A Survey of Soil Nematodes
Across Western Oregon
Caroline Hilburn
Mentor: 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
Sample collection
Nematode extraction
Worm line cultivation
DNA extraction
PCR amplification
DNA sequencing
BLAST search
Nematode identification
Corrolation of molecular
and ecological data
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
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Species Abundance Across Soil Types
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Species
Cultivated land
City Parks
Natural Areas
Compost
Rotting Fruit
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Before Sampling
After Sampling
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Next Steps
Photo: Dr. David Wharton
• Caenorhabditis:
continue sampling
• Panagrolaimus:
continue exploring
the new strains and
how they relate to
the evolution of
different
reproductive modes
Acknowledgements
•
•
•
•
•
Howard Hughes Medical Institute: Funding
Dr. Kevin Ahern
Dr. Dee Denver: Mentor
Dana Howe
Sampling Sites:
–
–
–
–
–
–
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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.”