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bioRxiv · 10.1101/2020.06.11.147595

Simple Assay, Kinetics, and Biochemical Trends for Soil Microbial Catalases

Chabot, M.·Morales, E.·Cummings, J.·Rios, N.·Giatpaiboon, S. A.·Mogul, R.
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Abstract

In this report, we expand upon the enzymology and biochemical ecology of soil catalases through development and application of a simple kinetic model and assay based upon volume displacement. Through this approach, we (A) directly relate apparent Michaelis-Menten terms to the catalase reaction mechanism, (B) obtain upper estimates of the intrinsic rate constants for the catalase community [Formula] and moles of catalase per 16S rRNA gene copy number, (C) utilize catalase specific activities (SAs) to obtain biomass estimates of soil and permafrost communities (LOD, ~104 copy number gdw-1), and (D) relate kinetic trends to changes in bacterial community structure. This model represents a novel approach to the kinetic treatment of soil catalases, while simultaneously incorporating barometric adjustments to afford comparisons across field measurements. As per our model, and when compared to garden soils, biological soil crusts exhibited ~2-fold lower values for [Formula], [≥]105-fold higher catalase moles per biomass (250-1200 zmol copy number-1), and ~104-fold higher SAs per biomass (74-230 fkat copy number-1). However, the highest SAs were obtained from permafrost and high-elevation soil communities (5900-6700 fkat copy number-1). In sum, these total trends suggest that microbial communities which experience higher degrees of native oxidative stress possess higher basal intracellular catalase concentrations and SAs per biomass, and that differing kinetic profiles across catalase communities are indicative of phylum and/or genus-level changes in community structure. For microbial ecology, therefore, these measures effectively serve as markers for microbial activity and abundance, and additionally provide insights into the community responses to exogenous stress. ImportanceThe efficient management of oxidative stresses arising from environmental pressures are central to the homeostasis of soil microbial communities. Among the enzymes that manage oxidative stress are catalases, which degrade hydrogen peroxide into oxygen gas and water. In this report, we detail the development and application of a simple kinetic model and assay to measure catalase reaction rates and estimate soil biomass. Our assay is based upon volume displacement, and is low-cost, field-amenable, and suitable for scientists and educators from all disciplines. Our results suggest that microbial communities that experience higher degrees of native oxidative stress possess higher basal intracellular catalase concentrations and specific activities when expressed per biomass. For microbial ecology, therefore, these measures serve as biochemical markers for microbial activity and abundance, and provide insights into the community responses to exogenous stress; thereby providing a novel means to study active microbial communities in soils and permafrost.

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Chabot, M., Morales, E., Cummings, J., Rios, N., Giatpaiboon, S. A., Mogul, R.. 2020-06-12. Simple Assay, Kinetics, and Biochemical Trends for Soil Microbial Catalases. https://doi.org/10.1101/2020.06.11.147595

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