Sikes Microbial Lab​
People
Benjamin (Ben) A. Sikes
I spent a formative semester in the Florida Keys as an undergraduate and the rest is history. I've worked on lobster vision, pollination and invasion, population genetics and restoration. I went belowground for my PhD (University of Guelph) to study mycorrhizal fungi and succession and haven't come up since. Since completing my grad work, I've worked on soil fungi in restoration (Smith Fellowship at UT-Austin) and the accumulation of pathogens in non-native New Zealand plants (Bioprotection Research Centre). A ton of fantastic people have helped me get this far including (but certainly not limited to): David J. Fox, Diego Vazquez, Dan Simberloff, Jim Fleming, Steven Travis, John Klironomos, Hafiz Maherali, Christine Hawkes (UT), Eric Menges (Archbold Biological Station), Doria Gordon (TNC-UF), Richard Duncan ​and Phil Hulme.
I'm currently a full professor and senior scientist in Microbial Ecology, cross appointed between the Department of Ecology and Evolutionary Biology at KU and the Kansas Biological Survey.
Kit Savoy
Kit is a PhD student and 2025-2029 Madison and Lila Self Graduate Fellow with a passion for space exploration. They are investigating the evolution and characteristics of interactions of fungal propagules with triboelectricity (i.e., static) in dispersal, deposition, and adhesion for applications in the construction of biological life support systems and extraterrestrial human habitats (e.g., spacecraft). They are also working to describe the response of soil crust microbiomes to space-like stresses (radiation and freezing).
Rashmi Liyanage
I am a master’s student in Ecology at the University of Kansas, originally from Sri Lanka. My research investigates how soil microbial communities, structured by prairie plant assemblages under contrasting rainfall regimes and varying levels of species richness and phylogenetic diversity, influence plant performance both above and below ground. I am particularly interested in understanding the microbial mechanisms that drive plant productivity and ecosystem function, with applications for ecological restoration and sustainable agriculture.
Holly Andres
Holly is a PhD student currently assisting with DNA sequencing of endosphere and rhizosphere soils and roots in support of the New Roots for Restoration/BII. She is exploring potential research directions focused on soil microbial ecology, plant–fungal interactions, and how fungi shape ecosystem resilience.
Malik Ali Zaidi Pons
My name is Malik A. Zaidi Pons, and I recently earned a B.S. in Biomedical Sciences from the Pontifical Catholic University of Puerto Rico. I am currently an NSF RaMP Scholar at the University of Kansas, where I focus on microbial ecology and stress response. My research investigates dormancy in arbuscular mycorrhizal (AM) fungi, with particular emphasis on the role of melanin transcription in spore viability and trade-offs under multiple stress conditions. This work is being developed to align with the goals and expectations of the NSF GRFP.
Outside the lab, I enjoy playing video games and staying active through pickleball.
Rigel Parker
Rigel is a second-year student at KU. He is majoring in microbiology and minoring in philosophy. His project is exploring how soil properties, microbes, and enzymes move across ecological edges beteeen prairie monoliths and surrounding degraded land uses. In his free time, he enjoys drawing, painting, and getting fancy about coffee.
Grace Francis
Grace is a second-year microbiology and biochemistry major at KU. Her project involves studying the effect of differently trained microbiomes on photosynthetic traits. In her free time, she enjoys running, baking, and exploring walking trails around Lawrence.
Abby Hout
Abby is a sophomore majoring in Microbiology. She is measuring hyphal density in response to different crop treatments. Additionally, she began an independent project to explore how exposure to lake water shapes sand microbiomes. When she is not in the lab or studying, she loves to spend time with her cat, Cardio.
Sikes Lab Fungal Foray (Fall 2023) at Breidenthal Tract, Baldwin Woods: Margot Lockwood, Tamar Kopadze, Dilshini Thathsarani, Josh Williams, Rigel Parker, Kaitlyn Savoy, and Ben.
Recent Sikes Lab Alums
Dilshini Sandanika Thathsarani
Dilshini is a Master's student who is exploring the response and function of soil microbial systems to plant diversity as part of the New Roots for Restoration BII. She is quantifying fungal hyphal density in response to different perennial cropping treatments, including intercropping. She is also measuring how plant root traits respond to microbial inoculum derived from plant prairie communities with increasing diversity and exposed to different rainfall over 5 years. Prior to joining the lab, Dilshini completed her honours degree in Plant Biotechnology at the University of Colombo in Sri Lanka. Her undergraduate project helped isolate and characterize heavy-metal tolerant microbes from serpentine soils.
Carlos Schwindt
Carlos completed his pre-med microbiology major at KU and is received a full scholarship to the Scholars in Rural Health program at KU Med. During his time in the lab, Carlos won a K-INBRE fellowship and several UGRAs which supported his COVID inspired work on the "mycobiomes" of masks. We are now finalizing this work for publication.
Theo (Thorbot) Michaels
Theo completed her PhD in Spring 2023 focusing on ecological paradigms in grassland restoration. Her main project explores nucleation and island biogeography in restoration. She moved large monoliths of prairie into sites with different land use histories. These monoliths are huge (1.27m diameter X 1.1m deep) and are either alone, or clustered into different patch sizes. The goal is to see what effect clustering and the background matrix of land use history has on the ability of these monoliths (their microbes and plants) to spread out or be invaded. Theo has a diverse set of experiences, with adventures in creative writing and applied ecology out in California. She is now a postdoctoral scholar at the University of Nebraska, Lincoln in the Center for Resilience in Agricultural Working Landscapes.
Dr. Jacob Hopkins - Postdoc at OSU in Bennett Lab
Jacob was a PhD student in the lab whose research focused on feedbacks between fire, plants and soil microbes. Jacob explored how fire alters microbial decomposition of fuels and shifts production of pyrogenic plant species. He was supported by a prestigious NSF Graduate Research Fellowship to study the mycorrhizal component and look at post-fire fungal succession with deep sequencing. Prior to coming to KU, he spent 4 years as an undergraduate in the Bever/Schultz lab at Indiana University. He has worked extensively on field and greenhouse experiments, many of which focused on AM fungi.
Paige Hansen - Ph.D. at CSU in Cotrufu Lab
Paige was an undergraduate then Master's student in the lab. Her Master's work explores how historical precipitation regimes and land use impact the communities of fungi and bacteria living at different soil depths. Her project is a key component of the MAPS-EPSCoR research and Paige was a Self Graduating Senior Fellow. As an undergrad, Paige pioneered the use of ddPCR to assess how fungal abundance changes in response to fire history, presenting her work at national conferences, and receiving both a UGRA and K-INBRE awards.
Dr. Thomas McKenna - Assistant Research Professor at KBS-CER
Tom has been an awesome postdoctoral researcher who led a major collaborative project with the Land Institute. The project seeks to maximize perennial crop diversity, soil management, and soil microbes in a shift to sustainable agriculture. Tom's work has been funded by the Perennial Agriculture Project Research Fellowship Program through the Malone Family Land Preservation Foundation. Tom's research has been very successful, and he's now an assistant research professor at KBS, starting to build his own lab. We continue to work closely together. Tom's has amazing prior research including native ecosystem restoration for the State of Hawaii; as a black bear technician for Sequoia and Kings Canyon, Three Rivers, California; and in prairie restoration for Applied Ecological Services, Baldwin City, Kansas. His PhD is from the University of North Dakota in 2016 where he worked with Kathyrn Yurkonis.
Dr. Tatiana (Tanya) Semenova - Analytical Development Scientist at WuXi Tech
After 3 fantastic years, Tanya recently moved on from her postdoctoral researcher position. Tanya has led the effort to sequence microbial communities (and fungi in particular) in response to fire, and how these changes may alter future fires. Apart from generating amazing data, doing incredible outreach, and publishing cool papers (more to come), she also was a model lab member. Her husband Don was a great friend to the lab and they had a lovely daughter, Evangeline, while in Lawrence. Tanya continues to work with us to analyze fungal responses to fire (as a KBS affiliate), and has taken a cool position in industry at at WuXi AppTec in Philadelphia working on pharmaceuticals. Tanya received her doctoral degree in the Netherlands (2016) on the impacts of climate change on soil fungal communities in arctic Alaska. Her undergraduate studies involved conservation of red-listed polypores in Finland, assessments of enzyme profiles in “fungus gardens” in Denmark, and purification of fungal peptidases in Russia.