Independent Research Projects.–A major objective of the REU Program is to give undergraduate students an opportunity to conduct independent research.  Mentors for the REU Program have expertise in a broad range of ecological and evolutionary disciplines, and could advise on a range of topics related to the ecology and genomics of organisms of the tallgrass prairie.  Mentors have been invited to describe specific projects that would be available to students participating in the REU Site program.  New project abstracts will be added here in Fall 2009.  Here are some of the topics that have been proposed for the REU Site Program in Summer 2010 (sorted by mentor names):

Grassland Restoration Ecology (Mentor: Blair).  REU students may participate in ongoing long-term restoration projects at the Konza LTER site that addresses the application of basic ecological principles to restoration ecology.   For example, on-site grasslands restoration experiments in former agricultural fields provide opportunities for students to investigate the recovery of plant communities and/or ecosystem properties and processes.  Studies of the use of fire to reverse the spread of woody vegetation and enhance recovery of herbaceous grassland communities are also possible.  Many opportunities exist for student research in plant, soil and invertebrate ecology within the context of restoration ecology, and I am willing to work with students to design specific research projects that address their interests. 

Ecosystem Responses to Fire and Grazing (Mentor: Blair).  The structure and function of tallgrass prairies is strongly affected by three interacting drivers - fire, grazing by large herbivores, and climate.  As part of an ongoing project to assess the interactive effects of fire and grazers in grasslands, we have established grazing exclosures in areas grazed by bison and that are burned either annually, every four years or every twenty years.  REU students may participate in research that addresses the combined effects of grazing and different fire frequencies on a suite of plant and soil responses.  Potential areas of interest include effects on soil nutrient availability, soil C dynamics, and plant nutrient status.  I am also willing to work with students to develop projects that address other specific questions within this general research area.

Temperature sensitivity and soil carbon (Mentor-Craine).  Soil carbon is one of the most important pools in determining the fate of atmospheric carbon dioxide levels and global warming. In conjunction with a separate NSF-funded project that is examining patterns of soil carbon temperature sensitivity at the continental scale, 1-2 REU students will be hired to examine patterns of the temperature sensitivity of soil carbon at Konza.  The goal of this specific project is to examine patterns of the temperature sensitivity of soil carbon across Konza.  Students will learn a host of field and laboratory ecosystem measurements as part of this project.  In conjunction with Noah Fierer at the University of Colorado, Boulder, students will also have a chance to examine patterns of microbial communities along side the soil carbon dynamics.

Impact of the Roots and Rhizosphere of a Dominant Prairie Grass on the Soil Fungal Communities (Mentors: Blair and Jumpponen).  Plant roots dramatically alter the physical, chemical and biological properties in the surrounding soil and create an environment known as the rhizosphere.  The rhizosphere selects fungal communities suspected to be specifically adapted to this environment and having a potential role in plant nutrient uptake and cycling.  To assess the rhizosphere effect on the fungal communities, we will use molecular techniques to compare the fungal communities in soil, rhizosphere and the roots of Andropogon gerardii – a dominant warm season (C₄) grass in the tallgrass prairie.  To do this, A. gerardii plants will be grown in exclusion chambers that preclude invasion by non-target roots.  Whole plants with their roots and the adhering rhizosphere soils as well as the bulk soil not in direct contact with the roots will be subjected to nucleic acid extraction.  The substrate-inhabiting fungi will be PCR-amplified and the mixed populations of PCR amplicons will be cloned and sequenced.  Differences among the three substrates will be inferred from frequency and phylogenetic analyses of the communities detected in the three substrates.

Interactive Effects of Hydrology and Species Composition on Ecosystem Functioning of Intermittent Streams (Mentors: Dodds and Gido).  The consensus of general circulation models is that both frequency of precipitation events and drought occurrences are very likely to increase by the end of the 21st century. These changes in hydrology will greatly influence intermittent streams, which will either expand or contract during these extreme events. In 2003, we began a series of experiments that quantified how natural changes in hydrology interact with key biotic elements (i.e., strong interacting species) to regulate ecosystem function (stream metabolism) in intermittent prairie streams (i.e., Kings Creek on Konza Prairie). Specifically, we tested the interaction between flood frequency and stream minnows on ecosystem metabolism and nutrient retention in both experimental streams at Konza Prairie and in Kings Creek.  In 2006, we will build on this body of research.  Potential REU projects include an investigation of the specific roles of different species in regulating system processes, quantifying species interactions, developing methods to detect changes in stream metabolism and nutrient retention, and quantifying ecosystem processes across the longitudinal gradient of Kings Creek.  Data from these experiments will be used to help predict how prairie streams respond to future climate scenarios that may include changes in hydrologic variance and species composition.

Ecological Genomics of Soil Nematode Community Responses: Model and Non-model Approaches (Mentors: Herman, Blair and Todd). This research project will use native prairie microbial-feeding soil nematode populations sampled from the Konza Prairie Biological Station to link organismal responses to environmental change. Extensive genomic tools are currently available for one model species of soil nematode, C. elegans. Our group has shown that microbial-feeding nematode and bacterial communities differentially respond to altered disturbance regimes and nutrient enrichment (Jones et al. 2006a,b; Jones et al., submitted). We have modeled interactions in the lab and used transcriptional profiling to identify C. elegans candidate genes involved in bacterial interactions. Moreover, functional tests were used to determine which induced genes have the greatest impact in a changing bacterial environment (Coolon et al., submitted). REU students will be involved in two new exciting projects. One lab-based project will involve functional characterization of candidate genes identified in C. elegans and native species of nematodes. The second project will be field-based and will involve use of molecular methods to document and quantify specific microbial-nematode interactions.

Behavioral Ecology of Amphibians and Reptiles (Mentor: Horne).  There are a variety of species of herpetofauna on Konza Prairie with interesting behavioral traits for study.  My particular areas of interest that could generate good REU projects include the effects of mite parasitism on mate-choice behaviors in collared lizards, agonistic behaviors of Great Plains skink, visual territorial and courtship displays in cricket frogs, auditory courtship in chorus frogs, competition among tadpole species in temporary pools, and tail autotomy in glass lizards and skinks.  A non-herpetofauna behavioral project that could be very promising is the territorial and courtship behavior of dragonflies at local ponds.

Habitat Heterogeneity and Insect Diversity (Mentor: Joern).  Spatial heterogeneity in key vegetation attributes of tallgrass prairie develops in response to major ecosystem drivers (fire, grazing, climate and topography). Arthropod community diversity varies according to the degree of heterogeneity that results from such interactions.  This project will carefully measure arthropod community responses to spatial heterogeneity in response to (a) natural responses to influences of ecosystem drivers, and (b) experimentally developed heterogeneity in order to understand underlying mechanisms that link spatial heterogeneity of vegetation structure and species composition to its effect on species diversity in arthropods. Observational and manipulative studies of insect herbivores (primarily grasshoppers) will assess the role of nutrient acquisition rate, thermal characteristics of the habitat as they affect feeding and digestion, and risk from predators as it affects individual performance in the context of habitat heterogeneity. In this project, the student will work with a research team, develop individual experiments that address some or all of these factors, and then present results to the research group at Kansas State University.  This project has the potential of developing over more than one field season.

Ecotypic Variation and Functional Genetic Responses of an Ecologically Dominant Grass Under Natural and Reduced Precipitation: Genes to Ecosystem Response (Mentor: Johnson).  The overall goal of this research is to provide an integrative and mechanistic understanding (spanning from genetics to whole plant physiology to regulation of ecosystem function) of the response of the ecologically dominant prairie grass, Andropogon gerardii (Vitman), to natural and simulated changes in precipitation.  A. gerardii (big bluestem) represents the dominant species across a sharp precipitation gradient from 400 mm/yr in western Kansas to >1200 mm/yr in eastern Illinois.  We will use a common garden approach of reciprocally transplanted single and multiple source genotypes of A. gerardii established under ambient and reduced rainfall across a precipitation gradient to test whether ecotypes are locally or broadly adapted to climate variation, identify the extent of genetic diversity and functional genetic variation accounting for these putatively drought adapted phenotypes, and whether functional genetic variation scales to influence ecosystem processes through response of the dominant C4 grass species.  Thus, understanding the degree of and genetic basis for drought tolerance in A. gerardii across the precipitation gradient of tallgrass prairie and in response to reduced precipitation is needed to forecast the responses of prairie ecosystems to climate change a broad geographic area.  Potential REU projects include characterizing the ecophysiological response of ecotypes of big bluestem to drought under controlled environment conditions, and characterizing genetic diversity of source big bluestem populations across the geographic range of big bluestem.

Symbiosis Between Arabidopsis thaliana and Compatible Root-associated Endophytic Fungi (Mentor: Jumpponen).  Root-associated fungi are important determinants of many ecosystem functions because they control community dynamics, population dynamics, and net primary productivity of their host plants.  Mycorrhizal fungi are an abundant and relatively well-understood group of such mutualists.  However, our recent observations challenge the overwhelming abundance of the mycorrhizal root symbionts: non-mycorrhizal endophytes in Konza Prairie Long Term Ecological Research site equal or exceed the mycorrhizal fungi in abundance.  During experiments aiming to determine the plant host ranges of these endophytes, we discovered that at least two of the fungal endophytes form functional symbioses with Arabidopsis thaliana.  These symbioses, depending on the fungal individual, range from mutualisms increasing the host’s growth two- to four-fold to parasites and pathogens that may either significantly reduce host growth or kill seedlings. This finding provides a great experimental system: variation in A. thaliana responses to endophytes allows evaluation of the nature of these symbioses as well as determination of the mechanisms of the differential host responses.  We aim to take advantage of this unique and fortuitous mutualism to further our understanding of the function of root-associated symbioses.  In this REU project, we will compare a large number of fungal individuals in simple experiments in endophyte-inoculated plants are compared with non-inoculated control plants.  We expect to find an array of different host responses to con-specific fungi.

Speciation and the Rapid Evolution of Barriers to Fertilization in Crickets (Mentor: Marshall). Our recent research has focused on identification of the genes and proteins that underlie reproductive incompatibilities (e.g., fertilization success, sperm competition, egg-laying induction) among grassland crickets (Allonemobius socius complex) in North America. REU student projects will include gene-identification studies, fertilization experiments utilizing gene-silencing techniques, and field studies to assess gene flow of incompatibility alleles among nearby populations of conspecifics and other closely related species. Our research program offers a diverse training environment because REU students will be able to combine molecular techniques (e.g., proteomics, RNA and DNA techniques, and RNAi) with behavioral experiments in mating arenas, and field sampling of natural populations of crickets.

Genetic Basis of Adaptive Coloration in Garter Snakes (Mentors: Morgan).  Many pressing questions in medicine and agriculture require that we understand the evolution of traits that are affected by multiple genes. I study the evolution of color traits, which are the product of many genes, and ask how color traits evolve over geographic space and over relatively short time scales. Populations of garter snakes are known to show significant differences in color traits even when gene flow between populations is high, suggesting that selection is driving the evolution of snake color traits on a small geographic scale. The crucial question now is to understand this process in terms of the actual genes that underlie the traits of interest. I use molecular approaches, including candidate gene sequencing and AFLP analysis, to search for the signature of selection on particular genes as well as on a genome-wide basis. The project will involve both laboratory work (DNA and RNA extraction, PCR) and fieldwork (snake collection and tissue sampling).

Ecological Genomics of Adaptive Trait Variation (Mentor: Morgan).  Research in my lab is motivated by the fact that most species are subdivided into finite systems of subpopulations and that the pattern of phenotypic and genetic variation within and among populations provides crucial information about evolutionary processes in nature.  Determining the relative roles of diverse evolutionary processes in population differentiation and local adaptation has and remains one of the central questions in evolutionary biology.  My lab currently uses Drosophila melanogaster as a model system to address larger questions in evolutionary and ecological genomics.  These broad questions include what are the genes that underlie ecologically-relevant phenotypic variation?  What evolutionary processes have influenced (and currently influence) the molecular genetic variation at these functional loci?  And how does molecular variation in these loci and networks influence ecologically relevant phenotypic variation in nature?   Potential summer projects that fit under the umbrella of my lab include: a study that seeks to link the role of functional genetic variation to phenotypic variation via a candidate gene approach, a study documenting the presence or absence of standing level of functional genetic variation among locally adapted populations for thermal stress phenotypes, as well as project investigating the level of phenotypic differentiation and local adaptation among populations sampled along a latitudinal cline.  Each of these projects would involve a combination of whole organism and molecular genetic analysis.  No prior experience is necessary for success in these summer REU projects!

Plant Responses to Environmental Variability (Mentor: Nippert).  Our ability to predict future plant-environmental interactions is constrained by incomplete information of current plant responses to heterogeneity.  This summer we are going to establish permanent high resolution weather stations. Weather data will be used to investigate the role of local environmental variability on species coexistence and resource competition.  I will assist REU students in the development of a project to investigate the role of heterogeneity (both biotic and abiotic) on individual mechanisms, traits, and plant responses contributing to patterns of community structure and ecosystem processes.

Physiological and Genetic Variation in Switchgrass Populations (Mentor: Nippert). Panicum virgatum (switchgrass) is a dominant plant species within tallgrass prairie ecosystems.  Switchgrass is genotypically and phenotypically diverse, and commonly exhibits broad adaptation to a range of environmental conditions.  During the summer 2008, we will plant rhizomes collected from 4 tallgrass prairie locations (S. Dakota, Kansas, Oklahoma, and Texas) in an outdoor mesocosm facility on Konza.  Using this common-garden approach, a REU student will examine the physiological and genetic differences among and between populations of switchgrass.  Ecological and evolutionary differences in these populations will provide a better understanding of potential climate change effects on switchgrass, as well as broader impacts for the tallgrass prairie ecosystem driven by the responses of a dominant plant species.

Landscape Ecology of Avian Vocal Culture (Mentor: Parker).  Many songbirds show distinct patterns of vocal culture, often referred to as song dialects. However, we know almost nothing about how ecological processes influence song dialects (or any aspect of avian culture).  Dr. Parker has been studying vocal culture in the Dickcissel, a songbird of the Great Plains, for the past 3 years.  Previous REU students on this project have demonstrated that neighboring birds share song types, and that similarity in song between birds is a function of distance – most birds within 500 m or 1 km of each other tend to be very similar, but birds several km apart show less (or even no) song similarity, and birds 10 km apart typically do not sound like each other at all.  This coming summer, the goal is to explain the substantial variation in the effects of distance on song sharing by linking the distribution and quality of habitat with Dickcissel population variables (such as site fidelity and density).  REU students will capture, band, and re-sight birds, record songs, and analyze sound recordings.

Ecology of Large River Fishes in the Great Plains (Mentors: Paukert).  Large rivers in the Great Plains offer a diverse fish community that has evolved to become established in these harsh conditions. However, many of these rivers are now imperiled because of anthropogenic causes, which have altered habitat, flow regimes, and fish community composition (including invasive species). The REU project would likely focus on the ecology of fishes in the Kansas River, a large prairie river located near Manhattan, Kansas, and complement current graduate student research on large river fish ecology and science in the region. Possible projects may include habitat selection/use of native and non-native fishes, current and historical changes in large river fish communities, anthropogenic effects on the population dynamics (e.g., abundance, growth, year class strength) of large river fishes (e.g., shovelnose sturgeon, blue sucker, channel catfish, or others). Data from these projects would further our understanding of the effects of anthropogenic alterations on large river fishes.

Investigating Avian Mating Systems with Molecular Markers (Mentors: Sandercock and Wisely). Molecular tools have provided new insights into avian reproductive strategies, including extra-pair mating by males and intraspecific nest parasitism by females. Most studies of avian mating systems have been based upon terrestrial songbirds, but patterns of parentage may differ in other lineages of birds. This REU project will use behavioral and molecular methods to investigate the mating system of the Upland Sandpiper (Bartramia longicauda), a grassland bird of conservation concern. Results from an 8-year field study suggest that the social mating system is monogamy, with a low incidence of mate-switching and social groups other than mated pairs. Sandpipers will be radio-marked, eggs will be collected and hatched in artificial incubators, and blood samples will be collected from all birds. In the lab, DNA will be extracted from blood samples, birds will be sexed with molecular markers based on the CHD-gene, and each family group will be genotyped with six optimized microsatellite markers. REU students will be jointly mentored by a behavioral ecologist (Sandercock) and a conservation geneticist (Wisely). The combination of field and laboratory activities will provide interdisciplinary research opportunities, and project results will inform management efforts for a migratory bird.

Effects of Grazing and Burning on the Community Dynamics of Butterflies in the Tallgrass Prairie (Mentor: Sandercock).  Konza Prairie Biological Station is subdivided into 60 or so management units that are exposed to a range of different burning and grazing treatments.  The effects of these land use practices on plant, grasshopper and bird communities are fairly well understood, but prairie butterflies have been a neglected component of the consumer communities.  Species lists are available for Konza Prairie and for Kansas, but detailed population studies have not yet been conducted. Elsewhere, butterflies are useful indicator species for evaluating the ecosystem health of natural areas.  In this project, the REU student will develop standardized methods for assessing grassland butterflies across a range of experimental habitats that span the range of vegetative structure found in natural and managed grassland ecosystems.  Species richness will be estimated with new mark-recapture models for estimation of occupancy rates, corrected for the probability of detection.  Relative abundance will be estimated with transect survey methods.  This project has the potential to provide useful baseline information that will aid conservation efforts for degraded native tallgrass prairie sites elsewhere in the Flint Hills. 

Ecological Genomics of Grassland Plants (Mentor: Ungerer).  Research in my laboratory is focused primarily on evolutionary and ecological genomics in plants. We use a combination of molecular, statistical, and ecological approaches in an attempt to better understand the origin of new plant species and how existing species evolve to become better adapted to their environment. Currently, there are two different research foci in the lab. The first seeks to understand the genetic basis of ecologically and evolutionarily relevant phenotypic variation in members of the plant family Brassicaceae (the mustard family) and how natural selection acts on this variation. We are currently using the model plant species Arabidopsis thaliana for this work because of the tremendous genetic and genomic resources available. The second focus seeks to understand genome structure and evolution in wild sunflower species. Two different sunflower projects are currently underway. The first examines the forces governing the amplification and evolution of retrotransposons (genetic elements related to viruses) in sunflower species of diploid hybrid origin. The second project examines the genomic consequences of allopolyploidization (the doubling of genome size following interspecific hybridization).

Life History Variation in a Perennial Sunflower (Mentors: Ungerer and Morgan).  Species with broad geographic ranges typically exhibit considerable within-species variation in morphology, physiology, and development.  This variation is often most pronounced along environmental gradients (e.g., latitudinal and/or altitudinal) where differences in climatic factors can result in strong natural selection for ecological divergence.  Traits that exhibit such patterns of variation represent excellent phenotypes for studies of adaptive evolution, especially when phenotypic differences among populations can be linked functionally to diverse environments and selection pressures.  We are investigating population level differences in life history characteristics in a perennial sunflower (Maximilian sunflower) across a broad latitudinal range from Texas to Manitoba, Canada.  Populations from different geographic regions exhibit striking differences in germination rates, developmental rates, and flowering time that are consistent with climate differences of their places of origin.  A combination of approaches is being employed to examine these ecologically relevant differences in further detail.  REU projects include detailed phenotypic characterization of population-level differences via common garden experiments and/or population genetic analysis of clinal variation using molecular markers.

Clinal variation in freezing tolerance in Arabidopsis thaliana (Mentor: Ungerer). The model plant Arabidopsis thaliana is found over a broad geographic range. We have documented remarkable latitudinal variation in the freezing tolerance of Arabidopsis. Plants from northern populations are more tolerant of low temperatures than plants from southern populations. Our findings suggest a major role for natural selection in shaping variation among wild populations. We will investigate the underlying genetic and physiological basis of natural variation in freezing tolerance by examining functional variation in important candidate genes. We will examine variation in global metabolite and lipid profiles because our ongoing work has indicated that metabolites play an important proximate role in the development of improved freezing tolerance in individual plants. The latter set of experiments will utilize the Kansas Lipidomics Research Center at K-State.

Environmental Factors Controlling the Dynamics of Archaea Communities in Grassland Ecosystem (Mentors: Welti, Jeannotte, and Blair). Archaea are a component of prokaryotic communities not only in extreme environments but also in natural soils.  The presence of Archaea as well as the environmental factors that regulate their populations in a grassland ecosystem such as the Konza tallgrass prairie are not documented up to now.  An interesting feature of Archaea is their specific ether polar lipids that could be used as biomarkers to trace them in the environment.  We propose a project in which an REU student will study, using a signature lipid biomarker approach, the dynamics of Archaea populations and the environmental factors (water manipulation, fire, aboveground diversity, nitrogen and phosphorus inputs, etc.) that control them in the Konza tallgrass prairie.  The REU student will be involved in the design of the experiment in collaboration with other K-State researchers using the experimental plots at the Konza Prairie research station, the development of a quantitative mass spectrometry method that will be used to profile Archaea lipids in soil, to sample the relevant experimental plots, to extract soil lipids and analyze them by mass spectrometry. 

Soil Algae in the Konza Prairie Grassland Ecosystem (Mentors: Welti, Jeannotte, and Blair).  Soil algae perform important functions in terrestrial ecosystems: transformation of inorganic nutrients into organic molecules by their photoautotrophic nutrition, food source for bacteria and invertebrates, production of biological active molecules that will affect other components of soil biota.  Algal biomasses in soils ranges from 0 to 108 cells per gram of soil.  Algal communities are sensitive to type of vegetation, soil properties, climatic conditions and other environmental factors.  However, algae are understudied in soil ecosystems compared to bacteria and fungi.  Previous studies on soil algae mainly used culture-based method and taxonomic identification.  Recently, specific lipid biomarkers have been extensively studied and used to trace algae in aquatic ecosystems.  We propose a project in which an REU student will participate in the development of a signature lipid biomarker method that will allow to profile algal communities and to better understand the environmental factors (water manipulation, fire, aboveground diversity, nitrogen and phosphorus inputs, etc.) that control algae in tallgrass prairie.  The student will be involved in the design of the experiment in collaboration with other K-State researchers using the experimental plots at the Konza Prairie research station, in the development of a quantitative mass spectrometry method that will be used to profile algal lipids in soil, to sample the experimental plots, to extract soil lipids, analyze them by mass spectrometry.

Molecular Characterization of Grassland Soil Ecosystem by Mass Spectrometry (Mentors: Welti, Jeannotte, and Blair).  We would like to offer the opportunity to a student that is interested in interfacing biochemistry and ecology in order to understand the functioning of a grassland ecosystem like the Konza tallgrass prairie.  Living and non-living pools of organic matter are short and long-term memory of what happens to an ecosystem.  We want to offer the opportunity to an REU student to develop a research project that will target the molecular characterization of soil biota and-or non-living organic matter in the Konza in response to environmental factors (water manipulation, fire, aboveground diversity, grazing, nitrogen and phosphorus inputs, etc.) using mass spectrometry tools.  We will assist the student in the elaboration of the project, in the laboratory and field work to realize it. This is an unique opportunity to be trained in mass spectrometry applied to understand soil ecological processes.

Disease Dynamics in Wild Populations of Carnivores (Mentor: Wisely).  To understand the altered epizootic potential of rabies in the Midwestern United States due to urban and suburban development, we are constructing a model of human exposure risk based on ecological parameters of the host species, striped skunk (Mephitis mephitis), and current and predicted anthropogenic changes.   As a first step towards model development, we are comparing habitat use, survival, and fecundity of striped skunks in urban and rural habitats.   REU students would help to trap skunks in the town of Manhattan, assist in radio-tracking collared skunks both on Konza prairie and in Manhattan, and work with gathered data to estimate the number of susceptible animals and habitat-specific encounter rates in each environment.

Parasitic Hymenoptera of the Prairie (Mentor: Zolnerowich). The order Hymenoptera accounts for approximately 75% of all insect parasites.  Food chains that involve green plants, insect herbivores, and parasites contain more than half of all known metazoan species.  Hymenopterans that act as predators or parasites interact with more species of insect prey than any other order of insect in terrestrial habitats.  Chalcidoidea is one of the most diverse groups of Hymenoptera known, with 20 families and over 18,000 species in 1,900 genera worldwide.  Because they are parasites of other insects, chalcidoids represent an important trophic level in ecosystems.  However, despite their impact on the environment and their ability to regulate host populations, the chalcidoid fauna remains poorly known and baseline studies of natural enemy communities for many areas are lacking.  The project is an excellent fit for an REU student and will include sampling various watersheds with different colored pan traps, sorting and curating samples, identification of taxa, analysis of data, and digital photography of specimens.