Plant Ecological Genomics
Current Research Focus-Ecological Genomics
The emerging field of Ecological Genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field, requiring a multidisciplinary approach that combines field studies with laboratory experiments with in ecologically relevant framework. Thus, while traditionally, ecological and laboratory-based genetic/genomic studies have occupied different areas of biological investigation, Ecological Genomics seeks to integrate these disciplines by using genomic approaches in an ecological context.
So far, Ecological Genomics refers to the use of any genome-enabled approach, whether aimed at discovering the ecological functions of single or multiple genes. We can define ecological genomics as an integrative field of study that seeks to understand the genetic mechanisms underlying responses of organisms to their natural environment. These responses include modifications of biochemical, physiological, morphological, or behavioral traits of adaptive significance.
The Johnson lab has three projects related to plant ecological genomics.
- Title: Ecotypic variation and functional genetic response in the ecologically dominant prairie grass big bluestem along sharp natural precipitation gradients and in response to simulated precipitation change in Great Plains grasslands: genes to ecosystem response
Investigators: Loretta Johnson (Biology), Girardara Kumar Surabhi (post-doc in Biology), Karen Garrett (Plant Pathology), Ted Morgan (Biology), Eduard Akhunov (Plant Pathology), Paul St Amand (USDA) and Sara Baer (Southern Illinois University)
Background: The central grasslands of the United States are amongst the most productive rangelands. These grasslands are dominated by big bluestem, Andropogon gerardii, which persists across the sharp and often variable precipitation gradient, ranging from 1200 mm annual precipitation in Illinois to only 400 mm in western Kansas. Changes in amount and timing of precipitation, as predicted from climate change scenarios, are likely to be critical abiotic stressors in determining the future productivity and sustainability of these rangelands. We aim to investigate the degree of ecotypic variation across the range of big bluestem, predict the functional response of this species to climate change across its range, and elucidate the genetic basis for differential variation in function across the natural climate gradient and in response to experimentally altered conditions. We hypothesize that the steep precipitation gradient in the Midwest provided selection to favor the development of local ecotypes that will respond differentially to climate change due to variation in functional attributes [e.g., net rates of photosynthesis (A net), plant water status and water use efficiency efficiency (WUE), and carbon allocation above and belowground] that may underpin variation in physical characteristics resulting from local genetic adaptation.
Questions addressed: Are ecotypes of the dominant prairie grass big bluestem broadly or locally adapted to drought along a sharp precipitation gradient, how will ecotypes from different places across the gradient respond to precipitation change (natural and experimentally induced with rainout shelters). What is the genetic basis for these drought adaptations?
Objectives: 1) characterize functional attributes and genetic structure of locally adapted, phenotypically distinct populations of big bluestem across a precipitation gradient from western KS to IL;
2) quantify differential response of ecotypes to the natural precipitation gradient and simulated changes in amounts and timing of precipitation as predicted by climate change scenarios, and
3) to characterize the ecosystem consequences of the interaction between genetic differentiation (at the level of gene expression) and climate in newly assembled stands consisting of single v. multiple genotypes.
Approach: We will use a reciprocal common garden experiment, where seeds from three source populations (western KS, eastern KS, and IL) and all populations combined will be sown in replicated plots at each of the 3 source locations. Each reciprocal common garden experiment will also receive a rainfall manipulation, such that simulated droughts will be punctuated by larger, but less frequent precipitation events. Ecophysiological response variables to be measured will include net photosynthesis, WUE, water potential, chlorophyll florescence, relative growth rate, and above-and belowground biomass. We will also characterize the genetic structure of each of the source populations using AFLP techniques and characterize the functional consequences of genetic differentiation at the level of gene expression using cDNA-AFLP and/or cross-species microarray hybridization using Zea mays oligonucleotide microarray chips.
Significance: This research will provide a mechanistic understanding of how variation in a dominant forage grass is locally adapted to natural and simulated changes in precipitation (drought stress) and the genetic basis for this local adaptation. This research will provide data that will help inform land managers about how to restore tallgrass prairie and guide them in decisions about which ecotypes to plant where in the face of climate change.
Title: Occurrence and distribution of Big Bluestem (Andropogon gerardii) polyploids in tallgrass prairies: Ecological consequences of differences in genome size
Investigators: Loretta Johnson (Biology), Karen Garrett (Plant Pathology), Eduard Akhunov (Plant Pathology), Ted Morgan (Biology)
Background: Polyploidy is a very common occurrence in plants. About 70% of angiosperms have experienced recent or ancient whole genome duplication events (polyploidization). Furthermore, genome duplication is even more common in the grass family. Autopolyploids are polyploids that have acquired multiple chromosome sets from a single species due to unreduced gamete formation. Andropogon gerardii (big bluestem), an ecologically dominant tall grass of the Great Plains, is an autopolyploid with a base chromosome number of 10 and two common ploidy levels of 6 (6X) and 9 sets (9X) of chromosomes. Our first step was to briefly survey the occurrence and distribution of these ploidy levels, or cytotypes, across the Great Plains in order to better understand where, how and why the 9X cytotype forms and the ecological consequences of ploidy in this dominant species. We collected field grown plants (270) from 4 locations in the Hays area of W KS, 4 locations in the vicinity of Konza in E KS. We determined ploidy using flow cytometry calibrated with chromosome counts in root tip smears. We found that the 6X and 9X cytotypes occurred in roughly equal abundance in a mosaic throughout KS. In contrast, plants in the eastern range (Il, MO) are almost exclusively 6X. In the Hays area, the cytotype were biased toward 6X (79.6%). In contrast, in the Manhattan area, 6X and 9X cytotypes were more balanced in frequency (51.2% and 49.8%). We did not detect evidence for a ploidy-specific geographic differentiation across broad spatial scales (east-west) nor fine-scale local habitat differentiation (upland-lowland). Interestingly, the frequency of cytotypes in the field-grown leaves sharply contrasted with that of the seed rain; when seeds were collected from the same locations as field-grown leaves, those seeds germinated into almost entirely 6X cytotypes (n=~200 plants).
Objectives: First, we plan to survey over broad geographic areas the occurrence, distribution and abundance of 6 and 9X cytotypes and identify how and why the 9X forms and is maintained. Second, we plan to characterize if there is a morphological, physiological and genomic differentiation between 6X and 9X plants and the ecological consequences of differences in genome size in the dominant prairie grass big bluestem.
Questions: Where, how and why and how frequent does the 9X cytotype forms? Why do the 6X and 9X occur as a mosaic in Kansas and Colorado, yet 6X dominates in the eastern part of the range of big bluestem? Does the stress of precipitation variability or increasing temperature westward contribute to the formation of the 9X cytotype? Can and do the 6X and 9X interbreed? If not, what factors contribute to their reproductive isolation? How do the 6X and 9X remain growing together on the same site yet remain genetically distinct? We hypothesize that due to genome duplication, 9X plants will be more robust and vigorous vegetatively when compared to the 6X. We predict that the 9X will be taller, have longer leaf blades, more leaf biomass, taller flowering stalks, higher photosynthetic rates, higher water use efficiency, and altered stomatal density. We predict that the disadvantages of the 9X include fewer viable seeds and lower germination rates. The next step is to quantify these differences and test these predictions in common gardens of 6X and 9X cytotypes planted across the Great Plains.
Approach: We will test these predictions by quantifying differences in morphology, physiology, reproductive fitness, and genetic differentiation at the level of gene expression in 6X and 9X plants under controlled conditions. We will determine and test these predictions using flow cytometry to determine ploidy calibrated with chromosome counts in root tip smears. We will also conduct parallel field experiments of common gardens of 6X and 9X cytotypes planted across the precipitation gradient of the Great Plains to examine the role of abiotic factors on the success of the different cytotypes in different precipitation regimes.
Significance: Ancient and recent polyploids in the plant kingdom are ubiquitous. Yet we know precious little about ecological differentiation in polyploids and the role they may play in ecosystem function.
- Title: Chronic and transient effects of N saturation on root processes and gene expression in the dominant prairie grass big bluestem Andropogon gerardii: Can we detect signs of N saturation through gene expression profiles?
Investigators: Loretta Johnson (Biology), Jyoti Shah (University of North Texas), Girardara Kumar Surabhi (post-doc in Biology)
Background: Mesic tallgrass prairie is amongst the most productive grasslands. In tallgrass prairie, belowground processes dominate because aboveground plant biomass is often removed by grazers and frequent fires. Indeed, root productivity often exceeds that of aboveground foliage productivity. The high root productivity results in grassland soils containing about 15% of the world’s soil carbon, derived mainly from root inputs. In spite of the obvious importance of roots, especially in prairies and grassland, root processes remain poorly understood.
Goal: To understand the molecular and physiological response of roots of big bluestem to changes in the availability of N, a key factor important in prairie plant growth, to correlate changes in gene expression in roots with whole plant response at the cellular and physiological levels and to explore the possibility of detecting signs of N saturation through gene expression profiles of roots.
Approach: We are complementing our ongoing subtractive cDNA library approach with genome-wide expression analysis (microarray analysis) in big blue stem using heterologous hybridization with Zea mays spotted EST chips. We also take advantage of candidate genes that have been identified in model plants (Oryza and Zea mays) that are known to be involved in root processes, and are likely conserved among a range of plant groups, including the grass family. Information from model plants will provide a starting point for a better understanding of the roles of these genes in non-model prairie plants in field settings. The genetic, molecular and physiological responses to changes in nitrogen (N) will be assessed in ongoing long- and short term experimental plots at the Konza Prairie Biological Station. We have collected our roots from plots that have been chronically treated with 4 levels of N (0, 2.5, 5 and 10 gN/m2/yr) and a parallel set of plots that have been treated only once. This allows us to assess the short- and long–term response to N and also to detect thresholds of response by comparing root response in the low and high N plots. We will place our studies of gene expression in the ecological context necessary to interpret genetic and molecular mechanisms by correlating gene expression pattern with response at the cellular (metabolites), whole plant (physiology) and ecosystem (productivity) levels.
Ungerer, M., L. Johnson and M. Herman. 2008. Ecological genomics: finding gene functions in the natural environment. Special ecological genomics issue of Heredity 100:178-183.
McKinley, D.C., M.D. Norris, L.C. Johnson, and J.M. Blair. 2008. Biogeochemical changes associated with Juniperus virginiana encroachment into grasslands. Pages170-187, In Ecological Studies Series 196 - Western North American Juniperus Communities: A Dynamic Vegetation Type (O.W. Van Auken ed.), Springer-Verlag, NY.
Johnson L., M. Herman, S. Welch. 2007. Ecological Genomics: Extending the genome revolution to the environment around us. Merrill Series on the Research Mission of the Public Universities. A compilation of papers originally presented at a conference sponsored by the Merrill Advanced Studies Center June 2007. MASC Rept. 111, University of Kansas. Merrill Advanced Studies Center (Not peer-reviewed)
Kammenga, J., M. Herman, J. Ouborg, L. Johnson, and R. Breitling. 2007. Microarray Challenges in Ecology Trends in Ecology and Evolution 22: 273-279.
Norris, M.A., J.M. Blair and L.C. Johnson. 2007. Altered ecosystem nitrogen dynamics as a consequence of land cover change in tallgrass prairie. American Midland Naturalist 158:432-445.
Craine, J., B. Lee, L. Johnson, W. Bond, W.D. Williams. 2005. Roots of the world. Ecology 86:12-19.
Jumpponen, A. Trowbridge, J., Mandyam, K.G. and Johnson, L.C. 2005. Nitrogen deposition affects AM root colonization minimally but shifts community structure. Biology and Fertility of Soils 41:217-224.
Jumpponen, A. and Johnson, LC. 2005. Can rDNA analysis of diverse fungal communities in soil and roots detect effects of environmental manipulations-a case study from tallgrass prairie. Mycologia 97(6):1177.
Loya, W., L.C. Johnson, K. Nadelhoffer. 2004. Annual dynamics of leaf and root derived carbon in arctic tundra soils. Soil Biology and Biochemistry 36(4):655-666.
Smith, D.L. and L.C. Johnson. 2004. Changes in soil carbon cycling as forests expand into grassland: Vegetation-mediated changes in microclimate reduces soil respiration. Ecology 85 (12): 3348-3361.
Wessman, C., S.A. Archer, L.C. Johnson and G. Asner. 2004. Woodland expansion in US Grassland: Assessing land cover change and biogeochemical impacts. Peer-reviewed Book Chapter. In Land Use and Land Cover Change. Kluwer Publishing.
Smith, D.L. and L.C. Johnson. 2003. Expansion of Juniperus virginiana in the Great Plains: Changes in Soil Organic Carbon Dynamics. Global Biogeochemical Cycles 17(2):1-12.
McKane, R., L.C. Johnson, B. Fry, G. Shaver, K. Nadelhoffer, E. Rastetter, B. Fry, A. Giblin, K. Kielland, B. Kwaitkowski, J. Laundre, and G. Murray. 2002. Resource-based niches provide a basis for species diversity and dominance in an arctic plant community. Nature 415:68-71.
Norris, M., J. Blair, and L.C. Johnson. 2002. Changes in plant biomass, productivity, and nutrient stores following Juniperus expansion into grasslands. Can. J. Forestry Research 31:1940-1946.
Loya, W., L. C. Johnson, K. Nadelhoffer, G. Kling, J. King, W. Reeburgh. 2002. Pulse-labeling studies of carbon cycling in Arctic tundra ecosystems: the contribution of photosynthate to soil organic matter. Global Biogeochemical Cycles 16(4).
Nadelhoffer, K.J., L.C. Johnson, J. Laundre, A. Giblin. and G. Shaver. 2002. Fine root production and nutrient use in wet and moist arctic tundras as influenced by chronic fertilization. Plant and Soil 242 (1): 107-113.
King, J., W. Reeburgh, K. Nadelhoffer, G. Kling, W. Loya, and L.C. Johnson. 2002. Contribution of photosynthate of methane emission in tundra: A 14C labeling approach. Global Biogeochemical Cycles 4 (doi: 10.1029/2001GB001456).
Hoch, G., J. Briggs, and L. Johnson. 2002. Assessing the rate, mechanisms, and consequences of conversion of tallgrass prairie to Juniperus virginaian forest. Ecosystems 5:578-586.
Johnson, L.C. and J.R. Matchett. 2001. Fire and grazing regulate belowground processes in tallgrass prairie. Ecology 82:3377-3388.
Norris, M., J. Blair, and L.C. Johnson. 2001. Land cover change in eastern Kansas: litter dynamics of closed-canopy eastern red cedar forests in tallgrass prairie. Can. J. Botany 79:214-222.
Johnson, L.C., G. Shaver, D. Cades, A. Stanley, K. Nadelhoffer, A. Giblin. 2000. Plant carbon-nutrient interactions control CO2 exchange in Alaskan wet sedge tundra ecosystems. Ecology 81:453-469.
Hooper, David U. and L.C. Johnson. 1999. Nitrogen limitation in arid and semi-arid ecosystems: Response to geographic and temporal variation in precipitation. Biogeochemistry 46:247-293.
A.K. Knapp, J.M. Blair, J.M. Briggs, S.L. Collins, D.C. Hartnett, L.C. Johnson, and E.G.Towne. 1999. The keystone role of bison in North American tallgrass prairie. Bioscience 49:39-50.
Shaver, G. R., L.C. Johnson, D.H. Cades, G. Murray, J.A. Laundre, E.B. Rastetter, K. J. Nadelhoffer, and A.E. Giblin. 1998. Biomass and CO2 flux in wet sedge tundras: Responses to nutrients, temperature, and light. Ecological Monographs 68(1): 75-92.
Williams, M, E. B. Rastetter, D. N. Fernandez, M. Goulden, L. C. Johnson, G. R. Shaver. 1997. Predicting gross primary productivity in terrestrial ecosystems. Ecological Applications 7(3):882-894.
Nadelhoffer, K., G. R. Shaver, B. Fry, A. Giblin, L. Johnson, and R. McKane. 1996. Variation in 15N natural abundance in arctic tundra as an indicator of plant species N-use patterns. Oecologia 107:386-394.
Johnson, L.C., G.R. Shaver, K.J. Nadelhoffer, A. E.Giblin, E.B. Rastetter, J.A. Laundre, G.L. Murray. 1996. The effects of enhanced drainage and elevated temperature on carbon balance in tussock tundra microcosms. Oecologia 108:737-748.