Method for determining DNA extraction rate of soil sample

A soil sample and extraction rate technology, applied in the field of soil biochemistry, can solve problems such as low comparability, bias in microbial information, and inability to measure DNA concentration, and achieve the effects of simple preparation, simple culture method, and quick and simple operation.

Inactive Publication Date: 2018-02-02
ZHEJIANG UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The smaller the difference in the DNA adsorption performance of different soil samples, the smaller the difference in the amount of DNA extracted (extraction rate), and the stronger the comparability; At the same time, the amount of DNA extracted from the sample will also affect the results of amplicon and metagenomic sequencing. Rare microorganisms that play an important role in the system are not easily detected, resulting in bias in the final microbial information
At present, people can only measure the concentration of soil DNA after extraction, but the original DNA concentration of the soil sample cannot be measured, so it is impossible to calculate how much DNA is adsorbed by the soil sample during the extraction process

Method used

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  • Method for determining DNA extraction rate of soil sample
  • Method for determining DNA extraction rate of soil sample
  • Method for determining DNA extraction rate of soil sample

Examples

Experimental program
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Effect test

Embodiment 1

[0048] Embodiment 1, a kind of method for measuring all soil sample DNA extraction rates, carries out following steps successively:

[0049] A), purchase A.fischeri ATCC 7744T bacterial strain, cultivate at room temperature (25 ℃) on the tryptone soybean agar medium that concentration is 3%NaCl, use strong The DNA was extracted by the DNA extraction kit, and its concentration was measured by Qubit 3.0, which was used as an internal standard for determining the DNA extraction rate of the soil sample; it was used for future use.

[0050] B) A mineral soil (yellow soil), a black carbon obtained by pyrolysis at 300°C (black carbon 300) and a black carbon obtained by pyrolysis at 700°C (black carbon 700) were used as test materials. Among them, Heitan 300 is rich in aliphatic carbon structure, while Heitan 700 is rich in aromatic carbon structure. The carbon structure of the two is very different, which can be regarded as two different types of soil organic matter. At the same ti...

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Abstract

The invention discloses a use of Aliivibrio fischeri strain DNA. The Aliivibrio fischeri strain DNA is used for determining a DNA extraction rate of a soil sample. The invention also discloses a method for determining a DNA extraction rate of a soil sample. The method comprises the following steps: culturing the Aliivibrio fischeri ATCC 7744T strain, extracting DNA of the Aliivibrio fischeri ATCC7744T strain, and using as an internal standard for determining the DNA extraction rate of the soil sample; designing a specific primer of a 16S rRNA gene fragment in Aliivibrio fischeri; adding DNA of the internal standard in the soil sample, and then immediately extracting the DNA; determining the gene quantity of the internal standard added into the soil and the gene quantity of the internal standard in the soil sample after the extraction by adopting qPCR, and calculating the DNA extraction rate.

Description

technical field [0001] The invention belongs to the field of soil biochemistry, and in particular relates to a method applicable to the determination of DNA extraction rates of all soil samples. Background technique [0002] Soil microorganisms (bacteria, fungi, and archaea, etc.) are a very important class of life in soil ecosystems. This kind of microorganism has a wide variety, a large number, and various functions. It plays an important role in the degradation of soil organic matter, the transformation and cycle of soil nutrients, the growth and development of crops, the emission of greenhouse gases, and the fixation and degradation of pollutants. However, the vast majority of microorganisms in soil are non-culturable, and only a small number (0.1%-10%) of microorganisms can be obtained using traditional isolation and culture methods, which cannot fully reflect the composition, diversity and function of the microbial community structure in the soil environment feature. ...

Claims

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Application Information

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IPC IPC(8): C12Q1/6851
CPCC12Q1/6851C12Q2545/114C12Q2531/113
Inventor 戴中民徐建明
Owner ZHEJIANG UNIV
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