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Xie QY, Kuo LY, Chang CC, Lin CJ, Wang WH, Chen KH. Prevalent arbuscular mycorrhizae in roots and highly variable mycobiome in leaves of epiphytic subtropical fern Ophioderma pendulum. AMERICAN JOURNAL OF BOTANY 2024:e16319. [PMID: 38641926 DOI: 10.1002/ajb2.16319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/21/2024]
Abstract
PREMISE Endophytic and mycorrhizal fungi are crucial in facilitating plant nutrition acquisition and stress tolerance. In epiphytic habitats, plants face nutrition and water stress, but their roots are mostly nonmycorrhizal and especially lacking in arbuscular mycorrhizal associations. Ophioderma pendulum is an epiphytic fern with a partially mycoheterotrophic lifestyle, likely heavily reliant on symbiotic fungi. To characterize fungal associations in the sporophyte of O. pendulum, we focused on leaves and roots of O. pendulum, seeking to reveal the fungal communities in these organs. METHODS Roots and leaves from O. pendulum in a subtropical forest were examined microscopically to observe the morphology of fungal structures and determine the percentage of various fungal structures in host tissues. Fungal composition was profiled using metabarcoding techniques that targeted ITS2 of the nuclear ribosomal DNA. RESULTS Roots were consistently colonized by arbuscular mycorrhizal fungi (Glomeromycota), especially Acaulospora. Unlike previous findings on epiphytic ferns, dark septate endophytes were rare in O. pendulum roots. Leaves were predominantly colonized by Ascomycota fungi, specifically the classes Dothideomycetes (46.88%), Eurotiomycetes (11.51%), Sordariomycetes (6.23%), and Leotiomycetes (6.14%). Across sampling sites, fungal community compositions were similar in the roots but differed significantly in the leaves. CONCLUSIONS Ophioderma pendulum maintains stable, single-taxon-dominant communities in the roots, primarily featuring arbuscular mycorrhizal fungi, whereas the leaves may harbor opportunistic fungal colonizers. Our study underlines the significance of mycorrhizal fungi in the adaptation of epiphytic ferns.
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Affiliation(s)
- Qiao-Yi Xie
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taiwan
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing-Hua University, Hsinchu, Taiwan
| | - Chiung-Chih Chang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Jung Lin
- Fushan Research Center, Taiwan Forestry Research Institute, Yilan, Taiwan
| | - Wen-Hong Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ko-Hsuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Singha R, Sharma D, Saha AK, Das P. Foliar phenols and flavonoids level in pteridophytes: an insight to culturable fungal endophyte colonisation. Arch Microbiol 2024; 206:170. [PMID: 38491263 DOI: 10.1007/s00203-024-03880-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 03/18/2024]
Abstract
There are many available reports of secondary metabolites as bioactive molecules from culturable endophytes, nevertheless, there are scarce research pertaining to the levels of metabolites in plants with respect to the incidence and colonisation of fungal endophytes in the same foliar tissues. Therefore, the study was focussed to examine whether fungal endophyte colonisation and the accumulation of secondary metabolites, such as flavonoids and phenols, in the plants are related in any way. For this reason, the study aims to analyse phenols and flavonoids from the fronds of eleven pteridophytes along with the culture-dependent isolation of fungal endophytes from the host plants subsequently assigning them to morphological category and their quantitative analysis and further resolving its identities through molecular affiliation. The results revealed that nine morpho-categories of fungal endophytes were allotted based on culture attributes, hyphal patterns and reproductive structural characters. Highest numbers of species were isolated from Adiantum capillus-veneris and least was recorded from Pteris vittata and Dicranopteris linearis. Maximum phenol content was analysed from the fronds of P. vittata and lowest was recorded in A. capillus-veneris. Highest flavonoid content was measured in D. linearis and lowest was detected in Christella dentata. Significant negative correlation was observed between phenol content of ferns and species richness of fungi. Moreover, significant positive correlation was observed with the relative abundance of Chaetomium globosum and flavonoid content of ferns and negative significant relation was found between relative abundance of Pseudopestalotiopsis chinensis and phenol content of pteridophytes. The occurrence and the quantitative aspects of endophytes in ferns and their secondary metabolites are discussed.
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Affiliation(s)
- Royee Singha
- Microbiology Laboratory, Department of Botany, Tripura University, Suryamaninagar, Tripura, 799022, India
| | - Dipashree Sharma
- Microbiology Laboratory, Department of Botany, Tripura University, Suryamaninagar, Tripura, 799022, India
| | - Ajay Krishna Saha
- Mycology and Plant Pathology Laboratory, Department of Botany, Tripura University, Suryamaninagar, Tripura, 799022, India
| | - Panna Das
- Microbiology Laboratory, Department of Botany, Tripura University, Suryamaninagar, Tripura, 799022, India.
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Kuo LY, Su HJ, Koubínová D, Xie PJ, Whitehouse C, Ebihara A, Grant JR. Organellar phylogenomics of Ophioglossaceae fern genera. FRONTIERS IN PLANT SCIENCE 2024; 14:1294716. [PMID: 38288414 PMCID: PMC10823028 DOI: 10.3389/fpls.2023.1294716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024]
Abstract
Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.
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Affiliation(s)
- Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
| | - Darina Koubínová
- University of Neuchâtel, Laboratory of Evolutionary Genetics, Neuchâtel, Switzerland
| | - Pei-Jun Xie
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Jason R. Grant
- University of Neuchâtel, Laboratory of Evolutionary Genetics, Neuchâtel, Switzerland
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Guillen‐Otero T, Lee S, Chen C, Szoevenyi P, Kessler M. A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11523. [PMID: 37342167 PMCID: PMC10278937 DOI: 10.1002/aps3.11523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 06/22/2023]
Abstract
Premise Detailed studies of the fungi associated with lycophytes and ferns provide crucial insights into the early evolution of land plants. However, most investigations to date have assessed fern-fungus interactions based only on visual root inspection. In the present research, we establish and evaluate a metabarcoding protocol to analyze the fungal communities associated with fern and lycophyte roots. Methods We used two primer pairs focused on the ITS rRNA region to screen the general fungal communities, and the 18S rRNA to target Glomeromycota fungi (i.e., arbuscular mycorrhizal fungi). To test these approaches, we collected and processed roots from 12 phylogenetically distant fern and lycophyte species. Results We found marked compositional differences between the ITS and 18S data sets. While the ITS data set demonstrated the dominance of orders Glomerales (phylum Glomeromycota), Pleosporales, and Helotiales (both in phylum Ascomycota), the 18S data set revealed the greatest diversity of Glomeromycota. Non-metric multidimensional scaling (NMDS) ordination suggested an important geographical effect in sample similarities. Discussion The ITS-based approach is a reliable and effective method to analyze the fungal communities associated with fern and lycophyte roots. The 18S approach is more appropriate for studies focused on the detailed screening of arbuscular mycorrhizal fungi.
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Affiliation(s)
- Thais Guillen‐Otero
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Soon‐Jae Lee
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Cheng‐Wei Chen
- Biodiversity Program, Taiwan International Graduate ProgramAcademia Sinica and National Taiwan Normal UniversityTaipei115Taiwan
| | - Peter Szoevenyi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
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Ke BF, Wang GJ, Labiak PH, Rouhan G, Chen CW, Shepherd LD, Ohlsen DJ, Renner MAM, Karol KG, Li FW, Kuo LY. Systematics and Plastome Evolution in Schizaeaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:885501. [PMID: 35909781 PMCID: PMC9328107 DOI: 10.3389/fpls.2022.885501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
While the family Schizaeaceae (Schizaeales) represents only about 0.4% of the extant fern species diversity, it differs from other ferns greatly in gross morphologies, niche preferences, and life histories. One of the most notable features in this family is its mycoheterotrophic life style in the gametophytic stage, which appears to be associated with extensive losses of plastid genes. However, the limited number of sequenced plastomes, and the lack of a well-resolved phylogenetic framework of Schizaeaceae, makes it difficult to gain any further insight. Here, with a comprehensive sampling of ~77% of the species diversity of this family, we first inferred a plastid phylogeny of Schizaeaceae using three DNA regions. To resolve the deep relationships within this family, we then reconstructed a plastome-based phylogeny focusing on a selection of representatives that covered all the major clades. From this phylogenomic backbone, we traced the evolutionary histories of plastid genes and examined whether gene losses were associated with the evolution of gametophytic mycoheterotrophy. Our results reveal that extant Schizaeaceae is comprised of four major clades-Microschizaea, Actinostachys, Schizaea, and Schizaea pusilla. The loss of all plastid NADH-like dehydrogenase (ndh) genes was confirmed to have occurred in the ancestor of extant Schizaeaceae, which coincides with the evolution of mycoheterotrophy in this family. For chlorophyll biosynthesis genes (chl), the losses were interpreted as convergent in Schizaeaceae, and found not only in Actinostachys, a clade producing achlorophyllous gametophytes, but also in S. pusilla with chlorophyllous gametophytes. In addition, we discovered a previously undescribed but phylogenetically distinct species hidden in the Schizaea dichotoma complex and provided a taxonomic treatment and morphological diagnostics for this new species-Schizaea medusa. Finally, our phylogenetic results suggest that the current PPG I circumscription of Schizaea is non-monophyletic, and we therefore proposed a three-genus classification moving a subset of Schizaea species sensu PPG I to a third genus-Microschizaea.
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Affiliation(s)
- Bing-Feng Ke
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Paulo H. Labiak
- Depto. de Botânica, Universidade Federal do Paraná, Curitiba, Brazil
| | - Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, EPHE, UA, CNRS, Sorbonne Université, Paris, France
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Cheng-Wei Chen
- Department of Life Science, Biodiversity Program, Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | | | | | - Kenneth G. Karol
- The Lewis B. and Dorothy Cullman Program for Molecular Systematics, New York Botanical Garden, Bronx, NY, United States
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Biology Section, Cornell University, Ithaca, NY, United States
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
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