Understanding complex Earth systems is challenging for scientists and students alike, because of the characteristics (e.g. bifurcations, self-organization, chaotic response) that are associated with these systems. This research integrates two research strands which contribute to the scientific and pedagogical understanding of complex Earth systems. In the first strand, a method that characterizes volatile organic compounds (VOCs) as ecological proxies of soil microbial ecosystems was validated. Unlike other measures of microbial community structure (e.g. Biolog and FAME), VOCs are advantageous because they are non-destructive and can provide temporal and spatial data. Additionally they are rich sources of information that describe the microbial metabolism, community structure, and organic carbon substrates utilized by soil microorganisms. Statistical results indicate that the detected and identified VOCs were significant (p < 0.05) indicators of microbial community composition shift in soil microcosm studies. Geographical information systems (GIS) illustrates that VOCs varied with space and time in south Texas soils. The second strand focuses on a geoscience education study exploring student conceptual model development of complex Earth systems. The efficacy of multiple representations and inquiry was tested as the pedagogical strategy in upper and lower level undergraduate courses to support students’ conceptual model development of complex Earth systems. Comparisons in student performance were based on prior knowledge (low and high) and on exposure to the implemented pedagogy (control and experimental groups). Results indicate that an inquiry-based learning model coupled with the use of multiple representations had significant positive performance impacts on students’ conceptual model development and content knowledge. This dissertation model integrates science and education research and is particularly useful for graduate students who intend to pursue a career in academia and envision teaching as part of their professional duties. It allows for synergy between teaching and research to be achieved where the classroom becomes a laboratory for research. Ultimately, the research conducted in the classroom informs pedagogy and enhances scholarship. Graduates learn to bridge the gap between education and science departments where they become leaders in science who conduct cutting-edge scientific research and also value making a broader impact on society through enhancing public education.