CN102643794A - Method for extracting total DNA (deoxyribonucleic acid) of mulberry rhizosphere soil microorganisms by adopting plurality of measures - Google Patents
Method for extracting total DNA (deoxyribonucleic acid) of mulberry rhizosphere soil microorganisms by adopting plurality of measures Download PDFInfo
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Abstract
The invention discloses a method for extracting total DNA (deoxyribonucleic acid) of mulberry rhizosphere soil microorganisms by adopting a plurality of measures, which can achieve a good cell lysis effect by utilizing PVP (polyvinyl pyrrolidone) prewashing to remove humic acid, the synergy of CTAB (cetyltrimethyl ammonium bromide), lysozyme, protease and SDS (sodium dodecyl sulfate) to lyse cells and repetitively freezing and thawing the cells at the same time and utilizes PEG8000 to precipitate DNA, so that the purity of the obtained DNA is high. The adopted method is simple and convenient, and the DNA can be used in subsequent PCR (Polymerase Chain Reaction) analysis and DGGE (denaturing gradient gel electrophoresis) analysis without needing to be purified. The extracted DNA is so pure as to meet the requirement of direct subsequent molecular biology research, an extracted DNA fragment can be used in the amplification and DGGE map analysis of 16SrDNA, moreover, the specific band gel extraction and base sequencing of a DGGE band can be carried out, comparison with the sequence existing in an RDP (ribosomal database project) database can be carried out, or a new sequence probe can be established to identify unknown bacteria, so that the composition of a microbial community structure can be determined, and thereby laying a foundation for the future research of the community structure diversity and the ecological functions of the mulberry rhizosphere soil microorganisms.
Description
Technical field
The present invention relates to the molecular ecology technical field, be specifically related to the process for extracting of the total DNA of a kind of mulberry field soil microorganisms.
Background technology
For a long time, the Study on Diversity of relevant soil microorganisms realizes through separation and Culture.Yet most microbial populations still can not be realized pure culture, and this becomes a restrictive factor of soil microorganisms Study on Diversity.Along with deepening continuously of soil microbial community structural research; Avoided traditional research method can not obtain the defective of soil microorganisms diversity information by the research method of modern molecular biology technique such as PCR-RFLP, PCR-SSCP, PCR-DGGE etc. comprehensively; The variety that can show through soil microbial DNA; Earth microbial population structure situation is gone up in reflection truly; And efficient, the high-quality extraction of soil microbial community genome DNA is the precondition of the soil microbial community structure being studied from the molecular biology level.Because soil physical chemistry complicated component; Often containing humic acid, phenolic cpd, heavy metal ion etc. influences the material of dna molecular operation; Pedotheque processing and experiment condition are complicated; Length consuming time, thus acquisition high purity microbe genome DNA has certain difficulty from edatope, and therefore the DNA extraction technological innovation receives much concern.Reported multiple soil microorganisms total DNA extraction method at present.Roughly be divided into two types from the method for soil extract microorganism total DNA: direct extraction method and indirect extraction method.The DNA purity that indirect method is extracted is high, only accounts for 25%～50% of total flora but its shortcoming is the bacterium that obtains, and the DNA that direct method is extracted surpasses 60% of bacteria total DNA.Direct method because can extract more full DNA of bacteria, laborsaving, DNA output is high, thereby development is very fast.Use SDS such as Tsai and N,O-Diacetylmuramidase lysing cell extract total DNA; Tiedje etc. use PVP (Vinylpyrrolidone polymer) and CTAB (cetyl trimethylammonium bromide) to remove humic acid; Effect is fine; People such as Bourrain adopt this method from active sludge, to extract DNA, and people such as Reddy have extracted DNA from compost.
The generation of the formation of earth structure and improvement on variety of mulberry field soil microorganisms and vital movement and the mulberry field, soil fertility differentiation, mulberry tree root disease, the supply of mulberry tree nutritive substance and vine growth and development etc. are closely related, but do not see as yet at present to use and exempt from the multifarious report of culture method research mulberry field soil microorganisms.
Summary of the invention
The present invention is based on the molecular ecology experimental technique system of setting up mulberry tree rhizosphere soil biological community structure; Use for reference the process for extracting of the total DNA of existing soil microorganisms, a kind of mulberry field soil microorganisms total DNA extraction method that can directly be used for pcr analysis efficiently is provided.
For realizing above-mentioned purpose, the invention discloses following technical scheme:
One. material is selected
Supply examination soil on March 7th, 2011 pick up from Crop Institute, Hunan Academy of Agricultural Sciences production mulberry field (114 ° 19 of east longitude ', 30 ° 29 of north latitude ', height above sea level 29m) the mulberry tree rhizosphere, mulberry tree breed is "Hur" mulberry No. 32.Collection soil is a yellow clay, and sampling depth is 5～10cm topsoil, by 5 method samplings, puts into sterile bag behind the mixing, and the extraction of soil microorganisms genome DNA is accomplished in 4 ℃ of preservations in the 24h.
Two. reagent is selected
In the main agents that the present invention adopts: cetyl trimethylammonium bromide (CTAB), sodium laurylsulfonate (SDS), Vinylpyrrolidone polymer K30 (PVP K30), polyoxyethylene glycol 8000 (PEG8000), urea, deionized formamide are all available from magnificent biotechnology ltd; N,O-Diacetylmuramidase, proteolytic enzyme are all available from Sigma company; Silver Nitrate is available from the 9509 factory of the Chinese People's Liberation Army; λ DNA/HindIII digest DNA Marker, 2000DL DNA Marker and Taq HS are all available from the precious biotechnology in Dalian ltd; The 16SrDNA universal primer is synthetic by Shanghai English fine horse biotechnology ltd; Soil extract test kit
Soil DNA Kit (50) is available from Omega company.
Three. the total dna direct cleavage method of soil microorganisms
Method one CTAB-proteolytic enzyme-SDS-multigelation method
Get the 5g soil sample, to wherein adding 13.5mL DNA extraction liquid I (Tris-HCl 100mmol/L, EDTA 100mmol/L, Na
3PO
4100mmol/L, NaCl 1.5mol/L, 1%CTAB; PH 8.0) and a little silica sand, vortex oscillation device vibration 3min; Add 20mg/mL Proteinase K 15 μ L again, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 1.5mL 10%SDS, 65 ℃ of water-bath 1h; Multigelation 3 times, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic phenol/chloroform/primary isoamyl alcohol (volume ratio 25: 24: 1) extracting, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant, and is subsequent use.
Method two PVP pre-treatment-CTAB-N,O-Diacetylmuramidase-proteolytic enzyme-SDS-multigelation method
Get 5g soil sample adding 20g/L sodium-metaphosphate damping fluid and (contain 10g/L PVP-K30; PH 8.5) 30mL, shaking table vibration 15min, the centrifugal 5min of 8500r/min gets deposition, repeated washing 3 times; Get deposition, add 13.5mL DNA extraction liquid I (Tris-HCl 100mmol/L, EDTA 100mmol/L, Na
3PO
4100mmol/L, NaCl 1.5mol/L, 1%CTAB; PH 8.0) and a little silica sand, vortex oscillation device vibration 3min; Add 100mg/mL N,O-Diacetylmuramidase 150 μ L, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 20mg/mL Proteinase K 15 μ L again, mixing, 37 ℃ of water-bath 1h; Add 1.5mL 10%SDS, 65 ℃ of water-bath 1h; Multigelation 3 times, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic phenol/chloroform/primary isoamyl alcohol (volume ratio 25: 24: 1) extracting, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant, and is subsequent use.
Method three PVP pre-treatment-CTAB, CaCl
2, BSA-N,O-Diacetylmuramidase-proteolytic enzyme-SDS-multigelation method
Get 5g soil sample adding 20g/L sodium-metaphosphate damping fluid and (contain 10g/LPVP-K30; PH 8.5) 30mL, shaking table vibration 15min, the centrifugal 5min of 8500r/min gets deposition, repeated washing 3 times; Get deposition, add 13.5mL DNA extraction liquid II (Tris-HCl 100mmol/L, EDTA 100mmol/L, Na
3PO
4100mmol/L, NaCl 1.5mol/L, 1%CTAB, 2%CaCl
2, 1 μ g/mL BSA; PH 8.0) and a little silica sand, vortex oscillation device vibration 3min.Subsequent operations is identical with method two.
Method four CTAB, PVP, CaCl
2, BSA-N,O-Diacetylmuramidase, proteolytic enzyme-SDS-multigelation method
Get the 5g soil sample, add 13.5mL DNA extraction liquid III (Tris-HCl 100mmol/L, EDTA 100mmol/L, Na
3PO
4100mmol/L, NaCl 1.5mol/L, 1%CTAB, 2%CaCl
2, 1 μ g/mL BSA, 2%PVP; PH 8.0) and a little silica sand, vortex oscillation device concussion 3min; Add 150 μ L 100mg/mL N,O-Diacetylmuramidases, 15 μ L 20mg/mL Proteinase Ks, incubation 1h in the mixing, 37 ℃, 230r/min shaking table.Subsequent operations is identical with method two.
Method five CTAB, CaCl
2, BSA-N,O-Diacetylmuramidase, proteolytic enzyme-SDS, PVP-multigelation method
Get the 5g soil sample, add 13.5mL DNA extraction liquid II (Tris-HCl 100mmol/L, EDTA 100mmol/L, Na
3PO
4100mmol/L, NaCl 1.5mol/L, 1%CTAB, 2%CaCl
2, 1 μ g/mL BSA; PH 8.0) and a little silica sand, vortex oscillation device vibration 3min; Add 100mg/mL N,O-Diacetylmuramidase 150 μ L, 20mg/mL Proteinase K 15 μ L, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 1.5mL 10%SDS and 0.3g PVP, mixing, 65 ℃ of water-bath 1h; Multigelation 3 times.Subsequent operations is identical with method two.
Method six test kit methods
Adopt soil extract test kit
the Soil DNA Kit (50) of Omega company to extract.
Four. the total DNA intermediate processing of soil microorganisms
Method one isopropanol precipitating method
In supernatant, add 0.7 times of volume Virahol and 0.1 times of volume NaAc, 8500r/min is spent the night in-20 ℃ of placements; 4 ℃ of centrifugal 20min, deposition is used 70% washing with alcohol, the centrifugal 10min of 12500r/min; The deposition room temperature is dried, and adds 200 μ LTE dissolution precipitations ,-20 ℃ of preservations.
The method two PEG8000 precipitator method
In supernatant, add 0.5 times of volume 25%PEG 8000 and 0.1 times of volume 5mol/L NaCl, 8500r/min is spent the night in 4 ℃ of placements; 4 ℃ of centrifugal 20min, deposition is used 70% washing with alcohol, the centrifugal 10min of 12500r/min; The deposition room temperature is dried, and adds 200 μ LTE dissolution precipitations ,-20 ℃ of preservations.
Five. the quality examination of the total DNA of soil microorganisms
1.DNA purity and detection by quantitative measure D (230nm), D (260nm), D (280nm) value of dna solution with ultraviolet spectrophotometer; Calculate the mass concentration (ng/ μ L) of DNA according to multiple * 50 of formula dsDNA=D (260nm) * dilution; Converse the DNA amount that every gram soil extracts, and detect the purity of DNA according to D (260nm)/D (230nm), D (260nm)/D (280nm).Use 1% agarose gel electrophoresis check and analysis simultaneously.
2.16SrDNAV3 fragment PCR is that template is directly carried out PCR with the total DNA of mulberry field soil microorganisms that extracts.Forward and reverse primer is respectively: GC-F341 (5 '-CGCCCGCCG CGC GCG GCG GGC GGG GCG GGGGCACGGGGG G CCT ACG GGA GGC AGC AG-3 ') and R518 (5 '-ATTACC GCG GCT GCTGG-3 ').Reaction system: 10 * PCR buffer (containing Mg2+), 3 μ L, 2.5mmol/L dNTPs 2.4 μ L, each 0.6 μ L of 10 μ mol/L upstream and downstream primers, Taq enzyme 1U, template DNA 30ng adds ddH2O to 30 μ L at last.PCR program: 94 ℃ of preparatory sex change 5min; 94 ℃ of sex change 1min, annealing 1min, 72 ℃ are extended 1min, 36 circulations (annealing temperature is from 65 ℃～55 ℃, and each circulation reduces by 0.5 ℃, and 15 circulations subsequently keep 55 ℃); 72 ℃ of final 7min that extend.The PCR product detects through 2% agarose gel electrophoresis.Triplicate.
3. denaturing gradient gel electrophoresis separates 16SrDNA V3 fragment PCR products and uses JY-TD331 denaturing gradient gel electrophoresis appearance (Beijing monarch anticipate east electrophoresis equipment ltd) and separate the PCR product.Get 15 μ L PCR products; Add 10 μ L6 * loading buffer and carry out denaturing gradient gel electrophoresis (DGGE), deposition condition: 8% SEPIGEL 305, electrophoretic buffer are 1 * TAE; 50%～80% denaturing agent (urea and deionized formamide); 60 ℃ of temperature, voltage 100V, electrophoresis time 17h.Electrophoresis finishes back silver and dyes colour developing.
Six. interpretation of result
1. the preliminary screening of mulberry tree rhizosphere soil microorganism total DNA process for extracting
Adopt 5 kinds of different cells cleavage methods and 2 kinds of DNA intermediate processings to make up; Thereby obtain the method for 8 kinds of different direct extraction mulberry tree rhizosphere soil microorganism total DNAs; And be reference with the mulberry tree rhizosphere soil microorganism total DNA that the test kit method is extracted, utilize its D of determined by ultraviolet spectrophotometry (230nm), D (260nm), D (280nm) value.With the purity and the quality of D (260nm)/D (280nm) representation DNA, with the degree of humic acid pollution in D (260nm)/D (230nm) representation DNA.Table 1 data presentation the effect of Different Extraction Method.
Can know that by Fig. 1 the molecular mass of the DNA that different methods extracts more than 23kb, is a genomic dna all, and DNA do not interrupted, be large fragment DNA, can be used for follow-up molecular biological analysis.Take all factors into consideration DNA purity and quality, humic acid pollution level and productive rate, method 4,5,8,9 combines physics, chemistry, biological 3 kinds of method lysing cell, in DNA extraction liquid, adds PVP, BSA, CaCl
2Further remove humic acid; Save loaded down with trivial details pre-wash step, the DNA productive rate of acquisition is higher than 11.2 μ g/g, and D (260nm)/D (230nm) is greater than 2.11; D (260nm)/D (280nm) has reached the requirement of directly carrying out PCR greater than 1.71 on purity and humic acid pollution level.
The comparison of several kinds of mulberry tree rhizosphere soils of table 1 microorganism total DNA process for extracting
The not purified total DNA of mulberry tree rhizosphere soil microbial genome that extracts with different methods is a template; The direct V3 district of amplification bacterial 16 S rDNA; Thereby judge whether there is suppressor factor in the DNA extraction sample and is enough to suppress the Taq enzymic activity, cause it can not obtain amplified production.Amplified production is with 1.5% agarose gel electrophoresis detected result such as Fig. 2.Total DNA that employing method 4,5,8 and 9 is extracted can both success amplify 16SrDNA V3 fragment; And the template DNA that employing method 1,2,3,6,7 is extracted fails to amplify the purpose band; Explain that dna profiling is impure, contain certain impurity, suppressed subsequent P CR reaction.
Product after total DNA cloning of method 4,5,8 and 9 extractions is directly gone up appearance; Detect the variety of the mulberry field soil microbial community that shows through denaturing gradient gel electrophoresis; Thereby verify that further this test sets up the feasibility of mulberry tree rhizosphere soil microorganism total DNA process for extracting, the result is as shown in Figure 3.Total DNA of 4 kinds of method extractions all can obtain the bacterial flora variety collection of illustrative plates of rich, but the bacterium variety that method 8,9 is extracted is obviously wanted the height of ratio method 4,5.Hence one can see that, and it is very crucial to pcr amplification to extract highly purified dna profiling.
The present invention has following beneficial effect:
1. be directed against the singularity of mulberry field soil; When utilizing CTAB, N,O-Diacetylmuramidase, proteolytic enzyme and SDS acting in conjunction with lysing cell to its multigelation; Confirm CTAB, N,O-Diacetylmuramidase, proteolytic enzyme, the SDS concentration of suitable mulberry field soil treating, obtained the good cell lytic effect.
2. method therefor is simple and convenient, does not need purified promptly can be used for subsequent P CR analysis and DGGE analysis.CTAB, N,O-Diacetylmuramidase, protein enzyme K and SDS acting in conjunction lysing cell, and used the further smudge cells of multigelation method, confirmed to be suitable for the reaction conditions of mulberry field soil, improve the DNA productive rate.
3. to the singularity of mulberry field soil, this law has been saved tediously long, loaded down with trivial details DNA washing step, save time and avoid the DNA loss, and in DNA extraction liquid direct interpolation CaCl
2, BSA and PVP, confirmed the reaction conditions of suitable mulberry field soil, make easy and simple to handlely, the humic acid removal effect is obvious, this is an innovation part of the present invention.In addition, CTAB not only can be used for lysis, also helps to remove humic acid.The DNA purity that the PEG8000 precipitin reaction system that is suitable for mulberry field soil of establishing makes the present invention extract improves 5.3%-8.4% than existing extraction effect best technique, reaches the needs that directly carry out subsequent molecular.
4. the dna fragmentation that utilizes the inventive method to extract can carry out amplification and the DGGE atlas analysis of 16SrDNA; And can cut glue recovery, base order-checking to the specific band of DGGE bands of a spectrum; Compare with existing sequence in the RDP DB; Or discern unknown bacterium through setting up new sequence probe, thus confirm that biological community structure forms, lay the foundation for studying mulberry tree rhizosphere soil biological community structure variety and ecological functions from now on.
Description of drawings
Fig. 1 different methods extracts the electrophoretogram (M. λ DNA/HindIII molecule marker 1～9 different methods extracts total DNA, and the swimming lane numbering is consistent with table 1 numbering) of mulberry tree rhizosphere soil microorganism total DNA
Fig. 2 different methods extracts the 16S rDNA pcr amplification result (M.DL2000DNA molecule marker 1～9 different methods extracts the 16S rDNA amplification of total DNA, and the swimming lane numbering is consistent with table 1 numbering) of mulberry tree rhizosphere soil microorganism total DNA
Fig. 3 different methods extracts the DGGE collection of illustrative plates (the swimming lane numbering is consistent with table 1 numbering) of the 16S rDNA of mulberry tree rhizosphere soil microorganism total DNA
Embodiment
For simple and purpose clearly, hereinafter combines embodiment that the present invention is done further explanation:
Embodiment 1:
PVP pre-treatment-CTAB-N,O-Diacetylmuramidase-proteolytic enzyme-SDS-multigelation method.Get 5g soil sample adding 20g/L sodium-metaphosphate damping fluid and (contain 10g/L PVP-K30; PH 8.5) 30mL, shaking table vibration 15min, the centrifugal 5min of 8500r/min gets deposition, repeated washing 3 times; Get deposition, add 13.5mL DNA extraction liquid I and a little silica sand, vortex oscillation device vibration 3min; Add 100mg/mL N,O-Diacetylmuramidase 150 μ L, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 20mg/mL Proteinase K 15 μ L again, mixing, 37 ℃ of water-bath 1h; Add 1.5mL 10%SDS, 65 ℃ of water-bath 1h; Multigelation 3 times, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic phenol/chloroform/primary isoamyl alcohol (volume ratio 25: 24: 1) extracting, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant; Add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant; In supernatant, add 0.7 times of volume Virahol and 0.1 times of volume NaAc, 8500r/min is spent the night in-20 ℃ of placements; 4 ℃ of centrifugal 20min, deposition is used 70% washing with alcohol, the centrifugal 10min of 12500r/min; The deposition room temperature is dried, and adds 200 μ L TE dissolution precipitations, and-20 ℃ of preservations promptly obtain the total DNA of mulberry field soil microorganisms.Embodiment 2:
PVP pre-treatment-CTAB, CaCl2, BSA-N,O-Diacetylmuramidase-proteolytic enzyme-SDS-multigelation method are got 5g soil sample adding 20g/L sodium-metaphosphate damping fluid and (are contained 10g/L PVP-K30; PH 8.5) 30mL, shaking table vibration 15min, the centrifugal 5min of 8500r/min gets deposition, repeated washing 3 times; Get deposition, add 13.5mL DNA extraction liquid II and a little silica sand, vortex oscillation device vibration 3min; Add 100mg/mL N,O-Diacetylmuramidase 150 μ L, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 20mg/mL Proteinase K 15 μ L again, mixing, 37 ℃ of water-bath 1h; Add 1.5mL 10%SDS, 65 ℃ of water-bath 1h; Multigelation 3 times, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic phenol/chloroform/primary isoamyl alcohol (volume ratio 25: 24: 1) extracting, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant; In supernatant, add 0.7 times of volume Virahol and 0.1 times of volume NaAc, 8500r/min is spent the night in-20 ℃ of placements; 4 ℃ of centrifugal 20min, deposition is used 70% washing with alcohol, the centrifugal 10min of 12500r/min; The deposition room temperature is dried, and adds 200 μ L TE dissolution precipitations ,-20 ℃ of preservations.Promptly obtain the total DNA of mulberry tree soil microorganisms.
Embodiment 3:
CTAB, PVP, CaCl2, BSA-N,O-Diacetylmuramidase, proteolytic enzyme-SDS-multigelation method.Get the 5g soil sample, add 13.5mLDNA extracting solution III and a little silica sand, vortex oscillation device concussion 3min; Add 150 μ L 100mg/mL N,O-Diacetylmuramidases, 15 μ L20mg/mL Proteinase Ks, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 20mg/mL Proteinase K 15 μ L again, mixing, 37 ℃ of water-bath 1h; Add 1.5mL 10%SDS, 65 ℃ of water-bath 1h; Multigelation 3 times, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic phenol/chloroform/primary isoamyl alcohol (volume ratio 25: 24: 1) extracting, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant; In supernatant, add 0.7 times of volume Virahol and 0.1 times of volume NaAc ,-20 ℃ of placements are spent the night, 8500r/min, 4 ℃ of centrifugal 20min; Deposition is used 70% washing with alcohol, the centrifugal 10min of 12500r/min, and the deposition room temperature is dried; Add 200 μ L TE dissolution precipitations ,-20 ℃ of preservations promptly obtain the total DNA of mulberry field soil microorganisms.
Embodiment 4:
CTAB, CaCl2, BSA-N,O-Diacetylmuramidase, proteolytic enzyme-SDS, PVP-multigelation method.Get the 5g soil sample, add 13.5mLDNA extracting solution II and a little silica sand, vortex oscillation device vibration 3min; Add 100mg/mL N,O-Diacetylmuramidase 150 μ L, 20mg/mL Proteinase K 15 μ L, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 1.5mL 10%SDS and 0.3g PVP, mixing, 65 ℃ of water-bath 1h; Multigelation 3 times; The centrifugal 10min of 8500r/min; Get supernatant, add isopyknic phenol/chloroform/primary isoamyl alcohol (volume ratio 25: 24: 1) extracting, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant; In supernatant, add 0.7 times of volume Virahol and 0.1 times of volume NaAc ,-20 ℃ of placements are spent the night, 8500r/min, 4 ℃ of centrifugal 20min; Deposition is used 70% washing with alcohol, the centrifugal 10min of 12500r/min, and the deposition room temperature is dried; Add 200 μ LTE dissolution precipitations ,-20 ℃ of preservations promptly obtain the total DNA of mulberry field soil microorganisms.
Embodiment 5:
CTAB, PVP, CaCl2, BSA-N,O-Diacetylmuramidase, proteolytic enzyme-SDS-multigelation method.Get the 5g soil sample, add 13.5mLDNA extracting solution III and a little silica sand, vortex oscillation device concussion 3min; Add 150 μ L 100mg/mL N,O-Diacetylmuramidases, 15 μ L20mg/mL Proteinase Ks, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 20mg/mL Proteinase K 15 μ L again, mixing, 37 ℃ of water-bath 1h; Add 1.5mL 10%SDS, 65 ℃ of water-bath 1h; Multigelation 3 times, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic phenol/chloroform/primary isoamyl alcohol (volume ratio 25: 24: 1) extracting, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant; In supernatant, add 0.5 times of volume 25%PEG 8000 and 0.1 times of volume 5mol/L NaCl, 8500r/min is spent the night in 4 ℃ of placements; 4 ℃ of centrifugal 20min, deposition is used 70% washing with alcohol, the centrifugal 10min of 12500r/min; The deposition room temperature is dried, and adds 200 μ L TE dissolution precipitations ,-20 ℃ of preservations.Promptly obtain the total DNA of mulberry field soil microorganisms.
Claims (2)
1. a method that adopts many means to extract mulberry tree rhizosphere soil microorganism total DNA is characterized in that, comprises the steps:
Described method is specially PVP pre-treatment-CTAB, CaCl
2, BSA-N,O-Diacetylmuramidase-proteolytic enzyme-SDS-multigelation method, get the 5g soil sample and add 20g/L sodium-metaphosphate damping fluid 30mL, shaking table vibration 15min, the centrifugal 5min of 8500r/min gets deposition, repeated washing 3 times; Get deposition, add 13.5mL DNA extraction liquid II and a little silica sand, vortex oscillation device vibration 3min; Add 100mg/mL N,O-Diacetylmuramidase 150 μ L, incubation 1h in the mixing, 37 ℃, 230r/min shaking table; Add 20mg/mL Proteinase K 15 μ L again, mixing, 37 ℃ of water-bath 1h; Add 1.5mL 10%SDS, 65 ℃ of water-bath 1h; Multigelation 3 times, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic phenol/chloroform/primary isoamyl alcohol (volume ratio 25: 24: 1) extracting, the centrifugal 10min of 8500r/min; Get supernatant, add isopyknic chloroform/primary isoamyl alcohol (volume ratio 24: 1) extracting once more, the centrifugal 10min of 8500r/min gets supernatant; In supernatant, add 0.5 times of volume 25%PEG 8000 and 0.1 times of volume 5mol/L NaCl, 8500r/min is spent the night in 4 ℃ of placements; 4 ℃ of centrifugal 20min, deposition is used 70% washing with alcohol, the centrifugal 10min of 12500r/min; The deposition room temperature is dried, and adds 200 μ L TE dissolution precipitations ,-20 ℃ of preservations; Promptly obtain mulberry tree rhizosphere soil microorganism total DNA.
Said DNA extraction liquid II composition is Tris-HCl 100mmol/L, EDTA 100mmol/L, Na
3PO
4100mmol/L, NaCl 1.5mol/L, 1%CTAB, 2%CaCl
2, 1 μ g/mL BSA; PH 8.0.Described soil sample is picked up from the mulberry tree rhizosphere soil, and the degree of depth is 5～10cm topsoil, by 5 method samplings, puts into sterile bag behind the mixing, 4 ℃ of preservations.
2. the purposes of the method for extraction DNA as claimed in claim 1; It is characterized in that: this method is at the amplification of carrying out 16SrDNA and DGGE atlas analysis; Compare with existing sequence in the RDP DB; Or discern unknown bacterium, thereby confirm biological community structure composition, structure diversity and ecological functions thereof through setting up new sequence probe.
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Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN103820434A (en) * | 2014-03-19 | 2014-05-28 | 四川省农业科学院土壤肥料研究所 | Method for extracting total DNA (deoxyribonucleic acid) of fungal hyphae |
| CN104911178A (en) * | 2015-06-19 | 2015-09-16 | 厦门大学 | Method for simultaneously extracting microbial intracellular and extracellular DNAs (deoxyribonucleic acids) in sewage biological treatment water sample |
| CN106497913A (en) * | 2015-09-07 | 2017-03-15 | 粮华生物科技（北京）有限公司 | A kind of method for extracting soil microorganism STb gene and its application |
| CN110295162A (en) * | 2019-06-17 | 2019-10-01 | 广东省生态环境技术研究所 | A kind of DNA extraction reagent and extracting method for Fe-mn Nodules of Soils microorganism |
| CN110295163A (en) * | 2019-06-17 | 2019-10-01 | 广东省生态环境技术研究所 | The extraction reagent and extracting method of The Rhizosphere of Rice iron membrane micro DNA |
| CN110511977A (en) * | 2019-09-05 | 2019-11-29 | 武汉华大基因技术服务有限公司 | Extracting method, sequencing approach and the kit of genomic DNA |
| CN110914424A (en) * | 2017-08-22 | 2020-03-24 | 深圳华大基因股份有限公司 | Optimized large-fragment DNA extraction method |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1978453A (en) * | 2005-12-07 | 2007-06-13 | 浙江工业大学 | Method for extracting soil microbial DNA |
| CN101063174A (en) * | 2007-05-28 | 2007-10-31 | 中国热带农业科学院橡胶研究所 | Method for scale selection of microorganism alkaliproof related genes |
| CN102286463A (en) * | 2011-06-29 | 2011-12-21 | 内蒙古大学 | High-efficiency humus-removing environment sample total DNA extraction method |
-
2012
- 2012-04-05 CN CN2012100968210A patent/CN102643794A/en active Pending
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1978453A (en) * | 2005-12-07 | 2007-06-13 | 浙江工业大学 | Method for extracting soil microbial DNA |
| CN101063174A (en) * | 2007-05-28 | 2007-10-31 | 中国热带农业科学院橡胶研究所 | Method for scale selection of microorganism alkaliproof related genes |
| CN102286463A (en) * | 2011-06-29 | 2011-12-21 | 内蒙古大学 | High-efficiency humus-removing environment sample total DNA extraction method |
Non-Patent Citations (3)
| Title |
|---|
| 何丽鸿等: "堆肥中微生物总DNA的高效提取", 《微生物学报》 * |
| 李钧敏等: "一种高效可直接用于PCR分析的土壤总微生物DNA抽提方法", 《应用生态学报》 * |
| 蒋云霞等: "不同提取缓冲液对红树林土壤DNA提取品质的影响", 《热带海洋学报》 * |
Cited By (10)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN103820434A (en) * | 2014-03-19 | 2014-05-28 | 四川省农业科学院土壤肥料研究所 | Method for extracting total DNA (deoxyribonucleic acid) of fungal hyphae |
| CN104911178A (en) * | 2015-06-19 | 2015-09-16 | 厦门大学 | Method for simultaneously extracting microbial intracellular and extracellular DNAs (deoxyribonucleic acids) in sewage biological treatment water sample |
| CN106497913A (en) * | 2015-09-07 | 2017-03-15 | 粮华生物科技（北京）有限公司 | A kind of method for extracting soil microorganism STb gene and its application |
| CN110914424A (en) * | 2017-08-22 | 2020-03-24 | 深圳华大基因股份有限公司 | Optimized large-fragment DNA extraction method |
| CN110295162A (en) * | 2019-06-17 | 2019-10-01 | 广东省生态环境技术研究所 | A kind of DNA extraction reagent and extracting method for Fe-mn Nodules of Soils microorganism |
| CN110295163A (en) * | 2019-06-17 | 2019-10-01 | 广东省生态环境技术研究所 | The extraction reagent and extracting method of The Rhizosphere of Rice iron membrane micro DNA |
| CN110295163B (en) * | 2019-06-17 | 2022-02-11 | 广东省科学院生态环境与土壤研究所 | Reagent and method for extracting rice rhizosphere iron membrane microorganism DNA |
| CN110295162B (en) * | 2019-06-17 | 2022-03-29 | 广东省科学院生态环境与土壤研究所 | DNA extraction reagent and extraction method for soil iron-manganese nodule microorganisms |
| CN110511977A (en) * | 2019-09-05 | 2019-11-29 | 武汉华大基因技术服务有限公司 | Extracting method, sequencing approach and the kit of genomic DNA |
| CN110511977B (en) * | 2019-09-05 | 2023-07-21 | 武汉华大基因技术服务有限公司 | Genomic DNA extraction method, sequencing method and kit |
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