Technical Report on the PCR-DGGE Analysis of
Bacterial and Fungal Soil Communities

Ver. 3.3
Revised on June 10, 2010

National Institute for Agro-Environmental Sciences

Table of Contents
Page
1. Preparation of soil samples

1

2. DNA extraction

1

3. Polymerase chain reaction (PCR)
3-1. Bacteria

33-2. Fungi

5

4. Denaturing gradient gel electrophoresis (DGGE)

6

5. Examples

12

6. Troubleshooting

15

7. References

19For inquiries regarding this manual, please contact:
Seiya Tsushima, Yuko Matsushita
Natural Resources Inventory Center
National Institute for Agro-Environmental Sciences
E-mail: seya@affrc.go.jp, yuhko@affrc.go.jp
Tel.: +81-29-838-8351

1. Preparation of soil samples(1) Pass the collected soil sample through a sieve with a 2-mm mesh size to remove as much of
the plant residue as possible. Thoroughly mix the sieved soil in a large plastic bag to avoid
variability among the results of replicate soil samples.

(2) Put 0.4 g of the obtained soil in a tube for bead mill homogenization. If DNA is notextracted immediately, store the tubes at -20°C or lower. The sample number from eachfield should be about 3–5, depending on the characteristics of the target field (i.e., its scaleor diversity).

2. DNA extraction

DNA is extracted from the soil samples by using the commercially available kit described
below. The method includes the process of prevention of DNA adsorption to soil particles byadding skim milk1). The tubes used for bead mill homogenization and test reagents (excluding
skim milk) are included in the kit.

【Materials required】- FastDNA SPIN Kit for Soil (Q-BIOGene)- Skim milk
- Bead mill homogenizer (FP series from Q-BIOGene, Inc., Bead Smash from Wakenyaku, Co.,
Ltd., etc.)- High-speed microcentrifuge【Extraction procedure】(1) Add 978 μl of sodium phosphate buffer*1 and 122 μl of MT buffer to the 0.4 g sample in the
tube (Lysing Matrix E) used for bead mill homogenization and suspend the mixture.
*1 For soil types such as andosol, which strongly adsorb DNA, add 80–160 μl of 20%(w/v) skim milk solution when adding the sodium phosphate buffer. In this case, a1

volume equivalent to the skim milk solution must be reduced from the sodium
phosphate buffer. Since the optimum amount of skim milk to be added differs from soil
to soil, it is necessary to check the optimum amount in advance. To prevent DNA
contamination from skim milk, the skim milk solution should be heat-treated in advanceat 115°C for 5 min. It is recommended that the skim milk solution be put into tubes(capacity, approximately 2 ml) with screw caps and stored at -20°C.

(2) Set the tube in the bead mill homogenizer. At this time, ensure that the tube cap is tightly
closed, since failing to do so may cause the extract to leak. The standard speeds and times
for the FastPrep FP series and BeadSmash series are 5.5 m/s for 30 s and 5,000 rpm for 30 s,
respectively.

(3) Centrifuge at 14,000 ×g for 1 min, and then transfer the supernatant to a new 1.5-ml tube.
(4) Add 250 μl of PPS to the supernatant and mix well by flipping the tube upside down, andthen centrifuge at 14,000 ×g for 5 min.

(5) Transfer the supernatant to a new 15-ml tube, and add 1 ml of binding matrix suspension to
it. Since the binding matrix suspension precipitates easily, mix well to prevent unevenness
while dispensing.

(6) Mix gently using a rotator or by hand for 2 min, and then make the tube stand still in a rack
until the binding matrix settles.
(7) Remove 500 μl of the supernatant, avoiding removal of the binding matrix.
(8) Suspend the binding matrix again, and transfer 600 μl to a spin filter; then centrifuge at
14,000 ×g for 1 min.

(9) Decant the flow-through and pass the remaining suspension through the spin filter using thesame procedure, and then collect the binding matrix on the spin filter.
(10) Add 500 μl of salt ethanol wash solution (SEWS-M) to the collected binding matrix, and2then centrifuge at 14,000 ×g for 1 min.

(11) Decant the flow-through and centrifuge at 14,000 ×g for 2 min to completely remove the
SEWS-M, and then transfer the spin filter to a catch tube.
(12) Air-dry the matrix for 5 min, and then add 80 μl*2 of DES and gently suspend it. At thistime, ensure that no damage is caused to the filter by the head of the tip.
*2 Although the kit manual specifies the use of 50 μl of DES, we recommend 80 μl be
used since it is difficult to thoroughly suspend the matrix using 50 μl of DES.

(13) Centrifuge at 14,000 ×g for 1 min, and collect the eluate in a catch tube. Confirm DNA
extraction by performing agarose gel electrophoresis by using approximately 5–10 μl of
the eluted DNA solution*3. If the DNA solution is not used immediately, freeze-store it ata temperature of -20°C or lower.
*3 When humic soil is used, the solution appears to be slightly colored. In case PCR
inhibition occurs, additional purification must be performed using a commerciallyavailable DNA purification column etc.

3. PCR

3-1. Bacteria
Use the following primer set2), which targets the V6-8 variable region of eubacterial 16S
rRNA genes.

Forward primer: F984GC
5′-cgc ccg ggg cgc gcc ccg ggc ggg gcg ggg gca cgg ggg gaa cgc gaa gaa cct tac-3′
The underlined segment indicates a GC clamp.
Reverse primer: R1378
5′-cgg tgt gta caa ggc ccg gga acg-3′3

【PCR conditions】
Use TOYOBO “KOD-Plus-” under the following conditions:- The composition of the reaction mixture (Total volume, 50 μl)

AmountFinal concentration

Sterile distilled water

33 μl

10× buffer

5 μl

1×

dNTPs (2 mM)

5 μl

0.2 mM each

MgSO4 (25 mM)

2 μl

1 mM

F984GC (10 μM)

1 μl

0.2 μM

R1378 (10 μM)

1 μl

0.2 μM

BSA (20 mg/ml)*41 μl

0.4 μg/μl

KOD-Plus-

1 μl

Template DNA*5

1 μl*4 Bovine serum albumin solution (BSA; TaKaRa #2320). The inhibition of PCR, which may
be caused by humic substances, can be prevented by the addition of BSA.
*5 Add 1 μl of the DNA solution used in the extraction method described above. For thenegative control experiment, the mixture without the template DNA must be prepared.

- Reaction cycle
94°C (2 min)  [94°C (15 s), 55°C (30 s), 68°C (30 s)] × 34

【Detection and purification of PCR product】
To confirm that PCR product of the expected size has been obtained (approximately 470–480bp), perform agarose gel electrophoresis using approximately 2–3 μl of the PCR product. Purify
the remaining product using a commercially available PCR product purification kit (QIAGEN
QIAquick PCR Purification Kit etc.), and then measure the DNA concentration. If denaturing
gradient gel electrophoresis (DGGE) is not performed immediately, store the purified product at-20°C or lower.

4

3-2. Fungi
Use the following primer set3), which targets fungal 18S rRNA genes.

Forward primer: NS1
5′-gta gtc ata tgc ttg tct c-3′

Reverse primer: GCFung5′-cgc ccg ccg cgc ccc gcg ccc ggc ccg ccg ccc ccg ccc cat tcc ccg tta ccc gtt g-3′
The underlined segment indicates a GC clamp.

【PCR conditions】
Use TOYOBO “KOD-Plus-” under the following conditions:- The composition of the reaction mixture (Total volume, 50 μl)

AmountFinal concentration

Sterile distilled water

32 μl

10× buffer

5 μl

1×

dNTPs (2 mM)

5 μl

0.2 mM each

MgSO4 (25 mM)

2 μl

1 mM

NS1 (10 μM)

1.5 μl

0.3 μM

GCFung (10 μM)

1.5 μl

0.3 μM

BSA (20 mg/ml)*6

1 μl

0.4 μg/μl

KOD-Plus-

1 μl

Template DNA*7

1 μl*6 Bovine serum albumin solution (BSA; TaKaRa). The inhibition of PCR, which may becaused by humic substances, can be prevented by the addition of BSA.
*7 Add 1 μl of the DNA solution used in the extraction method described above. For thenegative control experiment, the mixture without the template DNA must be prepared.

- Reaction cycle

594°C (2 min)  [94°C (15 s), 50°C (30 s), 68°C (30 s)] × 30

【Detection and purification of PCR product】
Perform agarose gel electrophoresis using an approximately 2- to 3-µl aliquot of the PCR
product to confirm that a product of the expected size (approximately 390 bp) has been obtained.
Purify the remaining product using the same method used for common bacterial analysis, andthen measure the DNA concentration. If DGGE is not performed immediately, store the purified
product at -20°C or lower.

4. DGGE

Bio-Rad DCode system is used for DGGE. The procedure is the same as that for bacteria andfungi except for the electrophoresis conditions shown in Tables 1 and 2.

Table 1 Electrophoresis conditions
Condition

For bacteria

For fungi

Acrylamide/bis concentration

6%

7%

50%  70%

20%  45%

Temperature

58°C

60°C

Voltage

50 V

50 V

Time

18 h

20 h

Denaturing concentration
gradient

Table 2 Composition of the gel stock solution for DGGE*8
For bacteria

For fungi

50%
denaturingsolution70%
denaturingsolution20%
denaturingsolution45%
denaturingsolution

40% acrylamide/bis 37.5:1

15 ml

15 ml

17.5 ml17.5 ml

50× TAE

2 ml

2 ml

2 ml

2 ml

Formamide (deionized)

20 ml

28 ml

8 ml

18 ml

Urea

21 g

29.4 g8.4 g

18.9 gup to 100 ml

up to 100 ml

up to 100 ml

up to 100 ml

Composition

Ultrapure water*8 100% denaturing solution is equivalent to a combination of 7 M urea and 40% formamide.

6

【Materials required】- DCode system (Bio-Rad)(Main unit, casting stand, sandwich clamp, glass plate, spacer, syringes, tubes, needles, Y-fitting,comb, and gradient former)- Power supply- Suction filter (IWAKI membrane filter system #8110-250 etc.)- Vessel used for gel staining (polypropylene)- Gel imaging equipment- 40% acrylamide/bis 37.5:1 solution- 50× TAE
- Formamide (deionized)- Urea (molecular biology grade)- Ammonium persulfate- TEMED- Dye solution (see manual attached to DCode)- 2× loading dye (see manual attached to DCode)- SYBR Green I (TaKaRa #F0513 etc.)【Preparation of the stock solution for DGGE】(1) On the basis of the composition given in Table 2, prepare 2 kinds of gel stock solutions withdifferent denaturation concentrations. It is possible to cast the DGGE gel for 6 sheets using
100 ml of each stock solution. Unpolymerized acrylamide is toxic. Wear rubber gloves
when handling it.

(2) Filter the prepared solution using the suction filter to remove impurities.

(3) Store the solution in a light-resistant bottle at 4°C. Use within approximately 1 month*9.
*9 Since formamide is gradually degraded by moisture, the ability of DNA denaturation
will be reduced in the deteriorated gel stock, with the band declining toward thedownstream side. If this is observed, replace the stock solution regardless of the7preservation period.

【Casting Gels】(1) Assemble the plate following the instructions in the DCode manual*10. Secure the plate on
the casting stand, and tape the tube used for gel injection in the center of the plate.
*10 Ensure that the spacer and the edge of the glass plate are on a flat plane to prevent gelleakage.

(2) Prepare an adequate amount of 10% ammonium persulfate solution*11.
*11 Use approximately 300 μl per gel sheet. Prepare just before use.

(3) Pour 16 ml of each denatured gel stock solution into clean beakers etc.
(4) Add 100 μl of dye solution to the highly denaturing gel stock solution.
(5) Add 144 μl of ammonium persulfate solution prepared in Step (2) to both stock solutions
and lightly shake.
(6) Add 14.4 μl of TEMED to both stock solutions, lightly shake, and suction the whole amountof each solution into syringes with an attached tube. Remove air from inside the syringes
and tubes, set the syringes on a gradient former*12, and then connect the edge of each tube
to the tube used for gel injection with a Y-fitting.
*12 Ensure not to confuse the left and right of the gradient former. Firmly secure a highly
denaturing gel stock solution syringe on the right-hand side of the wheel and a slightly
denaturing gel stock solution syringe on the left-hand side. If they are not tightly
secured with screws, the syringe will become misaligned at the time of injection,
thereby causing variation in gel quantity. Rotate, in advance, the wheel of the gradient
former in the reverse direction of gel injection operation until it cannot be rotatedanymore.

(7) Slowly rotate the wheel of the gradient former toward yourself at a steady speed. Inject thesolution until it reaches the upper edge of the plate, disconnect the tubes, and then insert the
comb taking care to prevent the entry of air bubbles. Return the solution remaining in the8tubes and syringes to the container, and dispose of it after polymerization. Rinse the tubes
and syringes with distilled water so that acrylamide will not set in them.

(8) Polymerize for 3 h or longer.

Since polymerization of acrylamide starts as soon as TEMED is added, steps (6)–(8) must be
performed quickly for each gel. Because the polymerization of acrylamide progresses rapidly ata higher temperature, chill the gel stock solution well, in advance. If there is a large differencein temperature between the glass plate and the stock solution, polymerization will not progress
uniformly, thereby causing distortion of the denaturing gradient. It is recommended that, if
possible, gel casting be performed in a low-temperature room in order to keep the glass plate ata low temperature. In this case, polymerization will take longer (Return the product to room
temperature after it has been solidified to a certain degree).

【Electrophoresis】(1) Prepare 7 L of 1× TAE buffer, and pour it into the electrophoresis tank until it reaches
between the “Fill” and “Run” positions. Turn on the heater, and set the temperatureapproximately 5°C higher than the electrophoresing temperature*13. Perform this step while
gel polymerization is in progress, because it takes a long time for the buffer to be heated toan appropriate temperature.
*13 This is because the buffer temperature drops when the gel slabs are set later.

(2) Carefully pull the comb out of the sufficiently polymerized gel. Thoroughly remove any
extra gel from the plate surface, and cleanse the wells using an injector etc. Further,straighten the border of the wells.

(3) Attach the gel slab to the core of DCode, and set it on the electrophoresis tank. At this time,
if the entire core is sunk, the buffer will overflow. Therefore, put aside approximately 300
ml of the buffer from the electrophoresis tank in a separate vessel in advance, and after
setting the core, return the buffer in the separate vessel to the upper part of the core. DCodeenables electrophoresis with 2 gels simultaneously, but even when electrophoresing just one
gel, set the plates on both surfaces. In this case, you can use plates without a gel andspacers.

9

(4) Start the pump and fill the electrophoresis tank with the buffer to the “Maximum” line.
Check to see that the upper buffer retains a fixed water level as the pump is operated. Set
thetemperaturetoapproximately

2°C

higherthanthetemperatureduringelectrophoresis*14, and wait until the temperature stabilizes.
*14 This is because the buffer temperature drops during sample application.

(5) Prepare a sample for electrophoresis by mixing an equivalent of 200 ng (when a 16-wellcomb is used) of PCR product with the same quantity of 2× loading dye.

(6) Remove the upper unit, and apply the sample to each well. It is better not to use the wells
at the ends since they are likely to cause distortion in electrophoresis. Prepare marker
lanes*15 to compare the movement patterns between the different gels.
*15 Use of DGGE Marker III for bacteria and DGGE Marker IV for fungi isrecommended (both manufactured by Nippon Gene Co., Ltd.).

(7) Set the temperature given under the electrophoresis conditions in Table 1, and start thepump. At this time, if the buffer level does not reach the “Maximum” line of theelectrophoresis tank, replenish the buffer. After the temperature stabilizes, startelectrophoresis in accordance with the electrophoresis conditions shown in Table 1.

【Staining】
Although SYBR Green I used in the following procedure is considered less harmful thanethidium bromide, wear rubber gloves for safety during the staining operation. The gloves also
prevent gels from being soiled with sebum etc.

(1) Dissolve the core and remove the sandwich clamp from the glass plate.

(2) Remove the smaller glass plate from the gel by slowly and carefully lifting the spacer
along the edge.

(3) Carefully remove the gel from the larger glass plate, and transfer it to a vessel used forstaining. At this time, take care not to damage the gel.

10(4) Lightly rinse the gel with an appropriate quantity of 1× TAE buffer, and discard the buffer.

(5) Add 100 ml of 1× TAE buffer and 10 µl of SYBR Green I, and gently shake on a turntableetc., for 30 min. Read the manual for SYBR Green I thoroughly before handling it. Since
SYBR Green I is adsorbed to glass and polyethylene, use a vessel made of polypropylene
for staining.

(6) Generate an image of the electrophoretic profile following the instructions in the operation
manual for the imaging equipment used. The use of a large-size gel image scanner is ideal,
but by using a transilluminator together with a digital camera that has a manual exposure
function, it is possible to obtain a good electrophoretic profile if appropriate adjustments
are made. Minigel imaging equipment and Polaroid cameras usually lack resolution.

11

5. Examples

1. The extraction of DNA from the soil samples
Samples1

Field soil (andosol)

2

Field soil (yellow soil)

3

Field soil (gray lowland soil)

4

Field soil (low humic andosol)

5Greenhouse floor soil (low humic andosol)

6

Field soil (low humic andosol)

7

Field soil (brown lowland soil)

8

Field soil (low humic andosol)

9

Paddy field (andosol)

10 Paddy field (gray lowland soil)M

Kb DNA ladder (Stratagene)In accordance with this manual, 80 µl of DNA solution was extracted from 0.4 g of each soil
sample, 6 µl of which was used for agarose gel electrophoresis. On extraction, 80 µl of 20%
skim milk solution was used for samples 2 and 3, 120 µl for sample 1, and 160 µl for samples 4,
5, 6, and 8.

2. PCR【PCR of bacterial 16S rDNA】
Using the DNA extracted from theabovementioned soil samples as atemplate, PCR amplification ofbacterial 16S rDNA was performed.
Two microliters of each product
was

used

for

agarosegelelectrophoresis. N is the negative
control.

12

【PCR of fungal 18S rDNA】
Using the DNA extracted from theabovementioned soil samples as atemplate, PCR amplification of
fungal 18S rDNA was performed.
Two microliters of each product
was

used

for

agarosegelelectrophoresis. N is the negative
control.

3. DGGE【Bacteria】
After purifying the bacterial 16S
rDNA PCR products, an equivalentof 200 ng of each product wasused for electrophoresis under theconditions

specified

in

this

manual.
After staining with SYBR Green I,
imaging

was performed

using

PharosFX (Bio-Rad).
M is a marker optimized for the
analysisconditions(DGGE

Marker III; Nippon Gene Co.,
Ltd.).

13

【Fungi】
After purifying the fungal 18S
rDNA PCR products, an equivalentof 200 ng of each product wasused for electrophoresis under theconditions

specified

in

this

manual.
After staining with SYBR Green I,
imaging

was performed

using

PharosFX (Bio-Rad).
M is a marker optimized for the
analysisconditions(DGGE

Marker IV; Nippon Gene Co.,
Ltd.).

14

6. Troubleshooting【Problems related to DNA extraction】-DNA cannot be extracted, or the extracted amounts are extremely small.
 Change the amount of skim milk added. Depending on the soil, the yield of DNA may be
low because the original biomass is also low.

-Spin filter is broken and binding matrix falls off.
 Depending on the soil, this trouble may happen frequently. If this happens, collect thematrix that has fallen off, suspend it in SEWS-M, and transfer it to a new filter.

-The extracted DNA solution is colored.
 When highly humic soil is used, the extracted DNA solution may have a light brown color.
If PCR is inhibited, re-purify the DNA solution using a commercially available DNA
purification kit etc.

-The sample diffuses during the electrophoresis using the agarose gel.
 This may be because there is ethanol remaining in the sample. The binding matrix is not
sufficiently dried after it is cleaned with SEWS-M.

【Problems related to PCR】
-No amplification is obtained.
 When only a particular sample is not amplified, this problem is probably caused byinsufficient amount of template DNA or the presence of PCR-inhibiting contaminants(humic substances) in the DNA solution. If the DNA concentration is clearly low, change
the amount of skim milk that may improve the extraction efficiency. If a sufficientamount of DNA is not obtained even after implementing this measure, increase theamount of template DNA or the cycle number. If the DNA solution is clearly colored,
purify it using a commercial DNA purification kit etc.
 Reagents used for PCR should be completely dissolved and sufficiently mixed before use.
 Confirm the composition of the reaction mixture and the primer concentration.

15

-There are many nonspecific products.
 Ensure that excessive amounts of polymerase and Mg2+ are not present. Take maximum
care to prevent the polymerase, which is a highly viscous solution, from adhering to thepipette tips.
 If the template DNA concentration is extremely high, dilute it before use.

-Amplification is observed in the negative control.
 If the cause cannot be clearly identified, it is better to use new reagents. Since a large
quantity of PCR product is treated in the series of PCR-DGGE work, maximum careshould be taken to prevent contamination of the PCR product. The use of tips with filters
is recommended for the pipetting steps in PCR.

【Problems related to DGGE】-Acrylamide clots during gel casting.
 Polymerization progresses rapidly if the temperature of the gel stock solution is high.
Chill the stock solution well before use.

-Gels do not reach the upper edge of the plate even if the gradient former is rotated all the way.
 When assembling the glass plate, if the bottom surface is not flat, gels may leak during
injection.
 If the screws used to fix the syringe to the gradient former are not fully tightened, thesyringe itself is moved aside when the wheel is rotated and the piston is not fully pushed
in. In particular, this trouble is likely to happen if the syringe rubber plunger generates
large friction due to deterioration. In this case, replace the syringe with a new one.

-The electrophoretic profile is mottled with dirt.
 It is important to keep the instruments, particularly the glass plates, clean. Ensure that
dust does not adhere to the glass plates when assembling. Avoid wiping the glass platewith paper that is likely to leave fibers.
 If the gel stock itself contains impurities, refilter the stock.
 Ensure that the buffer and equipment used for staining and imaging capture are not dirty.

16

-Bands appear as a smear.
 Because of the structural characteristics of DCode, the bands on the back side gel tend tobe blurry. This problem can be improved by adding a magnetic stirrer to theelectrophoresis tank to stir the buffer during electrophoresis.
 If a sample that has been stored under poor conditions is electrophoresed, the band may
smear.
 If the timing of comb insertion is delayed, or air bubbles adhere to the comb, the wells
may become irregular, thereby affecting the electrophoresis profile.
 When injecting the sample to the well, take maximum care not to let the sample diffuse.

-The pattern is distorted.
 If the polymerization of acrylamide progresses rapidly, the denaturing gradient tends tobe distorted. To prevent the pattern from being distorted, chill the glass plate and the gelsolution in advance so that polymerization progresses slowly.

-The pattern reproducibility is poor.
 Since the deterioration of the syringe rubber plunger greatly influences pattern
reproducibility, the damaged syringes must be replaced immediately.
 Use of old gel stock or reuse of TAE buffer is not recommended for good reproducibility.
 Use deionized formamide. If formamide appears to be colored, it needs to be deionizedagain. To deionize formamide, add 10 g of AG501 X-8 resin (Bio-Rad) to 100 ml offormamide, stir for 1 h, and filter.
 If friction is experienced on the wheel of the gradient former, adjustment is necessary. It
may be improved by applying silicon spray to the part where friction is generated, but if
disassembly is necessary for adjustment, it is better to request the manufacturer.

-Upper buffer falls off.
 Ensure that the gasket is sandwiched between the core andthe plate with no space in between. There tends to be a gap
at the position marked by the red arrow in the diagram.

17

-The stirring shaft touches the plate, thereby making a noise.
 This is because the assembly of the core and the plate is incomplete, or the shaft is moved
aside. In the latter case, if the problem is not solved by adjusting the position, repair isnecessary. If electrophoresis is performed with the shaft touching the plate, the plate will
vibrate, thereby disturbing the electrophoresis profile.

18

7. References
1) Hoshino TY and Matsumoto N. 2004. An improved DNA extraction method using skim
milk from soils that strongly adsorb DNA. Microbes and Environments, 19(1), 13-19.

2) Heuer H, Kresk M, Baker P, Smalla K, and Wellington EM. 1997. Analysis of actinomycete
communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic
separation in denaturing gradients. Applied and Environmental Microbiology, 63(8),3233-3241.

3) May LA, Smiley B, and Schmidt MG. 2001. Comparative denaturing gradient gelelectrophoresis analysis of fungal communities associated with whole plant corn silage.
Canadian Journal of Microbiology, 47, 829-841.

19