A Survey of Soil Nematodes Across Western Oregon

Caroline HilburnMentor: Dr. Dee Denver

Zoology Department

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

Greater Implications• A mitochondrial deletion

heteroplasmy in C. briggsae was found recently in a gene known to affect aging and Parkinson’s 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

BLAST searchNematode identificationCorrolation of molecular

and ecological data

DNA extractionPCR amplificationDNA sequencing

Sample collectionNematode extractionWorm line cultivation

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

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

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

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

Total Species Abundance

0

10

20

30

40

50

60

Cephalobus sp

Rhabditis cf terricola Mesorhabditis sp Oscheius tipulae Panagrolaimus sp

Plectus sp

Panagrellus redivivus Halicephalobus gingivalis Rhabditoides inermiformis

Diplogaster sp

Choriorhabditis dudichi

Plectidae sp Pellioditis sp

Tylocephalus auriculatus

Rhabditella axei

Species

Abundance

Species Abundance Across Soil Types

0

10

20

30

40

50

60

Cephalobus sp

Rhabditis cf terricola Mesorhabditis sp

Oscheius sp

Panagrolaimus sp

Plectus sp

Halicephalobus sp

Rhabditoides inermiformis

Panagrellus redivivus Pristionchus lheritieri Choriorhabditis dudichi

Plectidae sp Pellioditis sp

Tylocephalus auriculatus

Rhabditella axei

Species

Abundance

Cultivated land City Parks Natural Areas Compost Rotting Fruit

Before Sampling After Sampling

PP

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

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 Kruger’s Farm– Liz Myers at Deerhaven Vineyard– Vitae Springs Vineyard– Oregon State Parks– Jan McNeilan, and the OSU Extension Services Offices

Background Photo: Hulusi Cinar

• 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 planet’s surface vanished, its “ghostly outline” could still be made out in the biomass of nematodes, almost all of species unknown.”