the development of Laccaria bicolor/Populus tremula × alba symbiosis. Our findings revealed that L. bicolor LbNox expression was significantly higher in ectomycorrhizal roots than in free-living mycelia. RNAi was used to silence LbNox, which resulted in decreased ROS signaling, limited formation of the Hartig net, and a lower mycorrhizal formation rate. Using Y2H library screening, BiFC and Co-IP, we demonstrated an interaction between the mitogen-activated protein kinase LbSakA and LbNoxR. LbSakA-mediated phosphorylation of LbNoxR at T409, T477 and T480 positively modulates LbNox activity, ROS accumulation and upregulation of symbiosis-related genes involved in dampening host defense reactions. These results demonstrate that regulation of fungal ROS metabolism is critical for maintaining the mutualistic interaction between L. bicolor and P. tremula × alba. Our findings also highlight a novel and complex regulatory mechanism governing the development of symbiosis, involving both transcriptional and posttranslational regulation of gene networks.
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Affiliation(s)
- Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zi Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Ju Hong Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hao Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wei Dong Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiao Yan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Ming Wen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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Chen P, Huang P, Yu H, Yu H, Xie W, Wang Y, Zhou Y, Chen L, Zhang M, Yao R. Strigolactones shape the assembly of root-associated microbiota in response to phosphorus availability. mSystems 2024; 9:e0112423. [PMID: 38780241 PMCID: PMC11237589 DOI: 10.1128/msystems.01124-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Plants rely on strigolactones (SLs) to regulate their development and form symbiotic relationships with microbes as part of the adaptive phosphorus (P) efficiency strategies. However, the impact of SLs on root-associated microbial communities in response to P availability remains unknown. Here, root microbiota of SL biosynthesis (max3-11) and perception (d14-1) were compared to wild-type Col-0 plants under different P concentrations. Using high-throughput sequencing, the relationship between SLs, P concentrations, and the root-associated microbiota was investigated to reveal the variation in microbial diversity, composition, and interaction. Plant genotypes and P availability played important but different roles in shaping the root-associated microbial community. Importantly, SLs were found to attract Acinetobacter in low P conditions, which included an isolated CP-2 (Acinetobacter soli) that could promote plant growth in cocultivation experiments. Moreover, SLs could change the topologic structure within co-occurrence networks and increase the number of keystone taxa (e.g., Rhizobiaceae and Acidobacteriaceae) to enhance microbial community stability. This study reveals the key role of SLs in mediating root-associated microbiota interactions.IMPORTANCEStrigolactones (SLs) play a crucial role in plant development and their symbiotic relationships with microbes, particularly in adapting to phosphorus levels. Using high-throughput sequencing, we compared the root microbiota of plants with SL biosynthesis and perception mutants to wild-type plants under different phosphorus concentrations. These results found that SLs can attract beneficial microbes in low phosphorus conditions to enhance plant growth. Additionally, SLs affect microbial network structures, increasing the stability of microbial communities. This study highlights the key role of SLs in shaping root-associated microbial interactions, especially in response to phosphorus availability.
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Affiliation(s)
- Pubo Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Pingliang Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Haiyang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Huang Yu
- School of Resource and Environment and Safety Engineering, University of South China, Hengyang, China
| | - Weicheng Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yuehua Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yu Zhou
- Hunan Institute of Microbiology, Changsha, China
| | - Li Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Meng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Ruifeng Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
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Guillen-Otero T, Hertel D, Quintanilla LG, Lehnert M, Schmid M, Kharazishvili D, Fawcett S, Kessler M. Comparative analysis of mycorrhizal communities associated with Struthiopteris spicant (L.) Weiss across Europe and North America. FRONTIERS IN PLANT SCIENCE 2024; 15:1402946. [PMID: 38899157 PMCID: PMC11186384 DOI: 10.3389/fpls.2024.1402946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
Introduction Ferns constitute the second largest group of vascular plants. Previous studies have shown that the diversity and composition of fern communities are influenced by resource availability and water stress, among other factors. However, little is known about the influence of these environmental factors on their biotic interactions, especially regarding the relationship between mycorrhizal fungi and ferns. The present study compares the mycorrhizal communities associated with 36 populations of Struthiopteris spicant L. Weiss across Europe and North America. This species exhibits a great tolerance to variations in light, nutrient, and pH conditions, and it can survive with and without mycorrhizae. Methods With the aim of determining which environmental factors impact the composition and abundance of the root-associated fungal communities in this species, we used an ITS-focused metabarcoding approach to identify the mycorrhizal fungi present and analyzed the influence of climatic and edaphic variables at global and regional scales. Results and discussion We encountered striking differences in the relative abundance of arbuscular mycorrhizal fungi (AMF) between S. spicant populations at both spatial levels. We recorded a total of 902 fungal ASVs, but only 2- 4% of the total fungal diversity was observed in each individual, revealing that each fern had a unique fungal community. Light availability and the interactive action of pH and soil nitrogen concentration showed a positive influence on AMF relative abundance, explaining 89% of the variance. However, environmental factors could only explain 4- 8% of the variability in AMF community composition, indicating that it might be determined by stochastic processes. These results support the hypothesis that ferns may be more independent of mycorrhization than other plant groups and interact with fungi in a more opportunistic manner.
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Affiliation(s)
- Thais Guillen-Otero
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Dietrich Hertel
- Albrecht von Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Luis G. Quintanilla
- School of Environmental Sciences and Technology, University Rey Juan Carlos, Móstoles, Spain
| | - Marcus Lehnert
- Geobotany and Botanical Garden Area, Herbarium, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Mattia Schmid
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Davit Kharazishvili
- Deputy Director of Research management of the Batumi Botanical Garden, Batumi, Georgia
| | - Susan Fawcett
- University and Jepson Herbaria, University of California, Berkeley, Berkeley, United States
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
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Rosling A, Eshghi Sahraei S, Kalsoom Khan F, Desirò A, Bryson AE, Mondo SJ, Grigoriev IV, Bonito G, Sánchez-García M. Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis. BMC Genomics 2024; 25:529. [PMID: 38811885 PMCID: PMC11134847 DOI: 10.1186/s12864-024-10391-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid. RESULTS In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89. CONCLUSION Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.
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Affiliation(s)
- Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | | | | | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Abigail E Bryson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Stephen J Mondo
- Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
- Department of Forest Mycology and Plant Pathology, Uppsala Biocentre, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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9
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Mishra S, Duarte GT, Horemans N, Ruytinx J, Gudkov D, Danchenko M. Complexity of responses to ionizing radiation in plants, and the impact on interacting biotic factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171567. [PMID: 38460702 DOI: 10.1016/j.scitotenv.2024.171567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In nature, plants are simultaneously exposed to different abiotic (e.g., heat, drought, and salinity) and biotic (e.g., bacteria, fungi, and insects) stresses. Climate change and anthropogenic pressure are expected to intensify the frequency of stress factors. Although plants are well equipped with unique and common defense systems protecting against stressors, they may compromise their growth and development for survival in such challenging environments. Ionizing radiation is a peculiar stress factor capable of causing clustered damage. Radionuclides are both naturally present on the planet and produced by human activities. Natural and artificial radioactivity affects plants on molecular, biochemical, cellular, physiological, populational, and transgenerational levels. Moreover, the fitness of pests, pathogens, and symbionts is concomitantly challenged in radiologically contaminated areas. Plant responses to artificial acute ionizing radiation exposure and laboratory-simulated or field chronic exposure are often discordant. Acute or chronic ionizing radiation exposure may occasionally prime the defense system of plants to better tolerate the biotic stress or could often exhaust their metabolic reserves, making plants more susceptible to pests and pathogens. Currently, these alternatives are only marginally explored. Our review summarizes the available literature on the responses of host plants, biotic factors, and their interaction to ionizing radiation exposure. Such systematic analysis contributes to improved risk assessment in radiologically contaminated areas.
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Affiliation(s)
- Shubhi Mishra
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia
| | - Gustavo Turqueto Duarte
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium
| | - Nele Horemans
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium; Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Joske Ruytinx
- Department of Bio-engineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dmitri Gudkov
- Institute of Hydrobiology, National Academy of Sciences of Ukraine, 04210 Kyiv, Ukraine
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia.
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10
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Voller F, Ardanuy A, Taylor AFS, Johnson D. Maintenance of host specialisation gradients in ectomycorrhizal symbionts. THE NEW PHYTOLOGIST 2024; 242:1426-1435. [PMID: 37984824 DOI: 10.1111/nph.19395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/02/2023] [Indexed: 11/22/2023]
Abstract
Many fungi that form ectomycorrhizas exhibit a degree of host specialisation, and individual trees are frequently colonised by communities of mycorrhizal fungi comprising species that fall on a gradient of specialisation along genetic, functional and taxonomic axes of variation. By contrast, arbuscular mycorrhizal fungi exhibit little specialisation. Here, we propose that host tree root morphology is a key factor that gives host plants fine-scale control over colonisation and therefore opportunities for driving specialisation and speciation of ectomycorrhizal fungi. A gradient in host specialisation is likely driven by four proximate mechanistic 'filters' comprising partner availability, signalling recognition, competition for colonisation, and symbiotic function (trade, rewards and sanctions), and the spatially restricted colonisation seen in heterorhizic roots enables these mechanisms, especially symbiotic function, to be more effective in driving the evolution of specialisation. We encourage manipulation experiments that integrate molecular genetics and isotope tracers to test these mechanisms, alongside mathematical simulations of eco-evolutionary dynamics in mycorrhizal symbioses.
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Affiliation(s)
- Fay Voller
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
| | - Agnès Ardanuy
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
- Université de Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, 31320, France
| | - Andy F S Taylor
- Ecological Sciences Group, James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK
| | - David Johnson
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
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11
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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. THE NEW PHYTOLOGIST 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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12
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Mujica MI, Herrera H, Cisternas M, Zuniga-Feest A, Sagredo-Saez C, Selosse MA. Mycorrhizas in South American Ericaceae. MYCORRHIZA 2024; 34:1-18. [PMID: 38512497 DOI: 10.1007/s00572-024-01141-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Mycorrhizal symbioses (mycorrhizas) of Ericaceae, including ericoid mycorrhiza (ErM), have been mainly studied in the Northern Hemisphere, although the highest diversity of ericaceous plants is located in the Southern Hemisphere, where several regions remain largely unexplored. One of them is South America, which harbors a remarkably high diversity of Ericaceae (691 species and 33 genera) in a wide range of environmental conditions, and a specific mycorrhizal type called cavendishioid. In this review, we compile all available information on mycorrhizas of Ericaceae in South America. We report data on the mycorrhizal type and fungal diversity in 17 and 11 ericaceous genera, respectively. We show that South American Ericaceae exhibit a high diversity of habitats and life forms and that some species from typical ErM subfamilies may also host arbuscular mycorrhiza. Also, a possible geographical pattern in South American ErM fungal communities is suggested, with Sebacinales being the dominant mycorrhizal partners of the Andean clade species from tropical mountains, while archetypal ErM fungi are common partners in southern South America species. The gathered information challenges some common assumptions about ErM and suggests that focusing on understudied regions would improve our understanding of the evolution of mycorrhizal associations in this intriguing family.
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Affiliation(s)
- María Isabel Mujica
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
| | - Héctor Herrera
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Mauricio Cisternas
- Instituto de Investigaciones Agropecuarias, INIA-La Cruz, La Cruz, Chile
| | - Alejandra Zuniga-Feest
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Cristiane Sagredo-Saez
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (UMR 7205-CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005, Paris, France
- Faculty of Biology, University of Gdańsk, ul. Wita Stwosza 59, 80-308, Gdańsk, Poland
- Institut Universitaire de France (IUF), Paris, France
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13
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Rehneke L, Schäfer P. Symbiont effector-guided mapping of proteins in plant networks to improve crop climate stress resilience: Symbiont effectors inform highly interconnected plant protein networks and provide an untapped resource for crop climate resilience strategies. Bioessays 2024; 46:e2300172. [PMID: 38388783 DOI: 10.1002/bies.202300172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/21/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe-derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the potential of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno-suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution-driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments.
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Affiliation(s)
- Laura Rehneke
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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14
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Guillen T, Kessler M, Homeier J. Fern mycorrhizae do not respond to fertilization in a tropical montane forest. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2024; 5:e10139. [PMID: 38560414 PMCID: PMC10979390 DOI: 10.1002/pei3.10139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Ferns are known to have a lower incidence of mycorrhization than angiosperms. It has been suggested that this results from carbon being more limiting to fern growth than nutrient availability, but this assertion has not been tested yet. In the present study, we took advantage of a fertilization experiment with nitrogen and phosphorus on cloud forest plots of the Ecuadorean Andes for 15 years. A previous analysis revealed changes in the abundances of fern species in the fertilized plots compared to the control plots and hypothesized that this might be related to the responses of the mycorrhizal relationships to nutrient availability. We revisited the plots to assess the root-associated fungal communities of two epiphytic and two terrestrial fern species that showed shifts in abundance. We sampled and analyzed the roots of 125 individuals following a metabarcoding approach. We recovered 1382 fungal ASVs, with a dominance of members of Tremellales (Basidiomycota) and Heliotales (Ascomycota). The fungal diversity was highly partitioned with little overlap between individuals. We found marked differences between terrestrial and epiphytic species, with the latter fundamentally missing arbuscular mycorrhizal fungi (AMF). We found no effect of fertilization on the diversity or relative abundance of the fungal assemblages. Still, we observed a direct impact of phosphorus fertilization on its concentration in the fern leaves. We conclude that fern-fungi relationships in the study site are not restricted by nutrient availability and suggest the existence of little specificity on the fungal partners relative to the host fern species.
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Affiliation(s)
- Thais Guillen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Jürgen Homeier
- Faculty of Resource ManagementUniversity of Applied Sciences and Arts (HAWK)GöttingenGermany
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15
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Guillen-Otero T, Lee SJ, Hertel D, Kessler M. Facultative mycorrhization in a fern (Struthiopteris spicant L. Weiss) is bound to light intensity. BMC PLANT BIOLOGY 2024; 24:103. [PMID: 38331718 PMCID: PMC10854079 DOI: 10.1186/s12870-024-04782-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND The establishment of mycorrhizal relationships between a fungus and a plant typically enhances nutrient and water uptake for the latter while securing a carbon source for the fungus. However, under a particular set of environmental conditions, such as low availability of light and abundant nutrients in the soil, the resources invested in the maintenance of the fungi surpass the benefits obtained by the host. In those cases, facultative mycorrhizal plants are capable of surviving without symbiosis. Facultative mycorrhization in ferns has been overlooked until now. The present study measured the response of Struthiopteris spicant L. Weiss, and its root-associated fungi to different levels of light and nutrient availability in terms of growth, mycorrhizal presence, and leaf nutrient content. This fern species exhibits a great tolerance to variable light, nutrient, and pH conditions, and it has been found with and without mycorrhizae. We conducted a greenhouse experiment with 80 specimens of S. spicant and three factors (Light, Phosphorus, and Nitrogen) resulting in eight treatments. RESULTS We found a significant influence of the factor light on fungal community composition, plant biomass, and nutrient accumulation. Departing from a lack of colonization at the initial stage, plants showed a remarkable increment of more than 80% in the arbuscular mycorrhizal fungi (AMF) richness and abundance in their roots when grown under high light conditions, compared with the ones in low light. We also observed an upward trend of C:P and C:N ratios and the above- and belowground biomass production when AMF abundance increased. Furthermore, the compositional analysis of the whole fungal communities associated with S. spicant roots revealed clear differences among low-light and high-light treatments. CONCLUSIONS This study is the first to investigate the importance of light and nutrient availability in determining fern-AMF relationships. We confirmed that Struthiopteris spicant is a facultative mycorrhizal plant. The composition and diversity of AMF found in the roots of this fern are strongly influenced by light and less by nutrient conditions. Our study shows that ferns respond very sensitively to changes in environmental factors, leading to shifts in the associated mycorrhizal communities.
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Affiliation(s)
- Thais Guillen-Otero
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.
| | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Dietrich Hertel
- Albrecht von Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
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16
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Ma X, Vanneste S, Chang J, Ambrosino L, Barry K, Bayer T, Bobrov AA, Boston L, Campbell JE, Chen H, Chiusano ML, Dattolo E, Grimwood J, He G, Jenkins J, Khachaturyan M, Marín-Guirao L, Mesterházy A, Muhd DD, Pazzaglia J, Plott C, Rajasekar S, Rombauts S, Ruocco M, Scott A, Tan MP, Van de Velde J, Vanholme B, Webber J, Wong LL, Yan M, Sung YY, Novikova P, Schmutz J, Reusch TBH, Procaccini G, Olsen JL, Van de Peer Y. Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment. NATURE PLANTS 2024; 10:240-255. [PMID: 38278954 PMCID: PMC7615686 DOI: 10.1038/s41477-023-01608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 12/05/2023] [Indexed: 01/28/2024]
Abstract
We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.
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Affiliation(s)
- Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jiyang Chang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Luca Ambrosino
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Kerrie Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Till Bayer
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | | | - LoriBeth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Justin E Campbell
- Coastlines and Oceans Division, Institute of Environment, Florida International University-Biscayne Bay Campus, Miami, FL, USA
| | - Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria Luisa Chiusano
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Agricultural Sciences, University Federico II of Naples, Naples, Italy
| | - Emanuela Dattolo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Centre, Palermo, Italy
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Guifen He
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marina Khachaturyan
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
- Institute of General Microbiology, University of Kiel, Kiel, Germany
| | - Lázaro Marín-Guirao
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain
| | - Attila Mesterházy
- Centre for Ecological Research, Wetland Ecology Research Group, Debrecen, Hungary
| | - Danish-Daniel Muhd
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jessica Pazzaglia
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Centre, Palermo, Italy
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Miriam Ruocco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Fano Marine Center, Fano, Italy
| | - Alison Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Min Pau Tan
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jozefien Van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Li Lian Wong
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Mi Yan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yeong Yik Sung
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Polina Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany.
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
- National Biodiversity Future Centre, Palermo, Italy.
| | - Jeanine L Olsen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
- Centre 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.
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17
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Zhang C, van der Heijden MGA, Dodds BK, Nguyen TB, Spooren J, Valzano-Held A, Cosme M, Berendsen RL. A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization. MICROBIOME 2024; 12:13. [PMID: 38243337 PMCID: PMC10799531 DOI: 10.1186/s40168-023-01726-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/18/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis. RESULTS Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization. CONCLUSIONS Our results highlight that AM fungi do not function in isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Video Abstract.
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Affiliation(s)
- Changfeng Zhang
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Bethany K Dodds
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Thi Bich Nguyen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Jelle Spooren
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alain Valzano-Held
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Marco Cosme
- Mycology, Earth and Life Institute, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
- Plants and Ecosystems, Biology Department, University of Antwerp, Antwerp, Belgium
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
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18
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Guo L, Deng M, Li X, Schmid B, Huang J, Wu Y, Peng Z, Yang L, Liu L. Evolutionary and ecological forces shape nutrient strategies of mycorrhizal woody plants. Ecol Lett 2024; 27:e14330. [PMID: 37866881 DOI: 10.1111/ele.14330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023]
Abstract
The associations of arbuscular mycorrhizal (AM) or ectomycorrhiza (EcM) fungi with plants have sequentially evolved and significantly contributed to enhancing plant nutrition. Nonetheless, how evolutionary and ecological forces drive nutrient acquisition strategies of AM and EcM woody plants remains poorly understood. Our global analysis of woody species revealed that, over divergence time, AM woody plants evolved faster nitrogen mineralization rates without changes in nitrogen resorption. However, EcM woody plants exhibited an increase in nitrogen mineralization but a decrease in nitrogen resorption, indicating a shift towards a more inorganic nutrient economy. Despite this alteration, when evaluating present-day woody species, AM woody plants still display faster nitrogen mineralization and lower nitrogen resorption than EcM woody plants. This inorganic nutrient economy allows AM woody plants to thrive in warm environments with a faster litter decomposition rate. Our findings indicate that the global pattern of nutrient acquisition strategies in mycorrhizal plants is shaped by the interplay between phylogeny and climate.
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Affiliation(s)
- Lulu Guo
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meifeng Deng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Xuefei Li
- Faculty of Science, Institute for Atmospheric and Earth System Research (INAR)/Physics, University of Helsinki, Helsinki, Finland
| | - Bernhard Schmid
- Department of Geography, Remote Sensing Laboratories, University of Zürich, Zürich, Switzerland
| | - Junsheng Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Yuntao Wu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyang Peng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lingli Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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19
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Meng Y, Davison J, Clarke JT, Zobel M, Gerz M, Moora M, Öpik M, Bueno CG. Environmental modulation of plant mycorrhizal traits in the global flora. Ecol Lett 2023; 26:1862-1876. [PMID: 37766496 DOI: 10.1111/ele.14309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023]
Abstract
Mycorrhizal symbioses are known to strongly influence plant performance, structure plant communities and shape ecosystem dynamics. Plant mycorrhizal traits, such as those characterising mycorrhizal type (arbuscular (AM), ecto-, ericoid or orchid mycorrhiza) and status (obligately (OM), facultatively (FM) or non-mycorrhizal) offer valuable insight into plant belowground functionality. Here, we compile available plant mycorrhizal trait information and global occurrence data (∼ 100 million records) for 11,770 vascular plant species. Using a plant phylogenetic mega-tree and high-resolution climatic and edaphic data layers, we assess phylogenetic and environmental correlates of plant mycorrhizal traits. We find that plant mycorrhizal type is more phylogenetically conserved than plant mycorrhizal status, while environmental variables (both climatic and edaphic; notably soil texture) explain more variation in mycorrhizal status, especially FM. The previously underestimated role of environmental conditions has far-reaching implications for our understanding of ecosystem functioning under changing climatic and soil conditions.
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Affiliation(s)
- Yiming Meng
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - John T Clarke
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maret Gerz
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - C Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Pyrenean Institute of Ecology, IPE-CSIC, Jaca, Spain
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20
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Worobiec G, Worobiec E, Gedl P, Kowalski R, Peryt D, Tietz O. Fossil history of fungus host-specificity: Association of conidia of fossil Asterosporium asterospermum with macro- and microremains of Fagus. Fungal Biol 2023; 127:1312-1320. [PMID: 37821153 DOI: 10.1016/j.funbio.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 10/13/2023]
Abstract
Fossil staurosporous conidia almost identical to modern conidia of Asterosporium asterospermum were found from three Central European localities ranging from the Late Oligocene (Germany) to Middle/Late Miocene (Poland). Extant A. asterospermum is strictly host-specific and found only on branches or bark of various Fagus species from Europe, Asia and North America. Conspicuous association of conidia of A. asterospermum with numerous macro- and microremains of Fagus were reported from all the localities where fossil conidia of Asterosporium were found confirming the host-specificity of fossil A. asterospermum to ancient beeches. The host-specific relationship of A. asterospermum and beech was presumably established early in the history of the Fagus genus.
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Affiliation(s)
- Grzegorz Worobiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland.
| | - Elżbieta Worobiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Przemysław Gedl
- Institute of Geological Sciences, Polish Academy of Sciences, Research Centre in Cracow, Senacka 1, 31-002 Kraków, Poland
| | - Rafał Kowalski
- Museum of the Earth in Warsaw, Polish Academy of Sciences, Al. Na Skarpie 27, 00-488 Warszawa, Poland
| | - Danuta Peryt
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warszawa, Poland
| | - Olaf Tietz
- Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, Germany
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21
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Rúa-Giraldo ÁL. Fungal taxonomy: A puzzle with many missing pieces. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:288-311. [PMID: 37721899 PMCID: PMC10588969 DOI: 10.7705/biomedica.7052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/24/2023] [Indexed: 09/20/2023]
Abstract
Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.
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22
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Groten K, Yon F, Baldwin IT. Arbuscular mycorrhizal fungi influence the intraspecific competitive ability of plants under field and glasshouse conditions. PLANTA 2023; 258:60. [PMID: 37535207 PMCID: PMC10400695 DOI: 10.1007/s00425-023-04214-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
MAIN CONCLUSION Nicotiana attenuata's capacity to interact with arbuscular mycorrhizal fungi influences its intraspecific competitive ability under field and glasshouse conditions, but not its overall community productivity. Arbuscular mycorrhizal (AM) fungi can alter the nutrient status and growth of plants, and they can also affect plant-plant, plant-herbivore, and plant-pathogen interactions. These AM effects are rarely studied in populations under natural conditions due to the limitation of non-mycorrhizal controls. Here we used a genetic approach, establishing field and glasshouse communities of AM-harboring Nicotiana attenuata empty vector (EV) plants and isogenic plants silenced in calcium- and calmodulin-dependent protein kinase expression (irCCaMK), and unable to establish AM symbioses. Performance and growth were quantified in communities of the same (monocultures) or different genotypes (mixed cultures) and both field and glasshouse experiments returned similar responses. In mixed cultures, AM-harboring EV plants attained greater stalk lengths, shoot and root biomasses, clearly out-competing the AM fungal-deficient irCCaMK plants, while in monocultures, both genotypes grew similarly. Competitive ability was also reflected in reproductive traits: EV plants in mixed cultures outperformed irCCaMK plants. When grown in monocultures, the two genotypes did not differ in reproductive performance, though total leaf N and P contents were significantly lower independent of the community type. Plant productivity in terms of growth and seed production at the community level did not differ, while leaf nutrient content of phosphorus and nitrogen depended on the community type. We infer that AM symbioses drastically increase N. attenuata's competitive ability in mixed communities resulting in increased fitness for the individuals harboring AM without a net gain for the community.
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Affiliation(s)
- Karin Groten
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany.
| | - Felipe Yon
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ian T Baldwin
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
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23
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Osborne R, Rehneke L, Lehmann S, Roberts J, Altmann M, Altmann S, Zhang Y, Köpff E, Dominguez-Ferreras A, Okechukwu E, Sergaki C, Rich-Griffin C, Ntoukakis V, Eichmann R, Shan W, Falter-Braun P, Schäfer P. Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion. Nat Commun 2023; 14:4065. [PMID: 37429856 DOI: 10.1038/s41467-023-39885-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
Plants have benefited from interactions with symbionts for coping with challenging environments since the colonisation of land. The mechanisms of symbiont-mediated beneficial effects and similarities and differences to pathogen strategies are mostly unknown. Here, we use 106 (effector-) proteins, secreted by the symbiont Serendipita indica (Si) to modulate host physiology, to map interactions with Arabidopsis thaliana host proteins. Using integrative network analysis, we show significant convergence on target-proteins shared with pathogens and exclusive targeting of Arabidopsis proteins in the phytohormone signalling network. Functional in planta screening and phenotyping of Si effectors and interacting proteins reveals previously unknown hormone functions of Arabidopsis proteins and direct beneficial activities mediated by effectors in Arabidopsis. Thus, symbionts and pathogens target a shared molecular microbe-host interface. At the same time Si effectors specifically target the plant hormone network and constitute a powerful resource for elucidating the signalling network function and boosting plant productivity.
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Affiliation(s)
- Rory Osborne
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Laura Rehneke
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Silke Lehmann
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Laboratory of Biotechnology and Marine Chemistry LBCM, EA3884, IUEM, Southern Brittany University, 56000, Vannes, France
| | - Jemma Roberts
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Melina Altmann
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany
| | - Stefan Altmann
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany
| | - Yingqi Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Eva Köpff
- Institute of Molecular Botany, Ulm University, 89069, Ulm, Germany
| | | | - Emeka Okechukwu
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Pascal Falter-Braun
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany.
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University München, 82152, Planegg-Martinsried, Germany.
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany.
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24
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Enebe MC, Erasmus M. Susceptibility and plant immune control-a case of mycorrhizal strategy for plant colonization, symbiosis, and plant immune suppression. Front Microbiol 2023; 14:1178258. [PMID: 37476663 PMCID: PMC10355322 DOI: 10.3389/fmicb.2023.1178258] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Plants and microbes (mycorrhizal fungi to be precise) have evolved together over the past millions of years into an association that is mutualist. The plants supply the fungi with photosynthates and shelter, while the fungi reciprocate by enhancing nutrient and water uptake by the plants as well as, in some cases, control of soil-borne pathogens, but this fungi-plant association is not always beneficial. We argue that mycorrhizal fungi, despite contributing to plant nutrition, equally increase plant susceptibility to pathogens and herbivorous pests' infestation. Understanding of mycorrhizal fungi strategies for suppressing plant immunity, the phytohormones involved and the signaling pathways that aid them will enable the harnessing of tripartite (consisting of three biological systems)-plant-mycorrhizal fungi-microbe interactions for promoting sustainable production of crops.
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Affiliation(s)
- Matthew Chekwube Enebe
- Centre for Mineral Biogeochemistry, University of the Free State, Bloemfontein, South Africa
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25
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Mitchell RL, Kenrick P, Pressel S, Duckett J, Strullu-Derrien C, Davies N, McMahon WJ, Summerfield R. Terrestrial surface stabilisation by modern analogues of the earliest land plants: A multi-dimensional imaging study. GEOBIOLOGY 2023; 21:454-473. [PMID: 36779552 DOI: 10.1111/gbi.12546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/23/2022] [Accepted: 01/05/2023] [Indexed: 06/13/2023]
Abstract
The evolution of the first plant-based terrestrial ecosystems in the early Palaeozoic had a profound effect on the development of soils, the architecture of sedimentary systems, and shifts in global biogeochemical cycles. In part, this was due to the evolution of complex below-ground (root-like) anchorage systems in plants, which expanded and promoted plant-mineral interactions, weathering, and resulting surface sediment stabilisation. However, little is understood about how these micro-scale processes occurred, because of a lack of in situ plant fossils in sedimentary rocks/palaeosols that exhibit these interactions. Some modern plants (e.g., liverworts, mosses, lycophytes) share key features with the earliest land plants; these include uni- or multicellular rhizoid-like anchorage systems or simple roots, and the ability to develop below-ground networks through prostrate axes, and intimate associations with fungi, making them suitable analogues. Here, we investigated cryptogamic ground covers in Iceland and New Zealand to better understand these interactions, and how they initiate the sediment stabilisation process. We employed multi-dimensional and multi-scale imaging, including scanning electron microscopy (SEM) and X-ray Computed Tomography (μCT) of non-vascular liverworts (Haplomitriopsida and complex thalloids) and mosses, with additional imaging of vascular lycopods. We find that plants interact with their substrate in multiple ways, including: (1) through the development of extensive surface coverings as mats; (2) entrapment of sediment grains within and between networks of rhizoids; (3) grain entwining and adherence by rhizoids, through mucilage secretions, biofilm-like envelopment of thalli on surface grains; and (4) through grain entrapment within upright 'leafy' structures. Significantly, μCT imaging allows us to ascertain that rhizoids are the main method for entrapment and stabilisation of soil grains in the thalloid liverworts. This information provides us with details of how the earliest land plants may have significantly influenced early Palaeozoic sedimentary system architectures, promoted in situ weathering and proto-soil development, and how these interactions diversified over time with the evolution of new plant organ systems. Further, this study highlights the importance of cryptogamic organisms in the early stages of sediment stabilisation and soil formation today.
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Affiliation(s)
- Ria L Mitchell
- Science Group, The Natural History Museum, London, UK
- Sheffield Tomography Centre (STC), Kroto Research Institute, The University of Sheffield, Sheffield, UK
| | - Paul Kenrick
- Science Group, The Natural History Museum, London, UK
| | | | - Jeff Duckett
- Science Group, The Natural History Museum, London, UK
| | - Christine Strullu-Derrien
- Science Group, The Natural History Museum, London, UK
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205, Muséum National d'Histoire naturelle, Sorbonne Université, CNRS, Paris, France
| | - Neil Davies
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - William J McMahon
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
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26
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Priyashantha AKH, Dai DQ, Bhat DJ, Stephenson SL, Promputtha I, Kaushik P, Tibpromma S, Karunarathna SC. Plant-Fungi Interactions: Where It Goes? BIOLOGY 2023; 12:809. [PMID: 37372094 PMCID: PMC10295453 DOI: 10.3390/biology12060809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Fungi live different lifestyles-including pathogenic and symbiotic-by interacting with living plants. Recently, there has been a substantial increase in the study of phytopathogenic fungi and their interactions with plants. Symbiotic relationships with plants appear to be lagging behind, although progressive. Phytopathogenic fungi cause diseases in plants and put pressure on survival. Plants fight back against such pathogens through complicated self-defense mechanisms. However, phytopathogenic fungi develop virulent responses to overcome plant defense reactions, thus continuing their deteriorative impacts. Symbiotic relationships positively influence both plants and fungi. More interestingly, they also help plants protect themselves from pathogens. In light of the nonstop discovery of novel fungi and their strains, it is imperative to pay more attention to plant-fungi interactions. Both plants and fungi are responsive to environmental changes, therefore construction of their interaction effects has emerged as a new field of study. In this review, we first attempt to highlight the evolutionary aspect of plant-fungi interactions, then the mechanism of plants to avoid the negative impact of pathogenic fungi, and fungal strategies to overcome the plant defensive responses once they have been invaded, and finally the changes of such interactions under the different environmental conditions.
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Affiliation(s)
- A. K. Hasith Priyashantha
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China; (A.K.H.P.); (D.-Q.D.)
| | - Dong-Qin Dai
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China; (A.K.H.P.); (D.-Q.D.)
| | - Darbhe J. Bhat
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
- Biology Division, Vishnugupta Vishwavidyapeetam, Gokarna 581326, India
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | | | - Saowaluck Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China; (A.K.H.P.); (D.-Q.D.)
| | - Samantha C. Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China; (A.K.H.P.); (D.-Q.D.)
- National Institute of Fundamental Studies (NIFS), Hantana Road, Kandy 20000, Sri Lanka
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27
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Guillen‐Otero T, Lee S, Chen C, Szoevenyi P, Kessler M. A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11523. [PMID: 37342167 PMCID: PMC10278937 DOI: 10.1002/aps3.11523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 06/22/2023]
Abstract
Premise Detailed studies of the fungi associated with lycophytes and ferns provide crucial insights into the early evolution of land plants. However, most investigations to date have assessed fern-fungus interactions based only on visual root inspection. In the present research, we establish and evaluate a metabarcoding protocol to analyze the fungal communities associated with fern and lycophyte roots. Methods We used two primer pairs focused on the ITS rRNA region to screen the general fungal communities, and the 18S rRNA to target Glomeromycota fungi (i.e., arbuscular mycorrhizal fungi). To test these approaches, we collected and processed roots from 12 phylogenetically distant fern and lycophyte species. Results We found marked compositional differences between the ITS and 18S data sets. While the ITS data set demonstrated the dominance of orders Glomerales (phylum Glomeromycota), Pleosporales, and Helotiales (both in phylum Ascomycota), the 18S data set revealed the greatest diversity of Glomeromycota. Non-metric multidimensional scaling (NMDS) ordination suggested an important geographical effect in sample similarities. Discussion The ITS-based approach is a reliable and effective method to analyze the fungal communities associated with fern and lycophyte roots. The 18S approach is more appropriate for studies focused on the detailed screening of arbuscular mycorrhizal fungi.
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Affiliation(s)
- Thais Guillen‐Otero
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Soon‐Jae Lee
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Cheng‐Wei Chen
- Biodiversity Program, Taiwan International Graduate ProgramAcademia Sinica and National Taiwan Normal UniversityTaipei115Taiwan
| | - Peter Szoevenyi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
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28
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Arévalo-Granda V, Hickey-Darquea A, Prado-Vivar B, Zapata S, Duchicela J, van ‘t Hof P. Exploring the mycobiome and arbuscular mycorrhizal fungi associated with the rizosphere of the genus Inga in the pristine Ecuadorian Amazon. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1086194. [PMID: 37746118 PMCID: PMC10512398 DOI: 10.3389/ffunb.2023.1086194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/20/2023] [Indexed: 09/26/2023]
Abstract
This study explored the composition of the mycobiome in the rhizosphere of Inga seedlings in two different but neighboring forest ecosystems in the undisturbed tropical Amazon rainforest at the Tiputini Biodiversity Station in Ecuador. In terra firme plots, which were situated higher up and therefore typically outside of the influence of river floods, and in várzea plots, the lower part of the forest located near the riverbanks and therefore seasonally flooded, tree seedlings of the genus Inga were randomly collected and measured, and the rhizosphere soils surrounding the root systems was collected. Members of the Fabaceae family and the genus Inga were highly abundant in both forest ecosystems. Inga sp. seedlings collected in terra firme showed a lower shoot to root ratio compared to seedlings that were collected in várzea, suggesting that Inga seedlings which germinated in várzea soils could invest more resources in vegetative growth with shorter roots. Results of the physical-chemical properties of soil samples indicated higher proportions of N, Mo, and V in terra firme soils, whereas várzea soils present higher concentrations of all other macro- and micronutrients, which confirmed the nutrient deposition effect of seasonal flooding by the nearby river. ITS metabarcoding was used to explore the mycobiome associated with roots of the genus Inga. Bioinformatic analysis was performed using Qiime 2 to calculate the alpha and beta diversity, species taxonomy and the differential abundance of fungi and arbuscular mycorrhizal fungi. The fungal community represented 75% of the total ITS ASVs, and although present in all samples, the subphylum Glomeromycotina represented 1.42% of all ITS ASVs with annotations to 13 distinct families, including Glomeraceae (72,23%), Gigasporaceae (0,57%), Acaulosporaceae (0,49%). AMF spores of these three AMF families were morphologically identified by microscopy. Results of this study indicate that AMF surround the rhizosphere of Inga seedlings in relatively low proportions compared to other fungal groups but present in both terra firme and várzea Neotropical ecosystems.
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Affiliation(s)
- Valentina Arévalo-Granda
- Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Institute of Microbiology, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
| | - Aileen Hickey-Darquea
- Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
| | - Belén Prado-Vivar
- Institute of Microbiology, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
| | - Sonia Zapata
- Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Institute of Microbiology, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Tiputini Biodiversity Station, Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
| | - Jéssica Duchicela
- Department of Life Sciences and Agriculture, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Pieter van ‘t Hof
- Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Institute of Microbiology, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
- Tiputini Biodiversity Station, Department of Biological and Environmental Sciences - COCIBA, Universidad San Francisco de Quito-USFQ, Quito, Ecuador
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Devi R, Verma R, Dhalaria R, Kumar A, Kumar D, Puri S, Thakur M, Chauhan S, Chauhan PP, Nepovimova E, Kuca K. A systematic review on endophytic fungi and its role in the commercial applications. PLANTA 2023; 257:70. [PMID: 36856911 DOI: 10.1007/s00425-023-04087-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
MAIN CONCLUSION EF have been explored for its beneficial impact on environment and for its commercial applications. It has proved its worth in these sectors and showed an impact on biological properties of plants by producing various bioactive molecules and enzymes. Endophytes are plant mutualists that live asymptomatically within plant tissues and exist in almost every plant species. Endophytic fungi benefit from the host plant nutrition, and the host plant gains improved competitive abilities and tolerance against pathogens, herbivores, and various abiotic stresses. Endophytic fungi are one of the most inventive classes which produce secondary metabolites and play a crucial role in human health and other biotic aspects. This review is focused on systematic study on the biodiversity of endophytic fungi in plants, and their role in enhancing various properties of plants such as antimicrobial, antimycobacterial, antioxidant, cytotoxic, anticancer, and biological activity of secondary metabolites produced by various fungal endophytes in host plants reported from 1994 to 2021. This review emphasizes the endophytic fungal population shaped by host genotype, environment, and endophytic fungi genotype affecting host plant. The impact of endophytic fungi has been discussed in detail which influences the commercial properties of plants. Endophytes also have an influence on plant productivity by increasing parameters such as nutrient recycling and phytostimulation. Studies focusing on mechanisms that regulate attenuation of secondary metabolite production in EF would provide much needed impetus on ensuring continued production of bioactive molecules from a indubitable source. If this knowledge is further extensively explored regarding fungal endophytes in plants for production of potential phytochemicals, then it will help in exploring a keen area of interest for pharmacognosy.
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Affiliation(s)
- Reema Devi
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, H.P., 173229, India
| | - Rachna Verma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, H.P., 173229, India.
| | - Rajni Dhalaria
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, H.P., 173229, India
| | - Ashwani Kumar
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, Uttarakhand, 249405, India
| | - Dinesh Kumar
- School of Bioengineering and Food Technology, Shoolini University of Biotechnology and Business Management, Solan, H.P., 173229, India
| | - Sunil Puri
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, H.P., 173229, India
| | - Monika Thakur
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, H.P., 173229, India
| | - Saurav Chauhan
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, H.P., 173229, India
| | - Prem Parkash Chauhan
- Lal Bahadur Shastri Government Degree College, Saraswati Nagar, Shimla, H.P., 171206, India
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003, Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003, Hradec Kralove, Czech Republic.
- Biomedical Research Center, University Hospital Hradec Kralove, 50005, Hradec Kralove, Czech Republic.
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Kaur H, Tashima, Singh S, Kumar P. Reconditioning of plant metabolism by arbuscular mycorrhizal networks in cadmium contaminated soils: Recent perspectives. Microbiol Res 2023; 268:127293. [PMID: 36586201 DOI: 10.1016/j.micres.2022.127293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 11/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Cadmium (Cd) is one of the most perilous nonessential heavy metal for plants, owing to its high water solubility and obstruction with various physiological and biochemical processes. It enters food chain via plant uptake from contaminated soil, posing a grave menace to ecosystem and mankind. Green remediation comprises approaches intended at prudent use of natural resources for increasing profits to humans and environment. Arbuscular mycorrhizal (AM) fungi are considered a promising green technological tool for remedial of Cd-polluted soils. They are naturally associated with root system of plants in Cd-contaminated soils, evidencing their tolerance to Cd. AM can decrease Cd uptake by plants broadly through two strategies: (1) extracellular mechanisms involving Cd chelation by root exudates, binding to fungal cell wall/structures or to the glycoprotein glomalin; (2) intracellular means involving transfer via hyphal network, detoxification and vacuolar sequestration mediated by complexation of Cd with glutathione (GSH), phytochelatins (PCs), metallothioneins (MTs) and polyphosphate granules. Additionally, mycorrhizal symbiosis facilitates reconditioning of plants' metabolism primarily through dilution effect, increased water and mineral uptake. Recently, AM-induced remodelling of root cell wall synthesis has been reported to improve plant vigor and survival under Cd stressed environments. The present article highlights Cd impacts on AM growth, its diversity in Cd contaminated soils, and variations among diverse AM fungal species for imparting plant Cd tolerance. The most recent perspectives on AM-mediated Cd tolerance mechanisms in plants, including cellular and molecular studies have also been reviewed for successful utilization of these beneficial microbes in sustainable agriculture.
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Affiliation(s)
- Harmanjit Kaur
- Department of Botany, University of Allahabad, Prayagraj 211002, Uttar Pradesh, India..
| | - Tashima
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
| | - Sandeep Singh
- Department of Botany, Kanya Maha Vidyalaya, Jalandhar, Punjab 144004, India
| | - Pankaj Kumar
- Department of Microbiology, Dolphin (PG) Institute of Biomedical and Natural Sciences, Manduwala, Dehradun, Uttarakhand 248007, India.
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Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry ( Vaccinium floribundum Kunth). Microorganisms 2023; 11:microorganisms11020399. [PMID: 36838364 PMCID: PMC9961955 DOI: 10.3390/microorganisms11020399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, an endemic species of the Andean region that has not been domesticated or cultivated. Using high-throughput sequencing of the 16S rRNA and ITS region, we characterized 39 rhizosphere samples of V. floribundum from four plant genetic clusters in two soil regions from the Ecuadorian Highlands. Our results showed that Proteobacteria and Acidobacteria were the most abundant bacterial phyla and that fungal communities were not dominated by any specific taxa. Soil region was the main predictor for bacterial alpha diversity, phosphorous and lead being the most interesting edaphic factors explaining this diversity. The interaction of plant genotype and altitude was the most significant factor associated with fungal diversity. This study highlights how different factors govern the assembly of the rhizosphere microbiome of a wild plant. Bacterial communities depend more on the soil and its mineral content, while plant genetics influence the fungal community makeup. Our work illustrates plant-microbe associations and the drivers of their variation in a unique unexplored ecosystem from the Ecuadorian Andes.
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Kapoor B, Kumar P, Verma V, Irfan M, Sharma R, Bhargava B. How plants conquered land: evolution of terrestrial adaptation. J Evol Biol 2023; 36:5-14. [PMID: 36083189 DOI: 10.1111/jeb.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023]
Abstract
The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.
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Affiliation(s)
- Bhuvnesh Kapoor
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, USA
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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33
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Role of carbohydrate-active enzymes in mycorrhizal symbioses. Essays Biochem 2022; 67:471-478. [PMID: 36562143 DOI: 10.1042/ebc20220127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
Mycorrhizal fungi form mutually beneficial interactions with a wide range of terrestrial plants. During this symbiosis, the associated fungus provides mineral nutrients, such as phosphorus and nitrogen, to its host plant in exchange of photosynthesis-derived carbohydrates. Genome sequencing of mycorrhizal fungi has shown that arbuscular mycorrhizal fungi and ectomycorrhizal fungi have a restricted set of plant-cell wall degrading enzymes (PCWDE) genes, while orchid and ericoid mycorrhizal fungi have an extended PCWDE repertoire similar to soil decomposers and wood-decay fungi. On the other hand, mycorrhizal fungi have retained a substantial set of carbohydrate active enzymes (CAZymes) acting on microbial polysaccharides. Functional analysis has shown that several of the remaining PCWDEs are involved in the fungal root colonization and establishment of the symbiotic interface. In this review, we highlight the current knowledge on the evolution and function of PCWDEs in mycorrhizal fungi.
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34
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Bowman JL. The origin of a land flora. NATURE PLANTS 2022; 8:1352-1369. [PMID: 36550365 DOI: 10.1038/s41477-022-01283-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
The origin of a land flora fundamentally shifted the course of evolution of life on earth, facilitating terrestrialization of other eukaryotic lineages and altering the planet's geology, from changing atmospheric and hydrological cycles to transforming continental erosion processes. Despite algal lineages inhabiting the terrestrial environment for a considerable preceding period, they failed to evolve complex multicellularity necessary to conquer the land. About 470 million years ago, one lineage of charophycean alga evolved complex multicellularity via developmental innovations in both haploid and diploid generations and became land plants (embryophytes), which rapidly diversified to dominate most terrestrial habitats. Genome sequences have provided unprecedented insights into the genetic and genomic bases for embryophyte origins, with some embryophyte-specific genes being associated with the evolution of key developmental or physiological attributes, such as meristems, rhizoids and the ability to form mycorrhizal associations. However, based on the fossil record, the evolution of the defining feature of embryophytes, the embryo, and consequently the sporangium that provided a reproductive advantage, may have been most critical in their rise to dominance. The long timeframe and singularity of a land flora were perhaps due to the stepwise assembly of a large constellation of genetic innovations required to conquer the terrestrial environment.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Victoria, Australia.
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35
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Ablimit R, Li W, Zhang J, Gao H, Zhao Y, Cheng M, Meng X, An L, Chen Y. Altering microbial community for improving soil properties and agricultural sustainability during a 10-year maize-green manure intercropping in Northwest China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 321:115859. [PMID: 35985268 DOI: 10.1016/j.jenvman.2022.115859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Maize is a crop that is cultivated worldwide. The Hexi Oasis is one of the most important areas for high-yield maize seed production in China. Green manure, a plant fertilizer, has great potential for increasing crop yield and agricultural sustainability. However, the role of microorganisms in soil health and the microbiological mechanism of green manure in improving soil fertility and crop production in the Hexi Oasis area remain unknown. The effects of maize-green manure intercropping on the soil microbial community structure and diversity and the mechanism of soil improvement were investigated in a 10-year field experiment. The study revealed that microbial phylotypes were grouped into four major ecological clusters. Module #2 is a soil core ecological cluster enriched with many plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi. The application of green manure led to significantly increased soil pH, nutrient contents, and enzyme activities, and significantly reduced the relative abundance of potential plant pathogens compared with monocropping, which should ensure high and stable maize yield under long-term continuous cropping. It also increased the economic benefits by 56.39% compared with monocropping, owing to the additional products produced by the green manure. These improvements were associated with changes in the microbial community structure and activity, consistent with the structural equation model results. Therefore, soil microorganisms are the key drivers of the potential benefits of maize-green manure on agricultural sustainability.
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Affiliation(s)
- Ruxangul Ablimit
- School of Life Sciences, Lanzhou, 730000, China; The Key Laboratory of Cell Activity and Adversity Adaptation, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Weikun Li
- School of Life Sciences, Lanzhou, 730000, China; The Key Laboratory of Cell Activity and Adversity Adaptation, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jiudong Zhang
- Institute of Soil, Fertilizer, and Water Saving Agriculture, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, 730070, China
| | - Haining Gao
- Key Laboratory of the Hexi Corridor Resources Utilization of Gansu, Zhangye, 734000, China
| | - Yiming Zhao
- School of Life Sciences, Lanzhou, 730000, China
| | | | - Xueqin Meng
- School of Life Sciences, Lanzhou, 730000, China
| | - Lizhe An
- School of Life Sciences, Lanzhou, 730000, China.
| | - Yong Chen
- School of Life Sciences, Lanzhou, 730000, China; The Key Laboratory of Cell Activity and Adversity Adaptation, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Effects of High Temperature-Triggered Transcriptomics on the Physiological Adaptability of Cenococcum geophilum, an Ectomycorrhizal Fungus. Microorganisms 2022; 10:microorganisms10102039. [PMID: 36296315 PMCID: PMC9607556 DOI: 10.3390/microorganisms10102039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
High temperature stress caused by global warming presents a challenge to the healthy development of forestry. Cenococcum geophilum is a common ectomycorrhizal fungus (ECMF) in the forest system and has become an important fungus resource with application potential in forest vegetation restoration. In this study, three sensitive isolates of C. geophilum (ChCg01, JaCg144 and JaCg202) and three tolerant isolates of C. geophilum (ACg07, ChCg28 and ChCg100) were used to analyze the physiological and molecular responses to high temperature. The results showed that high temperature had a significant negative effect on the growth of sensitive isolates while promoting the growth of tolerant isolates. The antioxidative enzymes activity of C. geophilum isolates increased under high temperature stress, and the SOD activity of tolerant isolates (A07Cg and ChCg100) was higher than that of sensitive isolates (ChCg01 and JaCg202) significantly. The tolerant isolates secreted more succinate, while the sensitive isolates secreted more oxalic acid under high temperature stress. Comparative transcriptomic analysis showed that differentially expressed genes (DEGs) of six C. geophilum isolates were significantly enriched in "antioxidant" GO entry in the molecular. In addition, the "ABC transporters" pathway and the "glyoxylate and dicarboxylic acid metabolic" were shared in the three tolerant isolates and the three sensitive isolates, respectively. These results were further verified by RT-qPCR analysis. In conclusion, our findings suggest that C. geophilum can affect the organic acid secretion and increase antioxidant enzyme activity in response to high temperature by upregulating related genes.
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Guy P, Sibly R, Smart SM, Tibbett M, Pickles BJ. Mycorrhizal type of woody plants influences understory species richness in British broadleaved woodlands. THE NEW PHYTOLOGIST 2022; 235:2046-2053. [PMID: 35622460 PMCID: PMC9543792 DOI: 10.1111/nph.18274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Mature temperate woodlands are commonly dominated by ectomycorrhizal trees, whereas understory plants predominantly form arbuscular mycorrhizal associations. Due to differences in plant-fungus compatibility between canopy and ground layer vegetation the 'mycorrhizal mediation hypothesis' predicts that herbaceous plant establishment may be limited by a lack of suitable mycorrhizal fungal inoculum. We examined plant species data for 103 woodlands across Great Britain recorded in 1971 and in 2000 to test whether herbaceous plant species richness was related to the proportion of arbuscular mycorrhizal woody plants. We compared the effect of mycorrhizal type with other important drivers of woodland plant species richness. We found a positive effect of the relative abundance of arbuscular mycorrhizal woody plants on herbaceous plant species richness. The size of the observed effect was smaller than that of pH. Moreover, the effect persisted over time, despite many woodlands undergoing marked successional change and increased understorey shading. This work supports the mycorrhizal mediation hypothesis in British woodlands and suggests that increased abundance of arbuscular mycorrhizal woody plants is associated with greater understory plant species richness.
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Affiliation(s)
- Petra Guy
- School of Biological SciencesUniversity of Reading, Health and Life Sciences BuildingWhiteknightsReadingRG6 6EXUK
- School of Agriculture, Policy, and DevelopmentUniversity of ReadingWhiteknightsReadingRG6 6BZUK
| | - Richard Sibly
- School of Biological SciencesUniversity of Reading, Health and Life Sciences BuildingWhiteknightsReadingRG6 6EXUK
| | - Simon M. Smart
- UK Centre for Ecology & HydrologyLibrary Avenue, BailriggLancasterLA1 4APUK
| | - Mark Tibbett
- School of Agriculture, Policy, and DevelopmentUniversity of ReadingWhiteknightsReadingRG6 6BZUK
| | - Brian J. Pickles
- School of Biological SciencesUniversity of Reading, Health and Life Sciences BuildingWhiteknightsReadingRG6 6EXUK
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Perez-Lamarque B, Petrolli R, Strullu-Derrien C, Strasberg D, Morlon H, Selosse MA, Martos F. Structure and specialization of mycorrhizal networks in phylogenetically diverse tropical communities. ENVIRONMENTAL MICROBIOME 2022; 17:38. [PMID: 35859141 PMCID: PMC9297633 DOI: 10.1186/s40793-022-00434-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/27/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND The root mycobiome plays a fundamental role in plant nutrition and protection against biotic and abiotic stresses. In temperate forests or meadows dominated by angiosperms, the numerous fungi involved in root symbioses are often shared between neighboring plants, thus forming complex plant-fungus interaction networks of weak specialization. Whether this weak specialization also holds in rich tropical communities with more phylogenetically diverse sets of plant lineages remains unknown. We collected roots of 30 plant species in semi-natural tropical communities including angiosperms, ferns, and lycophytes, in three different habitat types on La Réunion island: a recent lava flow, a wet thicket, and an ericoid shrubland. We identified root-inhabiting fungi by sequencing both the 18S rRNA and the ITS2 variable regions. We assessed the diversity of mycorrhizal fungal taxa according to plant species and lineages, as well as the structure and specialization of the resulting plant-fungus networks. RESULTS The 18S and ITS2 datasets are highly complementary at revealing the root mycobiota. According to 18S, Glomeromycotina colonize all plant groups in all habitats forming the least specialized interactions, resulting in nested network structures, while Mucoromycotina (Endogonales) are more abundant in the wetland and show higher specialization and modularity compared to the former. According to ITS2, mycorrhizal fungi of Ericaceae and Orchidaceae, namely Helotiales, Sebacinales, and Cantharellales, also colonize the roots of most plant lineages, confirming that they are frequent endophytes. While Helotiales and Sebacinales present intermediate levels of specialization, Cantharellales are more specialized and more sporadic in their interactions with plants, resulting in highly modular networks. CONCLUSIONS This study of the root mycobiome in tropical environments reinforces the idea that mycorrhizal fungal taxa are locally shared between co-occurring plants, including phylogenetically distant plants (e.g. lycophytes and angiosperms), where they may form functional mycorrhizae or establish endophytic colonization. Yet, we demonstrate that, irrespectively of the environmental variations, the level of specialization significantly varies according to the fungal lineages, probably reflecting the different evolutionary origins of these plant-fungus symbioses. Frequent fungal sharing between plants questions the roles of the different fungi in community functioning and highlights the importance of considering networks of interactions rather than isolated hosts.
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Affiliation(s)
- Benoît Perez-Lamarque
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP39, 57 rue Cuvier, 75 005, Paris, France.
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75 005, Paris, France.
| | - Rémi Petrolli
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP39, 57 rue Cuvier, 75 005, Paris, France
| | - Christine Strullu-Derrien
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP39, 57 rue Cuvier, 75 005, Paris, France
- Science Group, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Dominique Strasberg
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical, UMR PVBMT, Université de La Réunion, 97 400, Saint-Denis, La Réunion, France
| | - Hélène Morlon
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75 005, Paris, France
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP39, 57 rue Cuvier, 75 005, Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
- Institut Universitaire de France (IUF), Paris, France
| | - Florent Martos
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP39, 57 rue Cuvier, 75 005, Paris, France
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39
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Marro N, Grilli G, Soteras F, Caccia M, Longo S, Cofré N, Borda V, Burni M, Janoušková M, Urcelay C. The effects of arbuscular mycorrhizal fungal species and taxonomic groups on stressed and unstressed plants: a global meta-analysis. THE NEW PHYTOLOGIST 2022; 235:320-332. [PMID: 35302658 DOI: 10.1111/nph.18102] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/08/2022] [Indexed: 05/25/2023]
Abstract
The great majority of plants gain access to soil nutrients and enhance their performance under stressful conditions through symbiosis with arbuscular mycorrhizal fungi (AMF). The benefits that AMF confer vary among species and taxonomic groups. However, a comparative analysis of the different benefits among AMF has not yet been performed. We conducted a global meta-analysis of recent studies testing the benefits of individual AMF species and main taxonomic groups in terms of plant performance (growth and nutrition). Separately, we examined AMF benefits to plants facing biotic (pathogens, parasites, and herbivores) and abiotic (drought, salinity, and heavy metals) stress. AMF had stronger positive effects on phosphorus nutrition than on plant growth and nitrogen nutrition and the effects on the growth of plants facing biotic and abiotic stresses were similarly positive. While the AMF taxonomic groups showed positive effects on plant performance either with or without stress, Diversisporales were the most beneficial to plants without stress and Gigasporales to plants facing biotic stress. Our results provide a comprehensive analysis of the benefits of different AMF species and taxonomic groups on plant performance and useful insights for their management and use as bio-inoculants for agriculture and restoration.
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Affiliation(s)
- Nicolás Marro
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
- Department of Mycorrhizal Symbioses, Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Gabriel Grilli
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
| | - Florencia Soteras
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
| | - Milena Caccia
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
| | - Silvana Longo
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
| | - Noelia Cofré
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
| | - Valentina Borda
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
| | - Magali Burni
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
| | - Martina Janoušková
- Department of Mycorrhizal Symbioses, Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Carlos Urcelay
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, FCEFyN, Universidad Nacional de Córdoba, CC, 495, 5000, Córdoba, Argentina
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40
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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. THE NEW PHYTOLOGIST 2022; 235:306-319. [PMID: 35383395 DOI: 10.1111/nph.18143] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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41
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Wu B, Hao W, Cox MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biol 2022; 20:144. [PMID: 35706021 PMCID: PMC9202105 DOI: 10.1186/s12915-022-01346-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. Results By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. Conclusions The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01346-8.
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Affiliation(s)
- Baojun Wu
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
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Almario J, Fabiańska I, Saridis G, Bucher M. Unearthing the plant-microbe quid pro quo in root associations with beneficial fungi. THE NEW PHYTOLOGIST 2022; 234:1967-1976. [PMID: 35239199 DOI: 10.1111/nph.18061] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Mutualistic symbiotic associations between multicellular eukaryotes and their microbiota are driven by the exchange of nutrients in a quid pro quo manner. In the widespread arbuscular mycorrhizal (AM) symbiosis involving plant roots and Glomeromycotina fungi, the mycobiont is supplied with carbon through photosynthesis, which in return supplies the host plant with essential minerals such as phosphorus (P). Most terrestrial plants are largely dependent on AM fungi for nutrients, which raises the question of how plants that are unable to form a functional AM sustain their P nutrition. AM nonhost plants can form alternative, evolutionarily younger, mycorrhizal associations such as the ectomycorrhiza, ericoid and orchid mycorrhiza. However, it is unclear how plants such as the Brassicaceae species Arabidopsis thaliana, which do not form known mycorrhizal symbioses, have adapted to the loss of these essential mycorrhizal traits. Isotope tracing experiments with root-colonizing fungi have revealed the existence of new 'mycorrhizal-like' fungi capable of transferring nutrients such as nitrogen (N) and P to plants, including Brassicaceae. Here, we provide an overview of the biology of trophic relationships between roots and fungi and how these associations might support plant adaptation to climate change.
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Affiliation(s)
- Juliana Almario
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Claude Bernard Lyon1, 43 Boulevard du 11 novembre 1918, Villeurbanne, 69622, France
| | - Izabela Fabiańska
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Georgios Saridis
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Marcel Bucher
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50931, Germany
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43
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Yan H, Freschet GT, Wang H, Hogan JA, Li S, Valverde-Barrantes OJ, Fu X, Wang R, Dai X, Jiang L, Meng S, Yang F, Zhang M, Kou L. Mycorrhizal symbiosis pathway and edaphic fertility frame root economics space among tree species. THE NEW PHYTOLOGIST 2022; 234:1639-1653. [PMID: 35243647 DOI: 10.1111/nph.18066] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
The root economics space (RES) is multidimensional and largely shaped by belowground biotic and abiotic influences. However, how root-fungal symbioses and edaphic fertility drive this complexity remains unclear. Here, we measured absorptive root traits of 112 tree species in temperate and subtropical forests of China, including traits linked to functional differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) hosts. Our data, from known mycorrhizal tree species, revealed a 'fungal-symbiosis' dimension distinguishing AM from ECM species. This divergence likely resulted from the contrasting mycorrhizal evolutionary development of AM vs ECM associations. Increased root tissue cortical space facilitates AM symbiosis, whereas increased root branching favours ECM symbiosis. Irrespective of mycorrhizal type, a 'root-lifespan' dimension reflecting aspects of root construction cost and defence was controlled by variation in specific root length and root tissue density, which was fully independent of root nitrogen content. Within this function-based RES, we observed a substantial covariation of axes with soil phosphorus and nitrate levels, highlighting the role played by these two axes in nutrient acquisition and conservation. Overall, our findings demonstrate the importance of evolved mycorrhizal symbiosis pathway and edaphic fertility in framing the RES, and provide theoretical and mechanistic insights into the complexity of root economics.
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Affiliation(s)
- Han Yan
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Grégoire T Freschet
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, Moulis, 09200, France
| | - Huimin Wang
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - James Aaron Hogan
- Department of Biological Sciences, Institute of Environment, International Center of Tropical Biodiversity, Florida International University, Miami, FL, 33199, USA
- Department of Biology, University of Florida, Gainesville, FL, 32605, USA
| | - Shenggong Li
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Oscar J Valverde-Barrantes
- Department of Biological Sciences, Institute of Environment, International Center of Tropical Biodiversity, Florida International University, Miami, FL, 33199, USA
| | - Xiaoli Fu
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruili Wang
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Xiaoqin Dai
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Jiang
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengwang Meng
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fengting Yang
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Liang Kou
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
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Adnan M, Islam W, Gang L, Chen HYH. Advanced research tools for fungal diversity and its impact on forest ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45044-45062. [PMID: 35460003 DOI: 10.1007/s11356-022-20317-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Fungi are dominant ecological participants in the forest ecosystems, which play a major role in recycling organic matter and channeling nutrients across trophic levels. Fungal populations are shaped by plant communities and environmental parameters, and in turn, fungal communities also impact the forest ecosystem through intrinsic participation of different fungal guilds. Mycorrhizal fungi result in conservation and stability of forest ecosystem, while pathogenic fungi can bring change in forest ecosystem, by replacing the dominant plant species with new or exotic plant species. Saprotrophic fungi, being ecological regulators in the forest ecosystem, convert dead tree logs into reusable constituents and complete the ecological cycles of nitrogen and carbon. However, fungal communities have not been studied in-depth with respect to functional, spatiotemporal, or environmental parameters. Previously, fungal diversity and its role in shaping the forest ecosystem were studied by traditional and laborious cultural methods, which were unable to achieve real-time results and draw a conclusive picture of fungal communities. This review highlights the latest advances in biological methods such as next-generation sequencing and meta'omics for observing fungal diversity in the forest ecosystem, the role of different fungal groups in shaping forest ecosystem, forest productivity, and nutrient cycling at global scales.
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Affiliation(s)
- Muhammad Adnan
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liu Gang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Han Y H Chen
- Faculty of Forestry and the Forest Environment, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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Han X, Tsuda K. Evolutionary footprint of plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102209. [PMID: 35430538 DOI: 10.1016/j.pbi.2022.102209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
There are pieces of evidence from genomic footprints and fossil records indicating that plants have co-evolved with microbes after terrestrialization for more than 407 million years. Therefore, to truly comprehend plant evolution, we need to understand the co-evolutionary process and history between plants and microbes. Recent developments in genomes and transcriptomes of a vast number of plant species as well as microbes have greatly expanded our knowledge of the evolution of the plant immune system. In this review, we summarize recent advances in the co-evolution between plants and microbes with emphasis on the plant side and point out future research needed for understanding plant-microbial co-evolution. Knowledge of the evolution and variation of the plant immune system will better equip us on designing crops with boosted performance in agricultural fields.
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Affiliation(s)
- Xiaowei Han
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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46
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Perez‐Lamarque B, Öpik M, Maliet O, Afonso Silva AC, Selosse M, Martos F, Morlon H. Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont. Mol Ecol 2022; 31:3496-3512. [PMID: 35451535 PMCID: PMC9321572 DOI: 10.1111/mec.16478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022]
Abstract
Analysing diversification dynamics is key to understanding the past evolutionary history of clades that led to present-day biodiversity patterns. While such analyses are widespread in well-characterized groups of species, they are much more challenging in groups for which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyse the diversification dynamics of this clade in the past 500 million years. We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 million years ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.
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Affiliation(s)
- Benoît Perez‐Lamarque
- Institut de biologie de l’École normale supérieure (IBENS)École Normale SupérieureCNRSINSERMUniversité PSLParisFrance
- Institut de Systématique, Évolution, Biodiversité (ISYEB)Muséum National d’histoire NaturelleCNRSSorbonne UniversitéEPHE, UA, CP39ParisFrance
| | | | - Odile Maliet
- Institut de biologie de l’École normale supérieure (IBENS)École Normale SupérieureCNRSINSERMUniversité PSLParisFrance
| | - Ana C. Afonso Silva
- Institut de biologie de l’École normale supérieure (IBENS)École Normale SupérieureCNRSINSERMUniversité PSLParisFrance
- University of LilleCNRS, UMR 8198 ‐ Evo‐Eco‐PaleoLilleFrance
| | - Marc‐André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB)Muséum National d’histoire NaturelleCNRSSorbonne UniversitéEPHE, UA, CP39ParisFrance
- Department of Plant Taxonomy and Nature ConservationUniversity of GdanskGdanskPoland
| | - Florent Martos
- Institut de Systématique, Évolution, Biodiversité (ISYEB)Muséum National d’histoire NaturelleCNRSSorbonne UniversitéEPHE, UA, CP39ParisFrance
| | - Hélène Morlon
- Institut de biologie de l’École normale supérieure (IBENS)École Normale SupérieureCNRSINSERMUniversité PSLParisFrance
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47
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Bennett AE, Groten K. The Costs and Benefits of Plant-Arbuscular Mycorrhizal Fungal Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:649-672. [PMID: 35216519 DOI: 10.1146/annurev-arplant-102820-124504] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi is often perceived as beneficial for both partners, though a large ecological literature highlights the context dependency of this interaction. Changes in abiotic variables, such as nutrient availability, can drive the interaction along the mutualism-parasitism continuum with variable outcomes for plant growth and fitness. However, AM fungi can benefit plants in more ways than improved phosphorus nutrition and plant growth. For example, AM fungi can promote abiotic and biotic stress tolerance even when considered parasitic from a nutrient provision perspective. Other than being obligate biotrophs, very little is known about the benefits AM fungi gain from plants. In this review, we utilize both molecular biology and ecological approaches to expand our understanding of the plant-AM fungal interaction across disciplines.
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Affiliation(s)
- Alison E Bennett
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio, USA;
| | - Karin Groten
- Max Planck Institute for Chemical Ecology, Jena, Germany;
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Jiang D, Lin R, Tan M, Yan J, Yan S. The mycorrhizal-induced growth promotion and insect resistance reduction in Populus alba × P. berolinensis seedlings: a multi-omics study. TREE PHYSIOLOGY 2022; 42:1059-1069. [PMID: 35022794 DOI: 10.1093/treephys/tpab155] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/13/2021] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are an alternative to chemical insecticides or fertilizers, and there is an urgent need to extend the application of AM fungi to woody plants. This study aims to investigate the growth and resistance against the gypsy moth larvae (Lymantria dispar) in Glomus intraradices-colonized Populus alba × P. berolinensis seedlings, and to unravel the transcriptome and metabolome phenotypes recruited by AM fungus colonization that affect plant growth and insect resistance. Our results showed a positive mycorrhizal growth response, i.e., growth and biomass of mycorrhizal seedlings were enhanced. However, AM fungus inoculation reduced the resistance of poplar to gypsy moth larvae, as evidenced by the decreased carbon/nitrogen ratio in leaves, as well as the increased larval growth and shortened larval developmental duration. Transcriptome analysis revealed that in both auxin and gibberellin signaling transductions, all nodes were responsive to AM symbiosis and most differentially expressed genes belonging to effectors were up-regulated in mycorrhizal seedlings. Furthermore, the two key enzymes (4-coumarate-CoA ligase and trans-cinnamate 4-monooxygenase) involved in the synthesis of p-Coumaroyl-CoA, an initial metabolite in flavonoid biosynthesis and the first rate-limiting enzyme (chalcone synthase) in flavonoid biosynthesis, were down-regulated at the transcriptional level. Consistent with the transcriptome results, metabolome analysis found that the amounts of all differentially accumulated flavonoid compounds (e.g., catechin and quercetin) identified in mycorrhizal seedlings were decreased. Taken together, these findings highlight the diverse outcomes of AM fungi-host plant-insect interaction and reveal the regulatory network of the positive mycorrhizal growth response and mycorrhizal-induced reduction of insect resistance in poplar.
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Affiliation(s)
- Dun Jiang
- Department of Forestry School of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
- College of Forestry Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
| | - Ruoxuan Lin
- Department of Economics College of Economics and Management, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R.China
| | - Mingtao Tan
- Department of Forestry School of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
- College of Forestry Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
| | - Junxin Yan
- Department of Landscape Architecture College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
| | - Shanchun Yan
- Department of Forestry School of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
- College of Forestry Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China
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Abstract
The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.
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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. THE NEW PHYTOLOGIST 2022; 233:2294-2309. [PMID: 34861049 DOI: 10.1111/nph.17892] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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