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bioRxiv · 10.1101/2025.06.27.661829

Internal DNA standards for Isopycnic Centrifugation of Environmental DNA in Quantitative Stable Isotope Probing

Schwartz, E.·Hayer, M.·Mau, R.·Hungate, B. A.·Blazewicz, S. J.·Allen, M.·Morrissey, E. M.·Tripathi, B.·Pett-Ridge, J.
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Abstract

Element assimilation rates or the DNA replication rate of microbial taxa can be measured in environmental samples through quantitative DNA-stable isotope probing (DNA-qSIP). Here, we introduce a set of DNA standards that may be used to quantify the density of DNA extracted from environmental samples after isopycnic centrifugation. The standards are approximately 9 Kbp PCR products with either isotopically enriched (98 atom% 15N, 13C) nucleotides or natural abundance nucleotides and have densities that differ by 0.051 g/mL. The internal standards were tested in a DNA-qSIP analysis of bacterial populations in soil exposed to 63 atom% H218O, performed in two different laboratories with different equipment and protocols. While fractionation results, including number of fractions taken and differences in density between adjacent fractions, between the two laboratories were different, the internal standards allowed the two data sets to be compared, and both research groups found similar Excess Atom Fraction (EAF) of oxygen-18 in the DNA of bacterial taxa. These internal DNA standards allow direct comparison of DNA-qSIP results from different experiments regardless of operator, tracer enrichment levels, protocol or equipment used and can support the creation of a large global database that contains qSIP results from many different laboratories. ImportanceDNA-qSIP is an important technique in microbial ecology that allows the growth and nutrient assimilation rates of microbial taxa, including those that have not yet been cultured, to be measured. Growth and assimilation rates are extremely variable parameters in microbial ecology because most of the microbial community is dormant and inactive, which complicates linking microbial populations to ecosystem processes. DNA-qSIP is increasingly practiced in a range of laboratories, using different equipment, isotopes, substrates, and protocols, making comparison of results among different research groups challenging. Here we describe the development of internal standards, 2 pieces of DNA with different isotopic content and hence buoyant density, that can be added to environmental DNA before isopycnic centrifugation. Our results show the internal DNA standards allow DNA-qSIP results to be compared across laboratories and could contribute to the formation of a large DNA-qSIP database that contains growth or nutrient assimilation rates of microbial taxa from many different experiments.

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Schwartz, E., Hayer, M., Mau, R., Hungate, B. A., Blazewicz, S. J., Allen, M., Morrissey, E. M., Tripathi, B., Pett-Ridge, J.. 2025-06-29. Internal DNA standards for Isopycnic Centrifugation of Environmental DNA in Quantitative Stable Isotope Probing. https://doi.org/10.1101/2025.06.27.661829

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