Category Archives: News

The South Australian bryophyte DigiVol project

The bryophyte collection in the State Herbarium. Photo: A. Thornhill.

In the middle of 2019, I began developing a project to make a database of the South Australian bryophyte collection. There are over 30.000 bryophyte specimens in the State Herbarium of South Australia (AD), most of them stored in envelopes with the information typed or hand written on to the front of the envelope (like most bryophyte collections in herbaria). All of the envelopes had accession numbers but very few of them had barcodes or were databased.

With the help of Nunzio Knerr from CSIRO we developed some scripts that would read printed barcodes from a digital image and put the barcode number in the file name. Another script read any typed information and turned it into a text file. At the same time I was told about DigiVol, an Australian initiative that has citizen scientists transcribe scientific information, such as institute collections or camera-trap images. With the help of Eleanor Crichton and Ainsley Calladine from the State Herbarium we developed a bryophyte transcription template to capture the information from each envelope.

The second stage was the biggest part of the project. At the end of 2019 and start of 2020 we began the task of recording accession numbers of each envelope, printing out a barcode, sticking the barcode onto the envelope, and taking a photo of each envelope.

A typical envelope containing a moss collection. Photo: A. Thornhill.

With the help of summer student scholars Joel Bowes and Sam Billings, as well as weekly volunteers Catherine Courtney and Bonnie Newman we started off with a bang and were processing around 500 envelopes a day. A number of test DigiVol “expeditions” were created, and we began to transcribe the envelopes with the idea that we would iron out errors before making the expeditions live.

At the end of March 2021, Covid-19 hit Australia and everything came to a screeching halt. No volunteers could come to the herbarium nor staff. What had started off so promising had now stopped. We had around 2.000 envelopes already imaged and set up as expeditions, but they were yet to be made live. At the end of April 2020, it was decided we should make the expeditions live and see what happen

Photographing the bryophyte envelopes. Photo: A. Thornhill.

The first expedition with 477 envelope images was made live in May. It was completed in five days. The second expedition was made live and finished just as quickly. Soon, we started running out of a bank of images. In mid-May there were a slight lifting of restrictions and we were allowed to return to work or one or two days a week. I made the decision that I would take the images by myself to try and keep ahead of the DigiVol volunteers. From June to October, I imaged around 15.000 envelopes and just managed to stay ahead of the volunteers, who transcribed at a rapid rate.

In November it was agreed that Bonnie could return as a volunteer and with her help the imaging productivity skyrocketed. By the end of 2020 we had barcoded and captured the image of 24.000 envelopes. At the start of January 2021, I dedicated two weeks to finish the remaining 6.000 envelopes, which we completed at the end of January.

State Herbarium bryophyte volunteers and student scholars busy at work. Photo: A. Thornhill.

As it currently stands the DigiVol volunteers have transcribed over 25.000 envelopes, which is about 80% of the collection. The transcribing is likely to be finished by the end of March at our current rate. Once this is done we will curate our records and then the information will be made available through the Australasian Virtual Herbarium.

When I designed the project I had no idea that it would be completed so quickly. The fact that many Australians had not much to do due to lockdown and so turned to DigiVol certainly helped, but it also helped that we had a dedicated team of volunteers, both at the herbarium and online, who dedicated many hours to complete this project so quickly. If you are interested to see what the DigiVol project looks like then it can be viewed here.

Written by State Herbarium botanist Andrew Thornhill.

State Herbarium closed

As you would be aware, the State Government has announced that South Australia will enter into a six-day lockdown from today in an effort to stop the spread of a COVID-19 outbreak in Adelaide.

This means that we will be closing Adelaide, Mount Lofty and Wittunga Botanic Gardens, and the State Herbarium, until at least Wednesday 25 November 2020.

Keep safe and we look forward to seeing you very soon.

WA Herbarium on TV

WA botanist Kelly Shepherd. Photo: K. Shepherd (Taxonomy Australia website).

Last week, in a segment on ABC’s Gardening Australia, our colleague Dr Kelly Shepherd from the Western Australian Herbarium was interviewed. She shares her passion for native plants and explains the work of a plant taxonomist and of the herbarium.

Online resources of the WA Herbarium include the State’s plant information system FloraBase, as well as Nuytsia, the journal of the Herbarium. To mark the 50th anniversary of the journal, the Herbarium aims to name 50 undescribed plants. More information, as well as profiles of each new plant, can be found on the institution’s  Facebook page.

Written by State Herbarium botanist Juergen Kellermann.

Journal and Flora website offline

EnviroDataSA title

Please note that the EnvirodataSA website, which hosts the State Herbarium’s journal Swainsona, the Flora of South Australia and other Herbarium publications, is currently offline and undergoing maintenance.

A back-up of all articles published in Swainsona is available here (Vol. 30-). Complete volumes are available on JSTOR.

The Journal of the Adelaide Botanic Gardens is available on JSTOR (Vols 1-30).

Chapters of the new Flora of South Australia (5th edition) can be accessed here.

Swainsona stipularis at Witchelina Station, 11 Oct. 2010. Photo: P.J. Lang.

Preliminary studies of the fungi in Flinders Chase National Parks after the 2020 fires

Peziza aff. petersii. Photo: David Catcheside.

Fungi play important roles after fire. Their fine, root-like hyphae bind soil particles, stabilising the soil and reducing erosion. Fungi provide nutrients for plants, helping to re-establish plant communities. They reduce the high pH of the ash bed. Many fungi break down the burnt litter and wood, returning nutrients to the soil. A previous Blog on fires and fungi in Flinders Chase National Park was written before a recent survey of the Park.

Plicaria recurva. Photo: David Catcheside.

In mid-July 2020, Pam and David Catcheside surveyed the fungi in Flinders Chase National Park, devastated after the previous summer bushfires. These surveys  augment those made after the 2007 bushfires in the Park (see references below) and enable comparisons to be made of the fungi fruiting after those fire events. In 2020, 96 % of Flinders Chase was burnt, more than the 85 % estimate for the 2007 fires. Preliminary analysis suggests that, although there is some overlap between the species that occurred after the 2007 and 2020 fires, there are differences both in species composition and species richness, perhaps reflecting the differences in severity of the fires.

Pulvinula archeri. Photo: David Catcheside.

In 2020, collections were made at a number of sites, all of which had been severely burnt: near Rocky River, Platypus Waterholes, the Ravine des Casoars, Gosselands and Kelly Hill Conservation Park. The fungi were similar at all sites, though fruiting was less at Gosselands and at Kelly Hill.

Disc fungi made up most of the fungi that were found. These fungi are important colonisers often fruiting in profusion soon after fire. They reduce the strongly alkaline pH (around pH 10) resulting from the ash closer to neutral (pH 7), a pH more favourable for plant growth. The most common species were a fawn to pinkish-brown species of Peziza, possibly P. petersii, black-brown Plicaria recurva (see images above) and the small, brilliant orange Pulvinula archeri. There were a few patches of orange Anthracobia maurilabra and A. muelleri.

Anthracobia aff. maurilabra. Photo: David Catcheside.

After the 2007 fires, Anthracobias were abundant, often in circles around the bases of Xanthorrhoea semiplana var. tateana in contrast with the few patches seen in 2020.  Also after the 2007 fires Pulvinula archeri, though present, was not in the profusion found in 2020. Disc fungi are often difficult to identify to species. Almost all require microscopic examination of often nuanced characters such as spore ornamentation. Samples of some of the disc fungi collected have been taken for molecular sequencing and analysis. Results should help to clarify the tentative identifications made so far on the collections.

Laccaria aff. canaliculata. Photo: David Catcheside.

A few gilled fungi were found, including a species of Laccaria. Laccarias are early colonisers of burnt and bare ground and are mycorrhizal, forming essential partnerships with plants.

In contrast with the fungi found after the 2007 fires, there were few fruit bodies of ‘stone fungi’, species of Laccocephalum.  Their hard, pored, mushroom-like fruit bodies come up almost immediately after fire from a sclerotium, an underground storage tuber. This year, fruit bodies of Laccocephalum tumulosum, the only species of Laccocephalum found, were much smaller than those seen after the 2007 fires, reaching only 5 cm in comparison with the up to 20 cm of the 2008 collections. In 2008 and 2009 five species of Laccocephalum were collected: L. tumulosum, L. mylittae, L. basilapiloides, L. minormylittae and L. sclerotinium. Their sclerotia can be mixtures of fungal tissue and sand (false sclerotia) or consist only of fungal tissue (true sclerotia).

Laccocephalum tumulosum. Photo: David Catcheside.

At one site at the Ravine des Casoars, an undescribed species of coral fungus, Ramaria or Ramariopsis, was pushing up the sandy soil over an area of several metres. When excavated, this fungus was seen to have a false sclerotium, a structure previously unknown for any species of coral fungus (see images below).

Fungal fruiting is rain and temperature dependent and it is difficult to select the optimal time for surveys and collections. June and July are usually good months for fungi in South Australia. In 2008 Pam and David spent a week in early June when they collected 14 species of disc fungi, approximately 17 species of gilled fungi, two boletes (soft pored fungi with a central stem), a few club, bracket and coral fungi, in all approximately 40 species. The conditions prior to their collecting trip in 2020 were dry and would have had a somewhat detrimental effect on fungal fruiting. Nonetheless, the results were unexpected: only nine species of disc fungi, four of gilled fungi, two coral fungi with a total of 18 species. These preliminary results from the two sets of surveys suggest that both species composition and richness are less after the more extensive and more severe summer fires of 2020.

Ramaria sp. Sclerotium (left) and habit (right). Photos: David Catcheside.

References

  1. Catcheside, P.S. (2009). The phoenicoid discomycetes on Kangaroo Island. Fungimap Newsletter 38: 5–7 (1.2mb PDF).
  2. Catcheside, P.S., May, T.W. & Catcheside, D.E.A. (2009). The larger fungi in Flinders Chase National Park, Kangaroo Island. Surveys 2008. Report for Wildlife Conservation Fund and Native Vegetation Council.
  3. Catcheside, P.S. & Catcheside, D.E.A. (2010). The larger fungi in Flinders Chase National Park, Kangaroo Island. Surveys 2009. Report for Wildlife Conservation Fund and Native Vegetation Council.

Contributed by Pam Catcheside (State Herbarium Hon. Associate)
David Catcheside (Flinders University).