Tuesday, November 10, 2015

A very helpful email exchange with Dr. Rodrigo Valverde of the LSU Department of Plant Pathology and Crop Physiology, November 8th, 2015.   Rodrigo published a discovery of a novel fern virus in 2008:  New Virus Causing Disease in Japanese Holly Fern.

 Questions from me are in italics, and Rodrigo's answers are in bold.

Finally I have some time to answer your questions. I talked to other plant pathologists and in general they agree with my thoughts about the fern problem. Ok, below are your questions and my answers.

The ferns appear to die over about 12-24 months — that is, they go from good health to full death in that length of time. Is this faster than what you saw in your 2009 paper?

The time is similar but the fern virus does not kill the ferns (entirely) only several leaves followed by a slow decline which may end up in death.

We do not see any insects around the plants, but I will look again knowing now that the usual suspects do not seem to be present.  Have you any tips (or suggestions of things I can read) in order to do a good job on insects?

Unless they are vectoring a pathogen, it is unlikely that insects will kill the ferns. And if that is the case, they (the insects) will be very visible.

Our local plant pathologists are stumped.  Are there standard strategies for tracking down as yet unrecognized fungal, bacterial or nematode causes?  

Yes and no! Most new pathogens are old on pathogenic agents that evolved into a pathogen due to changes in the environment. It is very difficult sometime to differentiate between a pathogen and a saprophyte.

Maybe things like:

  1) look at a completely dead fern for lingering pests,  or
  2) look at an only partly affected fern (under the assumption the pest is still operating, and can be more easily found)
  3) culture in the lab for fungus & bacteria, hoping they will grow until they can be recognized.

These points (2 and 3) make a lot of sense and I am sure that the plant pathologists there are considering them. However, if an abiotic factor is involved as primary cause, they will not work. 

or anything else, any other strategies?

My impression is that it could be a soil-borne pathogen or a soil abiotic factor (pH, salinity, etc) or a combination of both. The abiotic factor allows the "new" pathogen to thrive!  Soil nutrient analysis including pH will may provide some information.

Good luck and keep me posted of any new development of the fern problem.


Rodrigo

Tuesday, November 3, 2015

Narrative Summary: Autumn 2013 to Present

Autumn 2013: Catherine Alexander's Initial Report

The sword fern die-off was first noticed by Catherine Alexander (naturalist and daily visitor to Seward) in the autumn of 2013.  Here is her account, offered on  October 28th, 2014:

The Sword Ferns near the hatchery and along the northern end of the hidden trail above that area began to fail about a year ago, though the first signs were quite subtle - just a sense that they were somehow sagging, as if they'd been covered with cardboard for a week or two. At the time I estimated that perhaps 40% of the population was affected.

I kept watch over the winter, thinking that what I was seeing was a temporary thing, that the ferns would recover when their fiddleheads appeared in spring. That was not to be. None of the affected ferns produced fiddleheads this spring, and by late spring the remaining fronds withered and died.

By July I noticed that whatever was happening had spread beyond the initial 40%, though it could be that I just hadn't seen the first signs of failure in the seemingly unaffected population.  I monitored spore production in and around the affected areas this year, and noticed that many of the apparently healthy individuals either failed to produce sori, or that their sori were sparse and underdeveloped. Many of these individuals failed over the summer.

I haven't a clue as to the cause, though I have been thinking about it. Initially I looked for signs of
Aplodontia (mountain beaver) activity, thinking that a new and active colony might be destroying the fern roots. I found none of the signs I would expect from such activity - no burrows, no bitten off fronds - so think that Aplodontia is in the clear, at least this time.

November 2014: Seattle Parks staff visit to the affected area

Several members of the Friends of Seward Park (Paul Shannon, Paul Talbert, Al Smith) and Seattle Parks staff (Gail Takeoka, Jeanne Schollmeyer and plant ecologist Jillian Weed) visited the affected area.  General puzzlement was shared.  Jillian proposed an informal monitoring project: we planted  two young sword ferns in December; almost one year later these two ferns are growing slowly and seem to be healthy. I watered them weekly over the dry summer.

October 13th 2014:  Video walkthrough of the area

  https://www.youtube.com/watch?v=hX0p_nzL2gU


December 2014:  Report from Jenny Glass, Plant Diagnostician, WSU Puyallup Plant & Insect Diagnostic Laboratory

With funding from the Friends of Seward Park, Jenny Glass analyzed two entire ferns (one dead, one still with a few signs of life) in her laboratory in Puyallup.  Her report:

Microscopic observations and incubation of the sample in moist chamber have not revealed any evidence of a primary pathogen in the root zone or crown tissue at the soil line. A composite sample of tissue from these areas tested for the Phytophthora pathogen via an Agdia immunostrip test kit was negative for the presence of this disease group (nor do soil conditions seem to be poorly draining, conditions that promote the growth of Phytophthoras). 

Microscopic investigation of the fronds of the sword fern also have not shown any primary pathogenic activity that would be responsible for the occurrence of this dying patch of plants.

May 23rd 2015: Lab report from plant pathologist Dr. Olaf Ribiero 

Without charge, Dr. Ribiero  analyzed diseased sword fern samples in his Bainbridge Island lab, and visited Seward Park to consult with us.   His report:

 I examined the fern samples you brought over. I found a  little Rhizoctonia and Pythium in the roots. Both can  cause root rot problems in ferns. However, I am not  convinced that this is the cause of the problem since  both are present in low amounts in the roots.  The fronds   are infected with Glomerella fungus blight. Again, not in  sufficient amounts to cause complete dieback of the frond. No foliar nematodes (a problem reported on ferns),  were isolated from fronds tested.

The dieback is more typical of herbicide injury or some  other chemical injury. Was any herbicide applied on this  area? [We have no evidence for, or report of, herbicides  applied here.]  Rhizoctonia is a difficult pathogen to  control.

Autumn 2015: Dr. Tim Billo (UW Environmental Studies, field ecologist)

Tim, a frequent visitor to Seward Park's old-growth forest, noticed the die-off early in 2014. Catherine Alexander put us in touch.  Under Tim's direction,  with contributions from other UW faculty,  crucial guidance from Seattle Parks plant ecologist Lisa Cieko and Nelson Salisbury of Earth Corps, two undergraduate students (Tristan O'Mara and Kramer Canup) have begun a systematic monitoring program.

October 2015: Video and slideshow, with closeups of healthy, affected and dead fronds:
  
     view


October 2015: Additional Scientific Contacts

Dr. Robbin Moran, Curator of Ferns & Lycophytes at the New York Botanical Garden:

I am not sure what could be causing the die-off of Polystichum and have not seen anything like this in other extensive fern populations. I hope you can find out what is happening. It is a curious phenomenon, and worrisome that it might spread elsewhere. The world's expert in the taxonomy of the genus is Dr. David Barrington (dbarring@zoo.uvm.edu), from the University of Vermont, Burlington. Although not a plant pathologist, he might have some insight into the problem.

Dr. David Barrington, Professor of Plant Biology, University of Vermont:

I understand your concern about the sword fern, given the stark pattern you are observing in your part of the world.  I have never heard of a blight impacting species of Polystichum so unfortunately I have nothing to offer in the way of insights into what might be at the root of your dieback.

Dr. Rodrigo Valverde, LSU Plant Pathologist and author of a 2009 paper describing a dsRNA virus infecting ferns, generously responded to my inquiry, and after viewing the video, suggested:

I have over 30 years of experience dealing with  plant diseases, most of them viral diseases and diseases of unknown cause. After looking at the photographs, my first impressions (in order of most likely to less likely) are: 1, fungal, bacterial, or nematode disease; 2, physiological stress (lack/excess of water, pH imbalances, acidic most likely caused by acid rain); 3, viral disease. As you can see, I placed viral disease last because it is rare that viruses kill plants. However, the fern virus I worked with tend to cause a slow decline and eventually death on ferns. I did not mention insects or other arthropods damage but that is something that cannot be ruled out. However, a careful inspection will answer that.

I would rather make a "guess" based on actual/live inspection of the problem, but if I have to make a guess from pictures, I will guess a fungal or bacterial pathogen. This is because of the apparent pattern/distribution of the dead plants.

Monday, November 2, 2015

Research proposal and monitoring protocols



Polystichum Munitum Mortality in Seward Park, Seattle Washington


Kramer Canup, Tristan O’Mara, Tim Billo, Paul Shannon, Lisa Ciecko, Nelson Salisbury, Philip O'Reilly
  1. Research Direction
Aims

The objectives of this research will be to investigate the extent and causes of mortality for the Polystichum munitum (sword fern) population in Seward Park. Specifically this study will examine:
  1. What is the current boundary of ferns displaying symptoms of die off?
  2. Is the die off spreading?
  3. What are the ecological conditions (vegetative composition, soils, mountain beavers) associated with the die off?
  4. What is causing the die off? (fungus, drought, animal disturbance, soil nutrients/chemical composition of soil)

Hypothesis

  1. Ferns beyond the previously established boundary will be displaying symptoms of die off.
  2. The die off is spreading. Based on the observations from citizen science from 2013 to 2015, the fern die off has significantly increased in the past few years.
  3. The areas of die off will have abnormal vegetative composition, soil content and beavers will be active in some areas.
  4. Fungal pathogens, drought or a combined impact of these disturbances can be attributed to the die off seen in Seward Park

  1. Background

See Narrative Summary: Autumn 2013 to present. Posted on Blogger.

  1. Methods of Data Collection
Transect and Fern Monitoring Methods

Using 20 randomized gps coordinates, we have configured the locations of our study plots. Each plot will be anywhere from 0- 750 meter away from the epicenter of the fern die off. Within the vegetative plots we will track the mortality and causes of mortality for Polystichum munitum within Seward Park. The health of each fern will be monitored and fungal samples will be taken from each plot along with soil samples to be analyzed in a lab.

Identifying fern mortality/ die back


Each individual fern will be mapped and tagged from within each plot as focal subjects to assess fern growth or mortality.

  • Categorize stages of fern die back by surveying four times per year, once in each season( November, February, May, August).
    • To monitor the die back and overall health of each plot with all of the ferns combined from within each plot we will monitor:
      • total percent cover of sword fern
        • take average of estimates provided by two surveyors
      • the percent of ferns that appear to be affected by the die off
        • they can be counted and calculated as # of healthy fern / total # of ferns in plot.
      • mid-canopy and upper canopy cover with species composition
        • take average of estimates provided by two surveyors

    • Individual ferns displaying will be quantitatively monitored by:
      • number of live fronds per individual fern
        • count each individual live frond
      • % of upright standing fronds per individual fern
        • take average of estimates provided by two surveyors
      • Percent of browning or dead looking foliage on the fern
        • take average of estimates provided by two surveyors
      • Sori abundance will be taken by selecting five random fronds per individual and classifying, on a scale of 1-4, the percent of sori present on the top foot of the frond
        • 1: 0-25 (little to no sori present)
        • 2: 26-50 (some sori present)
        • 3: 51-75 (most of the sori is present)
        • 4: 76-100 (large, abundant amounts of sori present)

Fungal sampling Methods


Four different fungal pathogens have been found in the roots of ferns in the die off area. Fungal pathogens will be taken from ferns in healthy forest habitats as well as from the affected and ground zero zone to assess the impact of fungi on the ferns.  Fungal spores concentrations and diversity may be impacted by the changing of seasons and nutrient levels in the soil due to tree storing energy and carbohydrates in their roots in the fall and winter time.


To fully quantify if fungal spores are responsible for the die off, fungal samples will be taken from the ferns during November, February, May and potentially August. Spore quantity and diversity will be assessed in relation to the different populations of fern species.


  • Fern Collection: Waiting to configure until after we meet with Olaf and discuss analyzation protocols.
  • Fern root samples will be taken from one fern per plot, as close as possible to the center of the plot. Samples will be taken by cutting
  • Fungal analysis: Samples will be analyzed using PCR and molecular techniques to determine the specific fungi and abundance in each fern.

Soil Sampling Methods


Drought could be contributing stress on the sword fern population, which could be exacerbating and compounding the stress imposed by other factors such as fungal infections. Ultimately, drought induced stress could be playing a significant role 

  • soil moisture (use a drying oven to assess water loss from soil)
  • pH, nitrogen, potash and phosphorus will be sampled using a soil test kit
  • We may be able to send some samples into the Department of King County for free to assess the accuracy of our soil kit


Mountain Beaver Monitoring Methods


Mountain beavers have been found nesting in multiple locations within the die off zone. They are known to eat fern fronds and roots (Link 2005). Most of their feeding occurs above ground and within 15 meters of their burrows Campbell 2005). Mountain beavers create extensive burrows that can also impact soil structure (Link 2005). For now we look to quantify the presence of mountain beavers near our study sites through:


  • Counting the number of dens within a 10m radius from the center of each plot.
  • Camera Traps will be set up in our plots, (Two at a time). Traps will be left for a 1 week at a time and moved to plots in varying locations within our grid.
  • Mountain beavers are mostly active during dusk and dawn (Link 2005). In person terrestrial observations could be done to assess animal disturbances in our plots. In person observations should be taken at random plots at various times throughout the day to assess activity level.



Cost Estimates
  • Stakes: 120 total. Come in packs of 12 for 3.30$. 10 packs x 3.30 = 33$
  • Fungal lab tests: 30x 60$= 1800$
  • Soil test kits: 2x 20$= 40$
  • Soil lab tests: Not relevant yet
  • Other Materials:
    • Compass
    • Tape Measure
    • Light sensor?

Sources


Campbell D. 2005. Mountain Beavers and Control of Mountain Beaver Damage. ICWDM.org

Link R. 2005. Living with Wildlife Mountain Beavers. Washington Department of Fish and Wildlife. http://wdfw.wa.gov/living/mtn_beavers.pdf.