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Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

 

The promotion of global sustainability within environmental science courses requires a paradigm switch from knowledge-based teaching to teaching that stimulates higher-order cognitive skills. Non-major undergraduate science courses, such as environmental science, promote critical thinking in students in order to improve the uptake of scientific information and develop the rational decision making used to make more informed decisions. Science, engineering, technology and mathematics (STEM) courses rely extensively on visuals in lectures, readings and homework to improve knowledge. However, undergraduate students do not automatically acquire visual literacy and a lack of intervention from instructors could be limiting academic success. In this study, a visual literacy intervention was developed and tested in the face-to-face (FTF) and online sections of an undergraduate non-major Introduction to Environmental Science course. The intervention was designed to test and improve visual literacy at three levels: (1) elementary—identifying values; (2) intermediate—identifying trends; and (3) advanced—using the data to make projections or conclusions. Students demonstrated a significant difference in their ability to answer elementary and advanced visual literacy questions in both course sections in the pre-test and post-test. Students in the face-to-face course had significantly higher exam scores and higher median assessment scores compared to sections without a visual literacy intervention. The online section did not show significant improvements in visual literacy or academic success due to a lack of reinforcement of visual literacy following the initial intervention. The visual literacy intervention shows promising results in improving student academic success and should be considered for implementation in other general education STEM courses.