University of Oregon
Microbes are vital to every ecosystem on Earth, from soils and oceans to the human microbiome, driving essential processes that sustain life. They play key roles in primary production, organic matter decomposition, nutrient cycling, disease prevention, and symbiotic relationships, while their collective metabolism shapes global biogeochemical cycles and influences the health of both the planet and its inhabitants.
As a Microbial Ecologist, my research examines the ecological roles of microbial communities, with a particular focus on how shifts in diversity, gene expression, and metabolic activity respond to environmental change. More recently, my work has expanded to include synthetic biology and bioinformatics approaches to explore microbial function and evolution in both natural and engineered systems.
My work is highly integrative, combining biochemistry, microbiology, and ecology from the molecular to the ecosystem scale. I draw on more than a decade of field, laboratory, and computational experience, applying tools such as metagenomics, metatranscriptomics, and metabolomics, as well as synthetic gene library design and high-throughput functional assays to investigate microbial processes and their broader ecological significance.
For the projects listed below, I investigated changes in microbial diversity and gene expression in response to water table decline in boreal peatlands, chronic nitrogen deposition in temperate forests, and permafrost thaw in Arctic tundra. For my postdoctoral studies, I investigated spatial differences in the metabolomic profile of Trichodesmium colonies in the Red Sea and elucidated how antibiotic resistance emerges within microbial communities given different evolutionary starting points.
MS thesis to investigate microbial diversity in boreal peatlands and the mechanisms regulating their enzymatic expression in response to water table decline and shifts in dominant vegetation.
Research on molecular and physiological responses of microbes exposed to chronic nitrogen deposition in temperate forests.
PhD dissertation on the microbial response to permafrost thaw in arctic tundra and how microbial diversity across tundra types affects the functional potential of the microbiome to degrade recently thawed soil carbon.
Postdoctoral studies to characterize how Trichodesmium and their epibionts center and dissolve iron-rich dust particles from the Red Sea using single colony metabolite profiling.
Postdoctoral studies on the emergence of antibiotic resistance using a community-wide approach that relies on the synthesis of large libraries of genes encoding antibiotic targets.
My teaching draws primarily upon the strengths of a discussion-based learning environment where students engage in conversation with their peers to deepen their understanding of the course content. My goal has always been to create a classroom environment in which students are encouraged to ask questions and critically evaluate evidence for topics as far ranging as the origins of life to the effects of human activity on global climate change.
This course is intended for students who plan to major in one of seven biology majors. It is open to anyone seeking a rigorous overview of the major themes in ecology and evolution.
*Teaching Excellence Award (2019)
This course surveys the evolution and interaction of physical, chemical, and biological processes; how past changes on Earth help us predict the future; and how fundamental principles of science establish the sustainability of human activities on Earth.
My research has been featured in a variety of podcast episodes, newsletter articles, and news stories, highlighting its impact on both scientific and public audiences. These include podcast interviews on the ecological implications of permafrost thaw in the Arctic tundra, newsletter features on microbial ecology and permafrost thaw, and popular science articles recounting a high school science teacher’s participation in Arctic climate change research through PolarTREC—a program connecting educators with field scientists to promote public understanding of polar research. More recently, media coverage of my Science Advances study has showcased my synthetic biology–driven antibiotic resistance research, which develops large biological datasets for machine learning to help predict and prevent resistant bacteria before they emerge. An Environmental Molecular Sciences Laboratory (EMSL) science highlight also featured my metabolomics work comparing metabolites in natural and cultured marine algae. These diverse platforms have broadened the reach of my work, fostering greater awareness of microbial processes and their significance in addressing global challenges.
University of Oregon Knight Campus News feature on my Science Advances study showing how my postdoctoral work could generate biological datasets for machine learning to predict and prevent antibiotic resistance before it emerges.
GEN news feature on my Science Advances study using synthetic metagenomics to uncover genetic drivers of antimicrobial resistance in the DHFR protein family.
Research highlight from the Environmental Molecular Sciences Laboratory (EMSL) on our single-colony mass spectrometry imaging study comparing metabolites in natural and cultured marine algae.
Season 2, Episode 3: "Microbes Reawaken" examines how long-dormant permafrost microbes resurface as ice melts, influencing the Arctic's climate response and the global carbon cycle.
Season 2, Episode 2: "Layers" explores permafrost's complex structure—its active layer, transition zone, and frozen core—and how these layers shift with rising temperatures.
Research highlight in the Toolik Field Station Winter 2024 newsletter describing how my doctoral research revealed a dramatic shift in permafrost microbial communities during thaw.
David Walker, a science teacher at the Liberal Arts and Science Academy in Austin, TX, joined scientists in the Arctic to study climate change as part of PolarTREC, a program linking educators with field researchers to raise public awareness of polar research.
As a Data Scientist, an essential component of my research is to develop a reproducible workflow when performing data analysis. In this section, I provide links to GitHub repositories and rendered code for each research project associated with a reproducible bioinformatic workflow. All data analyses performed in the following manuscripts can be reproduced to verify the published results using these workflows.
Science Advances: Paper
GitHub: Repository
RPubs: Rendered Code
EnvMicro: Paper
GitHub: Repository
RPubs: Rendered Code
Soil Systems: Paper
GitHub: Repository
RPubs: Rendered Code
FEMS: Paper
GitHub: Repository
RPubs: Rendered Code
Karl J. Romanowicz, Carmen Resnick, Samuel R. Hinton, Calin Plesa. (2025) Exploring antibiotic resistance in diverse homologs of the dihydrofolate reductase protein family through broad mutational scanning. Science Advances
Karl J. Romanowicz, Futing Zhang, Siyuan Wang, Dušan Veličković, Rosalie K. Chu, Yeala Shaked, Rene M. Boiteau. (2024) Single-colony MALDI mass spectrometry imaging reveals spatial differences in metabolite abundance between natural and cultured Trichodesmium morphotypes. mSystems.
Karl J. Romanowicz, Byron C. Crump, George W. Kling. (2023) Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost. ISME Communications.
Karl J. Romanowicz, George W. Kling. (2022) Summer thaw duration is a strong predictor of the soil microbiome and its response to permafrost thaw in arctic tundra. Environmental Microbiology.
Karl J. Romanowicz, Byron C. Crump, George W. Kling. (2021) Rainfall alters permafrost soil redox conditions, but meta-omics show divergent microbial community responses by tundra type in the Arctic. Soil Systems.
Louis J. Lamit, Karl J. Romanowicz, Lynette R. Potvin, Jay T. Lennon, Susannah G. Tringe, Rodney A. Chimner, Randy K. Kolka, Evan S. Kane, Erik A. Lilleskov. (2021) Peatland microbial community responses to plant functional group and drought are depth-dependent. Molecular Ecology.
Donald R. Zak, William A. Argiroff, Zachary B. Freedman, Rima A. Upchurch, Elizabeth M. Entwistle, Karl J. Romanowicz. (2019) Anthropogenic N deposition, fungal gene expression, and an increasing soil carbon sink in the Northern Hemisphere. Ecology.
Elizabeth M. Entwistle, Karl J. Romanowicz, William A. Argiroff, Zachary B. Freedman, Jeffrey J. Morris, Donald R. Zak. (2018) Anthropogenic N deposition alters the composition of expressed class II fungal peroxidases. Applied and Environmental Microbiology.
Karl J. Romanowicz, Donald R. Zak. (2017) Activity of an introduced earthworm (Lumbricus terrestris) increases under future rates of atmospheric nitrogen deposition in northern temperate forests. Applied Soil Ecology.
Louis J. Lamit, Karl J. Romanowicz, Lynette R. Potvin, Adam R. Rivers, Kanwar Singh, Jay T. Lennon, Susannah G. Tringe, Evan S. Kane, Erik A. Lilleskov. (2017) Patterns and drivers of fungal community depth stratification in Sphagnum peat. FEMS Microbiology Ecology.
*Karl J. Romanowicz, Zachary B. Freedman, Rima A. Upchurch, William A. Argiroff, Donald R. Zak. (2016) Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: the influence of pH and soil moisture.
FEMS Microbiology Ecology.
Karl J. Romanowicz, Evan S. Kane, Lynette R. Potvin, Randall K. Kolka, Erik A. Lilleskov. (2015) Understanding drivers of peatland extracellular enzyme activity in the PEATcosm experiment: mixed evidence for enzymic latch hypothesis. Plant and Soil.
Zachary B. Freedman, Karl J. Romanowicz, Rima A. Upchurch, Donald R. Zak. (2015) Differential responses of total and active soil microbial communities to long-term N deposition.
Soil Biology & Biochemistry.
Feel free to reach out for more information or to discuss the potential for collaboration.