Karthik Anantharaman, assistant professor in the Department of Bacteriology, and Thea Whitman, assistant professor in the Department of Soil Science, were recently selected to receive National Science Foundation CAREER awards. These are the NSF’s most prestigious awards in support of early-career faculty who have the potential to serve as academic role models in research and education and to lead advances in the mission of their department or organization. Details about their funded projects are below.

CAREER awards, presented once each year, include a federal grant for research and education activities for five consecutive years.

Karthik Anantharaman, assistant professor in the Department of Bacteriology
Scalable approaches for systems virology

Viruses are the most abundant biological entities on Earth and are keystone components of environments and microbiomes whose contributions have mostly been overlooked. Understanding viruses is critical to the study and applications of microbiomes in diverse fields such as agriculture, medicine, biotechnology, ecosystem science, oceanography and biogeochemistry. In spite of this recognized importance, computational tools for studying viruses are lacking compared to similar tools for other microbes like bacteria. To that end, the goals of this project are to develop new machine learning-based approaches for the study of viruses and their ecology. The project has the potential to transform the study of microbiomes and the field of viral ecology by maximizing information gained from viruses and elucidating their roles in nature. The current SARS-CoV-2 epidemic is projected to vastly increase student interest in STEM and specifically, virology in the coming years. In parallel, there is an increasing demand for a workforce adept in bioinformatics and data science approaches in biology. The project aims to advance the development of a talented, educated, and skilled workforce and increase participation of underrepresented minorities and first-generation college students in STEM. The project will also increase literacy of virology and data science across K-12 and undergraduate education through teacher-training workshops & course-based undergraduate research experiences (CUREs) at the interface of bioinformatics, data science, and virology.

This project will develop algorithms and bioinformatic tools to enable the study of uncultivated viruses from mixed communities with little to no biases (bacterial/archaeal/eukaryotic, DNA/RNA, lytic/lysogenic). The goals of the project are to develop new genome and protein databases and machine learning approaches to identify viruses; network-based frameworks for reference-free prediction of viral hosts; and network and statistical approaches for determination of viral taxonomy and estimates of genome completion. These methods will be validated using simulated and real-world metagenomics and metatranscriptomics data and formalized through the development and release of open access databases and software. The approaches will be applied to study viral ecology of deep-sea hydrothermal ecosystems, and the role of viral infections in impacting nutrient cycling in the oceans. Additionally, the project will also enable investigation of fundamental questions in viral ecology governing the roles of viruses in diverse microbiomes and environments such as soils, human health, freshwater, and marine systems. Two CUREs will be developed in virus cultivation and bioinformatics, respectively, using novel interactive education approaches including blended learning, and are expected to reach in excess of 1000 students. A teacher-training workshop “Viruses in nature” will be conducted to train K-12 biology teachers (especially from rural and underrepresented communities). The workshop will develop lesson plans, and hands-on laboratory activities that integrate concepts of virology and bioinformatics into teaching units on biology. For more information visit: https://github.com/AnantharamanLab/NSF_CAREER.

Thea Whitman, assistant professor in the Department of Soil Science
Developing a Fire Ecology Framework for Soil Bacteria

Wildfires cause major ecological as well as economic disturbances. They are increasing in frequency and severity in many regions of the world and burn hundreds of millions of hectares of land every year. The burned landscape results in large losses of carbon and nitrogen from ecosystems. Microorganisms in the soil play a critical role in the recovery of wildfire-affected ecosystems through their roles in cycling nutrients and their interactions with plants. The ecological impacts of wildfires on plant life are somewhat understood. This is not the case for soil microbes. The goal of this NSF CAREER project is to develop a fire ecology framework for bacteria, to improve understanding of why certain bacteria are “pyrophilous” – i.e., why they thrive following exposure to fire. The approach will draw on field research on northern forest wildfires and controlled prairie burns, laboratory experiments, and genetic sequencing. At its core, improving our understanding of bacterial response to fires will help underpin our understanding of how fires and changing fire regimes will affect the climate, an issue of great societal importance. This project will realize a myriad of broader impacts through its education goals, which are tightly integrated with each research goal. Undergraduates will be trained in the lab throughout the grant, working with the University of Wisconsin-Madison Undergraduate Research Scholars program, which will help support full participation of women and members of underrepresented groups in STEM fields. A podcast about fire ecology, developed in collaboration with undergraduates in the Life Sciences Communication program, and a new public outreach booth, “What happens belowground during a fire?”, will both help increase public scientific literacy and engagement with science and fire ecology.

The proposed research will build on the PI’s prior results to strengthen and integrate a trait-based understanding of bacterial responses to fire. The overarching hypothesis is that fire survival will be most relevant shortly after wildfires (~1 year), fast growth will be relevant over longer timescales (~5 years), and pyrogenic organic matter degradation will be relevant over longer periods of time (~10 years). The first theme will address the patterns and traits of pyrophilous soil bacteria. In seeking to determine which bacteria and genetic characteristics are associated with burned soils, the research team will add a ten-year timepoint to a current one- and five-year timepoints in a 40-site wildfire field experiment, building toward what will ultimately become a long-term field study of boreal forest wildfires. In addition, the research team will apply an untargeted metagenomics-based approach at multiple time points to characterizing post-fire functional potential. Part of the proposed approach to strengthening a fire ecology framework for bacteria lies in experimentally investigating bacterial fire response through its separate components, such as heat tolerance. The second theme focuses on the interactive effects of temperature and drought on bacterial survival and post-fire carbon (C) mineralization. The approach will use laboratory experiments with bacterial isolates, intact soil cores, and gas flux tracing to determine the temperature ranges that pyrophilous bacteria can survive and whether prior drought stress affects bacterial survival of high temperatures and influences post-fire C mineralization rates. The third theme will aim to develop an integrative understanding of fire ecology for soil bacteria. Here, the research team will draw on current and emerging datasets and cross-domain collaborations to determine the relative importance of different traits in determining post-fire success of pyrophilous bacteria over time and across burn severities. Studies will compare how the traits that make bacteria successful fire-responders correspond to (or contrast with) equivalent strategies in other organisms. Overall, the project will advance our understanding of fundamental questions about the effects of fire on bacteria – critical players in post-fire ecosystem recovery. Undergraduate training will be coupled with mentorship training for a PhD student and a research technician, helping them become better future educators, themselves. To help support a globally competitive STEM workforce, the PI will develop new metagenomics tutorials for soil microbiology courses, which will provide cutting-edge bioinformatics skills to students. These tutorials will be developed with a postdoctoral researcher, who will also participate in UW-Madison teaching workshops, further helping to improve both STEM education and educator development.