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Durodola B, Blumenstein K, Akinbobola A, Kolehmainen A, Chano V, Gailing O, Terhonen E. Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum. BMC Microbiol 2023; 23:350. [PMID: 37978432 PMCID: PMC10655427 DOI: 10.1186/s12866-023-03099-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype. To explore the influence of host genetics and environmental factors on fungal composition, we examined the mycobiome associated with phloem and roots of Norway spruce (Picea abies (L.) Karst.) cuttings under varying watering conditions. To test the "mycobiome-associated-fitness" hypothesis, we compared seedlings artificially inoculated with Heterobasidion parviporum and control plants to evaluate mycobiome interaction on necrosis development. We aimed to 1) identify specific mycobiome species for the Norway spruce genotypes/families within the phloem and root tissues and their interactions with H. parviporum and 2) assess stability in the mycobiome species composition under abiotic disturbances (reduced water availability). The mycobiome was analyzed by sequencing the ribosomal ITS2 region. Our results revealed significant variations in the diversity and prevalence of the phloem mycobiome among different Norway spruce genotypes, highlighting the considerable impact of genetic variation on the composition and diversity of the phloem mycobiome. Additionally, specific mycobiome genera in the phloem showed variations in response to water availability, indicating the influence of environmental conditions on the relative proportion of certain fungal genera in Norway spruce trees. In the root mycobiome, key fungi such as Phialocephala fortinii and Paraphaeosphaeria neglecta were identified as conferring inhibitory effects against H. parviporum growth in Norway spruce genotypes. Furthermore, certain endophytes demonstrated greater stability in root ecosystems under low water conditions than ectomycorrhizal fungi. This knowledge can contribute to developing sustainable forest management practices that enhance the well-being of trees and their ecosystems, ultimately bolstering forest resilience.
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Affiliation(s)
- Blessing Durodola
- Forest Pathology Research Group, Büsgen-Institute, Department of Forest Botany and Tree Physiology, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Department of Forest Genetics and Forest Tree Breeding, Büsgen-Institute, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.
| | - Kathrin Blumenstein
- Forest Pathology Research Group, Büsgen-Institute, Department of Forest Botany and Tree Physiology, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
- Chair of Pathology of Trees, Institute of Forestry, Faculty of Environment and Natural Resources, University of Freiburg, Bertoldstr. 17, 79098, Freiburg, Germany
| | - Adedolapo Akinbobola
- Forest Pathology Research Group, Büsgen-Institute, Department of Forest Botany and Tree Physiology, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Anna Kolehmainen
- Forest Pathology Research Group, Büsgen-Institute, Department of Forest Botany and Tree Physiology, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
- Department of Cell Biology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Victor Chano
- Department of Forest Genetics and Forest Tree Breeding, Büsgen-Institute, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, Büsgen-Institute, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Eeva Terhonen
- Forest Pathology Research Group, Büsgen-Institute, Department of Forest Botany and Tree Physiology, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity, Latokartanonkaari 9, 00790, Helsinki, Finland
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Crown closure affects endophytic leaf mycobiome compositional dynamics over time in Pseudotsuga menziesii var. menziesii. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Transitions of foliar mycobiota community and transcriptome in response to pathogenic conifer needle interactions. Sci Rep 2022; 12:7832. [PMID: 35551491 PMCID: PMC9098639 DOI: 10.1038/s41598-022-11907-0] [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: 01/13/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022] Open
Abstract
Profiling the host–mycobiota interactions in healthy vs. diseased forest ecosystems helps understand the dynamics of understudied yet increasingly important threats to forest health that are emerging due to climate change. We analyzed the structural and functional changes of the mycobiota and the responses of Pinus contorta in the Lophodermella needle cast pathosystem through metabarcoding and metatranscriptomics. When needles transitioned from asymptomatic to symptomatic, dysbiosis of the mycobiota occurred, but with an enrichment of Lophodermella pathogens. Many pathogenicity-related genes were highly expressed by the mycobiota at the necrotrophic phase, showing an active pathogen response that are absent in asymptomatic needles. This study also revealed that Lophodermella spp. are members of a healthy needle mycobiota that have latent lifestyles suggesting that other pine needle pathogens may have similar biology. Interestingly, Pinus contorta upregulated defense genes in healthy needles, indicating response to fungal recognition, while a variety of biotic and abiotic stresses genes were activated in diseased needles. Further investigation to elucidate the possible antagonistic interplay of other biotic members leading to disease progression and/or suppression is warranted. This study provides insights into microbial interactions in non-model pathosystems and contributes to the development of new forest management strategies against emerging latent pathogens.
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Redondo MA, Oliva J, Elfstrand M, Boberg J, Capador-Barreto HD, Karlsson B, Berlin A. Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce. Environ Microbiol 2022; 24:3640-3654. [PMID: 35315253 PMCID: PMC9544151 DOI: 10.1111/1462-2920.15974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/28/2022]
Abstract
The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high‐throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.
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Affiliation(s)
- Miguel A Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Jonàs Oliva
- Department of Crop and Forest Sciences, University of Lleida, Alcalde Rovira Roure 191, Lleida, 25198, Spain.,Joint Research Unit CTFC-AGROTECNIO, Alcalde Rovira Roure 191, Lleida, 25198, Spain
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Johanna Boberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Hernán D Capador-Barreto
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Bo Karlsson
- Skogforsk, Svalöv, Ekebo 2250, 268 90, Sweden
| | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
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Optimization of Protocol for Construction of Fungal ITS Amplicon Library for High-Throughput Illumina Sequencing to Study the Mycobiome of Aspen Leaves. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.
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Flessa F, Harjes J, Cáceres MES, Rambold G. Comparative analyses of sooty mould communities from Brazil and Central Europe. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01700-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
AbstractTo gain an insight into fungal sooty mould communities on leaves of trees and shrubs in the tropics and in temperate regions, 47 biofilms of the Mata Atlântica rainforest relic and the Caatinga vegetation in the state of Sergipe, Northeast Brazil, and from Central European colline and alpine zones were compared. The four sampling sites clearly differed in composition of their epiphyllous fungal communities. The fungal OTUs from all sites belonged mainly to the Ascomycota, with Dothideomycetes being the dominant class. The core community group consisted of a few site-specific representatives in co-occurrence with the ubiquitous Mycosphaerella tassiana and Aureobasidium pullulans. Most species of the core community were dark pigmented and were accompanied by facultative unpigmented or lightly pigmented species. Among the cultivable fungal species, the proportion of melanised species was significantly more abundant in samples from the two European sites, which supports the theory of thermal melanism. The identity of the host plant had a stronger impact on fungal community composition than the presence of sap-feeding insects.
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Siddique AB, Biella P, Unterseher M, Albrectsen BR. Mycobiomes of Young Beech Trees Are Distinguished by Organ Rather Than by Habitat, and Community Analyses Suggest Competitive Interactions Among Twig Fungi. Front Microbiol 2021; 12:646302. [PMID: 33936005 PMCID: PMC8086555 DOI: 10.3389/fmicb.2021.646302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
Beech trees (Fagus sylvatica) are prominent keystone species of great economic and environmental value for central Europe, hosting a diverse mycobiome. The composition of endophyte communities may depend on tree health, plant organ or tissue, and growth habitat. To evaluate mycobiome communalities at local scales, buds, and twigs were sampled from two young healthy mountain beech stands in Bavaria, Germany, four kilometers apart. With Illumina high-throughput sequencing, we found 113 fungal taxa from 0.7 million high-quality reads that mainly consisted of Ascomycota (52%) and Basidiomycota (26%) taxa. Significant correlations between richness and diversity indices were observed (p < 0.05), and mycobiomes did not differ between habitats in the current study. Species richness and diversity were higher in twigs compared to spring buds, and the assemblages in twigs shared most similarities. Interaction network analyses revealed that twig-bound fungi shared similar numbers of (interaction) links with others, dominated by negative co-occurrences, suggesting that competitive exclusion may be the predominant ecological interaction in the highly connected twig mycobiome. Combining community and network analyses strengthened the evidence that plant organs may filter endophytic communities directly through colonization access and indirectly by facilitating competitive interactions between the fungi.
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Affiliation(s)
- Abu Bakar Siddique
- Department of Ecology and Environmental Sciences, Faculty of Science and Technology, Umeå University, Umeå, Sweden
| | - Paolo Biella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Oliva J, Ridley M, Redondo MA, Caballol M. Competitive exclusion amongst endophytes determines shoot blight severity on pine. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13692] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonàs Oliva
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
- Joint Research Unit CTFC‐AGROTECNIO Lleida Spain
| | - Maia Ridley
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
| | - Miguel A. Redondo
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Maria Caballol
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
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Küngas K, Bahram M, Põldmaa K. Host tree organ is the primary driver of endophytic fungal community structure in a hemiboreal forest. FEMS Microbiol Ecol 2020; 96:5673485. [PMID: 31825516 DOI: 10.1093/femsec/fiz199] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/10/2019] [Indexed: 01/21/2023] Open
Abstract
Despite numerous studies on plant endophytes, little is known about fungal communities associated with different aboveground tissues of living trees. We used high-throughput sequencing to compare the diversity and community structure of fungi inhabiting leaves, branches and trunks of Alnus incana and Corylus avellana growing at three hemiboreal forest sites. Our analysis revealed that tree organs are the main determinants of the structure of fungal communities, whereas the effects of host species and locality remained secondary and negligible, respectively. The structure of fungal communities in trunks was the most distinct compared to that in leaves and branches. The foliar fungal communities were more similar within than between individual trees, implying that certain fungi may grow through parts of the tree crown. The weak effect of locality compared to host organs and species identity suggests that the structural variation of fungal communities in the aboveground parts of trees depends mainly on deterministic factors rather than dispersal limitation.
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Affiliation(s)
- Kati Küngas
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., EE51005 Tartu, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden
| | - Kadri Põldmaa
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., EE51005 Tartu, Estonia
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