1
|
Shrestha A, Limay-Rios V, Brettingham DJL, Raizada MN. Maize pollen carry bacteria that suppress a fungal pathogen that enters through the male gamete fertilization route. FRONTIERS IN PLANT SCIENCE 2024; 14:1286199. [PMID: 38269134 PMCID: PMC10806238 DOI: 10.3389/fpls.2023.1286199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024]
Abstract
In flowering plants, after being released from pollen grains, the male gametes use the style channel to migrate towards the ovary where they fertilize awaiting eggs. Environmental pathogens exploit the style passage, resulting in diseased progeny seed. The belief is that pollen also transmits pathogens into the style. By contrast, we hypothesized that pollen carries beneficial microbes that suppress environmental pathogens on the style passage. No prior studies have reported pollen-associated bacterial functions in any plant species. Here, bacteria were cultured from maize (corn) pollen encompassing wild ancestors and farmer-selected landraces from across the Americas, grown in a common field in Canada for one season. In total, 298 bacterial isolates were cultured, spanning 45 genera, 103 species, and 88 OTUs, dominated by Pantoea, Bacillus, Pseudomonas, Erwinia, and Microbacterium. Full-length 16S DNA-based taxonomic profiling showed that 78% of bacterial taxa from the major wild ancestor of maize (Parviglumis teosinte) were present in at least one cultivated landrace. The species names of the bacterial isolates were used to search the pathogen literature systematically; this preliminary evidence predicted that the vast majority of the pollen-associated bacteria analyzed are not maize pathogens. The pollen-associated bacteria were tested in vitro against a style-invading Fusarium pathogen shown to cause Gibberella ear rot (GER): 14 isolates inhibited this pathogen. Genome mining showed that all the anti-Fusarium bacterial species encode phzF, associated with biosynthesis of the natural fungicide, phenazine. To mimic the male gamete migration route, three pollen-associated bacterial strains were sprayed onto styles (silks), followed by Fusarium inoculation; these bacteria reduced GER symptoms and mycotoxin accumulation in progeny seed. Confocal microscopy was used to search for direct evidence that pollen-associated bacteria can defend living silks against Fusarium graminearum (Fg); bacterial strain AS541 (Kluyvera intermedia), isolated from pollen of ancestral Parviglumis, was observed to colonize the susceptible style/silk entry points of Fg (silk epidermis, trichomes, wounds). Furthermore, on style/silk tissue, AS541 colonized/aggregated on Fg hyphae, and was associated with Fg hyphal breaks. These results suggest that pollen has the potential to carry bacteria that can defend the style/silk passage against an environmental pathogen - a novel observation.
Collapse
Affiliation(s)
- Anuja Shrestha
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Victor Limay-Rios
- Department of Plant Agriculture, University of Guelph, Ridgetown, ON, Canada
| | | | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
2
|
Hiruma K, Aoki S, Takino J, Higa T, Utami YD, Shiina A, Okamoto M, Nakamura M, Kawamura N, Ohmori Y, Sugita R, Tanoi K, Sato T, Oikawa H, Minami A, Iwasaki W, Saijo Y. A fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae. Nat Commun 2023; 14:5288. [PMID: 37673872 PMCID: PMC10482981 DOI: 10.1038/s41467-023-40867-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
Plant-associated fungi show diverse lifestyles from pathogenic to mutualistic to the host; however, the principles and mechanisms through which they shift the lifestyles require elucidation. The root fungus Colletotrichum tofieldiae (Ct) promotes Arabidopsis thaliana growth under phosphate limiting conditions. Here we describe a Ct strain, designated Ct3, that severely inhibits plant growth. Ct3 pathogenesis occurs through activation of host abscisic acid pathways via a fungal secondary metabolism gene cluster related to the biosynthesis of sesquiterpene metabolites, including botrydial. Cluster activation during root infection suppresses host nutrient uptake-related genes and changes mineral contents, suggesting a role in manipulating host nutrition state. Conversely, disruption or environmental suppression of the cluster renders Ct3 beneficial for plant growth, in a manner dependent on host phosphate starvation response regulators. Our findings indicate that a fungal metabolism cluster provides a means by which infectious fungi modulate lifestyles along the parasitic-mutualistic continuum in fluctuating environments.
Collapse
Affiliation(s)
- Kei Hiruma
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
- Department of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
| | - Seishiro Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-0882, Japan
| | - Junya Takino
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Takeshi Higa
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yuniar Devi Utami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Akito Shiina
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-cho, Utsunomiya, Tochigi, 321-8505, Japan
| | - Masami Nakamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Nanami Kawamura
- Department of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Yoshihiro Ohmori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryohei Sugita
- Radioisotope Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Toyozo Sato
- Genetic Resources Center, National Agriculture and Food Research Organization, Ibaraki, 305-8602, Japan
| | - Hideaki Oikawa
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong, 529020, China
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-0882, Japan
| | - Yusuke Saijo
- Department of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| |
Collapse
|
3
|
Reprogramming of Fundamental miRNA and Gene Expression during the Barley- Piriformospora indica Interaction. J Fungi (Basel) 2022; 9:jof9010024. [PMID: 36675845 PMCID: PMC9865155 DOI: 10.3390/jof9010024] [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: 11/12/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The interactions between plants and microorganisms, which are widely present in the microbial-dominated rhizosphere, have been studied. This association is highly beneficial to the organisms involved, as plants benefit soil microorganisms by providing them with metabolites, while microorganisms promote plant growth and development by promoting nutrient uptake and/or protecting the plant from biotic and abiotic stresses. Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and establishes various benefits for the plants. In this work, an interaction between barley and the P. indica was established to elucidate microRNA (miRNA)-based regulatory changes in miRNA profiles and gene expression that occurred during the symbiosis. Growth promotion and vigorous root development were confirmed in barley colonized by P. indica. The genome-wide expression profile analysis of miRNAs in barley root showed that 7,798,928, 6,418,039 and 7,136,192 clean reads were obtained from the libraries of mock, 3 dai and 7 dai roots, respectively. Sequencing of the barley genome yielded in 81 novel miRNA and 450 differently expressed genes (DEGs). Additionally, 11, 24, 6 differentially expressed microRNAs (DEMs) in barley were found in the three comparison groups, including 3 dai vs. mock, 7 dai vs. mock and 7 dai vs. 3 dai, respectively. The predicted target genes of these miRNAs are mainly involved in transcription, cell division, auxin signal perception and transduction, photosynthesis and hormone stimulus. Transcriptome analysis of P. indica identified 667 and 594 differentially expressed genes (DEG) at 3 dai and 7 dai. Annotation and GO (Gene Ontology) analysis indicated that the DEGs with the greatest changes were concentrated in oxidoreductase activity, ion transmembrane transporter activity. It implies that reprogramming of fundamental miRNA and gene expression occurs both in barley and P. indica. Analysis of global changes in miRNA profiles of barley colonized with P. indica revealed that several putative endogenous barley miRNAs expressed upon colonization belonging to known micro RNA families involved in growth and developmental regulation.
Collapse
|
4
|
Wang X, Wang M, Wang L, Feng H, He X, Chang S, Wang D, Wang L, Yang J, An G, Wang X, Kong L, Geng Z, Wang E. Whole-plant microbiome profiling reveals a novel geminivirus associated with soybean stay-green disease. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2159-2173. [PMID: 35869670 PMCID: PMC9616524 DOI: 10.1111/pbi.13896] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Microbiota colonize every accessible plant tissue and play fundamental roles in plant growth and health. Soybean stay-green syndrome (SGS), a condition that causes delayed leaf senescence (stay-green), flat pods and abnormal seeds of soybean, has become the most serious disease of soybean in China. However, the direct cause of SGS is highly debated, and little is known about how SGS affect soybean microbiome dynamics, particularly the seed microbiome. We studied the bacterial, fungal, and viral communities associated with different soybean tissues with and without SGS using a multi-omics approach, and investigated the possible pathogenic agents associated with SGS and how SGS affects the assembly and functions of plant-associated microbiomes. We obtained a comprehensive view of the composition, function, loads, diversity, and dynamics of soybean microbiomes in the rhizosphere, root, stem, leaf, pod, and seed compartments, and discovered that soybean SGS was associated with dramatically increased microbial loads and dysbiosis of the bacterial microbiota in seeds. Furthermore, we identified a novel geminivirus that was strongly associated with soybean SGS, regardless of plant cultivar, sampling location, or harvest year. This whole-plant microbiome profiling of soybean provides the first demonstration of geminivirus infection associated with microbiota dysbiosis, which might represent a general microbiological symptom of plant diseases.
Collapse
Affiliation(s)
- Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
| | - Mingxing Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Like Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Huan Feng
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
- Northwest A&F UniversityYanglingChina
| | - Xin He
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of AgricultureHenan UniversityKaifengChina
| | - Shihao Chang
- Zhoukou Academy of Agricultural SciencesZhoukouChina
| | - Dapeng Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
| | - Lei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of AgricultureHenan UniversityKaifengChina
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
| | - Guoyong An
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of AgricultureHenan UniversityKaifengChina
| | | | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of AgronomyShandong Agricultural UniversityTaianChina
| | - Zhen Geng
- Zhoukou Academy of Agricultural SciencesZhoukouChina
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
| |
Collapse
|
5
|
Poveda J, Díaz-González S, Díaz-Urbano M, Velasco P, Sacristán S. Fungal endophytes of Brassicaceae: Molecular interactions and crop benefits. FRONTIERS IN PLANT SCIENCE 2022; 13:932288. [PMID: 35991403 PMCID: PMC9390090 DOI: 10.3389/fpls.2022.932288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Brassicaceae family includes an important group of plants of great scientific interest, e.g., the model plant Arabidopsis thaliana, and of economic interest, such as crops of the genus Brassica (Brassica oleracea, Brassica napus, Brassica rapa, etc.). This group of plants is characterized by the synthesis and accumulation in their tissues of secondary metabolites called glucosinolates (GSLs), sulfur-containing compounds mainly involved in plant defense against pathogens and pests. Brassicaceae plants are among the 30% of plant species that cannot establish optimal associations with mycorrhizal hosts (together with other plant families such as Proteaceae, Chenopodiaceae, and Caryophyllaceae), and GSLs could be involved in this evolutionary process of non-interaction. However, this group of plants can establish beneficial interactions with endophytic fungi, which requires a reduction of defensive responses by the host plant and/or an evasion, tolerance, or suppression of plant defenses by the fungus. Although much remains to be known about the mechanisms involved in the Brassicaceae-endophyte fungal interaction, several cases have been described, in which the fungi need to interfere with the GSL synthesis and hydrolysis in the host plant, or even directly degrade GSLs before they are hydrolyzed to antifungal isothiocyanates. Once the Brassicaceae-endophyte fungus symbiosis is formed, the host plant can obtain important benefits from an agricultural point of view, such as plant growth promotion and increase in yield and quality, increased tolerance to abiotic stresses, and direct and indirect control of plant pests and diseases. This review compiles the studies on the interaction between endophytic fungi and Brassicaceae plants, discussing the mechanisms involved in the success of the symbiosis, together with the benefits obtained by these plants. Due to their unique characteristics, the family Brassicaceae can be seen as a fruitful source of novel beneficial endophytes with applications to crops, as well as to generate new models of study that allow us to better understand the interactions of these amazing fungi with plants.
Collapse
Affiliation(s)
- Jorge Poveda
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Sandra Díaz-González
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - María Díaz-Urbano
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG), Spanish National Research Council (CSIC), Pontevedra, Spain
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG), Spanish National Research Council (CSIC), Pontevedra, Spain
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| |
Collapse
|
6
|
Zhou J, Huang PW, Li X, Vaistij FE, Dai CC. Generalist endophyte Phomopsis liquidambaris colonization of Oryza sativa L. promotes plant growth under nitrogen starvation. PLANT MOLECULAR BIOLOGY 2022; 109:703-715. [PMID: 35522401 DOI: 10.1007/s11103-022-01268-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Fungal endophytes establish symbiotic relationships with host plants, which results in a mutual growth benefit. However, little is known about the plant genetic response underpinning endophyte colonization. Phomopsis liquidambaris usually lives as an endophyte in a wide range of asymptomatic hosts and promotes biotic and abiotic stress resistance. In this study, we show that under low nitrogen conditions P. liquidambaris promotes rice growth in a hydroponic system, which is free of other microorganisms. In order to gain insights into the mechanisms of plant colonization by P. liquidambaris under low nitrogen conditions, we compared root and shoot transcriptome profiles of root-inoculated rice at different colonization stages. We determined that genes related to plant growth promotion, such as gibberellin and auxin related genes, were up-regulated at all developmental stages both locally and systemically. The largest group of up-regulated genes (in both roots and shoots) were related to flavonoid biosynthesis, which is involved in plant growth as well as antimicrobial compounds. Furthermore, genes encoding plant defense-related endopeptidase inhibitors were strongly up-regulated at the early stage of colonization. Together, these results provide new insights into the molecular mechanisms of plant-microbe mutualism and the promotion of plant growth by a fungal endophyte under nitrogen-deficient conditions.
Collapse
Affiliation(s)
- Jun Zhou
- Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
- Centre for Novel Agricultural Products, Department of Biology, University of York, YO10 5DD, York, United Kingdom
| | - Peng-Wei Huang
- Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Xin Li
- Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Fabián E Vaistij
- Centre for Novel Agricultural Products, Department of Biology, University of York, YO10 5DD, York, United Kingdom
| | - Chuan-Chao Dai
- Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
| |
Collapse
|
7
|
Efficiency of Combining Strains Ag87 (Bacillus megaterium) and Ag94 (Lysinibacillus sp.) as Phosphate Solubilizers and Growth Promoters in Maize. Microorganisms 2022; 10:microorganisms10071401. [PMID: 35889120 PMCID: PMC9315647 DOI: 10.3390/microorganisms10071401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
Increasing phosphorus (P) use efficiency in agricultural systems is urgent and essential to significantly reduce the global demand for this nutrient. Applying phosphate-solubilizing and plant growth-promoting bacteria in the rhizosphere represents a strategy worthy of attention. In this context, the present work aimed to select and validate bacterial strains capable of solubilizing phosphorous and promoting maize growth, aiming to develop a microbial inoculant to be used in Brazilian agriculture. Bacterial strains from the maize rhizosphere were evaluated based on their ability to solubilize phosphate and produce indole acetic acid. Based on these characteristics, 24 strains were selected to be further evaluated under laboratory, greenhouse, and field conditions. Among the selected strains, four (I04, I12, I13, and I17) showed a high potential to increase maize root growth and shoot P content. Strains I13 (Ag87) and I17 (Ag94) were identified by genomic sequencing as Bacillus megaterium and Lysinibacillus sp., respectively. These strains presented superior yield increments relative to the control treatment with 30% P. In addition, combining Ag87 and Ag94 resulted in even higher yield gains, indicating a synergistic effect that could be harnessed in a commercial inoculant for Brazilian agriculture.
Collapse
|
8
|
Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth. mSystems 2022; 7:e0030422. [PMID: 35695510 PMCID: PMC9239174 DOI: 10.1128/msystems.00304-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonmycorrhizal root-colonizing fungi are key determinants of plant growth, driving processes ranging from pathogenesis to stress alleviation. Evidence suggests that they might also facilitate host access to soil nutrients in a mycorrhiza-like manner, but the extent of their direct contribution to plant nutrition is unknown. To study how widespread such capacity is across root-colonizing fungi, we surveyed soils in nutrient-limiting habitats using plant baits to look for fungal community changes in response to nutrient conditions. We established a fungal culture collection and used Arabidopsis thaliana inoculation bioassays to assess the ability of fungi to facilitate host's growth in the presence of organic nutrients unavailable to plants. Plant baits captured a representation of fungal communities extant in natural habitats and showed that nutrient limitation has little influence on community assembly. Arabidopsis thaliana inoculated with 31 phylogenetically diverse fungi exhibited a consistent fungus-driven growth promotion when supplied with organic nutrients compared to untreated plants. However, direct phosphorus measurement and RNA-seq data did not support enhanced nutrient uptake but rather that growth effects may result from changes in the plant's immune response to colonization. The widespread and consistent host responses to fungal colonization suggest that distinct, locally adapted nonmycorrhizal fungi affect plant performance across habitats. IMPORTANCE Recent studies have shown that root-associated fungi that do not engage in classical mycorrhizal associations can facilitate the hosts' access to nutrients in a mycorrhiza-like manner. However, the generality of this capacity remains to be tested. Root-associated fungi are frequently deemed major determinants of plant diversity and performance, but in the vast majority of cases their ecological roles in nature remain unknown. Assessing how these plant symbionts affect plant productivity, diversity, and fitness is important to understanding how plant communities function. Recent years have seen important advances in the understanding of the main drivers of the diversity and structure of plant microbiomes, but a major challenge is still linking community properties with function. This study contributes to the understanding of the cryptic function of root-associated fungi by testing their ability to participate in a specific process: nutrient acquisition by plants.
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Mahdi LK, Miyauchi S, Uhlmann C, Garrido-Oter R, Langen G, Wawra S, Niu Y, Guan R, Robertson-Albertyn S, Bulgarelli D, Parker JE, Zuccaro A. The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. THE ISME JOURNAL 2022; 16:876-889. [PMID: 34686763 PMCID: PMC8857181 DOI: 10.1038/s41396-021-01138-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 12/05/2022]
Abstract
Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.
Collapse
Affiliation(s)
- Lisa K. Mahdi
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany
| | - Shingo Miyauchi
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Charles Uhlmann
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Ruben Garrido-Oter
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Gregor Langen
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany
| | - Stephan Wawra
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Yulong Niu
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Rui Guan
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Senga Robertson-Albertyn
- grid.8241.f0000 0004 0397 2876University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Davide Bulgarelli
- grid.8241.f0000 0004 0397 2876University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Jane E. Parker
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Alga Zuccaro
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| |
Collapse
|
11
|
Grabka R, d’Entremont TW, Adams SJ, Walker AK, Tanney JB, Abbasi PA, Ali S. Fungal Endophytes and Their Role in Agricultural Plant Protection against Pests and Pathogens. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030384. [PMID: 35161365 PMCID: PMC8840373 DOI: 10.3390/plants11030384] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 05/06/2023]
Abstract
Virtually all examined plant species harbour fungal endophytes which asymptomatically infect or colonize living plant tissues, including leaves, branches, stems and roots. Endophyte-host interactions are complex and span the mutualist-pathogen continuum. Notably, mutualist endophytes can confer increased fitness to their host plants compared with uncolonized plants, which has attracted interest in their potential application in integrated plant health management strategies. In this review, we report on the many benefits that fungal endophytes provide to agricultural plants against common non-insect pests such as fungi, bacteria, nematodes, viruses, and mites. We report endophytic modes of action against the aforementioned pests and describe why this broad group of fungi is vitally important to current and future agricultural practices. We also list an extensive number of plant-friendly endophytes and detail where they are most commonly found or applied in different studies. This review acts as a general resource for understanding endophytes as they relate to potential large-scale agricultural applications.
Collapse
Affiliation(s)
- Rachel Grabka
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada; (R.G.); (P.A.A.)
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada; (T.W.d.); (S.J.A.); (A.K.W.)
| | - Tyler W. d’Entremont
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada; (T.W.d.); (S.J.A.); (A.K.W.)
| | - Sarah J. Adams
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada; (T.W.d.); (S.J.A.); (A.K.W.)
| | - Allison K. Walker
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada; (T.W.d.); (S.J.A.); (A.K.W.)
| | - Joey B. Tanney
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 Burnside Road West, Victoria, BC V8Z 1M5, Canada;
| | - Pervaiz A. Abbasi
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada; (R.G.); (P.A.A.)
| | - Shawkat Ali
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada; (R.G.); (P.A.A.)
- Correspondence:
| |
Collapse
|
12
|
Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S. Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nat Commun 2021; 12:7227. [PMID: 34893598 PMCID: PMC8664821 DOI: 10.1038/s41467-021-27479-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/11/2021] [Indexed: 02/03/2023] Open
Abstract
The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.
Collapse
Affiliation(s)
- Fantin Mesny
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Thorsten Thiergart
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Brigitte Pickel
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Lea Atanasova
- Research division of Biochemical Technology, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
- Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Magnus Karlsson
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Bruno Hüttel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kerrie W Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Diane Bauer
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - William Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elodie Drula
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, 13009, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Univ., 13009, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Annegret Kohler
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Tsinghua East Road Haidian District, Beijing, China.
| | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
| |
Collapse
|
13
|
Ray P, Guo Y, Chi MH, Krom N, Boschiero C, Watson B, Huhman D, Zhao P, Singan VR, Lindquist EA, Yan J, Adam C, Craven KD. Serendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1128-1142. [PMID: 34260261 DOI: 10.1094/mpmi-04-21-0084-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to Serendipita spp. colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain, S. vermifera, isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells to, finally, the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Furthermore, genes involved in phytohormone metabolism such as gibberellin, jasmonic acid, and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita spp. will inform our efforts to integrate them into forages and row crops for optimal plant-microbe functioning, thus facilitating low-input, sustainable agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Yingqing Guo
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Bonnie Watson
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - David Huhman
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Patrick Zhao
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Vasanth R Singan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Erika A Lindquist
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Juying Yan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Catherine Adam
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | | |
Collapse
|
14
|
Šečić E, Zanini S, Wibberg D, Jelonek L, Busche T, Kalinowski J, Nasfi S, Thielmann J, Imani J, Steinbrenner J, Kogel KH. A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis. BMC Biol 2021; 19:171. [PMID: 34429124 PMCID: PMC8385953 DOI: 10.1186/s12915-021-01104-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/16/2021] [Indexed: 01/15/2023] Open
Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Silvia Zanini
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, 35392, Giessen, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Sabrine Nasfi
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jennifer Thielmann
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jafargholi Imani
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jens Steinbrenner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany.
| |
Collapse
|
15
|
Wang K, Bi Y, Cao Y, Peng S, Christie P, Ma S, Zhang J, Xie L. Shifts in composition and function of soil fungal communities and edaphic properties during the reclamation chronosequence of an open-cast coal mining dump. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144465. [PMID: 33434846 DOI: 10.1016/j.scitotenv.2020.144465] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/06/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
The diversity, composition and ecological guilds of soil fungal communities in relation to revegetation were assessed during an open-cast mining dump reclamation chronosequence of the soil <1, 5, 10, 15 and 20 years after the start of reclamation. Soil pH and electrical conductivity, total nitrogen (TN), soil organic carbon (SOC), available potassium (AK), and available phosphorus (AP) contents, and soil phosphatase (Pha), urease (U) and invertase (INV) activities were measured. Using high-throughput sequence analysis on internal transcribed spacer (ITS) sequences, 1059 soil fungal operational taxonomic units (OTUs) were identified belonging to 64 orders and these were further categorized by ecological guild. Soil fungal diversity indices were significantly different between the early (<1 year) and later reclamation communities. Nonmetric multidimensional scaling (NMDS) analysis indicates that the composition and ecological guilds of soil fungal communities were significantly different early in the process and at the end of reclamation (P < 0.05). Co-occurrence network and structural equation model analyses show that soil fungal community structure and ecological guilds were correlated with edaphic properties and had an indirect effect on soil available nutrients through direct action on soil enzymes. Overall, the data suggest that soil fungal community composition and function within an open-cast coal mining dump reclamation chronosequence changed during the period following artificial re-vegetation, with interactions between edaphic properties and soil fungal communities associated with these changes.
Collapse
Affiliation(s)
- Kun Wang
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| | - Yinli Bi
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China; College of Geology and Environment, Xi'an University of Science and Technology, Shaanxi 710054, China.
| | - Yong Cao
- Shehua Group Zhungeer Energy CO., LTD, Ordos 017000, China
| | - Suping Peng
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| | - Peter Christie
- College of Geology and Environment, Xi'an University of Science and Technology, Shaanxi 710054, China
| | - Shaopeng Ma
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| | - Jiayu Zhang
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| | - Linlin Xie
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| |
Collapse
|
16
|
|
17
|
Muñoz-Guerrero J, Guerra-Sierra BE, Alvarez JC. Fungal Endophytes of Tahiti Lime ( Citrus citrus × latifolia) and Their Potential for Control of Colletotrichum acutatum J. H. Simmonds Causing Anthracnose. Front Bioeng Biotechnol 2021; 9:650351. [PMID: 33869159 PMCID: PMC8049634 DOI: 10.3389/fbioe.2021.650351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Colletotrichum acutatum is one of the causal agents of anthracnose in several crops, and of post-flowering fruit drop (PFD) in citrus and key lime anthracnose (KLA). The pathogen normally attacks flowers, causing lesions only in open flowers. Under very favorable conditions, however, it can also affect flower buds and small fruits, causing complete rotting of the fruit and a premature fall, resulting in major economic crop losses. We isolated endophytic fungi from Tahiti lime to evaluate its diversity, verify its antagonistic capacity against the phytopathogen Colletotrichum acutatum C-100 in dual tests, and evaluate the ability of various endophytic agents to control flowers with induced anthracnose. 138 fungal isolates were obtained from 486 fragments of branches, leaves, and fruit; from which 15 species were identified morphologically. A higher isolation frequency was found in branches and leaves, with a normal level of diversity compared to other citrus species. Of the 15 morphospecies, 5 were trialed against C. acutatum in antagonism tests, resulting in a finding of positive inhibition. 2 endophytic fungi from the antagonism tests demonstrated high inhibition of the phytopathogen, and were thus used in in vivo tests with Tahiti lime flowers, applied in a spore solution. Spore solutions of two molecularly identified species, Xylaria adscendens, and Trichoderma atroviride, reduced the lesions caused by the phytopathogen in these in vivo tests. The finding that these endophytes react antagonistically against C. acutatum may make them good candidates for further biological control research in an agroindustry that requires environmental sustainability.
Collapse
Affiliation(s)
- Jaider Muñoz-Guerrero
- Research Group in Agro-Environmental Biotechnology and Health, MICROBIOTA, Faculty of Exact Natural and Agricultural Sciences, University of Santander, Bucaramanga, Colombia
| | - Beatriz E Guerra-Sierra
- Research Group in Agro-Environmental Biotechnology and Health, MICROBIOTA, Faculty of Exact Natural and Agricultural Sciences, University of Santander, Bucaramanga, Colombia
| | - Javier C Alvarez
- Department of Biological Sciences, Eafit University, Medellín, Colombia
| |
Collapse
|
18
|
Suarez-Fernandez M, Sambles C, Lopez-Moya F, Nueda MJ, Studholme DJ, Lopez-Llorca LV. Chitosan modulates Pochonia chlamydosporia gene expression during nematode egg parasitism. Environ Microbiol 2021; 23:4980-4997. [PMID: 33496078 PMCID: PMC8518118 DOI: 10.1111/1462-2920.15408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 01/24/2021] [Indexed: 01/22/2023]
Abstract
Climate change makes plant‐parasitic nematodes (PPN) an increasing threat to commercial crops. PPN can be managed sustainably by the biocontrol fungus Pochonia chlamydosporia (Pc). Chitosan generated from chitin deacetylation enhances PPN parasitism by Pc. In this work, we investigate the molecular mechanisms of Pc for chitosan resistance and root‐knot nematode (RKN) parasitism, using transcriptomics. Chitosan and RKN modify the expression of Pc genes, mainly those involved in oxidation–reduction processes. Both agents significantly modify the expression of genes associated to 113 GO terms and 180 Pc genes. Genes encoding putative glycoproteins (Pc adhesives) to nematode eggshell, as well as genes involved in redox, carbohydrate and lipid metabolism trigger the response to chitosan. We identify genes expressed in both the parasitic and endophytic phases of the Pc lifecycle; these include proteases, chitosanases and transcription factors. Using the Pathogen—Host Interaction database (PHI‐base), our previous RNA‐seq data and RT‐PCR of Pc colonizing banana we have investigated genes expressed both in the parasitic and endophytic phases of Pc lifecycle.
Collapse
Affiliation(s)
- Marta Suarez-Fernandez
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, 03080, Spain.,Multidisciplinary Institute for Environmental Studies (MIES) Ramon Margalef, University of Alicante, Alicante, 03080, Spain
| | | | - Federico Lopez-Moya
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, 03080, Spain
| | - María J Nueda
- Mathematics Department, University of Alicante, Alicante, 03080, Spain
| | | | - Luis Vicente Lopez-Llorca
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, 03080, Spain.,Multidisciplinary Institute for Environmental Studies (MIES) Ramon Margalef, University of Alicante, Alicante, 03080, Spain
| |
Collapse
|
19
|
Vaz ABM, Fonseca PLC, Silva FF, Quintanilha-Peixoto G, Sampedro I, Siles JA, Carmo A, Kato RB, Azevedo V, Badotti F, Ocampo JA, Rosa CA, Góes-Neto A. Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs. PeerJ 2020; 8:e10487. [PMID: 33344092 PMCID: PMC7719295 DOI: 10.7717/peerj.10487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 11/12/2020] [Indexed: 11/20/2022] Open
Abstract
The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.
Collapse
Affiliation(s)
- Aline Bruna M Vaz
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Paula Luize C Fonseca
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe F Silva
- Graduate Program of Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Quintanilha-Peixoto
- Graduate Program of Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Inmaculada Sampedro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, C.S.I.C., Granada, Spain
| | - Jose A Siles
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, C.S.I.C., Granada, Spain
| | - Anderson Carmo
- Department of Genetics, Ecology, and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo B Kato
- Graduate Program of Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juan A Ocampo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, C.S.I.C., Granada, Spain
| | - Carlos A Rosa
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
20
|
Jack CN, Petipas RH, Cheeke TE, Rowland JL, Friesen ML. Microbial Inoculants: Silver Bullet or Microbial Jurassic Park? Trends Microbiol 2020; 29:299-308. [PMID: 33309525 DOI: 10.1016/j.tim.2020.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023]
Abstract
The appeal of using microbial inoculants to mediate plant traits and productivity in managed ecosystems has increased over the past decade, because microbes represent an alternative to fertilizers, pesticides, and direct genetic modification of plants. Using microbes bypasses many societal and environmental concerns because microbial products are considered a more sustainable and benign technology. In our desire to harness the power of plant-microbial symbioses, are we ignoring the possibility of precipitating microbial invasions, potentially setting ourselves up for a microbial Jurassic Park? Here, we outline potential negative consequences of microbial invasions and describe a set of practices (Testing, Regulation, Engineering, and Eradication, TREE) based on the four stages of invasion to prevent microbial inoculants from becoming invasive. We aim to stimulate discussion about best practices to proactively prevent microbial invasions.
Collapse
Affiliation(s)
- Chandra N Jack
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA.
| | - Renee H Petipas
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Tanya E Cheeke
- Department of Biological Sciences, Washington State University, Richland, WA 99354, USA
| | - Jennifer L Rowland
- AAAS Science and Technology Policy Fellow hosted by United States Department of Agriculture- APHIS Plant Protection and Quarantine, Riverdale, MD 20737, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA; Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| |
Collapse
|
21
|
Muñoz-Barrios A, Sopeña-Torres S, Ramos B, López G, Del Hierro I, Díaz-González S, González-Melendi P, Mélida H, Fernández-Calleja V, Mixão V, Martín-Dacal M, Marcet-Houben M, Gabaldón T, Sacristán S, Molina A. Differential Expression of Fungal Genes Determines the Lifestyle of Plectosphaerella Strains During Arabidopsis thaliana Colonization. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1299-1314. [PMID: 32720872 DOI: 10.1094/mpmi-03-20-0057-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The fungal genus Plectosphaerella comprises species and strains with different lifestyles on plants, such as P. cucumerina, which has served as model for the characterization of Arabidopsis thaliana basal and nonhost resistance to necrotrophic fungi. We have sequenced, annotated, and compared the genomes and transcriptomes of three Plectosphaerella strains with different lifestyles on A. thaliana, namely, PcBMM, a natural pathogen of wild-type plants (Col-0), Pc2127, a nonpathogenic strain on Col-0 but pathogenic on the immunocompromised cyp79B2 cyp79B3 mutant, and P0831, which was isolated from a natural population of A. thaliana and is shown here to be nonpathogenic and to grow epiphytically on Col-0 and cyp79B2 cyp79B3 plants. The genomes of these Plectosphaerella strains are very similar and do not differ in the number of genes with pathogenesis-related functions, with the exception of secreted carbohydrate-active enzymes (CAZymes), which are up to five times more abundant in the pathogenic strain PcBMM. Analysis of the fungal transcriptomes in inoculated Col-0 and cyp79B2 cyp79B3 plants at initial colonization stages confirm the key role of secreted CAZymes in the necrotrophic interaction, since PcBMM expresses more genes encoding secreted CAZymes than Pc2127 and P0831. We also show that P0831 epiphytic growth on A. thaliana involves the transcription of specific repertoires of fungal genes, which might be necessary for epiphytic growth adaptation. Overall, these results suggest that in-planta expression of specific sets of fungal genes at early stages of colonization determine the diverse lifestyles and pathogenicity of Plectosphaerella strains.
Collapse
Affiliation(s)
- Antonio Muñoz-Barrios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Sara Sopeña-Torres
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Brisa Ramos
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Irene Del Hierro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Sandra Díaz-González
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Pablo González-Melendi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Vanessa Fernández-Calleja
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Verónica Mixão
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marina Martín-Dacal
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| |
Collapse
|
22
|
Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 2020; 44:107614. [PMID: 32858117 DOI: 10.1016/j.biotechadv.2020.107614] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 08/15/2020] [Indexed: 10/25/2022]
Abstract
Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.
Collapse
Affiliation(s)
- Jakub Papik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Magdalena Folkmanova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Marketa Polivkova-Majorova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
| |
Collapse
|
23
|
Koskella B, Bergelson J. The study of host-microbiome (co)evolution across levels of selection. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190604. [PMID: 32772660 DOI: 10.1098/rstb.2019.0604] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.
Collapse
Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
24
|
Santos C, Santos da Silva BN, Amorim Ferreira e Ferreira AFT, Santos C, Lima N, da Silva Bentes JL. Fungal Endophytic Community Associated with Guarana ( Paullinia cupana Var. Sorbilis): Diversity Driver by Genotypes in the Centre of Origin. J Fungi (Basel) 2020; 6:E123. [PMID: 32751796 PMCID: PMC7558939 DOI: 10.3390/jof6030123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 12/29/2022] Open
Abstract
Guarana plant is a native of the Amazon region. Due to its high amount of caffeine and tannins, the seed has medicinal and stimulating properties. The guarana industry has grown exponentially in recent years; however, little information is available about associated mycobiota, particularly endophytic fungi. The present study aimed to compare the distribution and diversity of endophytic fungi associated with the leaves and seeds of anthracnose-resistant and susceptible guarana plants produced in Maués and Manaus, Amazonas State, Brazil. A total of 7514 endophytic fungi were isolated on Potato Dextrose Agar, Sabouraud and Czapek media, and grouped into 77 morphological groups. Overall, fungal communities in guarana leaves and seeds were mainly composed by Colletotrichum and Fusarium genera, but also by Chondrostereum, Clonostachys, Curvularia, Hypomontagnella, Lentinus, Neopestalotiopsis, Nigrospora, Peroneutypa, Phyllosticta, Simplicillium and Tinctoporellus. Obtained results indicate that some members of Colletotrichum and Fusarium genera may have experienced dysbiosis during the guarana domestication process, suggesting that some individuals may behave as latent pathogens. The susceptible guarana genotype cultivated in Manaus presented higher fungal diversity. The relative abundance of taxa and diversity among samples suggests that communities are structured by genotype and geographic location. This is the first report of mycobiota in both guarana leaves and seeds.
Collapse
Affiliation(s)
- Carla Santos
- CEB-Centre of Biological Engineering, Micoteca da Universidade do Minho, University of Minho, 4710-057 Braga, Portugal; (C.S.); (N.L.)
| | - Blenda Naara Santos da Silva
- Postgraduate Program in Tropical Agronomy, Federal University of Amazonas, Manaus-AM 69067-005, Brazil; (B.N.S.d.S.); (A.F.T.A.F.eF.); (J.L.d.S.B.)
- Department of Chemical Sciences and Natural Resources, BIOREN-UFRO, Universidad de La Frontera, Temuco 4811-230, Chile
| | | | - Cledir Santos
- Department of Chemical Sciences and Natural Resources, BIOREN-UFRO, Universidad de La Frontera, Temuco 4811-230, Chile
| | - Nelson Lima
- CEB-Centre of Biological Engineering, Micoteca da Universidade do Minho, University of Minho, 4710-057 Braga, Portugal; (C.S.); (N.L.)
| | - Jânia Lília da Silva Bentes
- Postgraduate Program in Tropical Agronomy, Federal University of Amazonas, Manaus-AM 69067-005, Brazil; (B.N.S.d.S.); (A.F.T.A.F.eF.); (J.L.d.S.B.)
| |
Collapse
|
25
|
Oses-Pedraza R, Torres-Díaz C, Lavín P, Retamales-Molina P, Atala C, Gallardo-Cerda J, Acuña-Rodríguez IS, Molina-Montenegro MA. Root endophytic Penicillium promotes growth of Antarctic vascular plants by enhancing nitrogen mineralization. Extremophiles 2020; 24:721-732. [PMID: 32699913 DOI: 10.1007/s00792-020-01189-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
Abstract
Fungal endophyte associations have been suggested as a possible strategy of Antarctic vascular plants for surviving the extreme environmental conditions of Antarctica. However, the mechanisms by which this occurs are still poorly understood. The role of root fungal endophytes in nitrogen mineralization and nutrient uptake, as well as their impact on the performance of Antarctic plants, were studied. We tested root endophytes, isolated from Colobanthus quitensis and Deschampsia antarctica, for lignocellulolytic enzyme production, nitrogen mineralization, and growth enhancement of their host plants. Penicillium chrysogenum and Penicillium brevicompactum were identified using a molecular approach as the main root endophytes inhabiting C. quitensis and D. antarctica, respectively. Both root endophytes were characterized as psychrophilic fungi displaying amylase, esterase, protease, cellulase, hemicellulase, phosphatase and urease enzymatic activities, mainly at 4 °C. Moreover, the rates and percentages of nitrogen mineralization, as well as the final total biomass, were significantly higher in symbiotic C. quitensis and D. antarctica individuals. Our findings suggest that root endophytes exert a pivotal ecological role based not only to breakdown different nutrient sources but also on accelerating nitrogen mineralization, improving nutrient acquisition, and therefore promoting plant growth in Antarctic terrestrial ecosystems.
Collapse
Affiliation(s)
- Rómulo Oses-Pedraza
- Vicerrectoría de Investigación y Postgrado (VRIP), Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama (UDA), Avenida Copayapu N° 485, Copiapó, Chile. .,Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo N°1281, Coquimbo, Chile.
| | - Cristian Torres-Díaz
- Laboratorio de Genómica y Biodiversidad (LGB), Departamento de Ciencias Naturales, Universidad del Bío-Bío, Chillan, Chile
| | - Paris Lavín
- Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Patricio Retamales-Molina
- Laboratorio de Bacteriología Molecular, Facultad de Medicina, Universidad Diego Portales (UDP), República # 239, Santiago, Chile
| | - Cristian Atala
- Laboratorio de Anatomía y Ecología Funcional de Plantas (AEF), Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Jorge Gallardo-Cerda
- Centro de Ecología Molecular y Aplicaciones Evolutivas en Agroecosistemas (CEM), Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
| | - Ian S Acuña-Rodríguez
- Centro de Ecología Molecular y Aplicaciones Evolutivas en Agroecosistemas (CEM), Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
| | - Marco A Molina-Montenegro
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo N°1281, Coquimbo, Chile.,Centro de Ecología Molecular y Aplicaciones Evolutivas en Agroecosistemas (CEM), Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile.,Research Program "Adaptation of Agriculture To Climate Change" PIEI A2C2, Universidad de Talca, Región del Maule, Talca, Chile.,Centro de Investigaciones y Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile
| |
Collapse
|
26
|
Adamo M, Chialva M, Calevo J, De Rose S, Girlanda M, Perotto S, Balestrini R. The Dark Side of Orchid Symbiosis: Can Tulasnella calospora Decompose Host Tissues? Int J Mol Sci 2020; 21:E3139. [PMID: 32365577 PMCID: PMC7247694 DOI: 10.3390/ijms21093139] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 01/02/2023] Open
Abstract
Photosynthetic orchids associate with mycorrhizal fungi that can be mostly ascribed to the "rhizoctonia" species complex. Rhizoctonias' phylogenetic diversity covers a variety of ecological/nutritional strategies that include, beside the symbiosis establishment with host plants, endophytic and pathogenic associations with non-orchid plants or saprotrophic soil colonization. In addition, orchid mycorrhizal fungi (OMF) that establish a symbiotic relationship with an orchid host can later proliferate in browning and rotting orchid tissues. Environmental triggers and molecular mechanisms governing the switch leading to either a saprotrophic or a mycorrhizal behavior in OMF remain unclear. As the sequenced OMF genomes feature a wide range of genes putatively involved in the degradation of plant cell wall (PCW) components, we tested if these transitions may be correlated with a change in the expression of some PCW degrading enzymes. Regulation of several genes encoding PCW degrading enzymes was evaluated during saprotrophic growth of the OMF Tulasnella calospora on different substrates and under successful and unsuccessful mycorrhizal symbioses. Fungal gene expression in planta was investigated in two orchid species, the terrestrial Mediterranean Serapias vomeracea and the epiphytic tropical Cattleya purpurata. Although we only tested a subset of the CAZyme genes identified in the T. calospora genome, and we cannot exclude therefore a role for different CAZyme families or members inside a family, the results showed that the degradative potential of T. calospora is finely regulated during saprotrophic growth and in symbiosis, often with a different regulation in the two orchid species. These data pose novel questions about the role of fungal PCW degrading enzymes in the development of unsuccessful and successful interactions.
Collapse
Affiliation(s)
- Martino Adamo
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy; (M.A.); (M.C.); (S.D.R.); (M.G.); (S.P.)
| | - Matteo Chialva
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy; (M.A.); (M.C.); (S.D.R.); (M.G.); (S.P.)
| | - Jacopo Calevo
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy; (M.A.); (M.C.); (S.D.R.); (M.G.); (S.P.)
| | - Silvia De Rose
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy; (M.A.); (M.C.); (S.D.R.); (M.G.); (S.P.)
| | - Mariangela Girlanda
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy; (M.A.); (M.C.); (S.D.R.); (M.G.); (S.P.)
| | - Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy; (M.A.); (M.C.); (S.D.R.); (M.G.); (S.P.)
| | - Raffaella Balestrini
- National Research Council, Institute for Sustainable Plant Protection, Viale Mattioli 25, 10125 Turin, Italy
| |
Collapse
|
27
|
Chandra P, Enespa, Singh R. Soil Salinity and Its Alleviation Using Plant Growth–Promoting Fungi. Fungal Biol 2020. [DOI: 10.1007/978-3-030-48474-3_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
28
|
|
29
|
Vidotti MS, Lyra DH, Morosini JS, Granato ÍSC, Quecine MC, de Azevedo JL, Fritsche-Neto R. Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense. PLoS One 2019; 14:e0222788. [PMID: 31536609 PMCID: PMC6752820 DOI: 10.1371/journal.pone.0222788] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/07/2019] [Indexed: 11/18/2022] Open
Abstract
Maize genotypes can show different responsiveness to inoculation with Azospirillum brasilense and an intriguing issue is which genes of the plant are involved in the recognition and growth promotion by these Plant Growth-Promoting Bacteria (PGPB). We conducted Genome-Wide Association Studies (GWAS) using additive and heterozygous (dis)advantage models to find candidate genes for root and shoot traits under nitrogen (N) stress and N stress plus A. brasilense. A total of 52,215 Single Nucleotide Polymorphism (SNP) markers were used for GWAS analyses. For the six root traits with significant inoculation effect, the GWAS analyses revealed 25 significant SNPs for the N stress plus A. brasilense treatment, in which only two were overlapped with the 22 found for N stress only. Most were found by the heterozygous (dis)advantage model and were more related to exclusive gene ontology terms. Interestingly, the candidate genes around the significant SNPs found for the maize-A. brasilense association were involved in different functions previously described for PGPB in plants (e.g. signaling pathways of the plant's defense system and phytohormone biosynthesis). Our findings are a benchmark in the understanding of the genetic variation among maize hybrids for the association with A. brasilense and reveal the potential for further enhancement of maize through this association.
Collapse
Affiliation(s)
- Miriam Suzane Vidotti
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- * E-mail: (MSV); (RFN)
| | | | - Júlia Silva Morosini
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - João Lúcio de Azevedo
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Roberto Fritsche-Neto
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- * E-mail: (MSV); (RFN)
| |
Collapse
|
30
|
Miura C, Saisho M, Yagame T, Yamato M, Kaminaka H. Bletilla striata (Orchidaceae) Seed Coat Restricts the Invasion of Fungal Hyphae at the Initial Stage of Fungal Colonization. PLANTS (BASEL, SWITZERLAND) 2019; 8:E280. [PMID: 31405202 PMCID: PMC6724134 DOI: 10.3390/plants8080280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 12/02/2022]
Abstract
Orchids produce minute seeds that contain limited or no endosperm, and they must form an association with symbiotic fungi to obtain nutrients during germination and subsequent seedling growth under natural conditions. Orchids need to select an appropriate fungus among diverse soil fungi at the germination stage. However, there is limited understanding of the process by which orchids recruit fungal associates and initiate the symbiotic interaction. This study aimed to better understand this process by focusing on the seed coat, the first point of fungal attachment. Bletilla striata seeds, some with the seed coat removed, were prepared and sown with symbiotic fungi or with pathogenic fungi. The seed coat-stripped seeds inoculated with the symbiotic fungi showed a lower germination rate than the intact seeds, and proliferated fungal hyphae were observed inside and around the stripped seeds. Inoculation with the pathogenic fungi increased the infection rate in the seed coat-stripped seeds. The pathogenic fungal hyphae were arrested at the suspensor side of the intact seeds, whereas the seed coat-stripped seeds were subjected to severe infestation. These results suggest that the seed coat restricts the invasion of fungal hyphae and protects the embryo against the attack of non-symbiotic fungi.
Collapse
Affiliation(s)
- Chihiro Miura
- Faculty of Agriculture, Tottori University, 4-101 Koyama Minami, Tottori 680-8553, Japan
| | - Miharu Saisho
- Faculty of Agriculture, Tottori University, 4-101 Koyama Minami, Tottori 680-8553, Japan
| | - Takahiro Yagame
- Mizuho Kyo-do Museum, 316-5 Komagatafujiyama, Mizuho, Tokyo 190-1202, Japan
| | - Masahide Yamato
- Faculty of Education, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba 263-8522, Japan
| | - Hironori Kaminaka
- Faculty of Agriculture, Tottori University, 4-101 Koyama Minami, Tottori 680-8553, Japan.
| |
Collapse
|
31
|
Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11070112] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present.
Collapse
|
32
|
Rodrigues CM, Takita MA, Silva NV, Ribeiro-Alves M, Machado MA. Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis, two fungi species that share the same host. BMC Genomics 2019; 20:554. [PMID: 31277573 PMCID: PMC6612112 DOI: 10.1186/s12864-019-5911-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 06/17/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Citrus are among the most important crops in the world. However, there are many diseases that affect Citrus caused by different pathogens. Citrus also hosts many symbiotic microorganisms in a relationship that may be advantageous for both organisms. The fungi Phyllosticta citricarpa, responsible for citrus black spot, and Phyllosticta capitalensis, an endophytic species, are examples of closely related species with different behavior in citrus. Both species are always biologically associated and are morphologically very similar, and comparing their genomes could help understanding the different lifestyles. In this study, a comparison was carried to identify genetic differences that could help us to understand the biology of P. citricarpa and P. capitalensis. RESULTS Drafts genomes were assembled with sizes close to 33 Mb for both fungi, carrying 15,206 and 14,797 coding sequences for P. citricarpa and P. capitalensis, respectively. Even though the functional categories of these coding sequences is similar, enrichment analysis showed that the pathogenic species presents growth and development genes that may be necessary for the pathogenicity of P. citricarpa. On the other hand, family expansion analyses showed the plasticity of the genome of these species. Particular families are expanded in the genome of an ancestor of P. capitalensis and a recent expansion can also be detected among this species. Additionally, evolution could be driven by environmental cues in P. citricarpa. CONCLUSIONS This work demonstrated genomic differences between P. citricarpa and P. capitalensis. Although the idea that these differences could explain the different lifestyles of these fungi, we were not able to confirm this hypothesis. Genome evolution seems to be of real importance among the Phyllosticta isolates and it is leading to different biological characteristics of these species.
Collapse
Affiliation(s)
- Carolina Munari Rodrigues
- Laboratório de Biotecnologia, Centro APTA Citros Sylvio Moreira, CP4, Cordeirópolis, SP 13490-970 Brazil
| | - Marco Aurélio Takita
- Laboratório de Biotecnologia, Centro APTA Citros Sylvio Moreira, CP4, Cordeirópolis, SP 13490-970 Brazil
| | - Nicholas Vinicius Silva
- Laboratório de Genômica e BioEnergia, Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | - Marcelo Ribeiro-Alves
- Laboratório de Pesquisa Clínica em DST/AIDS, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ 21040900 Brazil
| | - Marcos Antonio Machado
- Laboratório de Biotecnologia, Centro APTA Citros Sylvio Moreira, CP4, Cordeirópolis, SP 13490-970 Brazil
| |
Collapse
|
33
|
Kia SH, Pallesch S, Piepenbring M, Maciá-Vicente JG. Root endophytic fungi show low levels of interspecific competition in planta. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
34
|
Kerdraon L, Balesdent MH, Barret M, Laval V, Suffert F. Crop Residues in Wheat-Oilseed Rape Rotation System: a Pivotal, Shifting Platform for Microbial Meetings. MICROBIAL ECOLOGY 2019; 77:931-945. [PMID: 30834960 DOI: 10.1007/s00248-019-01340-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/05/2019] [Indexed: 05/13/2023]
Abstract
Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study, we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases over time with their likely progressive degradation and colonisation by other microorganisms. We characterised an entire fungal and bacterial community associated with 150 wheat and oilseed rape residue samples at a plurennial scale by metabarcoding. The impact of plant species on the residue microbiota decreased over time and our data revealed turnover, with the replacement of oligotrophs, often plant-specific genera (such as pathogens) by copiotrophs, belonging to more generalist genera. Within a single cropping season, the plant-specific genera and species were gradually replaced by taxa that are likely to originate from the soil. These changes occurred more rapidly for bacteria than for fungi, known to degrade complex compounds. Overall, our findings suggest that crop residues constitute a key fully-fledged microbial ecosystem. Taking into account this ecosystem, that has been neglected for too long, is essential, not only to improve the quantitative management of residues, the presence of which can be detrimental to crop health, but also to identify groups of beneficial microorganisms. Our findings are of particular importance, because the wheat-oilseed rape rotation, in which no-till practices are frequent, is particularly widespread in the European arable cropping systems.
Collapse
Affiliation(s)
- Lydie Kerdraon
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Matthieu Barret
- UMR IRHS, INRA, Agrocampus Ouest, Université d'Angers, 49071, Beaucouzé, France
| | - Valérie Laval
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
| | - Frédéric Suffert
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
| |
Collapse
|
35
|
Wawra S, Fesel P, Widmer H, Neumann U, Lahrmann U, Becker S, Hehemann JH, Langen G, Zuccaro A. FGB1 and WSC3 are in planta-induced β-glucan-binding fungal lectins with different functions. THE NEW PHYTOLOGIST 2019; 222:1493-1506. [PMID: 30688363 DOI: 10.1111/nph.15711] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
In the root endophyte Serendipita indica, several lectin-like members of the expanded multigene family of WSC proteins are transcriptionally induced in planta and are potentially involved in β-glucan remodeling at the fungal cell wall. Using biochemical and cytological approaches we show that one of these lectins, SiWSC3 with three WSC domains, is an integral fungal cell wall component that binds to long-chain β1-3-glucan but has no affinity for shorter β1-3- or β1-6-linked glucose oligomers. Comparative analysis with the previously identified β-glucan-binding lectin SiFGB1 demonstrated that whereas SiWSC3 does not require β1-6-linked glucose for efficient binding to branched β1-3-glucan, SiFGB1 does. In contrast to SiFGB1, the multivalent SiWSC3 lectin can efficiently agglutinate fungal cells and is additionally induced during fungus-fungus confrontation, suggesting different functions for these two β-glucan-binding lectins. Our results highlight the importance of the β-glucan cell wall component in plant-fungus interactions and the potential of β-glucan-binding lectins as specific detection tools for fungi in vivo.
Collapse
Affiliation(s)
- Stephan Wawra
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Philipp Fesel
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Heidi Widmer
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Ulla Neumann
- Central Microscopy (CeMic), Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Urs Lahrmann
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Stefan Becker
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Center for Marine Environmental Sciences, University of Bremen, MARUM, Bremen, 28359, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Center for Marine Environmental Sciences, University of Bremen, MARUM, Bremen, 28359, Germany
| | - Gregor Langen
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Alga Zuccaro
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| |
Collapse
|
36
|
Skiada V, Faccio A, Kavroulakis N, Genre A, Bonfante P, Papadopoulou KK. Colonization of legumes by an endophytic Fusarium solani strain FsK reveals common features to symbionts or pathogens. Fungal Genet Biol 2019; 127:60-74. [PMID: 30872027 DOI: 10.1016/j.fgb.2019.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/31/2019] [Accepted: 03/08/2019] [Indexed: 12/22/2022]
Abstract
Plant cellular responses to endophytic filamentous fungi are scarcely reported, with the majority of described colonization processes in plant-fungal interactions referring to either pathogens or true symbionts. Fusarium solani strain K (FsK) is a root endophyte of Solanum lycopersicum, which protects against root and foliar pathogens. Here, we investigate the association of FsK with two legumes (Lotus japonicus and Medicago truncatula) and report on colonization patterns and plant responses during the establishment of the interaction. L. japonicus plants colonized by FsK complete their life cycle and exhibit no apparent growth defects under normal conditions. We followed the growth of FsK within root-inoculated plants spatiotemporally and showed the capability of the endophyte to migrate to the stem. In a bipartite system comprising of the endophyte and either whole plants or root organ cultures, we studied the plant sub-cellular responses to FsK recognition, using optical, confocal and transmission electron microscopy. A polarized reorganization of the root cell occurs: endoplasmic reticulum/cytoplasm accumulation and nuclear placement at contact sites, occasional development of papillae underneath hyphopodia and membranous material rearrangements towards penetrating hyphae. Fungal hyphae proliferate within the vascular bundle of the plant. Plant cell death is involved in fungal colonization of the root. Our data suggest that the establishment of FsK within legume tissues requires fungal growth adaptations and plant cell-autonomous responses, known to occur during both symbiotic and pathogenic plant-fungal interactions. We highlight the overlooked plasticity of endophytic fungi upon plant colonization, and introduce a novel plant-endophyte association.
Collapse
Affiliation(s)
- Vasiliki Skiada
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Larissa 41500, Greece.
| | - Antonella Faccio
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10125, Italy.
| | - Nektarios Kavroulakis
- Hellenic Agricultural Organization "Demeter", Institute for Olive Tree, Subtropical Plants and Viticulture, Agrokipio-Souda, 73100 Chania, Greece.
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10125, Italy.
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10125, Italy.
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Larissa 41500, Greece.
| |
Collapse
|
37
|
Beneficial effects of endophytic fungi colonization on plants. Appl Microbiol Biotechnol 2019; 103:3327-3340. [DOI: 10.1007/s00253-019-09713-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
|
38
|
Sjokvist E, Lemcke R, Kamble M, Turner F, Blaxter M, Havis NHD, Lyngkjær MF, Radutoiu S. Dissection of Ramularia Leaf Spot Disease by Integrated Analysis of Barley and Ramularia collo-cygni Transcriptome Responses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:176-193. [PMID: 30681911 DOI: 10.1094/mpmi-05-18-0113-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ramularia leaf spot disease (RLS), caused by the ascomycete fungus Ramularia collo-cygni, has emerged as a major economic disease of barley. No substantial resistance has been identified, so far, among barley genotypes and, based on the epidemiology of the disease, a quantitative genetic determinacy of RLS has been suggested. The relative contributions of barley and R. collo-cygni genetics to disease infection and epidemiology are practically unknown. Here, we present an integrated genome-wide analysis of host and pathogen transcriptome landscapes identified in a sensitive barley cultivar following infection by an aggressive R. collo-cygni isolate. We compared transcriptional responses in the infected and noninfected leaf samples in order to identify which molecular events are associated with RLS symptom development. We found a large proportion of R. collo-cygni genes to be expressed in planta and that many were also closely associated with the infection stage. The transition from surface to apoplastic colonization was associated with downregulation of cell wall-degrading genes and upregulation of nutrient uptake and resistance to oxidative stresses. Interestingly, the production of secondary metabolites was dynamically regulated within the fungus, indicating that R. collo-cygni produces a diverse panel of toxic compounds according to the infection stage. A defense response against R. collo-cygni was identified in barley at the early, asymptomatic infection and colonization stages. We found activation of ethylene signaling, jasmonic acid signaling, and phenylpropanoid and flavonoid pathways to be highly induced, indicative of a classical response to necrotrophic pathogens. Disease development was found to be associated with gene expression patterns similar to those found at the onset of leaf senescence, when nutrients, possibly, are used by the infecting fungus. These analyses, combining both barley and R. collo-cygni transcript profiles, demonstrate the activation of complex transcriptional programs in both organisms.
Collapse
Affiliation(s)
- Elisabet Sjokvist
- 1 Scotlands Rural College, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JG, Scotland, U.K
- 2 Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, U.K
| | - Rene Lemcke
- 3 Department of Plant and Environmental Sciences, Copenhagen University, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Manoj Kamble
- 4 Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10, Aarhus, Denmark; and
| | - Frances Turner
- 5 Edinburgh Genomics, School of Biological Sciences, The University of Edinburgh; Scotland, U.K
| | - Mark Blaxter
- 2 Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, U.K
| | - Neil H D Havis
- 1 Scotlands Rural College, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JG, Scotland, U.K
| | - Michael F Lyngkjær
- 3 Department of Plant and Environmental Sciences, Copenhagen University, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Simona Radutoiu
- 4 Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10, Aarhus, Denmark; and
| |
Collapse
|
39
|
Kariman K, Barker SJ, Tibbett M. Structural plasticity in root-fungal symbioses: diverse interactions lead to improved plant fitness. PeerJ 2018; 6:e6030. [PMID: 30533314 PMCID: PMC6284451 DOI: 10.7717/peerj.6030] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 10/30/2018] [Indexed: 01/08/2023] Open
Abstract
Root-fungal symbioses such as mycorrhizas and endophytes are key components of terrestrial ecosystems. Diverse in trophy habits (obligate, facultative or hemi-biotrophs) and symbiotic relations (from mutualism to parasitism), these associations also show great variability in their root colonization and nutritional strategies. Specialized interface structures such as arbuscules and Hartig nets are formed by certain associations while others are restricted to non-specialized intercellular or intracellular hyphae in roots. In either case, there are documented examples of active nutrient exchange, reinforcing the fact that specialized structures used to define specific mycorrhizal associations are not essential for reciprocal exchange of nutrients and plant growth promotion. In feremycorrhiza (with Austroboletus occidentalis and eucalypts), the fungal partner markedly enhances plant growth and nutrient acquisition without colonizing roots, emphasizing that a conventional focus on structural form of associations may have resulted in important functional components of rhizospheres being overlooked. In support of this viewpoint, mycobiome studies using the state-of-the-art DNA sequencing technologies have unearthed much more complexity in root-fungal relationships than those discovered using the traditional morphology-based approaches. In this review, we explore the existing literature and most recent findings surrounding structure, functioning, and ecology of root-fungal symbiosis, which highlight the fact that plant fitness can be altered by taxonomically/ecologically diverse fungal symbionts regardless of root colonization and interface specialization. Furthermore, transition from saprotrophy to biotrophy seems to be a common event that occurs in diverse fungal lineages (consisting of root endophytes, soil saprotrophs, wood decayers etc.), and which may be accompanied by development of specialized interface structures and/or mycorrhiza-like effects on plant growth and nutrition.
Collapse
Affiliation(s)
- Khalil Kariman
- School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
| | - Susan Jane Barker
- School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
| | - Mark Tibbett
- Centre for Agri-Environmental Research & Soil Research Centre, School of Agriculture Policy and Development, University of Reading, Berkshire, United Kingdom
| |
Collapse
|
40
|
Perotto S, Daghino S, Martino E. Ericoid mycorrhizal fungi and their genomes: another side to the mycorrhizal symbiosis? THE NEW PHYTOLOGIST 2018; 220:1141-1147. [PMID: 29851103 DOI: 10.1111/nph.15218] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/08/2018] [Indexed: 05/20/2023]
Abstract
Contents Summary 1141 I. Introduction 1141 II. The ericoid mycorrhizal lifestyle 1141 III. Lessons from the mycorrhizal fungal genomes 1142 IV. ERM fungi: a discordant voice in the mycorrhizal choir 1143 V. An endophytic niche for ERM fungi 1144 VI. Specialised vs unspecialised mycorrhizal fungi? 1145 VII. Conclusions and perspectives 1145 Acknowledgements 1146 References 1146 SUMMARY: The genome of an organism bears the signature of its lifestyle, and organisms with similar life strategies are expected to share common genomic traits. Indeed, ectomycorrhizal and arbuscular mycorrhizal fungi share some genomic traits, such as the expansion of gene families encoding taxon-specific small secreted proteins, which are candidate effectors in the symbiosis, and a very small repertoire of plant cell wall-degrading enzymes. A large gene family coding for candidate effectors was also revealed in ascomycetous ericoid mycorrhizal (ERM) fungi, but these fungal genomes are characterised by a very high number of genes encoding degradative enzymes, mainly acting on plant cell wall components. We suggest that the genomic signature of ERM fungi mirrors a versatile life strategy, which allows them to occupy several ecological niches.
Collapse
Affiliation(s)
- Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Stefania Daghino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Elena Martino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| |
Collapse
|
41
|
Khare E, Mishra J, Arora NK. Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects. Front Microbiol 2018; 9:2732. [PMID: 30498482 PMCID: PMC6249440 DOI: 10.3389/fmicb.2018.02732] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/25/2018] [Indexed: 11/13/2022] Open
Abstract
Microbial endophytes are present in all known plant species. The ability to enter and thrive in the plant tissues makes endophytes unique, showing multidimensional interactions within the host plant. Several vital activities of the host plant are known to be influenced by the presence of endophytes. They can promote plant growth, elicit defense response against pathogen attack, and can act as remediators of abiotic stresses. To date, most of the research has been done assuming that the interaction of endophytes with the host plant is similar to the plant growth-promoting (PGP) microbes present in the rhizosphere. However, a new appreciation of the difference of the rhizosphere environment from that of internal plant tissues is gaining attention. It would be interesting to explore the impact of endosymbionts on the host’s gene expression, metabolism, and other physiological aspects essential in conferring resistance against biotic and abiotic stresses. A more intriguing and inexplicable issue with many endophytes that has to be critically evaluated is their ability to produce host metabolites, which can be harnessed on a large scale for potential use in diverse areas. In this review, we discuss the concept of endophytism, looking into the latest insights related to the multifarious interactions beneficial for the host plant and exploring the importance of these associations in agriculture and the environment and in other vital aspects such as human health.
Collapse
Affiliation(s)
- Ekta Khare
- Department of Microbiology, Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Jitendra Mishra
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Naveen Kumar Arora
- Department of Environmental Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| |
Collapse
|
42
|
Hiruma K, Kobae Y, Toju H. Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: evolutionary origins and host-symbiont molecular mechanisms. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:145-154. [PMID: 29738938 DOI: 10.1016/j.pbi.2018.04.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 05/02/2023]
Abstract
Brassicaceae plants have lost symbiotic interactions with mutualistic mycorrhizal fungi, but, nonmycorrhizal Brassicaceae associate with diverse taxonomic groups of mutualistic root-endophytic fungi. Distantly related fungal endophytes of Brassicaceae plants transfer phosphorus to the hosts and promote plant growth, thereby suggesting that the beneficial function was independently acquired via convergent evolution. These beneficial interactions appear tightly regulated by the tryptophan-derived secondary metabolite pathway, which specifically developed in Brassicaceae. Importantly, phosphate availability and types of colonizing microbes appear to influence the metabolite pathway. Thus, endophytes of Brassicaceae may have evolved to adapt to the Brassicaceae-specific traits. Future comparative functional analyses among well-defined endophytic fungi and their relatives with distinct life strategies and host plants will help understand the mechanisms that establish and maintain beneficial interactions.
Collapse
Affiliation(s)
- Kei Hiruma
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Yoshihiro Kobae
- Department of Sustainable Agriculture, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan; Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization (NARO) , 1 Hitsujigaoka, Toyohira-ku, Sapporo, Hokkaido 062-8555, Japan
| | - Hirokazu Toju
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| |
Collapse
|
43
|
Bernaola L, Cosme M, Schneider RW, Stout M. Belowground Inoculation With Arbuscular Mycorrhizal Fungi Increases Local and Systemic Susceptibility of Rice Plants to Different Pest Organisms. FRONTIERS IN PLANT SCIENCE 2018; 9:747. [PMID: 29922319 PMCID: PMC5996305 DOI: 10.3389/fpls.2018.00747] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/15/2018] [Indexed: 05/22/2023]
Abstract
Plants face numerous challenges from both aboveground and belowground stressors, and defend themselves against harmful insects and microorganisms in many ways. Because plant responses to biotic stresses are not only local but also systemic, belowground interactions can influence aboveground interactions in both natural and agricultural ecosystems. Arbuscular mycorrhizal fungi (AMF) are soilborne organisms that form symbiotic associations with many plant roots and are thought to play a central role in plant nutrition, growth, and fitness. In the present study, we focused on the influence of AMF on rice defense against pests. We inoculated rice plants with AMF in several field and greenhouse experiments to test whether the interaction of AMF with rice roots changes the resistance of rice against two chewing insects, the rice water weevil (Lissorhoptrus oryzophilus Kuschel, RWW) and the fall armyworm (Spodoptera frugiperda, FAW), and against infection by sheath blight (Rhizoctonia solani, ShB). Both in field and greenhouse experiments, the performance of insects and the pathogen on rice was enhanced when plants were inoculated with AMF. In the field, inoculating rice plants with AMF resulted in higher numbers of RWW larvae on rice roots. In the greenhouse, more RWW first instars emerged from AMF-colonized rice plants than from non-colonized control plants. Weight gains of FAW larvae were higher on rice plants treated with AMF inoculum. Lesion lengths and susceptibility to ShB infection were higher in rice plants colonized by AMF. Although AMF inoculation enhanced the growth of rice plants, the nutritional analyses of root and shoot tissues indicated no major increases in the concentrations of nutrients in rice plants colonized by AMF. The large effects on rice susceptibility to pests in the absence of large effects on plant nutrition suggest that AMF colonization influences other mechanisms of susceptibility (e.g., defense signaling processes). This study represents the first study conducted in the U.S. in rice showing AMF-induced plant susceptibility to several antagonists that specialize on different plant tissues. Given the widespread occurrence of AMF, our findings will help to provide a different perspective into the causal basis of rice systemic resistance/susceptibility to insects and pathogens.
Collapse
Affiliation(s)
- Lina Bernaola
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Marco Cosme
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Raymond W. Schneider
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Michael Stout
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| |
Collapse
|
44
|
Szűcs Z, Plaszkó T, Cziáky Z, Kiss-Szikszai A, Emri T, Bertóti R, Sinka LT, Vasas G, Gonda S. Endophytic fungi from the roots of horseradish (Armoracia rusticana) and their interactions with the defensive metabolites of the glucosinolate - myrosinase - isothiocyanate system. BMC PLANT BIOLOGY 2018; 18:85. [PMID: 29743024 PMCID: PMC5944135 DOI: 10.1186/s12870-018-1295-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 04/26/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND The health of plants is heavily influenced by the intensively researched plant microbiome. The microbiome has to cope with the plant's defensive secondary metabolites to survive and develop, but studies that describe this interaction are rare. In the current study, we describe interactions of endophytic fungi with a widely researched chemical defense system, the glucosinolate - myrosinase - isothiocyanate system. The antifungal isothiocyanates are also of special interest because of their beneficial effects on human consumers. RESULTS Seven endophytic fungi were isolated from horseradish roots (Armoracia rusticana), from the genera Fusarium, Macrophomina, Setophoma, Paraphoma and Oidiodendron. LC-ESI-MS analysis of the horseradish extract incubated with these fungi showed that six of seven strains could decompose different classes of glucosinolates. Aliphatic, aromatic, thiomethylalkyl and indolic glucosinolates were decomposed by different strains at different rates. SPME-GC-MS measurements showed that two strains released significant amounts of allyl isothiocyanate into the surrounding air, but allyl nitrile was not detected. The LC-ESI-MS analysis of many strains' media showed the presence of allyl isothiocyanate - glutathione conjugate during the decomposition of sinigrin. Four endophytic strains also accepted sinigrin as the sole carbon source. Isothiocyanates inhibited the growth of fungi at various concentrations, phenylethyl isothiocyanate was more potent than allyl isothiocyanate (mean IC50 was 2.30-fold lower). As a control group, ten soil fungi from the same soil were used. They decomposed glucosinolates with lower overall efficiency: six of ten strains had insignificant or weak activities and only three could use sinigrin as a carbon source. The soil fungi also showed lower AITC tolerance in the growth inhibition assay: the median IC50 values were 0.1925 mM for endophytes and 0.0899 mM for soil fungi. CONCLUSIONS The host's glucosinolates can be used by the tested endophytic fungi as nutrients or to gain competitive advantage over less tolerant species. These activities were much less apparent among the soil fungi. This suggests that the endophytes show adaptation to the host plant's secondary metabolites and that host metabolite specific activities are enriched in the root microbiome. The results present background mechanisms enabling an understanding of how plants shape their microbiome.
Collapse
Affiliation(s)
- Zsolt Szűcs
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, Debrecen, H-4010 Hungary
| | - Tamás Plaszkó
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, Debrecen, H-4010 Hungary
| | - Zoltán Cziáky
- Agricultural and Molecular Research and Service Institute, University of Nyíregyháza, Sóstói str. 31/b, Nyíregyháza, H-4400 Hungary
| | - Attila Kiss-Szikszai
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, H-4010 Hungary
| | - Tamás Emri
- Department of Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010 Hungary
| | - Regina Bertóti
- Department of Pharmacognosy, Semmelweis University, Üllői út 26, Budapest, H-1085 Hungary
| | - László Tamás Sinka
- Agricultural and Molecular Research and Service Institute, University of Nyíregyháza, Sóstói str. 31/b, Nyíregyháza, H-4400 Hungary
| | - Gábor Vasas
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, Debrecen, H-4010 Hungary
| | - Sándor Gonda
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, Debrecen, H-4010 Hungary
| |
Collapse
|
45
|
Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi. Sci Rep 2018; 8:6321. [PMID: 29679020 PMCID: PMC5910433 DOI: 10.1038/s41598-018-24686-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/06/2018] [Indexed: 01/09/2023] Open
Abstract
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.
Collapse
|
46
|
Dissanayake AJ, Purahong W, Wubet T, Hyde KD, Zhang W, Xu H, Zhang G, Fu C, Liu M, Xing Q, Li X, Yan J. Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine (Vitis vinifera). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0399-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
47
|
de Vries S, von Dahlen JK, Schnake A, Ginschel S, Schulz B, Rose LE. Broad-spectrum inhibition of Phytophthora infestans by fungal endophytes. FEMS Microbiol Ecol 2018; 94:4925062. [PMID: 29528408 PMCID: PMC5939626 DOI: 10.1093/femsec/fiy037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/05/2018] [Indexed: 11/12/2022] Open
Abstract
Phytophthora infestans is a devastating pathogen of tomato and potato. It readily overcomes resistance genes and applied agrochemicals and hence even today causes large yield losses. Fungal endophytes provide a largely unexplored avenue of control of Phy. infestans. Not only do endophytes produce a wide array of bioactive metabolites, they may also directly compete with and defeat pathogens in planta. Here, we tested 12 fungal endophytes isolated from different plant species in vitro for their production of metabolites with anti- Phytophthora activity. Four well-performing isolates were evaluated for their ability to suppress nine isolates of Phy. infestans on agar medium and in planta. Two endophytes reliably inhibited all Phy. infestans isolates on agar medium, of which Phoma eupatorii isolate 8082 was the most promising. It nearly abolished infection by Phy. infestans in planta. Our data indicate a role for the production of anti-Phytophthora compounds by the fungus and/or an enhanced plant defense response, as evident by an enhanced anthocyanin production. Here, we present a potential biocontrol agent, which can inhibit a broad-spectrum of Phy. infestans isolates. Such broadly acting inhibition is ideal, because it allows for effective control of genetically diverse isolates and may slow the adaptation of Phy. infestans.
Collapse
Affiliation(s)
- Sophie de Vries
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Janina K von Dahlen
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Anika Schnake
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Sarah Ginschel
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Barbara Schulz
- Institute of Microbiology, Technische Universitaet Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| |
Collapse
|
48
|
Daneshkhah R, Grundler FMW, Wieczorek K. The Role of MPK6 as Mediator of Ethylene/Jasmonic Acid Signaling in Serendipita indica-Colonized Arabidopsis Roots. PLANT MOLECULAR BIOLOGY REPORTER 2018; 36:284-294. [PMID: 29875545 PMCID: PMC5966479 DOI: 10.1007/s11105-018-1077-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Serendipita indica is an axenically cultivable fungus, which colonizes a broad range of plant species including the model plant Arabidopsis thaliana. Root colonization by this endophyte leads to enhanced plant fitness and performance and promotes resistance against different biotic and abiotic stresses. The involvement of MPK6 in this mutualistic interaction had been previously shown with an mpk6 A. thaliana mutant, which failed to respond to S. indica colonization. Here, we demonstrate that mpk6 roots are significantly less colonized by S. indica compared to wild-type roots and the foliar application of plant hormones, ethylene, or jasmonic acid, restores the colonization rate at least to the wild-type level. Further, hormone-treated mpk6 plants show typical S. indica-induced growth promotion effects. Moreover, expression levels of several genes related to plant defense and hormone signaling are significantly changed at different colonization phases. Our results demonstrate that the successful root colonization by S. indica depends on efficient suppression of plant immune responses. In A. thaliana, this process relies on intact hormone signaling in which MPK6 seems to play a pivotal role.
Collapse
Affiliation(s)
- R. Daneshkhah
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 24, 3430 Tulln on the Danube, Austria
| | - F. M. W. Grundler
- Institute of Crop Science and Resource Conservation, Molecular Phytomedicine, University Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany
| | - Krzysztof Wieczorek
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 24, 3430 Tulln on the Danube, Austria
| |
Collapse
|
49
|
Glynou K, Nam B, Thines M, Maciá-Vicente JG. Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species. THE NEW PHYTOLOGIST 2018; 217:1190-1202. [PMID: 29094363 DOI: 10.1111/nph.14873] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/02/2017] [Indexed: 05/02/2023]
Abstract
There is increasing knowledge on the diversity of root-endophytic fungi, but limited information on their lifestyles and dependence on hosts hampers our understanding of their ecological functions. We compared diversity and biogeographical patterns of cultivable and noncultivable root endophytes to assess whether their occurrence is determined by distinct ecological factors. The endophytic diversity in roots of nonmycorrhizal Microthlaspi spp. growing across Europe was assessed using high-throughput sequencing (HTS) and compared with a previous dataset based on cultivation of endophytes from the same root samples. HTS revealed a large fungal richness undetected by cultivation, but which largely comprised taxa with restricted distributions and/or low representation of sequence reads. Both datasets coincided in a consistent high representation of widespread endophytes within orders Pleosporales, Hypocreales and Helotiales, as well as similar associations of community structure with spatial and environmental conditions. Likewise, distributions of particular endophytes inferred by HTS agreed with cultivation data in suggesting individual ecological preferences. Our findings support that Microthlaspi spp. roots are colonized mostly by saprotrophic and likely facultative endophytes, and that differential niche preferences and distribution ranges among fungi importantly drive the assembly of root-endophytic communities.
Collapse
Affiliation(s)
- Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany
| | - Bora Nam
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany
| |
Collapse
|
50
|
Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. THE NEW PHYTOLOGIST 2018; 217:1213-1229. [PMID: 29315638 DOI: 10.1111/nph.14974] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/25/2017] [Indexed: 05/10/2023]
Abstract
Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis, Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto- and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis. The ERM fungal gene contents for polysaccharide-degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall-degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza-induced small secreted proteins (MiSSPs). The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes.
Collapse
Affiliation(s)
- Elena Martino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Emmanuelle Morin
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Gwen-Aëlle Grelet
- Manaaki Whenua - Landcare Research, Ecosystems and Global Change Team, Gerald Street, PO Box 69040, Lincoln, 7640, New Zealand
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Annegret Kohler
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Stefania Daghino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Kerrie W Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Nicolas Cichocki
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Rhyan B Dockter
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique - Aix-Marseille Université, Case 932, 163 Avenue de Luminy, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, 13288, France
| | - Rita C Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Erika A Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Jon Magnuson
- Pacific Northwest National Laboratory, Chemical and Biological Process Development Group, Richland, WA, 99354, USA
| | - Claude Murat
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Microbiology, Department of Biology, Utrecht University, 3508, TB Utrecht, the Netherlands
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Claire Veneault-Fourrey
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
- Laboratoire d'Excellence ARBRE, Faculté des Sciences et Technologies, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Université de Lorraine, Campus Aiguillettes, BP 70239, Vandoeuvre les Nancy cedex, 54506, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique - Aix-Marseille Université, Case 932, 163 Avenue de Luminy, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, 13288, France
- Department of Biological Sciences, King Abdulaziz University - KSA, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Francis M Martin
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| |
Collapse
|