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Sudden Oak Death Horticulture

PCR for DNA sequence analysis and identification of Oomycetes


PCR for DNA sequence analysis and identification of Oomycetes

Setting up PCR 5 24 2011 (click on photos to see larger photo).

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Katie Coats, molecular biologist, showing students pipetting skills. Accurate pipetting is very important in DNA analysis.

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Samples which were isolated onto V8 agar in pure culture will be tested.

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A master mix of chemicals used in PCR is prepared.

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Samples are centrifuged to mix thoroughly.

 

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A sterile pipet tip is scraped across the surface of a culture to obtain a sample for PCR.

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Then the chemicals are pipetted into microtubes for each sample.

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All samples are placed in the thermocycler for PCR, which runs about 2 hrs. Then the PCR product is sent off for sequencing.

Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013

Transferring Oomycetes to pure culture


Transferring Oomycetes to pure culture

5 17 2011 (click on photos to see larger photo).

Students visited the WSU-Puyallup plant pathology lab to transfer Oomycetes growing on the isolation plates to pure culture on V8 agar.

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Labelling plates is an important step in the process.

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Transferring colonies to pure culture is done in a laminar flow hood or bio-safety cabinet.

 

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Identifying colonies of Phytophthora or Pythium to be transferred.

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Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013

Isolating Oomycetes from leaf baits in the lab


Isolating Oomycetes from leaf baits in the lab

5 10 2011 (click on photos to see larger photo).

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Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013

Photos “bait in a bottle” method at Clarks Creek


Stream sampling using ”bait in a bottle” method at Clarks Creek

Sample collection 5 3 2011 (click on photos to see larger photo).

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Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013

Results of BOB sampling at Clarks Creek


Results of BOB sampling at Clarks Creek

The most commonly isolated group of Oomycetes was Pythium belonging to Clade B2. There was little difference among hosts, except for reed canarygrass from which only one Pythium sp. was isolated. Saprolegnia was isolated from three hosts. Two Phytophthoras belonging to Clade 6 were isolated, and these, as well as Pythiums in Clade B2, were commonly found at the other freshwater sites sampled in this study.

Phylogenetic trees from sequence data obtained in this study:

Phytophthora Pythium Saprolegnia

Host
species isolated
group or clade
Riparian/forest
# isolates
False lily of the valley Maianthemum dilatatum Fusarium spp. fungus
F
2
False lily of the valley Maianthemum dilatatum Phytophthora taxon ‘salixsoil’ 6
F
1
False lily of the valley Maianthemum dilatatum Pythium diclinum/lutarium B2
F
5
Grand fir Abies grandis Phytophthora taxon ‘pgchlamydo’ 6
F
1
Grand fir Abies grandis Pythium aquatile B2
F
1
Grand fir Abies grandis Pythium diclinum/lutarium B2
F
7
Licorice fern Polypodium glycorrhiza Mucor hiernalis zygomycete
F
1
Licorice fern Polypodium glycorrhiza Pythium aquatile B2
F
1
Licorice fern Polypodium glycorrhiza Pythium diclinum/lutarium B2
F
2
Licorice fern Polypodium glycorrhiza Pythium oopapillum B2
F
1
Rhododendron Rhododendron ‘Nova Zembla’ Pythium aquatile B2
F
1
Rhododendron Rhododendron ‘Nova Zembla’ Pythium diclinum/lutarium B2
F
5
Rhododendron Rhododendron ‘Nova Zembla’ Saprolegnia parasitica Saprolegnia
F
1
Red alder Alnus rubra Pythium diclinum/lutarium B2
R
5
Red alder Alnus rubra Pythium oopapillum B2
R
2
Red alder Alnus rubra Pythium undulatum H
R
1
Reed canary grass Phalaris arundinacea Pythium intermedium F
R
8
Salmonberry Rubus spectabilis Pythium diclinum/lutarium B2
R
8
Salmonberry Rubus spectabilis Pythium oopapillum B2
R
1
Salmonberry Rubus spectabilis Saprolegnia parasitica Saprolegnia
R
1
Skunk cabbage Lysichiton americanum Mortierella sp. zygomycete
R
1
Skunk cabbage Lysichiton americanum Pythium diclinum/lutarium B2
R
3
Skunk cabbage Lysichiton americanum Saprolegnia diclina Saprolegnia
R
1

Pierce College BOB 2011_allhosts

Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013

Stream sampling using “bait in a bottle” method at Clarks Creek


Stream sampling using ”bait in a bottle” method at Clarks Creek

Oomycetes are fungus-like organisms found in marine, freshwater, and terrestrial environments. Some, such as Phytophthora, Pythium, and Saprolegnia, are parasites of plants and animals. DNA sequence data has revealed that these organisms are not fungi, but are more closely related to brown algae and diatoms. We will be “fishing” for these organisms by using leaf baits from various plant species.

Objectives

  • Is there a relationship between host bait material and Oomycete species isolated?
  • Riparian vs forest plants – are riparian plants resistant to infection?
  • Has P. ramorum made it to Clarks Creek?

Each group will choose a plant species to use for bait. Pick fully expanded leaves that are relatively free of spots or other signs of infection. Punch out 20 leaf discs and put in bottle. Include one intact leaf. Put leaf baits in bottle of creek water and cap tightly. Rest bottle on its side for incubation.

After incubation leaf baits will be cultured on selective media for Oomycetes, transferred to pure culture, and identified using DNA sequencing.

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Students from Pierce College Biology 213 class collecting water samples at Clarks Creek.

Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013

Clarks Creek Headwaters 1103


Clarks Creek headwaters

Site #1103

Clarks Creek, near fish hatchery

This site also used for Pierce College “Bait in a Bottle” experiment.


Elevation 48 ft

Stream order 1


Clarks Creek Initiative

Results from 2011 monitoring

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2011 water temp data_14139_image021

Results from 2010 monitoring

1007

Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013

2011-1102 Clarks Creek downstream


Clarks Creek downstream

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Land use map 1102_350

Site #1102 Clarks Creek, Puyallup, WA


Elevation 24 ft Stream order 2


Clear/Clarks Creek Basin Plan 2006, Pierce County Public Works & Utilities USGS data for Clark’s Creek

Results from 2011 monitoring
 2011 sites species data_25436_image017
 2011 water temp data_14139_image017
 Results from 2010 monitoring
1001

Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013

Clarks Creek – headwaters


Clarks Creek – headwaters

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Site # 1007Baiting at Clarks Creek upstream, near fish hatchery by Biology 213 class from Pierce College. 4/15/10.

see results of the Shoe Experiment here

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Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA Last updated January 2, 2013

Clark’s Creek – downstream


Clark’s Creek – downstream

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DSC05863 350 labPHS students learning molecular identification techniques in the lab
DSC05328 sm Clarks Crkthumb Site #1001First bait deployment March 3, 2010 by Puyallup High School students in Dave Wetzel’s class

1001

Baiting period Bait leaf spp. Phytophthora spp. and others identified
1
Rhododendron P. gonapodyides (6), Trichoderma spp. (1)
1
Camellia P. gonapodyides (1), unknown (1)
2
Rhododendron P. gonapodyides (4), unknown (4)
2
Gold dust plant (Aucuba japonica ‘Variegata’) Pythium litorale or Py. sterilum (2)
3
Rhododendron P. gonapodyides (6), unknown (5)
3
Strawberry tree (Arbutus unedo) Pythium sp. or Py. undulatum (1), unknown (1)
4
Rhododendron P. gonapodyides (5), P. gonapodyides “A” (4), P. cryptogea (1), unknown (1)
4
Dwarf cherry laurel P. gonapodyides (2), unknown (2)
5
Rhododendron P. gonapodyides (7), unknown (5)
5
unknown (2)
6
Rhododendron P. gonapodyides (4), unknown (8)
6
Red tip Photinia P. gonapodyides (2)

Viewing Chum Salmon in Clark’s Creek

WDFW 2000 Clear/Clark’s Creek Basin Plan Pierce County 2005

Pink salmon in Clarks Creek near Puyallup NWIFC Blog Sept. 2007

 

Contact: Gary Chastagner, 253-445-4528 | WSU Puyallup Research & Extension Center, 2606 West Pioneer, Puyallup, WA, 98371-4998 USA
Last updated January 2, 2013