Biodiversity Data Journal :
Data Paper (Biosciences)
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Corresponding author: Roland Kirschner (kirschner@ntu.edu.tw)
Academic editor: Christian Wurzbacher
Received: 15 Dec 2022 | Accepted: 03 Feb 2023 | Published: 17 Feb 2023
© 2023 Yu-Hung Yeh, Roland Kirschner
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Yeh Y-H, Kirschner R (2023) The diversity of cultivable endophytic fungi of the sand coast plant Ipomoea pes-caprae in Taiwan. Biodiversity Data Journal 11: e98878. https://doi.org/10.3897/BDJ.11.e98878
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Ipomoea pes-caprae is a plant of sand coasts and it can tolerate stresses, such as high salinity, strong wind and sand movements and lack of nutrients. It plays an important role in coast protection and preventing erosion. Fungal endophytes show high biodiversity and have a strong influence on the survival of plants under different stress factors. Although this plant is important for sand coast ecosystems, little is known about the associated fungi. In this study, we isolated and identified endophytic fungi of Ipomoea pes-caprae, a dominant plant along the shore of Taiwan. The dataset contains 896 records, which correspond to 177 species. The geographical scope of the dataset covers the northern subtropical area of the main island of Taiwan, with its sand coasts in New Taipei, Taoyuan, Hsinchu and Taichung and two botanical gardens in Taipei and Taichung. The detailed original data of fungal diversity are rarely publicly shared under strictly formalised and, thus, reusable standards. As an example for such an approach, the complete occurrence dataset was made available in the Darwin Core Archive format via the Global Biodiversity Information Facility (GBIF) under Version 1.13, Taiwan Biodiversity Information Facility (TaiBIF) https://doi.org/10.15468/9h9rcg. In this first data paper on endophytic fungi, the scientific name and associated DNA sequence in the dataset were directly linked to other free online resource (Index Fungorum, GenBank), which shows the potential of GBIF for linking together different online data repositories.
We describe a dataset, in which the diversity of endophytic fungi of the sand coast plant Ipomoea pes-caprae in Taiwan was investigated.
biodiversity, coast plant, endophytic fungi, sandy beach
Taiwan has abundant coastal terrains. The most widespread coastal ecosystems are sand dunes and sandy beaches especially along the northern and western coast of the main island. Herbaceous vegetation at sand coasts consists of specific plants which can tolerate high salinity, strong wind and sand movements and lack of nutrients and is, therefore, important for coast protection and preventing erosion (
Endophytes are microorganisms, mainly fungi, growing within plant tissues for all or part of their life cycle, but causing no apparent disease (
The aim of the study was to study cultivable endophytic fungi of I. pes-caprae and to analyse whether fungi were specific to plant species and plant organs (root, stem, leaf). We also collected I. pes-caprae from botanical gardens located in the inland of the island for comparing the fungal communities between natural and artificial habitats in order to obtain insights about the influence of the habitat on the occurrence of endophytic fungi. The study of composition and diversity of fungi from I. pes-caprae provided new data about the geographical and host distribution of fungi. New isolates and DNA data were deposited for future systematic and biotechnological studies and applications.
Although studies of endophytic fungi yield high numbers of strains, species and associated DNA sequence data, the complete original data are often not presented in detail in publications; or when provided (usually as supplementary materials), the standards of species identification, as well as selection and format of data, vary between different publications. The divergent standards limit the reusability of the data. On the other hand, the data of a single mycological diversity study become scattered in different repositories, such as strain numbers (strain catalogues), specimens numbers (collection databases), DNA sequence accession numbers (DNA databases) and repositories of scientific names. The Darwin Core within the Global Biodiversity Information Facility (GBIF) allows bringing back such data into a single dataset in a unified format so that datasets from different researchers, areas and times can be analysed together (
Potential for reuse and interoperability of the dataset
As far as we know, complex original data of endophytic fungi have hitherto not been published in the form of a data paper, based on a GBIF dataset. GBIF is a system that helps to mobilise digitised data globally for biodiversity informatics (
Primary biodiversity data can principally be divided into “specimen-based” data with high cost and high quality and the low cost and low quality “observation” (
Due to the inflation of taxonomic names and rapid changes of names, we consider the Darwin Core “scientificNameID” to be particularly important, because it allows a direct link of a scientific name to a constantly updated name repository. For enhancing interoperability of our dataset, scientific names and DNA sequences were directly linked to the databases Index Fungorum and GenBank so that updates in these databases can be retrieved conveniently. Although for specimens and strains, accession numbers are available in certain online collection databases, there was no option for linking them directly. Many not yet fully identifiable or presumably conspecific strains and specimens could not be deposited in the collections according to their policies due to limited capacities. These deficits of professional collections indicate the potential for their future improvement by adequate funding and management. Vouchers that could not be deposited in the future may be found to represent cryptic species, which will hardly be resolved under the present policies.
The English spelling of place names is very confusing, particularly in Taiwan, where names changed during the Japanese rule and after the retrocession, while currently different spellings also exist for the same place. For pragmatic reasons, we chose the spelling used in the online database of the national postal service. Using the same place names as the local postal service may also be useful in other countries without widely accepted unified English spelling of names.
1. The effect of ex-situ preservation on the diversity of endophytic fungi in the coastal plant Ipomoea pes-caprae.
2. Taxonomic study of fungi on marattioid ferns in Taiwan I & II.
Yu-Hung Yeh - School of Forestry & Resource Conservation, National Taiwan University, 10617 Taipei City, Daan District, Roosevelt Rd. Sec. 4 No. 1.
1. Ministry of Science & Technology of Taiwan (MOST 108-2621-B-002-007).
2. Ministry of Science & Technology of Taiwan (MOST 109-2621-B-002-004, 110-2621-B-002-001-MY2).
One individual plant was collected per sampling (twice per year, representing the hot summer in one sampling event and another, cooler season from autumn to spring for the other collection event). 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-sterilised. Plant fragments were surface-sterilised under sterile conditions by agitation in 95% ethanol for 1 minute, 6–12% sodium hypochlorite (Hung Ei Chemical Co., Ltd., Taipei) for 3 minutes (for stems) or 1.5 minutes (for roots and leaves), 95% ethanol for 0.5 minutes 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 roots and two segments of the leaf lamina and the petiole were immediately placed on to malt extract agar (MEA) or corn meal 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 in 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). Since BCRC and TNM presently do not accept several specimens or strains from the same species, nor do they deposit collections without full scientific names of species or genus, samples which did not meet the criteria for deposit were not noted as PreservedSpecimen, but only as HumanObservation in the column basisOfRecord.
Since surface-sterilisation has to be adjusted whenever endophytes are isolated from a plant species which was hitherto uninvestigated with respect to endophytes, we optimised the methods for surface sterilisation for the different plant parts of I. pes-caprae. The effectiveness was further controlled regularly by the imprint technique, i.e. by pressing the surface-sterilised plant fragments on to control media after surface disinfection, before placing the fragments on to other media for growth of the fungi. Only if no growth occurred on the control media, but in the media with plant fragments, then the surface sterilisation procedure was neither too weak nor too rigorous (
Primers used in this study with the abbreviated names for the gene and forward and reverse primer, primer sequence and reference.
DNA region* |
Primer name |
Primer sequence (5’-3’) |
References |
ITS |
ITS1F |
CTTGGTCATTTAGAGGAAGTAA |
( |
ITS |
ITS4 |
TCCTCCGCTTATTGATATGC |
( |
ITS |
ITS5 |
GGAAGTAAAAGTCGTAACAAGG |
( |
LSU |
NL1 |
GCATATCAATAAGCGGAGGA AAAG |
( |
LSU |
NL4 |
GGTCCGTGTTTCAAGACGG |
( |
TUB |
TUB2Fd |
GTBCACCTYCARACCGGYCAR TG |
( |
TUB |
TUB4Rd |
CCRGAYTGRCCRAARACRAAGTTG TC |
( |
TUB |
Bt2a |
GGTAACCAAATCGGTGCTGCTTTC |
( |
TUB |
Bt2b |
ACCCTCAGTGTAGTGACCCTTGGC |
( |
HIS3 |
H3F1 |
TGGCAAGGCCCCTCGCAAGC |
( |
HIS3 |
H3R1 |
TTGGACTGGATRGTAACACGC |
( |
ELO |
ELO2-F |
CACTCTTGACCGTCCCTTCGG |
( |
ELO |
ELO2-R |
GCGGTGATGTACTTCTTCCACCAG |
( |
RPB2 |
RPB2-F |
GACGACCGTG ATCACTTTGG |
( |
RPB2 |
RPB2-R |
CCCATGGCCTGTTTGCCCAT |
( |
TEF |
EF1 |
ATGGGTAAGGARGACAAGAC |
( |
TEF |
EF2 |
GGARGTACCAGTSATCATGTT |
( |
TEF |
EF1-728F |
CATCGAGAAGTTCGAGAAGG |
( |
TEF |
EF1-986R |
TACTTGAAGGAACCCTTACC |
( |
TEF |
TEF-F |
GCCCCCGGCCATCGTGACTTCAT |
( |
TEF |
TEF-R |
ATGACACCGACAGCGACGGTCTG |
( |
*Abbreviations of DNA regions/genes: ELO: Fatty acid elongase 1 gene, HIS3: Histone 3 gene, ITS: Internal transcribed spacer of the rRNA genes (partial SSU rRNA gene, ITS1, 5.8S rRNA gene, ITS2, partial LSU rRNA gene), LSU: Large-subunit rRNA gene, RPB2: RNA polymerase II second largest subunit genes, TEF: Translation elongation factor 1-α gene, TUB: β-tubulin gene.
Strains of endophytic fungi were identified by both morphological and molecular characteristics. The following characteristics were used in the characterisation and identification of morphospecies: colony appearance, colour and structure of mycelia and in anamorphic fungi the type of conidiogenous cells, conidiophores and conidia. The microscopic samples were mounted in 5–10% (w/v) aqueous potassium hydroxide (KOH) solution. For molecular identification of fungi, DNA sequences of the internal transcribed spacer regions (ITS) and/or the ribosomal large subunit RNA gene (LSU rDNA) were generated for a preliminary identification. Additionally, depending on the species resolution in certain genera, where rDNA barcodes are insufficient, other barcodes were applied. Genomic DNA was extracted with Genomic DNA Spin Kit (Bioman Scientific Co., Ltd., Taiwan) according to the manufacturer’s protocol. The PCR products were synthesised with different primers, based on published phylogenetic analyses of specific genera or species complexes of fungi (Table
Ipomoea pes-caprae was collected from the six beach sites and two botanical gardens in the northern and central parts of the main island of Taiwan characterised by a subtropical climate. The dataset covers natural vegetation at sand coasts of New Taipei City (Bali District and Shihmen District), Taoyuan City (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. 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)
24.156172 and 25.292212 Latitude; 120.583286 and 121.414081 Longitude.
This dataset contains data from the Kingdom Fungi, Divisions 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. Classes and orders included in the dataset are given in Table
Classes |
Orders |
Agaricomycetes |
Agaricales, Cantharellales, Corticiales, Polyporales, Hymenochaetales |
Agaricostilbomycetes |
Agaricostilbales |
Cystobasidiomycetes |
Cystobasidiales |
Dothideomycetes |
Botryosphaeriales, Capnodiales, Dothideales, Mycosphaerellales, Pleosporales |
Eurotiomycetes |
Chaetothyriales, Eurotiales |
Exobasidiomycetes |
Exobasidiales |
Leotiomycetes |
Chaetomellales, Helotiales |
Malasseziomycetes |
Malasseziales |
Microbotryomycetes |
Sporidiobolales |
Mucoromycetes |
Mucorales |
Saccharomycetes |
Saccharomycetales |
Sordariomycetes |
Amphisphaeriales, Chaetosphaeriales, Diaporthales, Glomerellales, Hypocreales, Lulworthiales, Magnaporthales, Microascales, Sordariales, Xylariales |
Tremellomycetes |
Tremellales |
Ustilaginomycetes |
Ustilaginales |
Samples of I. pes-caprae were collected in Taiwan during the years 2013–2015 and 2019–2020.
This dataset contains data from the Kingdom Fungi, Divisions Ascomycota, Basidiomycota and Zygomycota from Taiwan. It contains 896 records, which correspond to 177 species. The Darwin Core definitions are arranged according to their sequence in the dataset and
Column label | Column description |
---|---|
OccurrenceID | An identifier for the Occurrence (the occurrenceID globally unique). |
basisOfRecord | The nature of the related resource. Three kinds of basisOfRecord were used in this study. 1. PreservedSpecimen: A fungal specimen was preserved as living or dried culture. 2. LivingSpecimen: Only a living strain was preserved. 3. HumanObservation: Only human observation was based on morphospecies classification of a strain without preserving a permanent fungal specimen. Since the collections BCRC and TNM presently do not accept several specimens or strains from the same species, nor are collections without full scientific names of species or genus permitted, samples which did not meet the criteria for deposit or for other reasons could not be deposited (because of loss due to contamination etc.) were recorded as HumanObservation only. |
scientificName | The full scientific name of isolates was given as in Index Fungorum (http://www.indexfungorum.org/). |
scientificNameID | An identifier for the nomenclatural details of a scientific name. The full scientific name of isolates was directly linked to the Index Fungorum Registration Identifier (http://www.indexfungorum.org/). |
identificationQualifier | A brief phrase or a standard term (e.g.: "sp. 1", "sp. 2", or “aff.”) to express the determiner's doubts about the scientific name. In this study, this qualifier is used to distinguish different species of the same genus, while it was not possible to provide a full binomial name. |
taxonRank | The taxonomic rank of the most specific name in the scientificName. In this study, it expresses the taxonomic rank of the identification. In species labelled with “aff.” in the identificationQualifier, the full scientific name was given in the scientificNameID and “species” in taxonRank according to the requirement of the Darwin Core. Adding “aff.” to the species name means that the species similar to, but distinct from, the given species. |
kingdom | The full scientific name of the kingdom in which the taxon is classified. |
phylum | The full scientific name of the phylum or division in which the taxon is classified. |
class | The full scientific name of the class in which the taxon is classified. |
order | The full scientific name of the order in which the taxon is classified. |
associatedTaxa | Host plant associated with the fungi. |
degreeOfEstablishment | Referring to the host plant whether it is native or introduced from its native place (coast) to an inland place (botanical garden). |
occurrenceRemarks | Comments or notes about the Occurrence. In this study, this qualifier refers to the specific plant tissues from which endophytes were isolated. |
country | The name of the country in which the Location occurs. |
countryCode | The standard code for the country in which the Location occurs. |
county | The full, unabbreviated name of the next smaller administrative region than stateProvince (county, city etc.) in which the Location occurs. |
locality | The specific name of the collection place. The spelling of the Chinese names follows Chunghua Post Co., Ltd. (https://www.post.gov.tw/post/internet/Postal/index.jsp?ID=207). |
decimalLatitude | The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic centre of a Location. |
decimalLongitude | The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic centre of a Location. |
geodeticDatum | The ellipsoid, geodetic datum or spatial reference system (SRS) upon which the geographic coordinates given in decimalLatitude and decimalLongitude are based. |
coordinateUncertaintyInMetres | The horizontal distance (in metres) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. In our dataset, we estimated 100 m for the coastal sites and 3 m for the plantations of I. pes-caprae in the botanical gardens. |
eventDate | The date-time during which collection occurred in the field. |
recordedBy | The primary collector or observer responsible for recording the original occurrence. |
identifiedBy | A list of names of people who identified the fungus. |
institutionCode | The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record. In this study, it followed Index Herbariorum sweetgum.nybg.org/science/ih/herbarium-list) using TNM for the National Museum of Natural Science where dried fungal specimens were deposited. |
catalogNumber | An identifier (preferably unique) for the record within the dataset or collection. In this study, it means the identifier of TNM as provided in the online collection database (http://collection.nmns.edu.tw/scripts/fungi.dll). |
otherCatalogNumbers | Alternate fully qualified catalogue numbers for the same Occurrence in the current dataset. In this study, it means an identifier of the Bioresource Collection and Research Center (BCRC) where cultures were deposited and can be retrieved under the identifier (https://catalog.bcrc.firdi.org.tw/) in addition to the PreservedSpecimen. |
recordNumber | The personal identifier of representative isolates in this study. |
associatedSequences | The URI of genetic sequence information associated with the Occurrence with direct link to GenBank (https://www.ncbi.nlm.nih.gov/nucleotide/). |
We thank the Content Manager of Taiwan Biodiversity Information Facility (TaiBIF) Ms. Melissa Liu and Dr. Robert Mesibov for guidance and technical assistance. The study was supported by the Ministry of Science & Technology of Taiwan (MOST 108-2621-B-002-007, 109-2621-B-002-004, 110-2621-B-002-001-MY2). The technical foundations for this study were laid by annual workshops about GBIF/TaiBIF since 2016 supported by MOST and organised by the Biodiversity Research Center, Academia Sinica, Taipei. The permits for collection in the botanical gardens of Taipei City and National Museum of Natural Science, Taichung, are gratefully acknowledged. Two reviewers, Dr. Marc-André Lachance and Mr. Jerome Chie-Jen Ko, are thanked for improving the text.