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• W3021890906 endingPage "105938" @default.
• W3021890906 startingPage "105938" @default.
• W3021890906 abstract "DNA-SIP (DNA-based stable isotope probing) is increasingly being employed in soil microbial ecology to identify those microbes assimilating the 13 C/ 15 N labelled substrate. Isopycnic gradient centrifugation is the primary experimental process for conducting DNA-SIP. However, diverse centrifugal conditions have been used in various recent studies. In order to get the optimum conditions of centrifugation for DNA-SIP, centrifugation time (36, 42, 48, 60 h), speed (45,000, 55,000 rpm) and the initial buoyant density (1.69, 1.71, 1.725 g ml −1 ), as were used extensively in related studies, were tested in this experiment with the Vti 65.2 rotor. DNA with either 13 C-labelling or unlabelled was extracted from a paddy soil pre-incubated with either 13 C-labelled or natural abundance glucose. After ultracentrifugation, the gene abundance of bacterial 16S rRNA, fungal 18S rRNA, bacterial and archaeal amoA within the fractioned DNA was detected. The results showed that centrifugation for 48 h was enough for the DNA to reach stabilization in the CsCl solution. The initial density of the mixed solution was best adjusted to 1.71 g ml −1 to ensure that most of the genes were concentrated on the middle fractions of the density gradient. Increasing the centrifugation speed would increase the density gradient of fractions; therefore, 45,000 rpm (184,000 g) was recommended so as to obtain the more widespread pattern of DNA in the centrifugal tube. We hope these findings will assist future researchers to conduct optimum ultracentrifugation for DNA-SIP. • Optimal centrifugation conditions for DNA-SIP of soil sample were explored. • Centrifugation for 48 h was enough for DNA equilibrium with the Vti 65.2 rotor. • The optimal initial buoyant density for DNA-SIP is 1.71 g cm −3 . • Low centrifuge speed was better for widespread of DNA in gradients." @default.
• W3021890906 created "2020-05-13" @default.
• W3021890906 creator A5018892762 @default.
• W3021890906 creator A5071067099 @default.
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• W3021890906 date "2020-06-01" @default.
• W3021890906 modified "2023-09-25" @default.
• W3021890906 title "Optimizing ultracentrifugation conditions for DNA-based stable isotope probing (DNA-SIP)" @default.
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• W3021890906 doi "https://doi.org/10.1016/j.mimet.2020.105938" @default.
• W3021890906 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/32360380" @default.
• W3021890906 hasPublicationYear "2020" @default.
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