Changes in nematode species composition in response to environmental cues: a genomic approach

We are using resident nematode populations sampled from the Konza Tallgrass Prairie Biological Station near Manhattan, Kansas to link the responses of organisms to environmental change at the genetic level. We hypothesize that different species may have varying genetic capacities to respond to changes in the environment; either by differences in the genes they possess or in how those genes are regulated. We have been testing these possibilities by examining the responses of bacterial feeding nematodes to changes in soil chemistry caused by nitrogen addition and fire. We are also addressing this in the laboratory using the genetic model nematode Caenorhabditis elegans (a Rhabditid). We are using C. elegans to model nematode environments on Konza in order to discover genes that are induced or repressed in response to environmental changes. Our strategy is to document responses of the soil nematode community to changes in the environment, identifying potential drivers and mechanisms, then to model these interactions in the lab with C. elegans to identify relevant genes and to test these candidate genes in native soil nematodes. This will lead to the identification of genes that are important for interactions of nematodes with their biotic and abiotic environment.

Our field experiments aimed to set the stage for investigations of gene functions responsible for the ability of different nematode taxa to persist in different environments. Previous observations at Konza documented changes at the taxonomic level of family (Todd, 1996; Todd, 1999). However, to be able to identify gene functions, we needed higher taxonomic resolution and the extent to which differential responses occurs at the genus level or below was unclear. Thus, we used molecular methods to quantify the responses of microbial-feeding nematodes to nitrogen addition and changes in fire frequency at the lowest levels of taxonomic resolution. Using DNA sequencing and quantitative polymerase chain reaction (PCR) probes for the 18S ribosomal RNA gene and the ITS1 region (Jones, 2006a), we identified 19 microbial-feeding nematode taxa across four families. When nematodes were sampled across treatments, we found that some taxa within a family responded similarly to nitrogen and burning treatments, while other taxa within the same family responded quite differently. Additionally, although nematodes from different families on average responded differently to nitrogen addition and burning, similar responses were seen in nematode taxa that spanned three taxonomic families (Jones, 2006b).

In the lab, C. elegans is normally grown on agar plates seeded with E. coli.  We have modeled both the abiotic and biotic aspects of the environment in the laboratory by examining the role of pH, ions and native soil bacteria on nematode responses. For example, we used cDNA microarrays to identify 204 candidate genes in C. elegans that are induced in response to the microbial aspects of the biotic environment. We have used loss of function mutants to test contributions of some of these genes to fitness in a given environment and found specific, significant correlations between expression levels and mutant life history data. Thus it seems that not only are the expression of specific genes induced in response to a change in environment, but some of these genes contribute to fitness traits. These results demonstrate that assessing C. elegans gene functions in more natural environments can allow new functions to be assigned to genes of unknown function, validating a prediction of Ecological Genomics. Interestingly, genes implicated in innate immune response were over represented in the genes identified and have used functional tests to determine that this defense response was not specific to C. elegans as we have found a variety of pathogen-associated effects in native nematode taxa in response to the native bacterial isolates.  Overall our results suggest that the nematode community responds to changes nutrient enrichment by expressing genes that increase fitness and the ability to defend against bacterial pathogens.

In addition, the altered nitrogen and burning regimes appear to cause changes in soil pH and ion concentration. We used KSU Targeted Excellence funding to explore the potential direct effects of alterations pH and osmolarity on native nematode fitness in the laboratory. Eventually, we plan microarray and subtractive hybridization experiments to discover the relevant genes involved.

References and recent ecological genomics publications

Jones, K.L., Todd, T.C., and Herman, M.A. 2006 Development of taxon-specific markers for high-throughput screening of microbial-feeding nematodes, Molecular Ecology Notes, 6, 712-714

Jones, K.L., Todd, T.C., Coolon, J.D., Blair, J. M., and Herman, M.A. 2006. Molecular approach for assessing responses of microbial-feeding nematodes to burning and chronic nitrogen enrichment in a native grassland, Mol. Ecol., 15, 2601-2609.

Kammenga, J.E., Herman, M.A., Ouberg. N.J., Johnson, L.C., Breitling, R. (2007), Microarray challenges in ecology, TREE, 22, 273-279.

Ungerer, M.C., Johnson, L.C., Herman, M.A. 2007 Ecological genomics: understanding gene functions in the natural environment. Heredity, 100, 178-183.

Todd, T.C. 1996. Effects of management practices on nematode community structure in tallgrass prairie. Applied Soil Ecology 3: 235-246.

Todd, T.C., J.M. Blair and G.A. Milliken. 1999. Effects of altered soil water availability on a tallgrass prairie nematode community. Applied Soil Ecology 13:45-55.