Gene Expression in Tomato Roots
Plant nutrient uptake and assimilation systems are highly responsive to soil nutrient availability. Expression levels of genes involved in these pathways may be sensitive indicators of nutrient cycling, serving as a “plant’s eye view” of the local soil environment. The plant’s perspective may be especially insightful in systems were nutrient cycling is dynamic, in which conventional measures of soil nutrient availability could be uninformative or misleading.
Previous research in our lab showed that gene expression in tomato roots responds rapidly to ephemeral patches of available nitrogen and phosphorus in both greenhouse and field settings using organically-managed soil. Microarrays and quantitative real time RT-PCR showed that genes involved in nitrogen uptake and assimilation, phosphorus uptake, and cell division and growth responded most strongly to these nutrients. Stable isotope additions showed that levels of plant nitrogen uptake were coupled to changes in gene expression. Additionally, mycorrhizal and non-mycorrhizal plants had unique strategies for nitrogen acquisition, especially at low nitrogen availability.
Current research by Tim Bowles involves examining how tomato root gene expression corresponds to soil bioassays for available nitrogen as well as gross nitrogen fluxes. We are also examining tomato root gene expression on farms with diverse organic management strategies across a gradient of soil organic matter (see Nutrient Cycling on Organic Farms across a California Landscape). These measurements are being coupled with detailed characterization of soil organic matter pools and composition (see FTIR indicators of soil organic matter quality across a landscape of organic management) and the microbial community. This analysis will yield process-based understanding of plant-soil-microbe nitrogen cycling and potentially lead to novel indicators of nitrogen availability for organic farms, or other soil environments where nitrogen cycling is rapid.
Bowles, T.M., Raab, R.A., Jackson, L.E. (2012). Rapid changes in root gene expression in response to nitrogen availability: Linking molecular biology, plant physiology, and soil biogeochemical processes. Ecological Society of America Conference, Portland,OR. (Bowles, ESA 2012)
Jackson, L.E., Bowles, T.M., Hodson A.K., Lazcano, C. (2012) Soil microbial-root and –microbial-rhizosphere processes to increase nitrogen availability and retention in agroecosystems. Current Opinion in Environmental Sustainability, in press. (Jackson et al, COSUST in press)
Ruzicka, D.R., Barrios-Masias, F.H., Hausmann, N.T., Jackson, L.E., Schachtman, D.P., 2010. Tomato root transcriptome response to a nitrogen-enriched soil patch. BMC Plant Biology 10, 1–19. (Ruzicka et al 2010)
Ruzicka, D.R., Hausmann, N.T., Barrios-Masias, F.H., Jackson, L.E., Schachtman, D.P., 2012. Transcriptomic and metabolic responses of mycorrhizal roots to nitrogen patches under field conditions. Plant and Soil 350, 145–162. (Ruzicka et al 2012)
Bowles, T.M., P.A. Raab, and L.E. Jackson. 2015. Root expression of nitrogen metabolism genes reflects soil nitrogen cycling in an organic agroecosystem. Plant and Soil 392: 175-189. (Bowles et al. 2015)
View a recent poster, "Rapid changes in root gene expression in response to nitrogen availability: Linking molecular biology, plant physiology, and soil biogeochemical processes" from ESA 2012 in Portland, OR.