Nontraditional EEB/MAPS REU student studies the effect of climate and land use on methanotrophic communities

Carrie Spanton

      This summer the Kansas NSF EPSCoR OIA-1656006 RII Track-1: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS) and the Department of Ecology & Evolutionary Biology (EEB): Research Experience for Undergraduates (REU) program at the University of Kansas (KU) have partnered to support three summer REU students. Through this collaboration, Carrie Spanton has been working with MAPS researcher, Terry Loecke on a project titled The effect of climate and land use on methanotrophic communities.
     Carrie is not your typical summer REU student. She grew up in Kentucky and lived in New Orleans for 20 years. She was living in New Orleans when hurricane Katrina hit in 2005. For Carrie, the hurricane was a trans-formative event and heavily influenced her decision to go back to school. Because the hurricane had stripped away everything she had once known and possessed, it left her thinking, "who am I?" All the things she thought defined her were suddenly gone.  Although the hurricane experience was devastating, she said “It was really liberating” too, because the ordeal gave her a chance to rediscover herself and the “guts to go back to school.”
     Kansas City is now Carrie's home, and she attends Metropolitan Community College at Penn Valley (MCCKC).  In addition to her studies, she is the president of Phi Theta Kappa, a prestigious honor society for two-year college students, and has been involved in the MCCKC Women on the Move program. She is also a Supplemental Instructor for an Ancient History/Biology community learning class, an active member of Project Success, a weekly volunteer at the food pantry, and a volunteer at North Kansas City Hospital Hospice.  Carrie stays active in student government and plans to start tutoring in the fall. Biology and Environmental Science became a focal interest for Carrie after she met her MCCKC mentor and biology instructor, Terry Davin. It was his teaching style that encouraged her to become a scientist and to apply for the KU summer EEB REU program.

Samples from the research

    As an EBB REU participant, Carrie has felt a sense of community with her cohort and has especially loved learning "how to conduct research." Learning research methodology from her REU mentor, Terry Loecke, she says, "has been life-changing." Carrie describes their REU research project as follows: "As global temperatures and net population simultaneously rise, so does the demand for food production.  The overall impacts of different land use management practices on the net global warming potential remain largely unknown.  Methane is a critical greenhouse gas that is both emitted and consumed by microbial communities in soil, contributing to climate change. We used a full fractal design experiment to measure how soil moisture and the addition of nitrogen, which is widely used as fertilizer, effect methane oxidation (consumption) in soils.  We used soil samples from east and west Kansas of agricultural land, post-agricultural land, and native prairie land to add varying moisture and nitrogen treatments.  We added methane to these treatments then took four samples sets at varying times."

     According to Carrie, this REU experience has positively "pushed her out of her comfort zone."  She has loved learning new things and “how to think like a scientist.”  She further commented, “I have watched my skill sets grow.... As a non-traditional student, I didn't know what I was capable of when I first started school.  Having this kind of support as I grow as a professional has been life-changing.  I have learned that I can, actually, really do this.” On a more personable note, she says her favorite part of this summer experience has been "showing my 16-year-old son what kind of opportunities are out there and getting him excited about his future.  He's my inspiration and my drive.” As for her future plans, Carrie plans on continuing her studies and staying in academia. This experience has also taught her what kind of “mentor/leader/researcher/instructor" she would like to be one day, and she hopes "to pass on this gift that others have given" to her.

Carrie will present her research findings at the 2018 EEB REU Poster Session, July 27, 2018.

Workforce Development, Education and Outreach funding for the Summer MAPS EEB 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 grant'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.

"Kansas Farmers" exhibit to open August 11, 2018 featuring photos from KS NSF EPSCoR Research Collaboration

     The Spencer Museum of Art on the University of Kansas (KU) campus will be hosting an exhibit titled Kansas Farmers beginning August 11, 2018 through January 6, 2019.  This exhibit highlights fifty photographs taken by artist and Distinguished Professor of Photography in the School of Art, Design, and Creative Industries at Wichita State University, Larry Schwarm.
     In 2010, Dr. Schwarm began a collaboration with Kansas NSF EPSCoR researchers involved in the RII Track-1 Award OIA-1656006  titled Phase VI Climate Change and Energy: Basic Science, Impacts, and Mitigation.  The collaborative project, titled Bio-fuels and Climate Change: Farmer’s Land Use Decisions, was a sub-project of the Track 1 Award. This particular study examined farmers decisions related to climate change, water availability and bio-fuel market opportunities.  The research team created a database on land use, water use, climate and weather, water availability, surface water quality and bio-fuel markets and used this data to identify the driving factors behind a farmer’s land and water use decisions.  Photographs taken by Larry Schwarm were integrated into the study and added to the database to provide the visual imagery associated with farmers' decisions.  The exhibit will showcase these fifty photographs illustrating the realities of contemporary farm life in Kansas.

     This collaboration also produced a 2018 book that features the photos taken during the research project titled Larry Schwarm: Kansas Farmers. The book includes an essay detailing the Kansas NSF EPSCoR research written by Dr. Dietrich Earnhart, an economics professor and director of the KU Center for Environmental Policy, and the photographs that will be presented in the exhibit.  The essay discusses the core themes of the Phase VI award that addressed farmer land use decisions, climate change, and bio-fuel prospects.  The photographs capture the legacy of Kansas farmers' independent spirit and raises awareness of how much is at stake as the farming communities of Kansas look to their future.

Kansas Teachers Conduct Field Research and Write Lesson Plans at The 2018 Ecosystems of Kansas Summer Institute

Teachers participate in field research and write related lesson plans to take back to their home schools.

     As part of the Microbiomes of Aquatic, Plant and Soil Systems (MAPS) across Kansas outreach initiatives, high school biology teachers from across the state the participated in the The 2018 Ecosystems of Kansas Summer Institute at the University of Kansas (KU) Field Station on June 4-8, 2018.  Eleven high school teachers were invited to attend.  The teachers participated in activities related to Aquatic and Terrestrial Ecosystems and Geographic Information Systems (GIS).  Prior to the workshop, teachers selected Aquatics, Terrestrial or GIS as an area of interest they wished to focus on for the week. University of Kansas (KU) MAPS faculty Helen Alexander, Jim Bever, and Peggy Schultz; Kansas Biological Survey faculty and staff, Jerry DeNoyelles, Ted Harris and Dana Peterson; UKan Teach faculty Steve Obenhaus and Michael Ralph; and Sarah Abeita, a biology teachers at Free State High School , led field activities, facilitated group discussions, and guided lesson planning.
     Each day began with a whole group field or water activity at either the KU Field Station or at the Free State High School Prairie Restoration Project, and was followed by afternoon breakout sessions focusing on the teachers’ area of interest.  The goal of each focus group was to create Next Generation Science Standards (NGSS) biology lessons and experiments that connected the teacher’s curriculum with MAPS current research.  Teachers were then asked to share their lessons with colleagues from across the state through in-service opportunities or by creating blog posts on the Kansas Association of Biological Teachers website. The institute also provided the opportunity for teachers to apply for funding to purchase the supplies needed to implement the lessons at their home campuses.  Faculty focus group leaders will continue to work with the teachers throughout the 2018-2019 school year by visiting schools and Skype conferencing.
     As for the comments on the overall Institute experience, one teacher said, “I loved the connections, both with teachers and facilitators, the most. The arrangements were well planned and organized.” Another teacher added “I think that it was fun to learn from the professors and understand what kind of research is being done.” All the teachers thought the morning field and aquatic activities were the highlight of the Institute.  In addition, teachers were asked to reflect on their focus group experience and one teacher commented “My focus group was great. The facilitators always were asking what WE wanted to get out of the experience,” and another shared, our focus group “came up with a great experimental design and all of the members in my group added their own twist or expertise.”  One teacher summed up the whole institute experience by saying, “I very much appreciated the flexibility … [the institute] … offered to allow us to choose our own professional development whilst also directing us to the relevant research they do. It was a transformative experience.”

Workforce Development, Education and Outreach funding for the Ecosystems of Kansas Summer Institute is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The grant'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.

REQUEST FOR PROPOSALS KANSAS NSF EPSCoR MAPS - Research & Education Innovation (REI) Awards - In Microbiome Research

Kansas NSF EPSCoR is announcing a funding opportunity for REI Awards in the area of microbiome research. REI Awards are for small projects that will either allow for networking and planning or for the immediate pursuit of larger projects for developing new transformational concepts. These are awarded for both research and education, given their close relationship. These awards are in the same spirit as and share goals with NSF EAGER (Early Concept Grants for Exploratory Research) awards, for high risk/high gain research ideas.

The current RII Track‐1 award funding REI Awards is titled Microbiomes of Aquatic, Plant and Soil Systems across Kansas (MAPS). Broadly, MAPS’ mission is to elucidate how microbiomes interact within native and agriculturally dominated aquatic, plant, and soil habitats, leveraging the steep precipitation gradient across Kansas as a means of projecting system response to environmental change. Only projects with research in areas that are related to the current Kansas NSF EPSCoR focus of microbiomes as broadly construed to be in aquatic, plant and/or soil systems are eligible for REI Awards.

Any individual with PI status at Kansas State University, University of Kansas, Wichita State University, Emporia State University, Fort Hays State University, Pittsburg State University or Washburn University.

Submission Deadline:
Proposals due by 5:00 pm on Friday,
June 29, 2018.

For More Information and to download RFP; Timeline Example; and NSF EPSCoR Budget Form go to: 

Kansas NSF EPSCoR
Research & Education Innovation (REI) Awards RFP 
Timeline Example

The source of funding for REI Awards is Kansas NSF EPSCoR, which receives its funding from the current National Science Foundation Established Program to Stimulate Competitive Research (EPSCoR) Research Infrastructure Improvement (RII) Track-1 award (OIA-1656006). Matching support is provided by the Kansas Board of Regents (KBOR) and the participating universities.

Free NSF Webinar to highlight NSF Funding Opportunities to Broaden Participation in STEM

The National Science Foundation Directorate for Education and Human Resources (EHR) is hosting a

FREE Webinar 

on June 14, 2018 from 1:00-3:30 pm ET 

The Webinar will feature and discuss current funding opportunities available at NSF aimed at broadening participation in science, technology, engineering, and mathematics (STEM) and targeting underrepresented groups and Minority Serving Institutions. Funding opportunities for programs like NSF INCLUDES, ADVANCE, LifeSTEM, IUSE, ITEST, GRFP and many others will be highlighted. NSF Program Officers and Staff from all four EHR Divisions will be represented.

Divisions include:

• Division of Research on Learning 
• Division of Graduate Education 
• Division of Undergraduate Education
• Division of Human Resource Development 

In addition, Q & A opportunities with Program Officers will be provided during the webinar.

Administrators, faculty, researchers, evaluators, and other STEM education leaders working to broaden participation in STEM in formal and or informal contexts are encouraged to attend.

Please register here as soon as possible 

Once you have registered, help spread the word about the webinar by forwarding this link to your STEM & broadening participation in STEM networks.

Kansas Students travel to Nebraska for the 2018 Women in Science Conference

     Eight Kansas high school students and their teachers from Topeka and Lawrence traveled to the University of Nebraska to attend the 20th Annual Women in Science Conference held April 6-7, 2018.  The conference was for students who want to meet and network with career and academic professional women in science. The attendees also had opportunities to interact with current female science undergraduate and graduate students as well as other high school girls interested in science.  In addition, the conference provided the students with the opportunity to discover and learn about professions in biology, geology, engineering, food science, computer science and various professions in the medical fields. Dr. Dayanna Patera, an  Internist with the Nebraska Internal Medicine PC, was the keynote speaker. 
     On Friday night at the banquet, the students listened to Dr. Patera and then Kansas had the opportunity to visit with current biomedical engineering students.  Saturday's agenda included hands-on activities at the Nebraska Union and lab activities at the Bead Center.  Some of the activities the Kansas students participated in were programing an EV3 robot to dance, building virus models, extracting plant and animal DNA, infect a tobacco leaf with bacteria, gram stain bacteria and practice sampling and organizing scientific data sets. 

     Marci Leuschen, a teacher from Free State High School in Lawrence, KS said "the graduate students leading the activities in the labs were encouraging and positive role models." One of her students, Lydia, commented "Personally, I thought the conference was such an amazing learning opportunity to meet other Women in the science fields that are so incredibly passionate. I enjoyed everything." And another student, Riddhi, said "The conference was a great experience!  It helped me discover professions that I had no idea existed before.  I was able to find professions that interest me and that can help me narrow in my search of personally interesting jobs as a future career."  Marci Leuschen shared, "The girls all came away from the conference energized about scientific research."

Education and outreach funding for the physics teacher workshop was provided by the Kansas and Nebraska NSF EPSCoR Track 2 Grant #1430519 titled: "Imaging and Controlling Ultrafast Dynamics of Atoms, Molecules, and Nanostructures."  The grant's 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 atomic/molecular/optical science.

Kansas NSF EPSCoR Announces MAPS First Award Recipients for 2017-2018

     Kansas NSF EPSCoR has awarded five assistant professors from institutions across the state to receive up to $100,000 in support of their research on topics that focus on Microbiomes of Aquatic, Plant and Soil Systems.  The purpose of the EPSCoR First Award Program is to assist early career faculty to become competitive for funding from the research directorates at the National Science Foundation.  It is designed to encourage early career faculty to submit proposals to NSF and accelerate the pace of the research as well as improve the quality of their subsequent proposals.  Any individual tenure track faculty member who is of the rank of assistant professor, currently untenured, has not received a prior First Award from another EPSCoR or EPSCoR like program in KS, and is or has not been a principal investigator on any research grant funded by a federal agency is eligible to apply. The 2017-2018 recipients are: Dong Lin, Colby Moorberg and Prathap Parameswaran from Kansas State University; Ali Eslami fromWichita State University, and Cuncong Zhoong from the University of Kansas.  Listed below are the award recipient submitted abstracts that summarize their proposed research.

Dong Lin  KSU

3D Printing Biomimetic and Hierarchical Wood Structure for Endosphere Microbiome Study

     Plants are regarded as superorganisms that rely on microbiomes for functions and traits. On the other side, plants feed the microbial community and influence their composition and activities. Nowadays, nanomaterials have been widely used in scientific research and everyday usage. The research about the influence of nanomaterials to the human-related microbiome has been intensively conducted, however limited attention has been paid to the plant based microbiome. Cellulose is the major composition of plant matter, and the most abundant organic and bio-degradable polymer on Earth. This research will focus on preparing cellulose/nanomaterials, including nanoparticles, carbon nanotubes, and aerogels, in order to study their effect on various bacteria. The cellulose/nanomaterials will be mixed and then subjected to freeze casting suspension. The materials will then be processed using the decomposition method to study their interaction with decomposed bacteria.

 Colby Moorberg  KSU

Quantifying the Impact of Weather Whiplash on Roots and Hyphae with an Automated Minirhizotron Camera System 
   
     Root exudation and turnover are primary soil carbon and energy sources for the rhizosphere microbiome. Plants are the interface between the atmosphere and the soil. Thus, plant stress from weather and climate events drive rhizosphere microbiome responses to stress. Current imaging technologies impede high-temporal-resolution root dynamics data. Minirhizotrons are commonly used for in situ monitoring of roots, and allow non-destructive tracking of root metrics overtime. However, high minirhizotron camera cost ($18,000+) and poor root-soil contrast prevent automated imaging and analysis. I propose to develop an inexpensive minirhizotron camera system using off-the-shelf computers (Raspberry Pi) and components to facilitate permanent camera deployment, high-temporal-resolution imaging, and automated image analysis using machine visioning. Experiments will complement work described in section 4.3.c.1.1 of the MAPS research proposal. Primary goals are to i) examine how weather whiplash impacts short-term (hours) and long-term (months) root dynamics, and ii) assess how root dynamics affect carbon inputs.

Prathap Parameswaran  KSU

Smart adaptation of enriched microbiomes in Recovered Nutrient Products (bio‐fertilizers) from anaerobic wastewater treatment to the native soil 

     Anaerobic Membrane Bioreactors (AnMBRs) are emerging as a viable option for municipalities and agro-businesses for energy positive wastewater treatment with simultaneous recovery of valuable nutrients (Nitrogen, Phosphorus) and water for indirect potable reuse. A pilot scale Anaerobic Membrane  Bioreactor (AnMBR) operated by the team including me at Ft. Riley, KS treating 1000 gallons per day of wastewater has consistently achieved these goals. More specifically, anaerobic microbial communities have been shown to vary in predominance with time and season, in the organic biosolids and inorganic nutrient product fractions from AnMBRs. The central hypothesis of the proposed research is that wastewater enriched microbial communities present in land applied nutrient products from the AnMBR will integrate with the soil microbiome to beneficially regulate the N and P release rates as well as the transformations of these two nutrients in the top soil layers. Understanding the transport and proliferation of these microbiomes can be achieved through plant uptake studies and field plot experiments. This research is very relevant to the current Kansas NSF EPSCoR program on microbiomes with a strong focus on the unexplored topic of microbiome interactions between the engineered/built environment such as wastewater treatment based bioreactors and the natural soil microbiome.

Ali Eslami  WSU

A Study of DNA Mutations through Error Control
Coding Theory

     Living beings, in particular, microorganisms, rely on DNA mutations for their evolution. Changes in the DNA sequence could be a result of random events such as DNA replication errors, or a result of intentional alterations introduced by genetic engineering. A similar phenomenon occurs in telecommunications when sequences of information are transmitted over a noisy channel, introducing multiple random errors. To overcome this problem, communication engineers “encode” each sequence before transmission, giving them the ability to correct errors later in the receiver. This is called “Error Control Coding”, a well-established area in communications, which started in 1948 and has been perfected over time. There are immense functional similarities between the DNA correction mechanisms in microorganisms and the error control techniques used in telecommunications. This research exploits these similarities and combines statistical methods with the powerful toolbox of algebraic error control coding to understand the behavior and evolution of microorganisms.

Cuncong Zhong  KU

Transforming Metagenomic Sequencing Data
Analysis with Scalable Assembly and Comprehensive Annotation

     The proposed research seeks to develop a series of computational methods and software for the analyses of metagenomic sequencing data. The proposed methods include de novo assembly methods with reduced computational requirement and enhanced parallelism, which facilitate the reconstruction of the metagenomes from huge-volume metagenomic datasets such as those collected form soil. They also include a series of annotation methods that improve the gene-calling, non-coding RNA discovery, gene cluster finding, and functional categorization of metagenomic data. Finally, novel phylogenetic reconstruction methods are also proposed to take advantage from the drastically improved annotation sensitivity and accuracy. The proposed methods can be directly applied on metagenomic and/or metatranscriptomic sequencing data generated from microbiome samples that are collected from environments such as aquatic, plant and/or soil systems.


Workforce Development, Education and Outreach funding is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: "Microbiomes of Aquatic, Plant, and Soil Systems across Kansas."  The grant'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.