University of Oregon
Microbes are vital to every ecosystem on Earth and contribute to fundamental ecological roles including primary production, organic matter decomposition, and symbiotic relationships. Microbes also impact the entire biosphere through metabolic processes that collectively control global biogeochemical cycles.
As a Microbial Ecologist, my research is focused on the ecological role of microbial communities, especially regarding shifts in microbial diversity, expression of metabolic genes, and the production of enzymes and metabolites in response to environmental change.
My work is highly integrative, combining biochemistry, microbiology, and ecology from the molecular to the ecosystem scale. My past studies employed the extensive application of state-of-the-art molecular biology techniques including metagenomics, metatranscriptomics, and metabolomics, combined with more than a decade of field, laboratory, and bioinformatics experience.
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.
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.
GitHub: Repository
RPubs: Rendered Code
GitHub: Repository
RPubs: Rendered Code
GitHub: Repository
RPubs: Rendered Code
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.