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Park JM, Hong JW, Lee W, Lee BH, You YH. Geographical Isolation and Root-Associated Fungi in the Marine Terrains: A Step Toward Establishing a Strategy for Acquiring Unique Microbial Resources. MYCOBIOLOGY 2021; 49:235-248. [PMID: 36999089 PMCID: PMC10049744 DOI: 10.1080/12298093.2021.1913826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/09/2021] [Accepted: 04/03/2021] [Indexed: 06/14/2023]
Abstract
This study aimed to understand whether the geo-ecological segregation of native plant species affects the root-associated fungal community. Rhizoplane (RP) and rhizosphere (RS) fungal microbiota of Sedum takesimense native to three geographically segregated coastal regions (volcanic ocean islands) were analyzed using culture-independent methods: 568,507 quality sequences, 1399 operational taxonomic units, five phyla, and 181 genera were obtained. Across all regions, significant differences in the phyla distribution and ratio were confirmed. The Chao's richness value was greater for RS than for RP, and this variance coincided with the number of genera. In contrast, the dominance of specific genera in the RS (Simpson value) was lower than the RP at all sites. The taxonomic identity of most fungal species (95%) closely interacting with the common host plant was different. Meanwhile, a considerable number of RP only residing fungal genera were thought to have close interdependency on their host halophyte. Among these, Metarhizium was the sole genus common to all sites. These suggest that the relationship between potential symbiotic fungi and their host halophyte species evolved with a regional dependency, in the same halophyte species, and of the same natural habitat (volcanic islands); further, the fungal community differenced in distinct geographical regions. Importantly, geographical segregation should be accounted for in national culture collections, based on taxonomical uniqueness.
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Affiliation(s)
- Jong Myong Park
- Water Quality Research Institute, Waterworks Headquarters Incheon Metropolitan City, Incheon, Republic of Korea
- Incheon Metropolitan City Institute of Public Health and Environment, Incheon, Republic of Korea
| | - Ji Won Hong
- Department of Hydrogen and Renewable Energy, Kyungpook National University, Daegu, Republic of Korea
| | - Woong Lee
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
| | - Byoung-Hee Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Young-Hyun You
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
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Šķipars V, Ruņģis D. Transcript Dynamics in Wounded and Inoculated Scots Pine. Int J Mol Sci 2021; 22:ijms22041505. [PMID: 33546141 PMCID: PMC7913219 DOI: 10.3390/ijms22041505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 11/16/2022] Open
Abstract
Comparative transcriptome analysis provides a useful tool for the exploration of plant-pathogen interaction by allowing in-depth comparison of gene expression between unaffected, inoculated and wounded organisms. Here we present the results of comparative transcriptome analysis in genetically identical one-year-old Scots pine ramets after wounding and inoculation with Heterobasidion annosum. We identified 230 genes that were more than 2-fold upregulated in inoculated samples (compared to controls) and 116 downregulated genes. Comparison of inoculated samp les with wounded samples identified 32 differentially expressed genes (30 were upregulated after inoculation). Several of the genes upregulated after inoculation are involved in protection from oxidative stress, while genes involved in photosynthesis, water transport and drought stress tolerance were downregulated. An NRT3 family protein was the most upregulated transcript in response to both inoculation and wounding, while a U-box domain-containing protein gene was the most upregulated gene comparing inoculation to wounding. The observed transcriptome dynamics suggest involvement of auxin, ethylene, jasmonate, gibberellin and reactive oxygen species pathways and cell wall modification regulation in response to H. annosum infection. The results are compared to methyl jasmonate induced transcriptome dynamics.
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Mukrimin M, Kovalchuk A, Ghimire RP, Kivimäenpää M, Sun H, Holopainen JK, Asiegbu FO. Evaluation of potential genetic and chemical markers for Scots pine tolerance against Heterobasidion annosum infection. PLANTA 2019; 250:1881-1895. [PMID: 31485774 DOI: 10.1007/s00425-019-03270-8] [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: 05/30/2019] [Accepted: 08/27/2019] [Indexed: 05/12/2023]
Abstract
Two terpene compounds and four genes were identified as potential biomarkers for further evaluation for Scots pine susceptibility or tolerance against Heterobasidion annosum. Scots pine (Pinus sylvestris) is one of the main sources of timber in the boreal zone of Eurasia. Commercial pine plantations are vulnerable to root and butt rot disease caused by the fungus Heterobasidion annosum. The pathogen affects host growth rate, causes higher mortality and decreases in timber quality, resulting in considerable economic losses to forest owners. Genetic and biochemical factors contributing to Scots pine tolerance against H. annosum infection are not well understood. We assessed the predictive values of a set of potential genetic and chemical markers in a field experiment. We determined the expression levels of 25 genes and the concentrations of 36 terpenoid compounds in needles of 16 Scots pine trees randomly selected from a natural population prior to artificial infection. Stems of the same trees were artificially inoculated with H. annosum, and the length of necrotic lesions was documented 5 months post inoculation. Higher expression level of four genes included in our analysis and encoding predicted α-pinene synthase (two genes), geranyl diphosphate synthase (GPPS), and metacaspase 5 (MC5), could be associated with trees exhibiting increased levels of necrotic lesion formation in response to fungal inoculation. In contrast, concentrations of two terpenoid compounds, β-caryophyllene and α-humulene, showed significant negative correlations with the lesion size. Further studies with larger sample size will help to elucidate new biomarkers or clarify the potential of the evaluated markers for use in Scots pine disease resistance breeding programs.
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Affiliation(s)
- Mukrimin Mukrimin
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland
- Department of Forestry, Faculty of Forestry, Hasanuddin University, Jln. Perintis Kemerdekaan Km. 10, 90245, Makassar, Indonesia
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland
| | - Rajendra P Ghimire
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, 70211, Kuopio, Finland
| | - Minna Kivimäenpää
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, 70211, Kuopio, Finland
| | - Hui Sun
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jarmo K Holopainen
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, 70211, Kuopio, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland.
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Forest Tree Microbiomes and Associated Fungal Endophytes: Functional Roles and Impact on Forest Health. FORESTS 2019. [DOI: 10.3390/f10010042] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term “microbiota” has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.
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Zeng Z, Wu J, Kovalchuk A, Raffaello T, Wen Z, Liu M, Asiegbu FO. Genome-wide DNA methylation and transcriptomic profiles in the lifestyle strategies and asexual development of the forest fungal pathogen Heterobasidion parviporum. Epigenetics 2019; 14:16-40. [PMID: 30633603 PMCID: PMC6380393 DOI: 10.1080/15592294.2018.1564426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/03/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022] Open
Abstract
Heterobasidion parviporum is the most devastating fungal pathogen of conifer forests in Northern Europe. The fungus has dual life strategies, necrotrophy on living trees and saprotrophy on dead woods. DNA cytosine methylation is an important epigenetic modification in eukaryotic organisms. Our presumption is that the lifestyle transition and asexual development in H. parviporum could be driven by epigenetic effects. Involvements of DNA methylation in the regulation of aforementioned processes have never been studied thus far. RNA-seq identified lists of highly induced genes enriched in carbohydrate-active enzymes during necrotrophic interaction with host trees and saprotrophic sawdust growth. It also highlighted signaling- and transcription factor-related genes potentially associated with the transition of saprotrophic to necrotrophic lifestyle and groups of primary cellular activities throughout asexual development. Whole-genome bisulfite sequencing revealed that DNA methylation displayed pronounced preference in CpG dinucleotide context across the genome and mostly targeted transposable element (TE)-rich regions. TE methylation level demonstrated a strong negative correlation with TE expression, reinforcing the protective function of DNA methylation in fungal genome stability. Small groups of genes putatively subject to methylation transcriptional regulation in response to saprotrophic and necrotrophic growth in comparison with free-living mycelia were also explored. Our study reported on the first methylome map of a forest pathogen. Analysis of transcriptome and methylome variations associated with asexual development and different lifestyle strategies provided further understanding of basic biological processes in H. parviporum. More importantly, our work raised additional potential roles of DNA methylation in fungi apart from controlling the proliferation of TEs.
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Affiliation(s)
- Zhen Zeng
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Jiayao Wu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Zilan Wen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Mengxia Liu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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Pepori AL, Michelozzi M, Santini A, Cencetti G, Bonello P, Gonthier P, Sebastiani F, Luchi N. Comparative transcriptional and metabolic responses of Pinus pinea to a native and a non-native Heterobasidion species. TREE PHYSIOLOGY 2019; 39:31-44. [PMID: 30137615 DOI: 10.1093/treephys/tpy086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/31/2018] [Indexed: 05/28/2023]
Abstract
Heterobasidion irregulare is a causal agent of root and butt-rot disease in conifers, and is native to North America. In 1944 it was introduced in central Italy in a Pinus pinea stand, where it shares the same niche with the native species Heterobasidion annosum. The introduction of a non-native pathogen may have significant negative effects on a naïve host tree and the ecosystem in which it resides, requiring a better understanding of the system. We compared the spatio-temporal phenotypic, transcriptional and metabolic host responses to inoculation with the two Heterobasidion species in a large experiment with P. pinea seedlings. Differences in length of lesions at the inoculation site (IS), expression of host genes involved in lignin pathway and in cell rescue and defence, and analysis of terpenes at both IS and 12 cm above the IS (distal site, DS), were assessed at 3, 14 and 35 days post inoculation (dpi). Results clearly showed that both species elicit similar physiological and biochemical responses in P. pinea seedlings. The analysis of host transcripts and total terpenes showed differences between inoculation sites and between pathogen and mock inoculated plants. Both pathogen and mock inoculations induced antimicrobial peptide and phenylalanine ammonia-lyase overexpression at IS beginning at 3 dpi; while at DS all the analysed genes, except for peroxidase, were overexpressed at 14 dpi. A significantly higher accumulation of terpenoids was observed at 14 dpi at IS, and at 35 dpi at DS. The terpene blend at IS showed significant variation among treatments and sampling times, while no significant differences were ever observed in DS tissues. Based on our results, H. irregulare does not seem to have competitive advantages over the native species H. annosum in terms of pathogenicity towards P. pinea trees; this may explain why the non-native species has not widely spread over the 73 years since its putative year of introduction into central Italy.
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Affiliation(s)
- Alessia Lucia Pepori
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Marco Michelozzi
- Institute of Biosciences and Bioresources, National Research Council (IBBR-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Alberto Santini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Gabriele Cencetti
- Institute of Biosciences and Bioresources, National Research Council (IBBR-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Pierluigi Bonello
- Department of Plant Pathology, The Ohio State University, 201 Kottman Hall, 2021 Coffey Rd, Columbus, OH, USA
| | - Paolo Gonthier
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini 2, Grugliasco, TO, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
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Finkina EI, Ovchinnikova TV. Plant Defensins: Structure, Functions, Biosynthesis, and the Role in the Immune Response. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018030056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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A Gene Encoding Scots Pine Antimicrobial Protein Sp-AMP2 (PR-19) Confers Increased Tolerance against Botrytis cinerea in Transgenic Tobacco. FORESTS 2017. [DOI: 10.3390/f9010010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kuo HC, Hui S, Choi J, Asiegbu FO, Valkonen JPT, Lee YH. Secret lifestyles of Neurospora crassa. Sci Rep 2014; 4:5135. [PMID: 24875794 PMCID: PMC4038807 DOI: 10.1038/srep05135] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/14/2014] [Indexed: 12/05/2022] Open
Abstract
Neurospora crassa has a long history as an excellent model for genetic, cellular, and biochemical research. Although this fungus is known as a saprotroph, it normally appears on burned vegetations or trees after forest fires. However, due to a lack of experimental evidence, the nature of its association with living plants remains enigmatic. Here we report that Scots pine (Pinus sylvestris) is a host plant for N. crassa. The endophytic lifestyle of N. crassa was found in its interaction with Scots pine. Moreover, the fungus can switch to a pathogenic state when its balanced interaction with the host is disrupted. Our data reveal previously unknown lifestyles of N. crassa, which are likely controlled by both environmental and host factors. Switching among the endophytic, pathogenic, and saprotrophic lifestyles confers upon fungi phenotypic plasticity in adapting to changing environments and drives the evolution of fungi and associated plants.
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Affiliation(s)
- Hsiao-Che Kuo
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Sun Hui
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, and Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Korea
| | | | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Yong-Hwan Lee
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, and Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Korea
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