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Researchers should cite this work as follows:
Yeh Y, Kirschner R (2022): The diversity of endophytic fungi of the sand coast plant Ipomoea pes-caprae in Taiwan. v1.11. Taiwan Biodiversity Information Facility (TaiBIF). Dataset/Occurrence. https://ipt.taibif.tw/resource?r=ipomoea-endophytes&v=1.11
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The publisher and rights holder of this work is Taiwan Biodiversity Information Facility (TaiBIF). This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.
This resource has been registered with GBIF, and assigned the following GBIF UUID: 42b98a7f-4252-42a0-a56e-069df3eb3a7d. Taiwan Biodiversity Information Facility (TaiBIF) publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Taiwan Biodiversity Information Facility.
Biodiversity; Coast Plant; Endophytic Fungi; Ipomoea pes-caprae; Sandy Beach; Occurrence; Specimen
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1. Taipei Botanical Garden in Taipei City (Latitude: 25.032205 Longitude: 121.509884) 2. Taichung Botanical Garden in Taichung City (Latitude: 24.156172 Longitude: 120.666314) 3. Wazihwei beach in New Taipei City (Latitude: 25.168699 Longitude: 121.414081) 4. Shimen beach in New Taipei City (Latitude: 25.292212 Longitude: 121.544561) 5. Daan beach in Taichung City (Latitude: 24.379000 Longitude: 120.583286) 6. Nanpu beach in Taichung City (Latitude: 24.343201 Longitude: 120.560261) 7. Sandy beach at Fongkeng fishing port in Hsinchu County (Latitude: 24.90521 Longitude: 120.96632) 8. Guanyin Beach in Taoyuan City (Latitude: 25.047 Longitude: 121.076)
|Bounding Coordinates||South West [21.739, 119.839], North East [25.483, 122.124]|
This dataset contains data from the Kingdom Fungi, Division Ascomycota, Basidiomycota and Zygomycota, corresponding to a total of 13 classes and 33 orders. It includes 177 different species of fungi for a total of 896 fungal strains.
The sand coast habitats are endangered by rising sea levels due to global warming and human activities. The effects on biodiversity and biological resources are widely unknown. Coastal plants are adapted to extremes of inundation and drought, poor soil nutrients, high salinity, strong wind and solar irradiation and are of utmost importance for protecting and stabilizing the threatened land along the sand shore of western Taiwan. When these habitats are lost, some coastal plants are still preserved ex-situ in botanical gardens. In our study designed for three years, we investigate the effect of such ex-situ conservation of on the biodiversity of microbes intimately associated with such plants at sand beaches. We choose Ipomoea pes-caprae as representative coastal plant which is widespread at tropical sand coasts, four natural coastal populations and two botanical gardens as collection sites, and the endophytic fungi associated with this plant as representative microbes. In a culture-dependent approach, endophytic fungi are isolated under axenic conditions and identified to species with the universal ITS marker as well as additional barcodes (TEF, TUB, RPB2, CAL and other genes) according to the specific taxonomic requirements in certain genera and species groups of fungi. In addition to this main topic yielding over one thousand new strains, next generation sequencing based on ITS markers is applied for testing at small scale whether this culture-independent method will reveal other species or species numbers. Also in collaboration parallel to this project, strains from the culture-dependent approach are to be screened for their application potential by their ability to degrade synthetic dyes which cause wastewater pollution. The species compositions and diversities between the natural and artificial collection sites are compared in order to provide data about the effects of ex-situ plant conservation on the associated microbial bioresources as foundation for decision-making in nature protection and bioconservation.
|Title||The effect of ex-situ preservation on the diversity of endophytic fungi in the coastal plant Ipomoea pes-caprae|
|Identifier||MOST 108-2621-B-002 -007|
|Funding||Ministry of Science & Technology Taiwan|
The personnel involved in the project:
One individual plant was collected per sampling (twice per year, representing the summer and the less hot seasons). Plants which were not conspicuously buried by sand during the collection time were removed with a trowel, individually placed in bags, returned to the laboratory and kept at 4°C until further processing for endophyte isolation within 48 hours after sampling. Altogether, 37 individuals of I. pes-caprae were collected from eight sites (27 from New Taipei, Taoyuan, Hsinchu and Taichung; 10 from Taipei and Taichung Botanical Gardens). Freshly collected healthy plants were cut into fragments (leaves, stems, roots) and surface-sterilized. Plant fragments were surface-sterilized under sterile conditions by agitation in 95% ethanol for 1 min, 6–12% sodium hypochlorite for 3 min (for stems) or 1.5 min (for roots and leaves), 95% ethanol for 0.5 min, and then rinsed in sterile water. All stems and roots were cut into six segments of approximately 1–2 cm, and each leaf into the petiole as well as three segments of ca. 0.6 cm diam. from the lamina. Three segments of stems and root and two segments of leaf lamina and the petiole were immediately placed onto malt extract agar (MEA) or corn extract agar (CMA) with 0.2% chloramphenicol. All isolates obtained from each plant sample were classified according to their morphological appearance into morphotypes. Representative isolates were identified to species as far as possible and deposited at the Bioresource Collection and Research Center, Hsinchu, Taiwan (BCRC). Dried cultures were deposited in the fungal specimen collection of the National Museum of Natural Science, Taichung, Taiwan (TNM).
|Study Extent||The study was conducted in northern and central Taiwan; The dataset covers natural vegetation at sand coasts of New Taipei City (Bali District and Shihmen District), Taoyuan (Guanyin District), Hsinchu County (Xinfeng Township) and Taichung City (Daan District and North District) and artificial plantations in the botanical gardens of Taipei City and Taichung City.|
|Quality Control||Since surface-sterilization has to be adjusted whenever endophytes are isolated from a hitherto uninvestigated plant species, we optimized the methods for surface sterilization for the different plant parts of I. pes-caprae. The effectiveness was further controlled regularly by the imprint technique, i.d. by temporarily pressing the surface-sterilized plant fragments onto control media. Only if no growth occurred on these control media, but in the media with plant fragments, then the surface sterilization procedure was neither too weak nor too rigorous (Rodrigruez et al. 2008). DNA sequencing was performed by Mission Biotech (Nankang, Taipei) with the same primers used for the PCR. The forward and reverse DNA sequences were edited using CodonCode Aligner version 4.0.1 (CodonCode Corp., USA) and submitted to GenBank and the DNA Data Bank of Japan. The sequences were submitted to BLAST searches at GenBank (https://blast.ncbi.nlm.nih.gov/). Depending on the similarities of the used barcode and verifiability by morphology, the strains were identified to species, genus or higher taxonomic ranks. Only sequences cited in publications were considered for identification. Scientific names were crosschecked and updated with Index Fungorum (http://www.indexfungorum.org).|
Method step description:
- Field collection, light microscopy, cultivation, DNA isolation, PCR, sequencing, sequence analyses
|Collection Name||Taipei Botanical Garden|
|Collection Name||Taichung Botanical Garden|
|Collection Name||Wazihwei beach in New Taipei City|
|Collection Name||Shimen beach in New Taipei City|
|Collection Name||Daan beach in Taichung City|
|Collection Name||Nanpu beach in Taichung City|
|Collection Name||Sandy beach at Fongkeng fishing port in Hsinchu County|
|Collection Name||Guanyin Beach in Taoyuan City|
|Specimen preservation methods||Dried|