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Zahn FE, Jiang H, Lee YI, Gebauer G. Mode of carbon gain and fungal associations of Neuwiedia malipoensis within the evolutionarily early-diverging orchid subfamily Apostasioideae. ANNALS OF BOTANY 2024; 134:511-520. [PMID: 38912975 PMCID: PMC11341671 DOI: 10.1093/aob/mcae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/22/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND AND AIMS The earliest-diverging orchid lineage, Apostasioideae, consists only of two genera: Apostasia and Neuwiedia. Previous reports of Apostasia nipponica indicated a symbiotic association with an ectomycorrhiza-forming Ceratobasidiaceae clade and partial utilization of fungal carbon during the adult stage. However, the trophic strategy of Neuwiedia throughout its development remains unidentified. To further improve our understanding of mycoheterotrophy in the Apostasioideae, this study focused on Neuwiedia malipoensis examining both the mycorrhizal association and the physiological ecology of this orchid species across various development stages. METHODS We identified the major mycorrhizal fungi of N. malipoensis protocorm, leafy seedling and adult stages using molecular barcoding. To reveal nutritional resources utilized by N. malipoensis, we compared stable isotope natural abundances (δ13C, δ15N, δ2H, δ18O) of different developmental stages with those of autotrophic reference plants. KEY RESULTS Protocorms exhibited an association with saprotrophic Ceratobasidiaceae rather than ectomycorrhiza-forming Ceratobasidiaceae and the 13C signature was characteristic of their fully mycoheterotrophic nutrition. Seedlings and adults were predominantly associated with saprotrophic fungi belonging to the Tulasnellaceae. While 13C and 2H stable isotope data revealed partial mycoheterotrophy of seedlings, it is unclear to what extent the fungal carbon supply is reduced in adult N. malipoensis. However, the 15N enrichment of mature N. malipoensis suggests partially mycoheterotrophic nutrition. Our data indicated a transition in mycorrhizal partners during ontogenetic development with decreasing dependency of N. malipoensis on fungal nitrogen and carbon. CONCLUSIONS The divergence in mycorrhizal partners between N. malipoensis and A. nipponica indicates different resource acquisition strategies and allows various habitat options in the earliest-diverging orchid lineage, Apostasioideae. While A. nipponica relies on the heterotrophic carbon gain from its ectomycorrhizal fungal partner and thus on forest habitats, N. malipoensis rather relies on own photosynthetic carbon gain as an adult, allowing it to establish in habitats as widely distributed as those where Rhizoctonia fungi occur.
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Affiliation(s)
- Franziska E Zahn
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental (BayCEER), University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Hong Jiang
- Yunnan Laboratory for Conservation of Rare, Endangered & Endemic Forest Plants, National Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, Yunnan, People’s Republic of China
| | - Yung-I Lee
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Gerhard Gebauer
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental (BayCEER), University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
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Wang D, Trimbos KB, Gomes SIF, Jacquemyn H, Merckx VSFT. Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR. THE NEW PHYTOLOGIST 2024; 242:1825-1834. [PMID: 37929750 DOI: 10.1111/nph.19385] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances. Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding. Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low-abundance families. This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.
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Affiliation(s)
- Deyi Wang
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, 2333 CC, Leiden University, Leiden, the Netherlands
| | - Sofia I F Gomes
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Heverlee, 3001, Leuven, Belgium
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
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3
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Merckx VSFT, Gomes SIF, Wang D, Verbeek C, Jacquemyn H, Zahn FE, Gebauer G, Bidartondo MI. Mycoheterotrophy in the wood-wide web. NATURE PLANTS 2024; 10:710-718. [PMID: 38641664 DOI: 10.1038/s41477-024-01677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
The prevalence and potential functions of common mycorrhizal networks, or the 'wood-wide web', resulting from the simultaneous interaction of mycorrhizal fungi and roots of different neighbouring plants have been increasingly capturing the interest of science and society, sometimes leading to hyperbole and misinterpretation. Several recent reviews conclude that popular claims regarding the widespread nature of these networks in forests and their role in the transfer of resources and information between plants lack evidence. Here we argue that mycoheterotrophic plants associated with ectomycorrhizal or arbuscular mycorrhizal fungi require resource transfer through common mycorrhizal networks and thus are natural evidence for the occurrence and function of these networks, offering a largely overlooked window into this methodologically challenging underground phenomenon. The wide evolutionary and geographic distribution of mycoheterotrophs and their interactions with a broad phylogenetic range of mycorrhizal fungi indicate that common mycorrhizal networks are prevalent, particularly in forests, and result in net carbon transfer among diverse plants through shared mycorrhizal fungi. On the basis of the available scientific evidence, we propose a continuum of carbon transfer options within common mycorrhizal networks, and we discuss how knowledge on the biology of mycoheterotrophic plants can be instrumental for the study of mycorrhizal-mediated transfers between plants.
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Affiliation(s)
- Vincent S F T Merckx
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, the Netherlands.
- Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands.
| | - Sofia I F Gomes
- Above-belowground Interactions, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Deyi Wang
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Cas Verbeek
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, the Netherlands
- Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Hans Jacquemyn
- Plant Population Biology and Conservation, Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium
| | - Franziska E Zahn
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Gerhard Gebauer
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
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Tanunchai B, Ji L, Schroeter SA, Wahdan SFM, Hossen S, Delelegn Y, Buscot F, Lehnert AS, Alves EG, Hilke I, Gleixner G, Schulze ED, Noll M, Purahong W. FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species. MICROBIAL ECOLOGY 2023; 85:411-428. [PMID: 35124727 PMCID: PMC9958157 DOI: 10.1007/s00248-022-01973-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/16/2023]
Abstract
Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.
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Affiliation(s)
- Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, 150040 Harbin, People’s Republic of China
| | - Simon Andreas Schroeter
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, 41522 Egypt
| | - Shakhawat Hossen
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Yoseph Delelegn
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ann-Sophie Lehnert
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Eliane Gomes Alves
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Gerd Gleixner
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
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Huang M, Gao D, Lin L, Wang S, Xing S. Spatiotemporal dynamics and functional characteristics of the composition of the main fungal taxa in the root microhabitat of Calanthe sieboldii (Orchidaceae). BMC PLANT BIOLOGY 2022; 22:556. [PMID: 36456905 PMCID: PMC9716840 DOI: 10.1186/s12870-022-03940-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Endophytic fungi play a critical ecological role in the growth and development of orchids, but little is known about the spatial and temporal dynamics of fungal diversity or the ecological functions of fungi during orchid growth and reproduction. Calanthe sieboldii Decne. is listed in the Chinese National Key Protected Wild Plants as a class I protected wild plant. To understand the community characteristics of root and soil fungi of the orchid during its reproductive seasons, we investigated the community composition, spatial and temporal dynamics, and functional characteristics of the orchid microhabitat fungi by using diversity and ecological functional analyses. RESULTS We discovered that there were three, seven, and four dominant fungal families in the orchid's roots, rhizoplane soil, and rhizosphere soil, respectively. Tulasnellaceae, Aspergillaceae, and Tricholomataceae were the dominant fungi in this endangered orchid's microhabitats. The closer the fungal community was to the orchid, the more stable and the less likely the community composition to change significantly over time. The fungal communities of this orchid's roots and rhizoplane soil varied seasonally, while those of the rhizosphere soil varied interannually. Saprophytic fungi were the most abundant in the orchid's fungal community, and the closer the distance to the orchid, the more symbiotic fungi were present. CONCLUSIONS The fungi in different parts of the root microhabitat of C. sieboldii showed different spatiotemporal dynamic patterns. The fungal community near the orchid roots was relatively stable and displayed seasonal variation, while the community further away from the roots showed greater variation. In addition, compared with the soil fungi, the dominant endophytic fungi were more stable, and these may be key fungi influencing orchid growth and development. Our study on the spatiotemporal dynamics and functions of fungi provides a basis for the comprehensive understanding and utilization of orchid endophytic fungi.
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Affiliation(s)
- Min Huang
- School of Ecology and Nature Conservation, Beijing Forestry University, Haidian, Beijing, 100083, China
| | - Dazhong Gao
- School of Ecology and Nature Conservation, Beijing Forestry University, Haidian, Beijing, 100083, China
| | - Lele Lin
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Haidian, Beijing, 100091, China
| | - Shengcai Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Haidian, Beijing, 100083, China
| | - Shaohua Xing
- School of Ecology and Nature Conservation, Beijing Forestry University, Haidian, Beijing, 100083, China.
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McCormick MK, Good KL, Mozdzer TJ, Whigham DF. Shade and drought increase fungal contribution to partially mycoheterotrophic terrestrial orchids Goodyera pubescens and Tipularia discolor. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1047267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Many photosynthetic plants supplement photosynthetic carbon with fungal carbon, but the mechanisms that govern dependence on mycoheterotrophic carbon are poorly understood. We used exclusion shelters to manipulate water and light availability to plants of the terrestrial orchids Goodyera pubescens and Tipularia discolor. We tracked changes in δ13C from photosynthesis and δ15N acquired from soil-derived inorganic nitrogen versus mycoheterotrophy, along with direct measures of photosynthesis in T. discolor. We hypothesized that shade would increase dependence on mycoheterotrophy compared to reference plants, while drought would decrease both photosynthesis and the abundance of potential mycorrhizal fungi. Drought and shade enriched 13C and 15N in both G. pubescens and T. discolor, compared to control plants, indicating increased fungal contribution to orchid tissues. Physiological measurements of T. discolor leaves showed that dark respiration, water use efficiency, and relative electron transport rate did not vary significantly, but shaded plants had greater quantum efficiency, suggesting they were light-limited. Light saturated photosynthesis of T. discolor leaves was lower in both shaded and drought-treated plants, indicating lower photosynthetic capacity, and likely greater dependence on mycoheterotrophy and corresponding enrichment in 13C and 15N. This study documented changes in orchid dependence on fungal carbon in response to manipulated environmental conditions. Both shade and drought increased the dependence of both orchids on mycoheterotrophically derived carbon and nitrogen.
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Peng HW, Lian L, Zhang J, Erst AS, Wang W. Phylogenomics, plastome degradation and mycoheterotrophy evolution of Neottieae (Orchidaceae), with emphasis on the systematic position and Loess Plateau-Changbai Mountains disjunction of Diplandrorchis. BMC PLANT BIOLOGY 2022; 22:507. [PMID: 36316655 PMCID: PMC9624021 DOI: 10.1186/s12870-022-03906-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Mycoheterotrophy is a unique survival strategy adapted to dense forests and has attracted biologists' attention for centuries. However, its evolutionary origin and related plastome degradation are poorly understood. The tribe Neottieae contains various nutrition types, i.e., autotrophy, mixotrophy, and mycoheterotrophy. Here, we present a comprehensive phylogenetic analysis of the tribe based on plastome and nuclear ITS data. We inferred the evolutionary shift of nutrition types, constructed the patterns of plastome degradation, and estimated divergence times and ancestral ranges. We also used an integration of molecular dating and ecological niche modeling methods to investigate the disjunction between the Loess Plateau and Changbai Mountains in Diplandrorchis, a mycoheterotrophic genus endemic to China that was included in a molecular phylogenetic study for the first time. RESULTS Diplandrorchis was imbedded within Neottia and formed a clade with four mycoheterotrophic species. Autotrophy is the ancestral state in Neottieae, mixotrophy independently originated at least five times, and three shifts from mixotrophy to mycoheterotrophy independently occurred. The five mixotrophic lineages possess all plastid genes or lost partial/all ndh genes, whereas each of the three mycoheterotroph lineages has a highly reduced plastome: one lost part of its ndh genes and a few photosynthesis-related genes, and the other two lost almost all ndh, photosynthesis-related, rpo, and atp genes. These three mycoheterotrophic lineages originated at about 26.40 Ma, 25.84 Ma, and 9.22 Ma, respectively. Diplandrorchis had presumably a wide range in the Pliocene and migrated southward in the Pleistocene. CONCLUSIONS The Pleistocene climatic fluctuations and the resultant migration resulted in the Loess Plateau-Changbai Mountains disjunction of Diplandrorchis. In the evolution of mycoheterotrophic lineages, the loss of plastid-encoded genes and plastome degradation are staged and irreversible, constraining mycoheterotrophs to inhabit understories with low light levels. Accordingly, the rise of local forests might have promoted the origin of conditions in which mycoheterotrophy is advantageous.
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Affiliation(s)
- Huan-Wen Peng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lian Lian
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Forestry College, Beihua University, Jilin, 132013, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Barrett CF, Santee MV, Fama NM, Freudenstein JV, Simon SJ, Sinn BT. Lineage and role in integrative taxonomy of a heterotrophic orchid complex. Mol Ecol 2022; 31:4762-4781. [PMID: 35837745 PMCID: PMC9452484 DOI: 10.1111/mec.16617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Mathilda V. Santee
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Nicole M. Fama
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - John V. Freudenstein
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 1315 Kinnear Rd., Columbus, Ohio, USA 43212
| | - Sandra J. Simon
- Department of Biology, West Virginia University Institute of Technology, Beckley, WV, USA
| | - Brandon T. Sinn
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, USA
- Department of Botany and Ecology, University of Latvia, Jelgavas iela 1, Riga, LV-1004, Latvia
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Zahn FE, Lee YI, Gebauer G. Fungal association and root morphology shift stepwise during ontogenesis of orchid Cremastra appendiculata towards autotrophic nutrition. AOB PLANTS 2022; 14:plac021. [PMID: 35673361 PMCID: PMC9167560 DOI: 10.1093/aobpla/plac021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
The chlorophyllous, terrestrial orchid Cremastra appendiculata from East Asia is unique concerning its fungal mycorrhiza partners. The initially mycoheterotrophic protocorms exploit rather specialized non-rhizoctonia saprotrophic Psathyrellaceae. Adult individuals of this orchid species are either linked to Psathyrellaceae being partially mycoheterotrophic or form mycorrhiza with fungi of the ubiquitous saprotrophic rhizoctonia group. This study provides new insights on nutrition mode, subterranean morphology and fungal partners across different life stages of C. appendiculata. We compared different development stages of C. appendiculata to surrounding autotrophic reference plants based on multi-element natural abundance stable isotope analyses (δ13C, δ15N, δ2H, δ18O) and total N concentrations. Site- and sampling-time-independent enrichment factors of stable isotopes were used to reveal trophic strategies. We determined mycorrhizal fungi of C. appendiculata protocorm, seedling and adult samples using high-throughput DNA sequencing. We identified saprotrophic non-rhizoctonia Psathyrellaceae as dominant mycorrhizal fungi in protocorm and seedling rhizomes. In contrast, the roots of seedlings and mature C. appendiculata were mainly colonized with fungi belonging to the polyphyletic assembly of rhizoctonia (Ceratobasidium, Thanatephorus and Serendipitaceae). Mature C. appendiculata did not differ in isotopic signature from autotrophic reference plants suggesting a fully autotrophic nutrition mode. Characteristic of orchid specimens entirely relying on fungal nutrition, C. appendiculata protocorms were enriched in 15N, 13C and 2H compared to reference plants. Seedlings showed an intermediate isotopic signature, underpinning the differences in the fungal community depending on their subterranean morphology. In contrast to the suggestion that C. appendiculata is a partially mycoheterotrophic orchid species, we provide novel evidence that mature C. appendiculata with rhizoctonia mycobionts can be entirely autotrophic. Besides an environmentally driven variability among populations, we suggest high within-individual flexibility in nutrition and mycobionts of C. appendiculata, which is subject to the ontogenetic development stage.
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Affiliation(s)
- Franziska E Zahn
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Yung-I Lee
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
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Chen J, Tang Y, Kohler A, Lebreton A, Xing Y, Zhou D, Li Y, Martin FM, Guo S. Comparative Transcriptomics Analysis of the Symbiotic Germination of D. officinale (Orchidaceae) With Emphasis on Plant Cell Wall Modification and Cell Wall-Degrading Enzymes. FRONTIERS IN PLANT SCIENCE 2022; 13:880600. [PMID: 35599894 PMCID: PMC9120867 DOI: 10.3389/fpls.2022.880600] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Orchid seed germination in nature is an extremely complex physiological and ecological process involving seed development and mutualistic interactions with a restricted range of compatible mycorrhizal fungi. The impact of the fungal species' partner on the orchids' transcriptomic and metabolic response is still unknown. In this study, we performed a comparative transcriptomic analysis between symbiotic and asymbiotic germination at three developmental stages based on two distinct fungi (Tulasnella sp. and Serendipita sp.) inoculated to the same host plant, Dendrobium officinale. Differentially expressed genes (DEGs) encoding important structural proteins of the host plant cell wall were identified, such as epidermis-specific secreted glycoprotein, proline-rich receptor-like protein, and leucine-rich repeat (LRR) extensin-like protein. These DEGs were significantly upregulated in the symbiotic germination stages and especially in the protocorm stage (stage 3) and seedling stage (stage 4). Differentially expressed carbohydrate-active enzymes (CAZymes) in symbiotic fungal mycelium were observed, they represented 66 out of the 266 and 99 out of the 270 CAZymes annotated in Tulasnella sp. and Serendipita sp., respectively. These genes were speculated to be involved in the reduction of plant immune response, successful colonization by fungi, or recognition of mycorrhizal fungi during symbiotic germination of orchid seed. Our study provides important data to further explore the molecular mechanism of symbiotic germination and orchid mycorrhiza and contribute to a better understanding of orchid seed biology.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanjing Tang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, INRAE Grand Est - Nancy, Champenoux, France
| | - Annie Lebreton
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, INRAE Grand Est - Nancy, Champenoux, France
| | - Yongmei Xing
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongyu Zhou
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Francis M. Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, INRAE Grand Est - Nancy, Champenoux, France
| | - Shunxing Guo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Weerasuriya NM, Kukolj K, Spencer R, Sveshnikov D, Thorn RG. Multiple Fungi May Connect the Roots of an Orchid ( Cypripedium reginae) and Ash ( Fraxinus nigra) in Western Newfoundland. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:805127. [PMID: 37746191 PMCID: PMC10512338 DOI: 10.3389/ffunb.2022.805127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/07/2022] [Indexed: 09/26/2023]
Abstract
Showy lady's slipper (Cypripedium reginae Walter, Orchidaceae) and black ash (Fraxinus nigra Marshall, Oleaceae) often co-occur in close proximity in fens in western Newfoundland, Canada. Metabarcoding of DNA extracted from root samples of both species following surface sterilization, and others without surface sterilization was used to determine if there were shared fungal endophytes in the roots of both species that could form a common mycorrhizal network between them. A wide variety of fungi were recovered from primers amplifying the nuclear ribosomal internal transcribed spacer region (ITS2). Sixty-six fungal sequences were shared by surface-sterilized roots of both orchid and ash, among them arbuscular mycorrhizal fungi (Claroideoglomus, Dominikia, Glomus and Rhizophagus), ectomycorrhizal fungi (Inocybe and Tomentella), the broad-host root endophyte Cadophora orchidicola, along with root pathogens (Dactylonectria, Ilyonectria, Pyricularia, and Xylomyces) and fungi of unknown function. There appear to be multiple fungi that could form a common mycorrhizal network between C. reginae and F. nigra, which might explain their frequent co-occurrence. Transfer of nutrients or carbon between the orchid and ash via one or more of the shared fungal endophytes remains to be demonstrated.
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Affiliation(s)
| | - Katarina Kukolj
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Rebecca Spencer
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Dmitry Sveshnikov
- School of Science and the Environment, Grenfell Campus, Memorial University, Corner Brook, NL, Canada
| | - R. Greg Thorn
- Department of Biology, University of Western Ontario, London, ON, Canada
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12
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Selosse MA, Petrolli R, Mujica MI, Laurent L, Perez-Lamarque B, Figura T, Bourceret A, Jacquemyn H, Li T, Gao J, Minasiewicz J, Martos F. The Waiting Room Hypothesis revisited by orchids: were orchid mycorrhizal fungi recruited among root endophytes? ANNALS OF BOTANY 2022; 129:259-270. [PMID: 34718377 PMCID: PMC8835631 DOI: 10.1093/aob/mcab134] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/25/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND As in most land plants, the roots of orchids (Orchidaceae) associate with soil fungi. Recent studies have highlighted the diversity of the fungal partners involved, mostly within Basidiomycotas. The association with a polyphyletic group of fungi collectively called rhizoctonias (Ceratobasidiaceae, Tulasnellaceae and Serendipitaceae) is the most frequent. Yet, several orchid species target other fungal taxa that differ from rhizoctonias by their phylogenetic position and/or ecological traits related to their nutrition out of the orchid roots (e.g. soil saprobic or ectomycorrhizal fungi). We offer an evolutionary framework for these symbiotic associations. SCOPE Our view is based on the 'Waiting Room Hypothesis', an evolutionary scenario stating that mycorrhizal fungi of land flora were recruited from ancestors that initially colonized roots as endophytes. Endophytes biotrophically colonize tissues in a diffuse way, contrasting with mycorrhizae by the absence of morphological differentiation and of contribution to the plant's nutrition. The association with rhizoctonias is probably the ancestral symbiosis that persists in most extant orchids, while during orchid evolution numerous secondary transitions occurred to other fungal taxa. We suggest that both the rhizoctonia partners and the secondarily acquired ones are from fungal taxa that have broad endophytic ability, as exemplified in non-orchid roots. We review evidence that endophytism in non-orchid plants is the current ecology of many rhizoctonias, which suggests that their ancestors may have been endophytic in orchid ancestors. This also applies to the non-rhizoctonia fungi that were secondarily recruited by several orchid lineages as mycorrhizal partners. Indeed, from our review of the published literature, they are often detected, probably as endophytes, in extant rhizoctonia-associated orchids. CONCLUSION The orchid family offers one of the best documented examples of the 'Waiting Room Hypothesis': their mycorrhizal symbioses support the idea that extant mycorrhizal fungi have been recruited among endophytic fungi that colonized orchid ancestors.
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Affiliation(s)
- Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Rémi Petrolli
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
| | - María Isabel Mujica
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile, & Instituto de Ecología and Biodiversidad (IEB), Alameda 340, Santiago, Chile
| | - Liam Laurent
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
| | - Benoît Perez-Lamarque
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, 75005 Paris, France
| | - Tomáš Figura
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague, Czech Republic
| | - Amelia Bourceret
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Taiqiang Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Jiangyun Gao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Julita Minasiewicz
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Florent Martos
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
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13
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Li YY, Boeraeve M, Cho YH, Jacquemyn H, Lee YI. Mycorrhizal Switching and the Role of Fungal Abundance in Seed Germination in a Fully Mycoheterotrophic Orchid, Gastrodia confusoides. FRONTIERS IN PLANT SCIENCE 2022; 12:775290. [PMID: 35095954 PMCID: PMC8792533 DOI: 10.3389/fpls.2021.775290] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Mycorrhizal associations are essential for orchid germination and seedling establishment, and thus may constrain the distribution and abundance of orchids under natural conditions. Previous studies have shown that germination and seedling establishment in several orchids often decline with increasing distance from adult plants, resulting in non-random spatial patterns of seedling establishment. In contrast, individuals of the fully mycoheterotrophic orchid Gastrodia confusoides often tend to have random aboveground spatial patterns of distribution within bamboo forests. Since G. confusoides is parasitic on litter-decaying fungi, its random spatial patterns of distribution may be due to highly scattered patterns of litter-decaying fungi within bamboo forests. To test this hypothesis, we first identified the main mycorrhizal fungi associating with developing seeds and adult plants at a bamboo forest site in Taiwan using Miseq high-throughput DNA sequencing. Next, we combined seed germination experiments with quantitative PCR (qPCR) analyses to investigate to what extent the abundance of mycorrhizal fungi affected spatial patterns of seed germination. Our results show that seed germination and subsequent growth to an adult stage in G. confusoides required a distinct switch in mycorrhizal partners, in which protocorms associated with a single Mycena OTU, while adults mainly associated with an OTU from the genus Gymnopus. A strong, positive relationship was observed between germination and Mycena abundance in the litter, but not between germination and Gymnopus abundance. Fungal abundance was not significantly related to the distance from the adult plants, and consequently germination was also not significantly related to the distance from adult plants. Our results provide the first evidence that the abundance of litter-decaying fungi varies randomly within the bamboo forest and independently from G. confusoides adults.
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Affiliation(s)
- Yuan-Yuan Li
- Beijing Key Laboratory of Seed Disease Testing and Control, College of Plant Protection, China Agricultural University, Beijing, China
| | - Margaux Boeraeve
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium
| | - Yu-Hsiu Cho
- Biology Department, National Museum of Natural Science, Taichung, Taiwan
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium
| | - Yung-I Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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14
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Mycorrhizal Fungal Partners Remain Constant during a Root Lifecycle of Pleione bulbocodioides (Orchidaceae). J Fungi (Basel) 2021; 7:jof7110994. [PMID: 34829281 PMCID: PMC8621020 DOI: 10.3390/jof7110994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Mycorrhizal mutualisms are vital for orchids through germination to adulthood. Fungal species diversity and community composition vary across seasons and plant development stages and affect plant survival, adaptation, and community maintenance. Knowledge of the temporal turnover of mycorrhizal fungi (OMF) remains poorly understood in the eco-physiologically diverse orchids (especially in epiphytic orchids), although it is important to understand the function and adaptation of mycorrhizae. Some species of Pleione are epiphytic plants with annual roots and may recruit different fungal partners during their root lifecycle. Based on continuous samplings of Pleione bulbocodioides during a whole root lifecycle, we characterized the fungal temporal dynamics using Illumina sequencing of the ITS2 region. Our data showed that the plants of P. bulbocodioides were quickly colonized by OMF at root emergence and had a constant OMF composition throughout one root lifecycle, although the OMF richness declined with root aging after a peak occurrence during root elongation. In contrast, the richness of root-inhabiting fungal endophytes kept increasing with root aging and more drastic turnovers were found in their species compositions. Our findings of OMF temporal turnover contribute to further understanding of mycorrhizal associations and adaptation of Orchidaceae and will benefit orchid resource conservation and utilization.
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