Transcriptomics of Soil Nematodes
A large number of nematodes in most soil samples feed on bacteria, or other small cells and particles that can be ingested. Some of these species are especially common in soils that have experiences a large, recent influx of nutrients that support rapid, and usually temporary, bacterial growth. These nematode species are called "enrichment type bacterial-feeding nematodes" because of the enriched nature of their environment, such as compost piles, agricultural fields amended with fertilizer or sewage sludge, or native soils adjacent to dung piles, decaying carcasses, or roting fruit. Many of these enrichment-type species are in the family Rhabditidae.
The head of a typical Rhabditidae (above) has a rather large, open buccal cavity through which bacteria and other small particles are ingested.
The ingested prey then pass through this large muscular bulb which crushes (most of) the bacteria cells.
Because these nematodes are exposed to a wide variety of bacteria in the soil, and might consume pathogenic or potentially harmful bacteria, we are interested in studying the effects of different bacteria on these nematodes and their ecology.
This individual (above) was fed E. coli that were transformed with a plasmid that causes the production of GFP, a green fluorescent protein. By overlaying the green channel from fluorescence microscopy on top of the DIC image demonstrates the location of lots of GFP-bacteria in the posterior part of the esophagus (just anterior to the bulb), and a few cells, but mostly just diffuse protein from broken cells, posterior to the bulb in the intestine.
Rhabditidae, and other enrichment-type nematodes, are not particularly abundant in native grassland soils, but in the right spots, such as adjacent to dung piles or decaying carcasses, you can find quite a few.
(Above) Collaborators Tim Todd, Corin White, and Michael Herman coming back from sampling soil nematodes on Konza Prairie. It's realtively easy to sample nematodes from the field and examine which species are associated with particular habitats or treatments, but the soil environment is complex and it is relatively difficult to determine how and whether the bacterial community affects the nematode community.
To address these questions, we've begun to develop genomic tools for non-model soil nematodes like these enrichment-type bacterivores. First, we sequenced de novo transcriptomes (using 454 Titanium chemistry) of four nematodes species native to Konza prairie (Kansas), Oscheius tipulae, Oscheius sp. FVV-2, Rhabditis sp., and Mesorhabditis sp. This resulted in several thousand newlys sequenced and assembled transcripts, or gene sequences. Secondly, we sequenced fragments of expressed transcriptomes (using Illumina GAIIx) of each of the four native nematodes (plus C. elegans N2) after being feed one of six different bacteria: Bacillus subtilis, B. thuringiensis, B. megaterium, Pseudomonas sp., Escherichia coli, and Stenotrophomonas maltophilia. Although the project is still in project, preliminary results suggest that we may be able to distinguish some genes that are differentially expressed when native nematodes are exposed to different bacteria.