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Changes in nematode species composition in response to environmental cues: a genomic approach
The ever-changing natural environment presents organisms with challenges that require both short-term ecological and long-term evolutionary responses. The disturbances caused by global environmental change are complex, involving changes in the biotic environment that include microbes, competitors and predators, as well as changes in the abiotic soil environment. To begin to sort out these interactions, we have focused on the responses of microbial-feeding nematodes to the microbial aspects of the grassland biotic environment by sampling resident soil nematode populations sampled from the Konza Tallgrass Prairie Biological Station near Manhattan, Kansas. We have employed an interdisciplinary approach using high throughput molecular techniques to first characterize shifts in the nematode community (Todd, 1996; Todd et al.1999; Jones et al., 2006b) as well as the interacting bacterial community (Coolon et al, 2013). Next, we have modeled these interactions using the genetic model organism Caenorhabditis elegans to begin to understand the interactions of genes with the environment in non-model systems such as the native grassland soil nematode community in grasslands at Konza Prairie.


We used transcriptional profiling to identify a set of 204 genes that were differentially expressed when C. elegans was exposed to grassland soil bacteria (Coolon et al, 2009). We then used mutations to inactivate 21 of the identified genes and demonstrated that most genes regulate life history traits such as lifespan (which is affected by bacterial infection) and population growth rates. Furthermore, we found that genes up-regulated in response to a particular bacteria were correlated with a loss in lifespan when knockout mutants of that same gene were grown on the same bacteria. This observation has important implications for studies of non-model species as it indicates that we can infer a portion of the relative functional importance of differentially expressed genes from transcriptomic studies of native nematodes that do not have well developed genetic systems. Advances in next generation sequence technology (primarily read length) now allow us to obtain de-novo sequence data to aid in identification of orthologs of candidate genes. We are currently applying this combination of approaches to identify the genes that matter in the taxa that matter as they interact with a changing environment.

References and recent ecological genomics publications

Darby, BJ, Herman, MA. 2014 Effect of prey richness on a consumer’s growth rate. Oecologia 175, 243-250.

Gomez-Montano L Jumpponen, A, Gonzales. MA, Cusicanqui, J, Valdivia, C, Motavalli, PP, Herman M, Garrett, KA.  2013. Do bacterial and fungal communities in soils of the Bolivian Altiplano change under shorter fallow periods? Soil Biology & Biochemistry 65: 50-59.

Darby, BJ, Todd, TC, Herman, MA 2013 High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure. Mol. Ecol., 22:5456-54-71, DOI: 10.1111/mec.12480.

Coolon, JD, Jones, KL, Todd, TC, Blair, JM, Herman, MA. 2013 Long-term nitrogen amendment alters soil bacterial diversity and assemblage in tallgrass prairie. PLoS One, Jun 28;8(6): e67884

Wheeler DC, Darby BD, Herman, MA 2012.  Several grassland soil nematodes species are insensitive to RNA-mediated interference. Journal of Nematology, 44:92-101.

Darby, B.J., Jones, K.L., Wheeler, D., and Herman, M.A. (2011). Normalization and centering of array-based heterologous genome hybridization based on divergent control probes. BMC Bioinformatics 12, 183

Coolon, JD, Jones, KL, Carr, BC, Todd, TC, Herman, MA. 2009. C. elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits. PLoS Genetics, 5(6): e1000503. doi:10.1371/journal.pgen.1000503.

Herman, MA; Coolon, JD; Jones, KL; Todd, TC. 2009. Ecological Genomics of Nematode Community Interactions: Model and Non-model Approaches. In Evolutionary Biology from Concept to Application II, ed. by Pierre Pontarotti, Springer: Heidelberg, Germany, p. 303-321.(PDF)

 



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