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Phytophthora

Earth Day with Vision Afrika

Tags: 
Citizen Science
Engagement
Phytophthora
Sample Collection
Education
Community Conservation
Plant Pathology

"Is this community conservation or environmental education?" asked Adam, a CPUT Work Integrated Learning student who volunteered his Earth Day with us this year. We answered: "Well... that's the great thing about citizen science, its both".

Cape Citizen Science is community conservation and environmental education smashed together to facilitate biological research about plant disease in the Cape Florisitc Region. This past weekend is a great example of what we're talking about. On Saturday, Earth Day, we provided an opportunity for 31 learners to release their inner scientist as citizen scientists in Jonkershoek Nature Reserve.

The story begins with some generous backers of a crowdfunding campaign on experiment.com. In February 2017, many individuals contributed funding so that we could cover the costs to engage youth from Kayamandi in our research. We also recevied financial support from the American Phytopathological Society through the Mathre Education Endowment Fund and the Promotion Fund from the British Society for Plant Pathology.

Thanks to those backers and awards, we were able to transport and provide food for 31 learners to travel to Jonkershoek Nature Reserve.

The youth we engaged are scholars involved in the after school learning program Vision Afrika. Spending Earth Day with us was a reward for spending the previous three saturdays studying at the Vision Afrika centre in Kayamandi.

Vision Afrika is an incredible program that fosters the success of many learners through after school learning activities and opportunities. On Saturday, we met with the learners at Vision Afrika and drove to the Cape Nature offices at Jonkershoek Nature Reserve.

 

Before our activity in the field, we started with a presentation in a Cape Nature conference room. The presentation introduced the learners to the reasons we do research, the importance of biodiversity, and the threats to the fynbos. We also introduced the concept of pathogen hunting, our earth day activity to sample diseased plants in the reserve. 

To involve the learners fully in the scientific process we generated a hypothesis to test during the activity. We hypothesized that we would find a greater diversity of Phytophthora species adjacent to a trail that received heavy traffic compared to a trail that had less traffic.

To test this hypothesis we chose two trails, a very popular trail to a waterfall, and a long and less popular trail called the Panorama hiking trail.

We set out into the beautiful Jonkershoek Nature Reserve after the presentation.

The field component of the activity involved hiking 30 minutes on two seperate trails, starting from the 10km loop road in the middle of the reserve.

We also made sure to take a few minutes to talk about the ecology and disturbances we saw. The first hike had lots of evidence of fire.

During the hikes we collected samples of sick looking plants along or close to the trails. Everyone collected at least one sample between the six different sites we stopped at (3 sites per trail).

We needed a break after the hikes so we hung out on the Eerste river for a bit.

Finally, it was time to Braai! So we headed back to the picnic area in the Assegaaibosch Nature Reserve. But the Science continued, we still needed to isolate pathogens from the sick plants we sampled.

After a quick demonstration, the learners took their pathogen hunting skills to the next level as they began primary isolations. For this, we cut small pieces of the infected plants and placed them into petri-plates containing 'pathogen food' (agar suspended maize meal).

By the end of the activity we had completed primary isolations for 72 samples. Incredible!

We consider Earth Day with Vision Africa a huge success and are grateful for the support we received from our backers, the American Phytopathological Society, and the British Society for Plant Pathology, and most especially, the Forestry and Agricultural Biotechnology Institute.

This is the first of many engagement activities with learners from impoverished communities. We look forward to doing it again. If you would like to contribute or join in the next one, please contact us.

Photo credit: Michelle Agne and Joey Hulbert 

 

The First Workshop

Tags: 
Workshops
Phytophthora
Kirstenbosch
Citizen Science

Our first workshop was offered on February 16-17, 2016 to the protea garden staff at Kirstenbosch National Botanical Garden. We expect to offer similar workshops every month in different locations throughout the Western Cape Province starting in May or June. Anyone will be welcome to attend and participate.

At this workshop we were fortunate to be in a beautiful area with a few examples of plant diseases. In future workshops, the organizer will likely bring plant samples showing symptoms of disease for participants to capture their own pathogens.

Workshops will generally include a short presentation about recognizing plant disease with an activity introducing the scientific process for identifying the cause of the disease. Activities to capture and culture Phytophthora species will also occur, with the cultures being included in the research.

Why are we interested in Phytophthora species? See this previous blog post for an introduction:

 

 

 

Two presentations were given during the first workshop, on separate days, provided below.

After the presentations, we walked around the garden and surrounding vegetation to observe symptoms and collect samples of a few dying plants. Below is a declining silver tree that we sampled.

Although it is difficult to see in the below image, we collected tissues from the blood red and brown discolored lesions present under the bark of the silver tree.

After we collected chips from the bark and inner tissues of the silver tree, we cut them into smaller pieces and placed them in a petri-plate for the microbe to grow. The petri-plate contains a agar based 'medium' that also includes a few antibiotics that prohibit bacteria from growing and help select for Phytophthora species.

After a few days of allowing the microorganisms to grow in the petri-plates, we remove a small piece of the agar and place it on another petri-plate to generate a petri-plate with only one organism growing, referred to as a pure culture. Once the culture is pure, we can work to identify whether it is a species of Phytophthora or from a different group.

On many occasions, more than one organism grows from the plant material originally placed on the petri-dish; in this case, we have to be careful to create seperate pure cultures. It makes it difficult to determine which organism is actually responsible for the disease, requiring further research; but collectively, with many samples, we should be able to tell an accurate story about the situation.

A major objective of this project is to raise awareness about invasive species. Invasive species seriously threaten the biodiversity in the fynbos biome.  They are not limited to plants or animals, microorganisms can be invasive too!

Detecting the arrival of a new microorganism is critical for controling invasive species. We need to act quickly! Thus, we are asking citizens in the Western Cape Province to report any dying plants they come across in the fynbos, their farms, or their gardens. You can report dying plants here:

 

Hunt'n Pathogens w/ Se7en

Tags: 
Citizen Science
Kirstenbosch
Phytophthora
Se7en
Engagement

We had an incredible time hunting pathogens in Kirstenbosch National Botanical Garden with a group of home school students (Se7en) in early November. The students were avid learners and natural citizen scientists, contributing much excitement to the afternoon's research extravaganza.

We spent the afternoon with two of the garden managers who have been battling root rot pathogens—microorganisms that attack plant roots and cause disease. The managers were kind enough to save some of the diseased plants for us to sample. Below are a few photos of us collecting plant samples. Each student collected at least one sample.

A citizen scientist using a knife to expose a lesion likely caused by Phytophthora cinnamomi. When isolating Phytophthora, we tried to collect pieces along the margin of living and dying tissue, because this was where the pathogens were still active. It was also critical to sterilize equipment/tools in between samples, to ensure we were not spreading the pathogens or contaminating our samples. 

We sterilized our tools in between samples by dipping the blades in ethanol and heating them with a lighter. Bleach or rubbing alcohol would also work. It was fun, but also educational!

We collected samples of leaves, stems, and roots for many different plant species present within the Proteaceae garden. Everyone had collected at least one sample by the end of the afternoon.

After collecting samples of dying plants, the next step was to try to isolate a species of Phytophthora. Phytophthora are not the only microbes causing disease in the fynbos, but it is the group that we are focusing on for our research. Phytophthora species cause serious issues around the world (e.g. Sudden Oak Death and the late blight of potato), and there is a lot to be learned about them in the fynbos. For more information about Phytophthora, see our previous blog post:

To isolate Phytophthora from our dying plant samples, we cut small pieces along the disease margin and placed them into selective agar media. This media has all of the nutrients that Phytophthora need, as well as some antibiotics to prevent growth of other fungi we are not interested in.

After we place the plant tissue pieces in the selective agar media, we watch carefully and replate the organisms that look like Phytophthora until we have a pure culture. Sometimes it takes many isolations before we have a pure Phytophthora culture.

We hope you enjoyed this blog post. Please contact us if you would like to organize a similar activity! Special thanks to Se7en and the managers at Kirstenbosch for a epic afternoon!

If you would like to see the activity from Se7en's perspective, you can see their incredible blog post about the afternoon here!

Partially Publically Funded

Tags: 
Crowdfunding
Funding
Phytophthora
Citizen Science

Crowdfunding

Crowdfunding is a form of fundraising where many people make contributions to reach a goal. Generally, if the project cannot reach its goal, it is not funded at all.

Success!

With contributions from more than 70 individuals, this project successfully reached its goal to raise $5,000 USD (~65,000 ZAR) through a web-platform called Experiment. This success demonstrates that there is public support for this research project.

Lab Notes

Lab Notes are a unique component of crowdfunding with Experiment. They are essentially blog posts created during the crowdfunding campaign. Below are a few selected Lab Notes relavent to becoming a pathogen hunter.

Surveying for Plant DestroyersFight them on the beaches or let the new order beginA recent excursion into sudden oak death infected lands

 

Teaser: 

With contributions from more than 70 individuals, $5,000 USD (~65,000 ZAR) was raised for this project, demonstrating that there is public support for this research project.

Plant Destroyers

Tags: 
Disease
Pathogens
Phytophthora

Intro to Plant Pathogens

Plant pathogens are microscopic organisms that cause disease in plants. They kill billions of plants each year! Some pathogens can infect many plant species (generalists), where others can only infect certain species (host specific). These organisms cause problems in agriculture and natural environments such as native forests and grasslands. Below are a few examples of diseases caused by plant pathogens.

Western Gall RustBlueberry Mummy BerryWheat Stripe Rust
Western Gall RustBlueberry Mummy BerryWheat Stripe Rust

Billions of rands are spent every year trying to control plant diseases. Plant pathogens threaten food security and the health of natural systems such as the fynbos or the native forests of South Africa. They also cause problems in plantations, ultimately increasing the cost of wood products.

Plant Destroyers

Phytophthora (pronounced Fy-TOFF-thor-uh) is a group of plant pathogens that are famous because of the dramatic disease outbreaks they cause. The word Phytophthora translates into 'plant destroyer' from Greek.

Phytophthora

phyto = plant
phthora = destroyer

Phytophthora infestans

Perhaps the most well known species is Phytophthora infestans, the species that is responsible for the Irish Potato Famine. P. infestans causes a disease in potatoes referred to as late blight. It can also infect tomatoes and even petunia hybrids. This species is present in South Africa, still causing problems more than a century after the Irish Potato Famine.

Blight Potato

Potato (Solanum tuberosum): Late blight, caused by Phytophthora infestans

Image Source: USDA, flickr.comImage Source: Scott Nelson, flickr.com

Phytophthora ramorum

Another Phytophthora species of concern is P. ramorum. This species is responsible for Sudden Oak Death in North America and Ramorum Disease in the United Kingdom. It has killed millions of oak trees in the North America and entire landscapes of Japanese larch have been removed to control the spread in the United Kingdom.

Landscape of Dead Tanoak TreesLesion on a Rhododendron
Dead Tanoak Canopy

More information about P. ramorum is presented in the below videos. Check them out!

Phytophthora ramorum is a generalist pathogen. It can infect more than a hundred different species of plants and it has practically eliminated mature tanoaks from the landscape in infected areas of California and Oregon, USA. If this species is allowed to spread to the fynbos, the consequences could be devastating!

Phytophthora ramorum, growing in v8 agar

Phytophthora cinnamomi

Finally, the last plant destroyer presented in this blog is Phytophthora cinnamomi—saving the best (or worst) for last! P. cinnamomi was originally described causing disease in cinnamon trees, hence its name. This species is also a generalist pathogen, causing root rot of many plants. It has been suggested to be the most ubiquitous Phytophthora species on the planet. It can infect thousands of plant species!

Phytophthora cinnamomi is present in the fynbos and has been implicated as the cause of root rot of many Proteaceae species. If you see a dying plant in the fynbos, there is a good chance P. cinnamomi is involved. However, despite knowing it is present, there is a lot that we don't know about it!

For example, we do not know:

  • where it is and where it is not
  • where it came from or whether it has always been in South Africa
  • which species it infects and how it is affecting the biodiversity of the fynbos
  • how it will respond to a changing climate
  • how it affects regeneration after a fire
  • its role in the decline of the silver tree near Table Mountain

    There is a lot to investigate! and you are invited to conduct the research with us!

    Start by registering as a pathogen hunter!

    Teaser: 

    A blog post about plant destroyers—a group of microscopic organisms that cause disease in plants. Read more to learn about the type of organisms we are hunting!