NSF-FUNDED GRADUATE POSITIONS AT KANSAS STATE UNIVERSITY IN MICROBIOMES OF AQUATIC, PLANT OR SOILS (MAPS)

     The Division of Biology at Kansas State University is recruiting diverse, highly-qualified graduate students to assist with understanding the linkages among microbiomes of aquatic, plant and soil (MAPS) ecosystems across the state ofKansas. 

The goal of MAPS is to understand:

1. How microbiome structure and function among these systems change across the precipitation gradient of Kansas and land use, and 
2. How those changes in microbiomes affect broader community and ecosystem properties. In all, the integrated and collaborative NSF-funded project is driven by >15 investigators, all of whom work collaboratively and train students in an interdisciplinary framework.

     If you are interested in developing skills in collaborative, team-based science focused on deploying cutting-edge tools in environmental microbiology and informatics, please contact the listed individuals who might serve as your graduate advisor. Students must discuss their interests with a potential advisor (by email or by scheduling a phone conversation by email) prior to submitting an application. 

• For Biology see https://www.k-state.edu/biology/grad/why.html; 
• For Agronomy see http://www.agronomy.k-state.edu/graduate/admissions/index.html; 
• For Plant Pathology see https://www.plantpath.k-state.edu/graduate/application-information/index.html).  We encourage students with experience in bioinformatics, molecular ecology, microbiology, field work and experimental design to apply. Experience working across multiple ecosystems or across environmental gradients will be preferred but not required.

Applications due by 

15 December for Fall or Summer 2019 start.

MAPS NSF Award information: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1656006

Agronomy:

• Chuck Rice (Soil Microbiology; http://www.agronomy.k-state.edu/people/faculty/rice-charles/)

Biology:

• Walter Dodds (Aquatic Ecology; http://www.k-state.edu/doddslab/)
• Ari Jumpponen (Fungal Ecology; https://www.k-state.edu/biology/people/tenure/jumpponen/index.html)
• Sonny Lee (Metagenomics, bioinformatics; http://www.k-state.edu/biology/people/tenure/stmlee)
• Thomas Platt (Microbial Evolution; http://www.platt-lab.com/)
• Lydia Zeglin (Microbial Ecology; https://www.k-state.edu/biology/people/tenure/zeglin/index.html)

Plant Pathology

• Sanzhen Liu (Bioinformatics; http://www.plantpath.k-state.edu/people/faculty/liu/)

Workforce Development, Education and Outreach funding for these MAPS graduate positions is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The award's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems

UIUC Actuarial Science major runs simulations to predict host infections in bird populations of the Hawaiian archipelago during KU REU

Megan Resurreccion

     Last spring, Megan Resurreccion met with her informatics adviser at the University of Illinois Urbanna-Champaign (UIUC) to discuss going to graduate school. During this meeting, she was encouraged to obtain research experience, so she decided to apply to a summer research experience for undergraduates program (REU). Megan specifically wanted a research experience that offered any kind of mathematical or statistical focus. In making her decision for where to apply, she commented, “Biology isn't normally my thing, but I wanted to see what computational work in that field was like.” Her search led her to a mathematical modeling project offered through the 2018 Ecology and Evolutionary Biology (EEB) summer REU program at the University of Kansas (KU) and supervised by Dr. Folashade B. Agusto, Assistant Professor in the EEB department at KU and part of the research team for the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas.

Her poster describing her study and results 

   
    Megan titled this project, Effects of Breeding Phenology on Avian Malaria Transmission Model. She described her research and her findings as follows: “In the Hawaiian archipelago, there is an infectious disease called avian malaria which has been affecting many native Hawaiian birds, transmitted by southern house mosquitoes. Simulations were run in Matlab to predict what total host infection rates of a bird species was based on differing breeding phenology (seasonality). The breeding phenology refers to the various times of year that the birds and mosquitoes had their breeding seasons in, so a single bird peak breeding season was estimated and compared with five other mosquito peak breeding seasons. The temporal distance between a mosquito breeding season and bird breeding season was then used to predict the infection rate. This was also tested in terms of low and high elevation since infection rates have been known to differ at various levels. The results concluded that when the mosquito breeding season was later than the bird breeding season, total host infection rates were higher. Then a simulation for differences in low and high elevations were run. For low elevations, total host infection rates were at their highest regardless of breeding phenology but were highest when the mosquito breeding season was before the bird breeding season. For high elevations, total host infection rates were highest when the mosquito breeding season was later than the bird breeding season. The importance of this is that it's important to preserve the biodiversity of the Hawaiian archipelago, and conservation measures should be implemented depending on when total host infection rates were. Our findings indicate a higher rate of total host infection at lower elevations than at higher elevations. Additionally, total host infection rates are higher when vector breeding season peaks occur after the breeding season peaks of native Hawaiian birds. Conclusively, based on the breeding season peak phenology, there should be measures taken to protect Hawaiian bird species since avian malaria is a prominent reason for population decline in these birds. If not, the population decline and potential extinction of bird species can have drastic effects on the biodiversity of the Hawaiian archipelago.”

     Megan said the best part of the summer research experience was “getting to know the undergraduates, learning what their research was about, and what kind of possibilities for research are out there, even if it isn't something I tend to explore more in depth.” She added that she also learned what it takes to conduct research such as “reading up on related literature, writing up a paper, running trials, fixing errors” and working in a lab.
     Currently, Megan is a student at the UIUC majoring in actuarial science and minoring in mathematical statistics, informatics, and creative writing. She also works as a Resident Advisor in University Housing at UIUC. In addition to her studies and work, Megan is a member of the Actuarial Science Club and is looking forward to serving as a Mathematics Ambassador for the UIUC Department of Mathematics. As for her future plans, Megan would like to attend graduate school for a masters or Ph.D. in statistics, and eventually pursue a career in the realm of statistics and data science.

MAPS investigator, Dr. Walter Dodds, receives the KSU Karen Ann Griffith Research Award

Karen Ann Griffith, Dr. Walter Dodds, Dr. Amit Chakrabarti

    Dr. Walter Dodds, University Distinguished Professor of Biology at Kansas State University (KSU) and co-principal investigator leading the aquatics team for the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS), has received the Karen Ann Griffith Research Award. He will be honored at a reception on October 10, 2018 from 4:00 pm to 5:30 in the Tadtman Boardroom of the KSU Alumni Center. This award has been granted to Dr. Dodds for his interdisciplinary research related to Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 and for connecting faculty from Biology, Agronomy, Plant Pathology and Geology in this collaborative research effort. Dr. Amit Chakrabarti, Dean of the KSU College of Arts and Sciences will deliver remarks. 

KU MAPS researchers receive NSF ERA award to examine soil properties in response to climate change using math models

Dr. Pam Sullivan and Dr. Sharon Billings
KU

   Dr. Pam Sullivan, Assistant Professor, Geography and Atmospheric Science, and Dr. Sharon Billings, Professor of Ecology and Evolutionary Biology and Senior Scientist, Kansas Biological Survey, at the University of Kansas (KU) have received an NSF Earth Sciences grant award to study the changes of soil properties in response to climate change. The title of their project is RAISE-SitS: Designing models to forecast how biogeochemical fluctuations in soil systems govern soil development, terrestrial water storage and ecosystem nutrient fluxes (NSF EAR #1841614).
     The researchers will develop new mathematical models to study the causes of changing soil structures and examine plant-soil-water responses to varying environmental conditions.  These new “models will allow the effects of soil structure fluctuations on ecosystem processes to be evaluated at diverse spatial and time scales,” and “may improve forecasting of future availability and quality of water resources, soils, and associated ecosystem services.” More specifically, the “soil ecosystem models (empirical and process-based) will be developed at multiple spatial scales to link soil structure and function in order to enhance the prediction of water and biogeochemical fluxes on timescales of decades to centuries. These models will be parameterized using soil, plant, and aquatic microbiome data collected across a strong precipitation gradient in the central USA (part of NSF Kansas Established Program to Stimulate Competitive Research, EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas) and continental-scale soil databases (e.g., the National Cooperative Soil Survey Soil Characterization Database, United States Department of Agriculture)."These models will also create and make available community tools to examine nutrient fluxes produced by soil, water and biogeochemical feedback, with an ultimate goal of addressing "nationwide problems such as managing the nitrogen cycle and the Gulf of Mexico dead zone" as well as “test climate driven changes in the soil fabric which prompt the emergence of integrated terrestrial responses that are more rapid than typically considered.”

For more information go to NSF EAR #1841614
And KU today 9/17/18

(Quotes in the article taken directly from the NSF EAR #1841614 award abstract)

MAPS REU student studies soil microbial communities in the tallgrass prairie

Lauren conducting field work,
working in the lab,
 and showing a soil sample

    Lauren Chartier has a broad interest in science, particularly Biology, but when she took an Environmental Science course, she became intrigued with soil science. It was her interest in studying microbe communities in soil systems that led her to apply for the Kansas NSF EPSCoR  RII track 1 OIA # 165006: Microbiomes of Aquatic, Plant and Soil systems across Kansas (MAPS) summer research experience for undergraduates (REU) offered at Kansas State University (KSU). Lauren was primarily interested in the KSU REU program because the research opportunity "tied microbiological and soil science to climate change." She liked the idea of conducting research that addressed issues related to "the acceleration of natural global climate change." So when offered an opportunity to work with Dr. Charles Rice, Distinguished Professor of Agronomy at KSU who specializes in soil microbiology, and who is the Co - Principal Investigator leading the soil systems investigation team for the MAPS project, she eagerly accepted it.

Some results from Lauren's study

      The title of Lauren’s study is the Impact of Drying and Re-wetting Cycles in Microbial Communities in the Tallgrass Prairie, and she describes her project as follows: “My research investigated the short-term effects of drying and re-wetting cycles on soil microbial communities.  Previous research done at the Konza Prairie Biological Station suggested that there might be a long-term, “legacy effect”, on microbial activity and biomass due to moisture variation in the grasslands.  However, new data is indicating that there is no legacy effect, so I investigated a 30 year-old experimental plot in Konza to take a closer look at what may be causing similarities between microbial groups. I tested the carbon dioxide concentration, fatty acid biomarkers, inorganic nitrogen, and soil mineral composition in correlation with microbial activity and development to determine whether there really is or is not a legacy effect and what short-term effects might be present.”
     Acquiring a new perspective for soil science and for graduate school was the best part of the experience for Lauren.  More specifically, she explained, “I gained clear and hands-on exposure to the life and level of performance in graduate schools, while learning about the dynamic and interdependent connections between soil, microbes, plants, and animals.” In addition, she said “I enjoyed learning how to perform the tests used to analyze soil microbes and various characteristics of soil health, but the fascinating thing is those tests can translate into many other scientific fields of study. I learned that in soil science, there is no clear-cut answer to anything. Conditions that apply in one place may not apply in another and the differences may be slight to drastic variations.”
     Lauren is from Williamsburg,VA and is currently a student at the University of Mary Washington (UMW) in Fredericksburg, VA. She is majoring in Biology with a minor in Environmental Science. In addition to her studies, Lauren is a Representative for the Honors Class of 2020, the Secretary of the Biology Student Association (BSA), and Co-Captain of the UMW Women’s Rowing Team. Once she completes her bachelor’s degree, she plans to pursue a master’s degree in an environmental field and possibly earn a PhD. As for her future career plans, Lauren commented, “Ultimately, I would like a career working outdoors with a focus on conservation, or in a field that protects people and nature from the negative repercussions of accelerated climate change.”

Workforce Development, Education and Outreach funding for the MAPS KSU summer REU program is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The award's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems

MAPS Researchers awarded NSF Earth Sciences Award to study Biochemical Drivers of IETs from iron reducers to methanogens

Matthew Kirk and Lydia Zeglin
KSU

     Two Kansas State University (KSU) researcher team members working on the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant and Soil Systems across Kansas (MAPS) project have received a NSF Earth Science award to explore Biogeochemical drivers of interspecies electron transfer from iron reducers to methanogens. Through this study, Matthew Kirk, Assistant Professor of Geology at KSU and a memeber of the MAPS soils focus group, and Lydia Zeglin, Assistant Professor of Biology at KSU and and a member of the MAPS aquatic focus group, will “1) identify environmental drivers that push interactions of methanogens and iron reducers between competition and interspecies electron transfer (IET), determine how changes in interactions between methanogens and iron reducers affect methane generation, and 3) evaluate the coupled role of enzyme properties and environmental chemistry in determining the nature of interactions.”  To address each of these goals the researchers “will integrate the results of bioreactor experiments with dynamic enzyme modeling.” The findings of the study “will create a roadmap for evaluating the environmental significance of IET between iron reducers and methanogens by defining an environmental context for this interaction,” as well as provide tools to better understand “the ecological underpinnings of the global methane cycle.”

For more details and information on this award go to: NSF EAR: #1753436
(Quotes in the article taken directly from the NSF EAR: #1753436 award abstract)

KS-LSAMP student studies agrobacterial genetic diversity

 

Veronica collecting samples from the Konza Prairie

     Veronica Mateo, a recent graduate of Dodge City Community College  (DC3) in Dodge City, Kansas, considers the well being of animals her passion. She commented, "Ever since I was a child I would find myself tending to the care and needs of my family pets." Caring for animals and knowing she could impact their lives was the main reason she decided to pursue an Associate’s degree in Wildlife Biology. Once she graduated, she knew she wanted to continue her education at Kansas State University (KSU).  So, she was excited to learn that during her transition to KSU, she had an opportunity to participate in the Research Immersions Pathways to STEM (RiPs) program.
     The RiPs program is a summer research experience offered by the Pathways to STEM: Kansas Louis Stokes Alliance for Minority Participation (KS-LSAMP) at KSU that provides students with a unique opportunity to work with faculty and conduct independent research. LSAMP is a National Science Foundation (NSF) program that recruits, supports, and encourages underrepresented minority students to pursue baccalaureate degrees in Science, Technology, Engineering and Math (STEM) fields. The KS-LSAMP RiPs program is specifically for Kansas community college students who intend to transfer to KSU or who are current KSU sophomores and juniors with no prior research experience.
     This summer, Veronica's research interests expanded to include the plant microbiology associated with ecosystems. She explained that because “Plants play a huge role in an animal’s ecosystem, the type of research I am interested in deals with plant pathogens.” Dr. Thomas Platt, Assistant Professor of Biology at KSU and a member of the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas plant systems research team, was her mentor. Veronica titled her project, the Degree of Agrobacterial Genetic Diversity within an infected plant and describes her research project as follows: “Agrobacterium tumefaciens are generally found in the root environment of the plants known as rhizosphere. Because interactions among different strains can influence pathogen dynamics, we aimed to determine the degree of agrobacterial diversity co-occurring on a single host. A typical diseased plant will harbor a gall or tumor on the crown. The samples were collected from Konza Prairie. We plated the samples collected onto a semi-selective media to identify and isolate biovar 1 agrobacteria seen as black, shiny colonies. We then used a biochemical test, then streak purified and preserved 360 isolates from these plants so that we could characterize the phenotypic and genetic attributes of the agrobacteria present. We used PCR to amplify and subsequently sequence the recA locus of the isolates from the infected sunflower to determine if the infected plant was colonized by one or several agrobacterial genotypes. We used a phylogenetic analysis that includes representatives of all 11 of the known genomovars of A. tumefaciens to determine which group or groups of agrobacteria were present. In the future we would like to determine if co-occurring genotypes significantly impact each other’s fitness. However, we are currently troubleshooting the recA locus at the moment.”

Veronica, Dr. Platt
and colleagues

     When asked what she learned from her KS-LSAMP RiPs experience, Veronica said, “Previously, I had never conducted actual research. The lab experience is definitely different from my science experience at the community college or even high school. You don’t always get the results right away, and you will be let down sometimes. However, that is science. We have to learn from our mistakes and analyze what went wrong. This research taught me, overall, about what a research lab experience is and how to be patient.” Her favorite part of the summer experience was working in the lab and meeting the people associated with Dr. Platt’s lab. She added, “When I had any issues or questions I did not hesitate to ask them and having that resource made it an enjoyable experience.”
     Veronica is from Dodge City, Kansas, and is currently a junior majoring in Biology at KSU. While studying at KSU, she plans to continue her research in Dr. Platt’s lab. As for her future plans, she said, “My career plan is to apply to the Veterinary program here at Kansas State University over the summer of 2019 and someday work in an environment surrounded by animals.”

Workforce Development, Education and Outreach funding for the KS-LSAMP  program is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The award's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems