Monday, July 25, 2016


Pathogen Detection Strategies: PCR and Sequencing

We do not know what is causing the sword fern die-off.  Mountain beaver and drought may be contributing causes.   But the spatial pattern of the die-off strongly suggests a pathogen is the driving cause:

  1. The die-off, unlike drought and mountain beavers, is limited to one region of the forest
  2. This region is growing approximately radially, as would infection
Phytophthora is a plausible candidate, but repeated WSU and Ribeiro lab studies have been unable to provide confirmation (see earlier blog entries for full reports).  New approaches may be needed, among which are PCR, and next-generation sequencing (NGS).  

Concerning PCR (polymerase chain reaction), Paul Talbert suggests (email, 6/8/2016)

Not to discourage the sequencing idea, which is unbiased with respect to pathogens, but I wonder if a simple PCR assay for Phytophthora would be a simpler first step (although we don't a Phytophthora sample have a positive control). The genomes of at least 8 species of Phytophthora have been sequenced, including P. cinnamomi (see attached for  six species, plus P. infestans and P.ramorum were sequenced several years ago).  Genome sequences of six Phytophthora species associated with forests in New Zealand.

Jenny Glass of the WSU Puyallup Plant diagnostics lab used the  agdia ImmunoStrip for Phytophthora.  If I understand her, and Marianne Elliott's subsequent lab techniques, PCR was not otherwise employed.  

Speculatively, and with no guarantee of success, we may wish to consider both PCR (with appropriate primers) and unbiased NGS sequencing of affected and unaffected samples.   Marianne provides this poster as a good starting point:  

NGS sequencing has proved successful in at least one somewhat-related field study:

Unfortunately, the genome of Western Sword Fern, polystichum munitum,  has not yet been sequenced:

Monday, June 6, 2016

Presentation to the Seattle Parks Field Committee, Thursday June 2nd 2016

At Lisa Cieko's invitation, I presented Kramer & Tristan's work to the Seatle Parks Field Committee.  UW's Tim Billo supervised this work, about which he said, 

"I think it would be worth reporting some of the stats from the analysis I did of Kramer and Tristan's data--so everyone knows that the decline over only a 6 month period is statistically significant and quite large (18% average decline). And it's also important to note that the decline is not equal across the whole area; in fact some areas actually showed an increase."

Note that the survey plots are limited to Ground Zero and the region of our informal survey of August 2015.

Saturday, May 14, 2016

Twenty UW Monitoring Plots, Data Collection Ongoing

Twenty random-placed monitoring plots, in and around Ground Zero

  • Initial and repeat surveys by Tristan Kramer and Tristan O'Mara
  • Third survey to be completed soon, after which we will summarize here

Saturday, February 20, 2016

Tristan and Kramer in action, establishing monitoring plots, mountain beaver evidence. January 2016

Mountain Beaver hole close-up 
In context (ground zero?

Paul Talbert's Skepticism regarding the Mountain Beaver Hypothesis

It seems likely that several interacting factors cause the sword fern die-off.   Phythophthora and mountain beavers have been proposed.  To promote discussion, and in hopes of eventually identifying causes and remedies through open debate, I am posting Paul Talbert's reply to an earlier mountain beaver post here, as a proper blog entry.   - Paul Shannon
I remain deeply skeptical of the mountain beaver hypothesis.

1) The area where the fern die-off is currently being documented has been riddled with mountain beaver burrows for years, as I discovered wandering through this area in 2008 when surveying social trails and possible alternative routes during our Comprehensive Trail Plan. However, the ferns were flourishing then.

2) Mountain beavers do eat sword ferns, but when I've seen them, they neatly clip off fronds and drag them into their burrows or eat them in the open. Instead we see fronds that look weak, then turn brown, then die, and eventually drop off. Once they have fallen off, they may resemble clipped fronds (and there also may be clipped fronds), but mountain beavers cannot cause drooping and browning on the plant unless possibly through underground activity that affects the roots. That doesn't seem plausible at ground zero, where there are no burrows.

3) Mountain beavers are found in many other locations, and have been throughout the Holocene at least, but we have not so far received any reports, current or historical, of ferns being laid to waste by mountain beavers.

4) It is possible that if Phytophthora or some other scourge is attacking the roots, mountain beavers may play a role in spreading the oospores, chlamydiospores, and sporangia from place to place. This might help explain the rapid spread, though the various spores can probably get around without assistance.

From the look of the photo, it seems that Oregon grape is still unaffected. While it is plausible that sword fern might be more susceptible to drought, enhanced by mountain beaver activity or not, if it is true that sword fern is being decimated while oregon grape is remaining untouched, that seems more like a species-specific pathogen than a drought, which I would expect to affect everything to some degree or other. 

It is great that you are gathering data that can help address these questions.

Saturday, January 9, 2016

Phytophthora: oft-proposed candidate pathogen

There are more than 100 species in this genus, whose name translates as "plant destroyer".    

P. ramorum is responsible for sudden oak death; P. infestus caused the Irish Potato Famine.  Lisa Cieko discovered a 1984 report:

We have not been able to verify the presence of Phytophthora at Seward Park.  

Seward Park Audubon's Kathryn Sechrist asked a San Francisco State botanist colleague to comment on our videos, and received this response:

As to the fern die-off ... I looked over the blog. Although not confirmed, it sure sounds like Phytophthora. It has become a huge problem here in CA, particularly with native plant propagation. I was just at a CNPS board meeting where a policy was passed to try to deal with protocols for raising natives. Huge burden on propagators! Really too bad. But, serious implications for natural systems as well."