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FBIP: Fungal Root Endophytes of Selected Erica species

Latest version published by South African National Biodiversity Institute on Sep 30, 2019 South African National Biodiversity Institute

Erica species are the second most dominant Fynbos plant group that associate with a specific group of fungi which form an ericoid mycorrhizal relationship with the plant roots. Little is known about the biodiversity of mycorrhizal fungi in general in South Africa and Ericoid mycorrhizas are no exception. This project's main objective it to investigate the biodiversity of root fungal endophytes of several Erica species which occur in the Albany Center of endemism.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 193 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

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Data as a DwC-A file download 193 records in English (10 KB) - Update frequency: unknown
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Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Dames J (2019): FBIP: Fungal Root Endophytes of Selected Erica species. v1.1. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=fungal&v=1.1

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is South African National Biodiversity Institute. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 2c511f3c-7055-4056-87e4-90b1a238a623.  South African National Biodiversity Institute publishes this resource, and is itself registered in GBIF as a data publisher endorsed by South African Biodiversity Information Facility.

Keywords

Endophtyic fungi; roots; Erica species; diversity; Specimen

Contacts

Who created the resource:

Joanna Dames
Head of Department & Associate Professor, Department of Biochemistry and Microbiology
Rhodes University Department of Biochemistry and Microbiology, Mycorrhizal Research Laboratory, P.O. Box 94 6139 Grahamstown Eastern Cape ZA 0466038443

Who can answer questions about the resource:

Joanna Dames
Head of Department & Associate Professor, Department of Biochemistry and Microbiology
Rhodes University Department of Biochemistry and Microbiology, Mycorrhizal Research Laboratory, P.O. Box 94 6139 Grahamstown Eastern Cape ZA 0466038443

Who filled in the metadata:

Joanna Dames
Head of Department & Associate Professor, Department of Biochemistry and Microbiology
Rhodes University Department of Biochemistry and Microbiology, Mycorrhizal Research Laboratory, P.O. Box 94 6139 Grahamstown Eastern Cape ZA 0466038443

Who else was associated with the resource:

Content Provider
Mahlatse Kgatla
FBIP Data Specialist
SANBI 2 Cussonia Avenue, Brummeria 0184 Pretoria Gauteng ZA 0128435196

Geographic Coverage

Eastern Cape, Makana

Bounding Coordinates South West [-33.5, 26.038], North East [-33.027, 26.911]

Taxonomic Coverage

Some specimen identified to Species level

Kingdom  Fungi

Temporal Coverage

Start Date / End Date 2013-01-01 / 2014-01-01

Project Data

Erica species are the second most dominant Fynbos plant group that associate with a specific group of fungi which form an ericoid mycorrhizal relationship with the plant roots. Little is known about the biodiversity of mycorrhizal fungi in general in South Africa and Ericoid mycorrhizas are no exception. This project's main objective it to investigate the biodiversity of root fungal endophytes of several Erica species which occur in the Albany Center of endemism.

Title Fungal Root Endophytes of Selected Erica species
Identifier IBSG13052418260
Funding Funding from Foundational Biodiversity Information Programme (FBIP)
Study Area Description Eastern Cape, Makana

The personnel involved in the project:

Principal Investigator
Joanna Dames

Sampling Methods

Assessment of fungal root endophyte diversity includes culturable isolates and unculturable fungi as well. DNA was extracted from surface sterilised and crushed root material and submitted for 454 sequencing at the GS Facility at Rhodes University. The sequences were compared with internal transcribed spacer (ITS) sequences available in the GenBank and UNITE databases by BLASTn search and the closest matches with homology greater than 95 % were included in the clustal alignment and phylogenetic analysis.Erica seeds were obtained from Kirstenbosch Botanical Gardens.

Study Extent Eastern Cape, Makana

Method step description:

  1. This is a current PhD project being undertaken by Ms Christine Bizabani. Ms Bizabani registered in 2012 and is due to complete at the end of 2014. Progress to date includes selection and collection or root material from Erica caffra, E. demissa, E. chamissonis, isolation and maintenance of culturable fungal root endophytes. Over 50 isolates have been morphologically and molecularly identified and have been sent to the National Fungal Culture Collection (see attached spreadsheet). Fungal isolates from E. glumifora, E cerinthoides and E. nemirosa are in process. An Honours student will contribute to a portion of the project in 2014. Assessment of fungal endophyte root biodiversity through DNA pyrosequencing and determination of phylogenetic relationships. Timeframe Jan 2014 - Oct 2014, Ms Bizabani (PhD Student). Timeframe Feb 2014- Oct 2014: An Honours student will be given one or two of the collected Erica species to work on in 2014. The student has not be identified. Assessment of fungal root endophyte diversity not only includes culturable isolates but unculturable fungi as well. DNA will be extracted from surface sterilised and crushed root material and submitted for 454 sequencing at the GS Facility at Rhodes University. The sequences will be compared with internal transcribed spacer (ITS) sequences available in the GenBank and UNITE databases by BLASTn search and the closest matches with homology greater than 95 % will be included in the clustal alignment and phylogenetic analysis. The sequences will be aligned using Clustal X. Phylogenetic analysis will be done using Molecular Evolutionary Genetics Analysis (MEGA) by the Neighbor-joining method. The robustness of the phylogeny will be analyzed by bootstrap analysis using 1000 iterations. The branches corresponding to partitions in less than 50 % bootstrap replicates will be collapsed. Positions containing gaps and missing data will be eliminated from the data set. This analysis will be conducted with the assistance of Dr Marieka Gryzenhout at the University of the Free State. Resynthesis and confirmation of endophyte status. Timeframe June 2013 - July 2014, Ms Bizabani (PhD Student) Commercial Erica seeds obtatined from Kirstenbosch will be used to test for ericoid mycorrhiza formation of selected isolates. The seeds will be surface sterilized with 3% bleach containing 100 μl l-1 Tween 20 for 1 min. The seeds will then be subsequently washed in sterile Milli-Q water twice. After sterilization the seeds will be pre treated prior to germination by soaking in Milli-Q water overnight or applying a smoke treatment. Seeds will be germinated on moist sterile filter paper and will be kept at 22 ⁰C during germination with 16 h light period and 8 h dark period. The germinated seedlings will then be transferred to sterile 150 ml square petri dishes measuring 120 mm x 15 mm containing 20 g of autoclaved vermiculite medium. Prior to seedling transfer the medium will be watered with 3 ml Sterile Milli-Q water and 0.5 ml of nutrient solution containing 15.0 μM KH2PO4, 17.0 μM MgSO4, 8.0 x 10-3 μM H3BO3, 4.0 x 10-3 μM MnCl2.4H2O, 3.0 x 10-4 μM ZnSO4.H2O, 8.0 x 10-5 μM CuSO4 and 8.0 x 10-6 μM (NH4) MO7O24.4H2O. Nine seedlings will be placed in each petri dish. After 3 weeks the root zones of the seedlings will be inoculated individually with 500 μl mycelial slurry of a particular isolated. There will be 3 replicate petri dishes (27 seedlings) for each treatment and uninoculated controls. If necessary Vaccinni corymbosium (Blueberry) micropropagated plantlets will be obtained through Amatola Berries in Stutterheim these will be inoculated in a pot trial. After 10-12 weeks roots from seedlings or plantlets will be excised and rinsed prior to clearing, staining and microscopic examination for mycorrhizal structures. Due to the length of time required for these resynthesis tests this will not form part of an Honours project. Ecological characterization of fungal isolates. Timeframe Sept 2013 - November 2014. Ms Bizabani (PhD Student) Timeframe Feb 2014- Oct 2014: A selection of isolates will assigned to an Honours student in 2014. The student has not be identified. Ecological activity of fungal endophytes will be assessed to determine biological control activity against other soil borne fungal pathogens, siderophore production, nitrogen and phosphate assimilation, phosphate solubilisation, lignocellulolytic activity and tolerance to metal toxicity. Antimicrobial screening will be conducted in dual culture between pathogens (Fusarium and Phytophthora) and endophytic isolates. Pathogen growth will be monitored daily. The endophytic isolates will also be tested for siderophore production which is a iron chelator using a Chrome Azurol S agar plate assay. The ability of the isolates to utilize organically bound nitrogen and phosphate will be assessed in a liquid basal medium amended with various organic (such as glutamine, arginine, BSA, glycerophosphate and RNA). Medium will be incubated for 7-10 days and filtered mycelium will be oven dried and biomass will be recorded. Phosphate solubilisation will be assessed on bromophenol blue medium containing insoluble Ca phosphate as the only P source. Development of yellow halo will indicate the presence of organic acids which contribute to the release of P. Linocellulolytic activity will be assessed using a basal medium amended with cellulose azure dye. A release of azure dye ndicates cellulose degradation. Tolerance to zinc, copper and cadmium will also be assessed in media amended with different concentrations of the metals. Fungal growth will be measure at regular intervals over an 8 week period.

Additional Metadata

Alternative Identifiers http://ipt.sanbi.org.za/iptsanbi/resource?r=fungal