CN102206630A - Method and kit for extracting total DNA of soil and sediment - Google Patents
Method and kit for extracting total DNA of soil and sediment Download PDFInfo
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Abstract
The invention relates to a method and a kit for extracting total DNA of soil and sediment. The method comprises the following steps of: dissolving and removing humic acid from the soil and sediment to the greatest extent by using a humic acid dissolving solution; performing complex-precipitation on the residual humic acid; randomly cracking and releasing genomic DNA in bacteria; centrifuging to remove complexed humic acid and protein from the solution; and regulating supernate containing DNA by using an acid-base regulating agent and a high-concentration salt solution, and specifically adsorbing by using a silica gel adsorption film to make the genomic DNA purified and recovered. By the method, a plurality of samples can be extracted in short time, the normal operating time is less than 70 minutes, and massive DNA samples having high purity and suitable for downstream analysis can be obtained. By the kit established according to the method, the obtained DNA samples have high purity without degradation and can be directly used for subsequent molecular biology analysis; meanwhile, a step of purifying the DNA by toxic reagents such as phenol and chloroform in the traditional DNA extraction method is avoided, and the invention has wide application prospect.
Description
Technical field
The invention belongs to soil microbe genome DNA separating and purifying technology field, be specifically related to a kind of soil and settling total DNA extraction method and extract test kit.
Background technology
The microbial ecological that the molecular fingerprint graphical spectrum technology has become field widespread usage such as microbial ecology, environmental, environmental engineering learns a skill, yet the extractive technique of (as soil, ocean and lake sediment etc.) total DNA gets more and more people's extensive concerning as the committed step and the core content of this technical system in the environmental sample.The specificity of total DNA extraction, concentration, purity etc. directly have influence on the objective reality of biological community structure in soil and the settling, are foreign periodical one of more contents of dispute in the process of going over a manuscript or draft in recent years.
At present,, still do not have the consistent preferred approach of admitting, and enzymatic lysis method of widespread usage, pharmaceutical chemicals extraction method etc. can only work at the sensitive organism in the sample, and can't remove the humic acid in the sample for from soil and settling, obtaining total DNA.The change that these methods are all artificial real biological community structure in the environment, and have following problem: 1) the DNA extraction process is numerous and diverse, overlong time, and need more large-scale instrument and equipment needs long water-bath process as enzyme extraction method; 2) the general dna leaching process is often used the chemical reagent of high malicious high pollution, as using " three cause " reagent such as phenol/chloroform in the DNA purge process; 3) DNA of Ti Quing is second-rate, and fragment is more, has pollutions such as humic acid, RNA, protein; 4) amount of DNA is especially obtained DNA very little from settling, can't satisfy the needs of downstream experiment.Therefore, set up a kind of method of effectively from soil and settling, extracting total DNA and become the task of top priority.
Summary of the invention
The purpose of this invention is to provide a kind of method that from soil and settling, obtains total DNA fast, and provide complete test kit product innovation, use this test kit, the investigator can obtain the DNA of needs fast from environmental sample, to carry out follow-up molecular biology research.
The present invention at first uses the humic acid lysate, farthest dissolve and remove humic acid in soil and the settling, to remain humic acid again and carry out complex-precipitation, do not have then and selectively discharge the intravital DNA of all bacteriums, complexing humic acid and the protein in the solution is removed in centrifugal back, the supernatant solution that contains DNA is able to purifying with the special absorption of silica gel adsorption film and reclaims then by after the high level salt solution adjusting.
Soil of the present invention and settling total DNA extraction method in turn include the following steps:
1) removes the most of humic acid of sample with the humic acid lysate, obtain precipitation;
2) add the humic acid complexing agent in the deposit sample of above-mentioned step 1), the precipitation that suspended makes the abundant complexing of remaining humic acid, and centrifugal humic acid complex compound and the bacteria samples of making fully precipitates;
3) to above-mentioned steps 2) precipitation in add cell pyrolysis liquid, vortex oscillation discharges bacteria total DNA, obtains containing the supernatant liquor of bacteria total DNA after centrifugal;
4) in the supernatant liquor of above-mentioned step 3), add acid-base modifier, the centrifugal supernatant solution that obtains removing protein and glucide;
5) in the supernatant solution of above-mentioned step 4), behind the high salt solvent of adding, cross silica gel adsorption film adsorption of DNA;
6) with above-mentioned steps 5) after the DNA of absorption cleans, obtain total DNA of sample with the elutriant wash-out.
Above-mentioned humic acid complexing agent is the calcium ion aqueous solution, is preferably calcium chloride solution, is 0.20mol/L, and pH 5.5~7.5; And the weight in wet base of soil or sediment sample is 1.5g/mmol/L with the adding proportion of calcium ion.
Above-mentioned acid-base modifier is 0.5~1.5mol/L Potassium ethanoate, and pH 4.8~5.0, has the regulator solution system to acid, with further precipitation humic acid and glucide, and the effect of denatured protein.
Above-mentioned step 3) vortex oscillation time of releasing is 10~12min.
Extraction test kit according to above-mentioned extracting method is set up comprises following component:
1) humic acid lysate and extra large sand, wherein extra large sand diameter is 1~2mm, the mass volume ratio of extra large sand and humic acid lysate is 0.2~0.3g/mL;
2) humic acid complexing agent: the 0.20mol/L calcium chloride solution, pH 5.5~7.5
3) cell pyrolysis liquid: 50~100mmol/L Tris-HCl, 1.5~3.5mol/L NaCl, 1%~3%CTAB, pH 8.0~10.0;
4) denaturing agent: 20%SDS, pH 9.0;
5) acid-base modifier: 0.5~1.5mol/L Potassium ethanoate, pH 4.8~5.0;
6) high salt solvent: 3.0~6.0mol/L Guanidinium hydrochloride, pH 5.0~8.0;
7) scavenging solution: 70% ethanol;
8) elutriant: 2~10mmol/L Tris-HCl, pH 8.0~9.0;
9) genomic dna adsorption column: the 2mL centrifuge tube suit that comprises silica gel adsorption film inner prop.
The test kit of setting up according to method of the present invention can extract a plurality of samples simultaneously at 70min in the time, the DNA sample purity height that obtains, there is not degraded, can be directly used in follow-up molecular biological analysis, avoided traditional DNA extraction method to need the step of toxic agent purify DNAs such as phenol/chloroform simultaneously, had broad application prospects.
Description of drawings
Fig. 1: use the different soils sample DNA electrophoresis result figure that test kit of the present invention extracts.
Fig. 2: different soils sample DNA 16S rRNA gene PCR amplification electrophoresis result.
Fig. 3: different soils sample DNA 16S rRNA gene V3 district pcr amplification electrophoresis result.
Fig. 4: different soils sample DNA ammonia oxidation bacteria distinguished sequence pcr amplification electrophoresis result.
Wherein, M is marker, and each fragment marks in figure right; 1,2,3 and 4 are respectively farmland soil, meadow soil, wetland soil, oceanic sediment, the negative contrast of C.
Embodiment
Below in conjunction with specific embodiment method of the present invention is described in detail.
The present invention obtains the method for total DNA from soil and settling, in turn include the following steps:
1) handle sample with extra large sand and humic acid lysate, the centrifugal deposit sample that obtains removing most of humic acid:
Get 0.3g diameter 1~2mm sea sand in the centrifuge tube of 2mL, carry out high pressure steam sterilization, add humic acid lysate (100~200mmol/L Tris, the 50~100mmol/LNa of 1.0~1.5mL sterilization
4P
2O
7, 50~100mmol/L Na
2EDTA, 1.0~3.0%PVP, 100~200mmol/L NaCl, 0.05~0.1%Triton X-100, pH 8.0~10.0), place room temperature standby;
Soil or sediment sample 0.3g are joined in the centrifuge tube that humic acid lysate and extra large sand are housed middling speed vortex vibration 1~3min, mixing fully, humic acid in the pedotheque is fully discharged, the centrifugal 30s of 10000 * g inhales as far as possible and abandons supernatant then, obtains deposit sample;
2) add the humic acid complexing agent in the deposit sample of above-mentioned step 1), the precipitation that suspended makes the abundant complexing of remaining humic acid, and centrifugal extra large sand, humic acid complex compound and the bacteria samples of making fully precipitates:
Add 1mL 0.20mol/L calcium chloride solution to the deposit sample of above-mentioned step 1), pH 5.5~7.5, middling speed vortex 1~3min then, and mixing fully, the centrifugal 30s of 10000 * g inhales as far as possible and abandons supernatant, obtains containing the precipitation of DNA.
Calcium ion can with electronegative larger molecular organics complexing, form infusible precipitate, humic acid, protein and DNA etc. are electronegative larger molecular organics under neutrallty condition, but this moment, bacterial cell was not broken as yet, DNA does not also discharge, so the calcium ion that adds only forms infusible precipitate with the humic acid complexing.And other humic acid complexometric reagent owing to can not form stable complex compound sediment with humic acid, can make humic acid enter in the sample system in follow-up lysis again.The present invention need select the calcium salt of good water solubility for use, preferably calcium chloride solution.
In addition, the calcium ion concn in the humic acid complexing agent of adding also produces significant effects to DNA extraction.Calcium ion concn is low excessively, will make in the sample humic acid complexing incomplete, and too high with remaining too much, influence output and the quality of follow-up DNA.Originally studies show that, in step 1), get under 0.3g soil or the sedimental condition, add 1mL 0.2mol/L calcium chloride solution (ratio that is sample weight in wet base and calcium ion is 1.5g/mmol/L) and just can will remain the complete complexing of humic acid, and less to the DNA yield effect.
3) to above-mentioned steps 2) precipitation in add cell pyrolysis liquid and denaturing agent and vortex oscillation and discharge bacteria total DNA, obtain containing the supernatant liquor of bacteria total DNA after centrifugal:
Add 720 μ L cell pyrolysis liquids, 50~100mmol/L Tris-HCl in the precipitation, 1.5~3.5mol/LNaCl, 1%~3%CTAB, pH 8.0~10.0; With 80 μ L denaturing agent 20%SDS, pH 9.0, top speed vortex oscillation 10~12min, and the centrifugal 60s of 10000 * g transfers to supernatant liquor (<650 μ L avoid drawing the upper strata bubble) in the new pipe;
4) in the supernatant liquor of above-mentioned step 3), add acid-base modifier, the centrifugal supernatant solution that obtains removing protein and glucide:
Add 100 μ L acid-base modifiers, 0.5~1.5mol/L Potassium ethanoate, pH 4.8~6.0; Put upside down mixing 5 times, 4 ℃ leave standstill 5min, the centrifugal 60s of 10000 * g, and supernatant (<700 μ L) moves to new pipe;
The supernatant liquor that obtains in the step 3) is less than 650 μ L, and the acid-base modifier of adding is 100 μ L, is to obtain comparatively ideal hydrochlorate regulating effect, and the volume ratio of the two needs greater than 6.5.
5) in the supernatant solution of above-mentioned step 4), behind the high salt solvent of adding, cross silica gel adsorption film adsorption of DNA:
In the supernatant solution of step 4), add the high salt solvent of 1400 μ L: 3.0~6.0mol/L Guanidinium hydrochloride, pH5.0~8.0; Behind the mixing, divide three times (getting 700 μ L) to add same silica gel adsorption film adsorption of DNA, the centrifugal 30s of 10000 * g at every turn;
In the supernatant solution that above-mentioned step 4) obtains, when the salts solution that adds high density is competed available water with dna molecular, dna molecular will be separated out and be combined with silica gel adsorption film in the organic phase.Guanidinium hydrochloride has the characteristic of salt, can high density be dissolved in water simultaneously, and this is that other salts are incomparable, and this also is the reason of applying high density Guanidinium hydrochloride of the present invention.
6) with above-mentioned steps 5) after the DNA of absorption cleans, obtain total DNA of sample with the elutriant wash-out:
Add 700 μ L70% ethanol, the centrifugal 60s of 10000 * g, after removing filtered solution, once centrifugal again, adsorption column is placed new pipe, use 100 μ L elutriants then: 2~10mmol/L Tris-HCl, pH 8.0~9.0 joins in the adsorption column, in 60 ℃ of water-bath 5min, and the centrifugal 60s of 10000 * g, collect filtered solution, in-20 ℃ of preservations.
Extraction test kit of the present invention comprises following component:
1) humic acid lysate and extra large sand, wherein extra large sand diameter is 1~2mm, the mass volume ratio of extra large sand and humic acid lysate is 0.2~0.3g/ml;
2) humic acid complexing agent: the 0.20mol/L calcium chloride solution, pH 5.5~7.5;
3) cell pyrolysis liquid: 50~100mmol/L Tris-HCl, 1.5~3.5mol/LNaCl, 1%~3%CTAB, pH 8.0~10.0;
4) denaturing agent: 20%SDS, pH 9.0;
5) acid-base modifier: 0.5~1.5mol/L Potassium ethanoate, pH 4.8~5.0;
6) high salt solvent: 3.0~6.0mol/L Guanidinium hydrochloride, pH 5.0~8.0;
7) scavenging solution: 70% ethanol;
8) elutriant: 2~10mmol/L Tris-HCl, pH 8.0~9.0;
9) genomic dna adsorption column: the 2ml centrifuge tube suit that comprises silica gel adsorption film inner prop.
Use this test kit, the simple device that only needs the laboratories such as general microbiology such as supercentrifuge, vortex oscillation device, water-bath and micropipet, molecular biology of conventional non-frozen type all to possess, for skilled investigator, extracting 6 sample DNA times simultaneously can foreshorten within the 70min, saved the researcher valuable time greatly, simultaneously can obtain high-quality DNA sample, the molecular biology operation unrestraint to the downstream shows great application potential.Extraction test by to total DNA in farmland soil, meadow soil, wetland soil, the oceanic sediment all obtains ideal results, and does not influence follow-up molecular biological analysis such as pcr amplification.
Embodiment 1: the selection of humic acid complexing agent concentration
Using this test kit, is object with wetland soil, oceanic sediment and farmland soil, inquires into the influence of humic acid complexing agent concentration to extraction efficiency.Sample size is 0.3g, and wherein calcium chloride solution concentration is respectively 0,0.1,0.2,0.3,0.4,0.5mol/L, and each adds 1ml, extracts about 60min of time spent according to method of the present invention.The DNA that extracts is carried out electrophoresis, dyeing, photograph, and use ultraviolet spectrophotometer and carry out qualitative and quantitative analysis.The result shows, calcium chloride solution concentration is respectively 0 and (the ratio of sample weight in wet base and calcium ion 〉=3g/mmol) during 0.1mol/L, though the rate of recovery of DNA is higher, be 10~15 μ g/g dry ground, but the dna solution that extracts is yellow, contains a large amount of humic acid, shows that humic acid is not removed fully, the calcium chloride relative quantity that adds is low excessively, and such DNA sample will have great restraining effect to the enzyme in the molecular biology experiment.Equally, using concentration and be 0.3mol/L above (is that the calcium chloride solution of the ratio≤1g/mmol/L) of sample weight in wet base and calcium ion is when being the humic acid complexing agent, though dna solution is transparent limpid, but the DNA rate of recovery is low excessively, be lower than the detection limit value during electrophoresis, ultraviolet detection shows and is lower than the 100ng/g dry ground that this shows that too high calcium chloride solution is residual too many, also complexing a large amount of dna moleculars, such DNA sample can't satisfy follow-up molecular biology needs.And when adding 1mL 0.2mol/L calcium chloride solution (ratio that is sample and calcium ion is 1.5g/mmol/L), the DNA concentration height of Ti Quing (5~7 μ g/g) not only, and quality can satisfy library construction, denaturing gradient gel electrophoresis follow-up molecular biological requirements such as (DGGE).
Embodiment 2: bacteria cell cracking vortex oscillation selection of time
Using this test kit, is object with 0.3g wetland soil, farmland soil respectively, and the vortex oscillation time that adds after cell pyrolysis liquid and the denaturing agent is optimized.Wherein the humic acid complexing agent is with the calcium chloride solution of the 0.2mol/L of 1ml, and pH 7.5, and the vortex oscillation time during lysis is selected 5min respectively, 10min, and 15min extracts according to method of the present invention, about 70min of time spent.DNA electrophoresis, dyeing, photograph, and use ultraviolet spectrophotometer and carry out qualitative and quantitative analysis.The result shows that the environmental sample DNA rate of recovery of vibration 5min is obviously on the low side, is lower than 1.0 μ g/g dry ground; And after being higher than 15min, the DNA rate of recovery there is no obvious increase, and a large amount of DNA fragments occurred, and this is unallowed for the molecular biology experiment that needs the long segment genomic dna, is advisable so duration of oscillation is chosen 10~12min.
Embodiment 3: extract total DNA from different pedotheques
The extraction conditions of using this test kit and determining extracts test to total DNA in farmland soil, meadow soil, wetland soil, the oceanic sediment respectively, extracts about 60min of time spent according to method of the present invention.Get 10 μ L DNA and carry out electrophoresis, gel dyes with EB, and gel imaging system is taken a picture, and uses ultraviolet spectrophotometer and carry out qualitative and quantitative analysis, and electrophoresis result as shown in Figure 1.According to this figure, total DNA that this test kit can obtain from different soil and settling, dna fragmentation length is at 10~20kb, and not degraded does not have RNA to pollute yet.Respectively each sample is carried out uv-absorbing and detect, show that the DNA sample that is obtained forms the DNA absorption peak of homogeneous at the 260nm place, do not have tangible albumen absorption peak OD to occur at the 280nm place
260/ OD
280=1.8~1.9, illustrate that the DNA that obtains is purer, there are not albumen and RNA to pollute, calculate and learn that the rate of recovery of DNA is 5~12 μ g/g dry ground.
For confirming that can use this test kit extraction DNA quality satisfy the molecular biology needs, DNA with acquisition is a template, use universal primer 8F/1541R, denaturing gradient gel electrophoresis (DGGE) the 16S rRNA gene V3 district special primer 341F/534R commonly used of bacterial 16 S rRNA full length gene respectively, and the special 16S rRNA gene primer CTO189f/CTO654r of ammonia oxidizing bacteria carries out pcr amplification.After PCR finishes, get 5 μ L electrophoresis, the result is respectively as Fig. 2, Fig. 3 and Fig. 4.Fig. 2 shows with 8F/1541R to be that primer obtains the 16S rna gene near total length, about 1500bp, and concentration is approximately 10ng/tL.The structure that can be used for 16S rRNA gene library behind this product purification is to resolve kind, composition and the ratio of microorganism in the environment.Fig. 3 shows that each sample has all obtained about 200bp target sequence, and concentration is approximately 20ng/ μ L, can be used for DGGE and analyzes, with the structure of analyzing microbial community and dynamically.It is after primer carries out PCR that Fig. 4 shows with TO189f/CTO654r, and each sample has all obtained the about 500bp target sequence of length, and concentration is approximately 10ng/ μ L.As seen, use this test kit, can from soil, sediment sample, extract high-quality DNA, can satisfy the biological needs of downstream molecules.
Claims (10)
1. soil and settling total DNA extraction method in turn include the following steps:
1) removes the most of humic acid of sample to be extracted with the humic acid lysate, obtain the sample precipitation;
2) in the sample precipitation to be extracted of above-mentioned step 1), add the humic acid complexing agent, make the abundant complexing of remaining humic acid, centrifugal humic acid complex compound and the bacteria samples precipitation of making;
3) to above-mentioned steps 2) precipitation in add cell pyrolysis liquid, vortex oscillation discharges bacteria total DNA, the centrifugal supernatant solution that obtains;
4) in above-mentioned step 3) supernatant solution, add acid-base modifier, the centrifugal supernatant liquor that obtains;
5) in above-mentioned step 4) supernatant liquor, add high salt solvent, cross silica gel adsorption film adsorption of DNA;
6) with above-mentioned steps 5) absorption DNA clean, obtain total DNA of sample with the elutriant wash-out.
2. extracting method as claimed in claim 1 is characterized in that described step 2) the humic acid complexing agent that adds in the sample to be extracted precipitation is the calcium ion aqueous solution.
3. extracting method as claimed in claim 2 is characterized in that the described calcium ion aqueous solution is calcium chloride solution.
4. extracting method as claimed in claim 2, the ratio that it is characterized in that the calcium ion of described sample to be extracted and interpolation is 1.5g:1mmol/L.
5. extracting method as claimed in claim 1 is characterized in that be 10~12min vortex oscillation time of releasing of described step 3).
6. extracting method as claimed in claim 1 is characterized in that the volume ratio of the acid-base modifier of supernatant solution in the described step 4) and adding is not less than 6.5.
7. extracting method as claimed in claim 1, the high salt solvent that it is characterized in that described step 5) is 3.0~6.0mol/L Guanidinium hydrochloride, pH 5.0~8.0.
8. soil and settling total DNA extraction test kit comprise following component:
1) efficient DNA separator column: comprise humic acid lysate and extra large sand;
2) humic acid complexing agent: the 0.20mol/L calcium chloride solution, pH 5.5~7.5;
3) cell pyrolysis liquid: 50~100mmol/L Tris-HCl, 1.5~3.5mol/L NaCl, 1%~3%CTAB, pH 8.0~10.0;
4) denaturing agent: 20%SDS, pH 9.0;
5) acid-base modifier: 0.5~1.5mol/L Potassium ethanoate, pH 4.8~6.0;
6) high salt solvent: 3.0~6.0mol/L Guanidinium hydrochloride, pH 5.0~8.0;
7) scavenging solution: 70% ethanol;
8) elutriant: 2~10mmol/L Tris-HCl, pH 8.0~9.0;
9) genomic dna adsorption column: the 2mL centrifuge tube suit that comprises silica gel adsorption film inner prop.
9. DNA extraction test kit as claimed in claim 8 is characterized in that the mass volume ratio g/mL of extra large sand and humic acid lysate is 0.2~0.3 in the described efficient DNA separator column.
10. DNA extraction test kit as claimed in claim 8 is characterized in that described efficient DNA separator column is that 2mL can found frozen pipe.
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CN102382821A (en) * | 2011-11-18 | 2012-03-21 | 重庆邮电大学 | Method for extracting DNA from genome |
CN103374566A (en) * | 2012-04-23 | 2013-10-30 | 内蒙古大学 | Efficient method for extracting purified total DNA (deoxyribonucleic acid) from lake sediment sample |
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2011
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Non-Patent Citations (2)
Title |
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《基因组学与应用生物学》 20091231 王丽娜等 三种土壤微生物总DNA提取方法的比较 正文第332页左栏第1.2节 1-10 , * |
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CN102382821A (en) * | 2011-11-18 | 2012-03-21 | 重庆邮电大学 | Method for extracting DNA from genome |
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CN103374566A (en) * | 2012-04-23 | 2013-10-30 | 内蒙古大学 | Efficient method for extracting purified total DNA (deoxyribonucleic acid) from lake sediment sample |
CN103627703A (en) * | 2013-12-19 | 2014-03-12 | 涂祖新 | Total DNA (deoxyribonucleic acid) extraction method and kit for synchronously removing humic acid and mycoprotein |
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CN114107286A (en) * | 2021-12-06 | 2022-03-01 | 哈尔滨市青蛙生物科技有限责任公司 | Universal soil genome DNA extraction kit and use method thereof |
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