A Survey of Soil Nematodes Across Western Oregon

1
A Survey of Soil Nematodes Across Western Oregon

• Caroline Hilburn
• Mentor Dr. Dee Denver
• Zoology Department

2
Background

• Nematode model
• Parasitic nematodes of interest to medicine
• Great variety of species
• Easily cultivated
• Small genome
• Caenorhabditis elegans was the first animal to
  have its complete genome sequenced
• C. remanei and C.briggsae are also being heavily
  studied as comparison species

Photo Lan D. Chin-Sang
3
Greater Implications

• A mitochondrial deletion heteroplasmy in C.
  briggsae was found recently in a gene known to
  affect aging and Parkinsons disease
• Nematode models, such as C. briggsae help
  understand mutation, the root of all genetic
  diseases.
• Parasitic nematodes cause Riverblindness,
  Elephantiasis, Hookworm

Photo Eric Haag
4
(No Transcript)
5
(No Transcript)
6
Ecology Methods

• Blocked experimental design, with sub-sites and
  samples nested within each of 8 major blocks.
• Nematode extraction from the soil using modified
  Baermann tubes
• Paul plates used for nematode cultivation
• New lines started by picking single worms to
  individual seeded Paul plates

7
Sampling

• 8 major sampling areas, Portland, Salem,
  Corvallis, Eugene, Lincoln City, Toledo, Lyons,
  and Sweet Home
• Five soil types natural areas, city parks,
  cultivated land, compost heaps, and rotting
  fruit
• Sampling
• 8 major blocks, up to 5 different soil types in
  each block, each with 4 sub-sites, and 4 soil
  samples from each sub-site

8
Molecular methods

• Nematode strain identification
• 18S ribosomal RNA gene targeted for conventional
  PCR amplification
• SPRI bead purification used to prepare PCR
  product for sequencing
• Product from the sequencing reactions taken to
  the Center for Genomics Research and
  Biotechnology for sequencing

9
Results

• 178 strains successfully sequenced
• Nematodes from 17 genera identified
  Acrobeloides, Cephalobus, Rhabditis,
  Mesorhabditis, Oscheius, Panagrolaimus, Plectus,
  Halicephalobus, Rhabditoides, Rhabditella,
  Choriorhabditis, Plectidae, Pristionchus,
  Pellioditis, Panagrellus, and Tylocephalus.
• 40 new nematode strains started
• 4 likely new species isolated

10
(No Transcript)
11
(No Transcript)
12
(No Transcript)
13
Before Sampling
After Sampling
P
P
14
(No Transcript)
15
Next Steps

• Caenorhabditis continue sampling
• Panagrolaimus continue exploring the new strains
  and how they relate to the evolution of different
  reproductive modes

Photo Dr. David Wharton
16
Acknowledgements

• Howard Hughes Medical Institute Funding
• Dr. Kevin Ahern
• Dr. Dee Denver Mentor
• Dana Howe
• Sampling Sites
• Portland parks and recreation department
• Cooper Mountain Organic Vineyard
• Don Kruger at Krugers Farm
• Liz Myers at Deerhaven Vineyard
• Vitae Springs Vineyard
• Oregon State Parks
• Jan McNeilan, and the OSU Extension Services
  Offices

Background Photo Hulusi Cinar
17

• From an interview with E.O.Wilson, author of
  Consilience
• Nematode worms, account for four of every
  five animals living on Earth - and are so
  abundant that if the planets surface vanished,
  its ghostly outline could still be made out in
  the biomass of nematodes, almost all of species
  unknown.