Quantitative DNA data extracted from four different soils and two subsurface rock samples

Cite as:

Medina, Diego; Horstmann, Lucas; Ganzert, Lars; Oses, Romulo; Friedl, Thomas; Wagner, Dirk (2023): Quantitative DNA data extracted from four different soils and two subsurface rock samples. GFZ Data Services. https://doi.org/10.5880/GFZ.3.7.2023.001

Status

I N R E V I E W : Medina, Diego; Horstmann, Lucas; Ganzert, Lars; Oses, Romulo; Friedl, Thomas; Wagner, Dirk (2023): Quantitative DNA data extracted from four different soils and two subsurface rock samples. GFZ Data Services. https://doi.org/10.5880/GFZ.3.7.2023.001

Abstract

This data publication presents quantitative DNA data obtained through fluorometric detection of genomic DNA and the estimation of 16S rRNA gene copies using quantitative Polymerase Chain Reaction (qPCR). The data encompasses various soil and rock samples collected across a climate gradient. The DNA was extracted using a protocol enabling the separate analysis of intracellular DNA (iDNA) and extracellular DNA (eDNA) from the same sample. The primary objective of this study was to enhance a previously established method developed by Alawi et al. (2014) for analyzing terrestrial samples by introducing modifications to the extraction buffer.

Phosphate buffers at two different concentrations (120 mM and 300 mM), EDTA (300 mM), and a high-concentration phosphate buffer in combination with EDTA (300 mM each) were tested in conjunction with a detergent mix (detailed in Medina et al., 2023; submitted). Thorough tests, including spiked DNA experiments and cell counts, were conducted on one low biomass sample to validate the extraction setups. The two most effective extraction protocols were then applied to all samples from the four designated sites and compared with the phosphate buffer described by Alawi et al. (2014), resulting in the calculation of improvement factors.

The resulting dataset provides valuable quantitative DNA information and estimates of 16S rRNA gene copies across diverse soil and rock samples along a climate gradient. The modifications made to the extraction buffer demonstrated improved efficiency in extracting especially iDNA compared to the original method. These findings contribute to the refinement and optimization of DNA extraction protocols for terrestrial samples, enabling more accurate and comprehensive analyses of microbial communities in different environments.

Additional Information

The DFG Priority Program 1803 "EarthShape - Earth Surface Shaping by Biota" (2016-2022; https://www.earthshape.net/) explored between scientific disciplines and includes geoscientists and biologists to study from different viewpoints the complex question how microorganisms, animals, and plants influence the shape and development of the Earth’s surface over time scales from the present-day to the young geologic past. All study sites are located in the north-to-south trending Coastal Cordillera mountains of Chile, South America. These sites span from the Atacama Desert in the north to the Araucaria forests approximately 1300 km to the south. The site selection contains a large ecological and climate gradient ranging from very dry to humid climate conditions.

Authors

Medina, Diego;GFZ German Research Centre for Geosciences, Potsdam, Germany
Horstmann, Lucas;Göttingen University, Goettingen, Germany
Ganzert, Lars;UiT The Arctic University of Norway, Tromsø, Norway
Oses, Romulo;Universidad de Atacama, Copiapó, Chile
Friedl, Thomas;Göttingen University, Goettingen, Germany
Wagner, Dirk;GFZ German Research Centre for Geosciences, Potsdam, Germany

Contact

Wagner, Dirk; GFZ German Research Centre for Geosciences, Potsdam, Germany;

Keywords

EarthShape, Chile, Coastal Cordillera, National Park Pan de Azúcar, Private Reserve Santa Gracia, National Park La Campana, National Park Nahuelbuta, biosphere > anatomy > tissue > genetic information > DNA, biosphere > anatomy > tissue > genetic information > gene, chemical > biochemical substance > nucleic acid