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CN114047036A - Site collection method of karst cave water environment DNA sample - Google Patents

Site collection method of karst cave water environment DNA sample Download PDF

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Publication number
CN114047036A
CN114047036A CN202111368669.2A CN202111368669A CN114047036A CN 114047036 A CN114047036 A CN 114047036A CN 202111368669 A CN202111368669 A CN 202111368669A CN 114047036 A CN114047036 A CN 114047036A
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China
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water
sample
dna
water sample
karst cave
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CN202111368669.2A
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罗福广
文衍红
王志强
黄杰
石国凡
杨军
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Liuzhou Fishery Technology Promotion Station
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Liuzhou Fishery Technology Promotion Station
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Priority to CN202111368669.2A priority Critical patent/CN114047036A/en
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    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00Sampling; Preparing specimens for investigation
    • G01N1/02Devices for withdrawing samples
    • G01N1/10Devices for withdrawing samples in the liquid or fluent state
    • G01N1/14Suction devices, e.g. pumps; Ejector devices
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00Sampling; Preparing specimens for investigation
    • G01N1/28Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/34Purifying; Cleaning

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • General Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Pathology (AREA)
  • Physics & Mathematics (AREA)
  • Hydrology & Water Resources (AREA)
  • Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Sampling And Sample Adjustment (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

The invention relates to a site collection method of a karst cave water environment DNA sample, which comprises the following steps: firstly, collecting water from a DNA detection point in a karst cave water environment by using a Beller tube, and putting the collected water sample into a disposable plastic basin for later use; and secondly, preliminarily filtering the DNA water sample of the karst cave environment acquired in the first step to remove large-particle impurities, thirdly, taking a disposable injector, absorbing the water sample after preliminary filtration, connecting the water sample to a replaceable membrane needle filter filled with a glass fiber membrane, manually extruding the injector at a constant speed to enable the water sample to be discharged after passing through the replaceable membrane needle filter, and putting the replaced filter membrane into a centrifugal tube filled with absolute alcohol for preservation at a low temperature. The method can collect the DNA sample of the karst cave water environment on site, solves the problems of DNA degradation, cross contamination and the like existing in the process of transporting the water sample to a laboratory for long distance and carrying out vacuum filtration, and has the advantages of low cost, simple and convenient operation and high accuracy of the collected sample.

Description

Site collection method of karst cave water environment DNA sample
Technical Field
The invention relates to a method for collecting a water environment DNA sample, in particular to a method for collecting a karst cave water environment DNA sample on site.
Background
The Guangxi karst cave fishes are rich in biological diversity and are one of hot areas for researching the cave fishes in the world. The traditional research method for the diversity of karst cave fishes mainly depends on collecting methods such as net fishing, electric shock and the like, and due to the complexity and the danger of the underground karst cave, the collection difficulty is extremely high, time and labor are consumed, the related research work progresses slowly, and the species protection work situation is severe. In recent years, the environmental DNA technology has become an important tool for researching biodiversity due to the characteristics of high sensitivity, high efficiency, low cost and the like, the research process of the diversity of karst cave fishes can be accelerated by applying the technology, and the important scientific demand of sustainable utilization of current biodiversity resources is met. Since the DNA of fish in a water sample at a target detection point is easily affected by external and artificial improper operation, false positive of detection data is caused, and misjudgment is caused, the exogenous DNA pollution of non-sampling points in sampling and filtering links is avoided as much as possible. At present, after a water sample is collected at a sampling point, the water sample is transported to a laboratory through medicine fixation or low temperature for vacuum filtration enrichment of DNA, and the method has more unpredictable pollution and DNA degradation risks in sampling, for example, exogenous DNA residue may be generated when sampling and a filter are repeatedly used, cross pollution is generated, DNA degradation in different degrees can be caused by overlong transportation of the water sample, and the potential influence of aerosol on the laboratory operation process and the like.
Chinese utility model patent 201620486713.8 discloses a water environment DNA sampling device, including the water pumper and the drinking-water pipeline of being connected with it, filter paper is installed to the other end of drinking-water pipeline, and filter paper is fixed through solid fixed ring, and the device still includes protection casing and pull pole, and the protection casing is installed on the drinking-water pipeline, and the pull pole passes through the vaulting pole and connects the protection casing. Although the scheme can complete the field collection work of the DNA of the water body environment, the following defects exist: 1. the water pump needs to be additionally provided with a power supply when used in the field, so that the use is inconvenient, and the water pump is large in equipment volume and relatively difficult to carry; 2. the water pump and the water pumping pipeline have cross contamination risk in the repeated sampling process, the cleaning step is complicated, more manpower and material resources are consumed in the cleaning process, and the sampling cost is increased.
Disclosure of Invention
The technical problem to be solved by the invention is as follows: the site collection method for the karst cave water environment DNA sample is provided, the site collection method can collect the karst cave water environment DNA sample on site, the problems that DNA is degraded and cross-polluted when the water sample is transported to a laboratory for a long distance in a vacuum filtration mode are solved, the cost is low, the operation is simple and convenient, and the collected sample is high in accuracy.
The technical scheme for solving the technical problems is as follows: a site collection method of a karst cave water environment DNA sample comprises the following steps:
firstly, before sampling, a sampling person needs to wear disposable latex gloves, and simultaneously the Beller tube and the disposable plastic basin are rinsed for 1-4 times by using a sampling point water sample; then, a traction rope with enough length is cut, two ends of the traction rope are respectively tied above the Beller tube and the traction rod, the Beller tube is pulled to a DNA detection point of the water environment of the karst cave through the traction rod to collect water, and the collected water sample is put into a disposable plastic basin for standby;
and secondly, preliminarily filtering the karst cave environment DNA water sample acquired in the first step, removing large-particle impurities, and specifically operating as follows: filling 2-4 layers of medical gauze packs into the inner side of a paper funnel, pouring a water sample in a karst cave environment into the paper funnel, and receiving and filtering the water sample by a disposable plastic cup for 1-2L for later use;
and thirdly, taking a disposable syringe, absorbing 500mL of the water sample subjected to the secondary primary filtration by 400-L of the disposable syringe, connecting the disposable syringe to a replaceable membrane needle filter filled with a glass fiber membrane, manually extruding the syringe at a constant speed to enable the water sample to pass through the replaceable membrane needle filter and then be discharged, replacing the disposable filter membrane by using disposable tweezers every time 500mL of the water sample is discharged, placing the replaced filter membrane into a centrifuge tube filled with absolute alcohol for preservation at the low temperature of 5-10 ℃, and completing sampling after filtering 1-2L of the water sample.
In the first step, the specific operation method of sampling is as follows: if the water depth of the karst cave is less than or equal to 2 meters, taking 1000mL of water sample which is 0.5m away from the water bottom; if the water depth of the karst cave is more than 2 meters and less than 10 meters, respectively mixing 1000mL of water samples which are 0.5m under the water and 0.5m away from the bottom for standby; if the water depth of the karst cave is more than or equal to 10 meters, 1000mL of water samples which are 0.5m underwater, 10m underwater and 0.5m away from the bottom are respectively taken and mixed for standby.
In the second step, the paper funnel is a 400 mesh paper funnel.
Due to the adoption of the technical scheme, the invention has the following beneficial effects:
1. the invention scientifically uses most standard, disposable and cheap medical and food packaging materials on the market as collecting tools, and the method can collect the DNA sample of the karst cave water environment on site, effectively avoids the problems of cross contamination and inaccurate data caused by DNA degradation, enables the reality of the collected sample data to have substantial great leap, and avoids the inconvenience of post data processing and analysis.
2. The cost is low. The tool used by the invention is disposable material (consumable) which is easy to purchase in the market, the cost of one-time sampling is about 50 yuan (wherein, 10 yuan for a Beller tube, 18 yuan for a 500mL syringe, 12 yuan for a replaceable membrane needle filter and about 10 yuan for other sporadic consumables), and compared with the unpredictable cost such as economy, time, manpower and the like generated by repeated data verification procedures such as repeated sampling, repeated subsequent sample detection and the like after the cross contamination occurs in the existing sampling method, the tool is relatively cheap.
3. The invention has simple operation, can reduce the risk of cross contamination to the greatest extent by using disposable consumables, has high accuracy of samples collected on site, provides an effective and easy-to-operate on-site sampling tool for related scientific research workers, and is suitable for popularization and application.
The technical characteristics of the method for collecting DNA samples in karst cave water environment in situ according to the present invention will be further described with reference to the accompanying drawings and examples.
Drawings
FIG. 1: the connecting schematic diagram of the Beller tube and the traction rope is provided.
FIG. 2: the invention discloses a schematic diagram of disposable sterilized medical gauze, a paper funnel and a disposable plastic cup.
FIG. 3: the disposable syringe and the replaceable membrane needle type filter are connected schematically.
FIG. 4: the box body of embodiment 1 of the present invention is schematically illustrated.
In the figure: 11-a belle tube, 12-a hauling rope, 21-disposable sterile medical gauze, 22-a paper funnel, 23-a disposable plastic cup, 31-a disposable injector, 32-a replaceable membrane needle type filter, 4-a set box body, 41-a rectangular storage tank, 42-an annular storage tank, 43-a storage tank I and 44-a storage tank II.
Detailed Description
Example 1: a site collection method of a karst cave water environment DNA sample comprises the following steps:
firstly, a sufficiently long hauling rope, namely a high-strength polyethylene fiber line, is cut, tied above the bailer tube and on a draw bar, the bailer tube is drawn to a DNA detection point in the water environment of the karst cave by the draw bar (bamboo pole, fishing rod, telescopic rod and the like) to collect water, and the collected water sample is put into a disposable plastic basin for standby. The method comprises the following steps: if the water depth of the karst cave is less than or equal to 2 meters, taking 1000mL of water sample which is 0.5m away from the water bottom; if the water depth of the karst cave is more than 2 meters and less than 10 meters, respectively mixing 1000mL of water samples which are 0.5m under the water and 0.5m away from the bottom for standby; if the water depth of the karst cave is more than or equal to 10 meters, 1000mL of water samples which are 0.5m underwater, 10m underwater and 0.5m away from the bottom are respectively taken and mixed for standby. The use of each sampling point is that the Beller tube is unused and the disposable plastic basin, and before the sampling, the sampling personnel need wear disposable latex gloves, rinses the Beller tube and the disposable plastic basin with the sampling point water sample 3 times simultaneously, avoids artificial external environment DNA to disturb as far as possible.
And step two, preliminarily filtering the karst cave environment DNA water sample acquired in the step one to remove large-particle impurities. The method comprises the following steps: three layers of medical gauze are stacked and placed on the inner side of a 400-mesh paper funnel, a karst cave environment water sample is poured into the paper funnel, and a disposable plastic cup is used for receiving and filtering the filtered water sample by 1-2L for later use.
And thirdly, taking a 500mL disposable syringe, absorbing 400-500mL water sample subjected to the secondary primary filtration, connecting the water sample to a replaceable membrane needle type filter membrane filter filled with a glass fiber membrane, and extruding the syringe at a constant speed by a manual machine to enable the water sample to pass through the filter and then be discharged, so that DNA in the water sample is attached to the filter membrane. And (3) replacing the filter membrane once by using a disposable forceps every time about 500mL of water sample is discharged, putting the replaced filter membrane into a 50mL centrifuge tube filled with absolute alcohol, and transporting the filter membrane back to the laboratory at the low temperature of 5-10 ℃ for next testing. Filtering 1-2L of water sample at each sampling point, if the water sample in the karst cave is turbid, replacing the filter membrane once every 200-300mL of water sample is discharged, and placing the filter membranes for filtering the water sample in the same batch into the same centrifugal tube. The appliances used at each sampling point are in principle disposable and, if they are to be reused, they must be washed 3 times with a chlorine-containing detergent and dried at a constant temperature of 60 ℃ for 3 days.
Note: the use of berer tubes, syringes, replaceable membrane needle filters, such as those that are rigorously cleaned, sterilized and disinfected, can also be reused to reduce sampling costs, but such an operation is not recommended.
The specific tool parameters used in this example are as follows:
the Beller tube is an underground water sampling tube, and has the specification: volume 1000mL, wall thickness 1mm, length 970mm, diameter 38mm, material: a highly transparent PC. The volume of the disposable plastic basin is 5L. The hauling cable is a high-strength polyethylene fiber wire with the wire diameter of 0.162mm-0.522 mm.
The medical gauze is disposable sterilized medical gauze with the size of 10cm multiplied by 15cm, the paper funnel with 400 meshes and the diameter of 19cm, and the volume of the disposable plastic cup is 1000 mL.
The disposable syringe is 500mL, the diameter of the replaceable membrane needle type filter is 5cm, the diameter of the glass fiber membrane is 47mm, the pore size is 0.7 micron, and the centrifuge tube is 50 mL.
The disposable forceps are disposable medical dressing forceps which are independently packaged, have a Y-shaped straight pointed end with the total length of 12.5cm and are made of polystyrene resin.
In this embodiment, can place the instrument that needs use and be convenient for carry in the box body that is furnished with the lid, the box body is provided with rectangle storage tank, annular storage tank, be located storage tank I of annular storage tank and be located the inside and outside storage tank II of annular storage tank (as shown in fig. 4), the bailer pipe that uses in the first step is placed in the rectangle storage tank, disposable plastic basin is placed in the annular storage tank, the disposable medical gauze of sterilizing that the second step used, paper funnel and disposable plastic cup are placed in storage tank I, use disposable latex gloves in the first step, the disposable syringe of haulage rope and telescopic link and third step use, interchangeable membrane needle formula filter, disposable tweezers, absolute alcohol, centrifuging tube and a plurality of glass fiber membrane are placed in storage tank II. As an alternative, the various tools that the present invention requires to be used with may also be placed in other ways.
The trial cases of the invention are as follows:
24/3/2021, applying the collection method of the invention, collecting water samples at four underground caverns or water outlets of a water sample of the six township village of the Suljun of the Suljunzhou, the water sample of the Suljunzhou province, respectively fixing the water sample of the filter membrane with absolute alcohol, then carrying out DNA extraction, designing a plurality of groups of primer amplification fragments and subsequent high-throughput sequencing analysis, and showing that the collection method can correspondingly find the fishes at four sampling points one by one in the detection result, and combine the specific fish data of the species, and the fish of which the known locations have not found cross contamination, for example, two fishes, namely, the water sample of the SulAnhuichi-tailed fish in the sampling points of the Suljunyun-wu mountain of the Sunnus albo mountain of the Sunnus albus, the data signal is strong; the detection signal data of a large amount of silurus meridionalis (scavenger) appears at six villages of towns in groups, and the detection signal data is matched with the actual situation that the foreign species invade the karst cave in the area to form threat; the method is characterized in that a high-townhutu in a Yangtze region detects special fishes with fine lines, and a Liuzhou city Liunanyuan Yangtze region detects sturgeons (related to sturgeon farms near the point), and the like. As the 4 sampling points are on the same day, the same person operates the samples collected on the site by the same method, the detected karst cave fish composition data all accord with the previous fishery resource investigation results, and some special fishes of each point do not appear in other sampling points, so that the sampling method is proved to have no cross contamination and is an effective and feasible karst cave water environment DNA on-site collection working method.

Claims (3)

1.一种溶洞水环境DNA样品的现场采集方法,其特征在于:包括以下步骤:1. a kind of on-site collection method of karst cave water environment DNA sample, is characterized in that: comprise the following steps: 第一步,在采样前,采样人员需佩戴一次性乳胶手套,同时将贝勒管和一次性塑料盆用采样点水样进行润洗1-4次;然后剪取足够长的牵引绳,两端分别系于贝勒管上方和牵引杆,通过牵引杆牵引贝勒管到溶洞水环境DNA检测点进行采水,采到的水样放入一次性塑料盆中待用;In the first step, before sampling, the sampling personnel need to wear disposable latex gloves, and at the same time rinse the Baylor tube and the disposable plastic basin with the sampling point water sample 1-4 times; Tie on the top of the Baylor tube and the drawbar, respectively, and use the drawbar to pull the Baylor tube to the DNA detection point of the cave water environment for water collection, and the collected water samples are placed in a disposable plastic pot for use; 第二步,将第一步采集获得的溶洞环境DNA水样初步过滤,去除大颗粒杂质,具体操作为:将医用纱布叠2-4层垫入纸漏斗内侧,将溶洞环境水样倒入到纸漏斗中,并用一次性塑料杯接过滤后水样1-2L备用;The second step is to preliminarily filter the DNA water sample of the cave environment collected in the first step to remove large particles of impurities. In a paper funnel, and use a disposable plastic cup to connect 1-2L of filtered water sample for use; 第三步,取一次性注射器,吸取400-500mL第二步初步过滤后的水样,连接到已经装入玻璃纤维膜的可换膜针式过滤器上,人工匀速挤压注射器使水样通过可换膜针式过滤器后排出,每排出200-500mL水样,用一次性镊子更换一次滤膜,将更换的滤膜放入装有无水酒精的离心管中于低温下5-10℃保存,过滤1-2L水样后采样完成。The third step is to take a disposable syringe, absorb 400-500mL of the water sample after preliminary filtration in the second step, connect it to the replaceable membrane needle filter that has been loaded with glass fiber membrane, and manually squeeze the syringe at a constant speed to make the water sample pass through. Replace the membrane needle filter and discharge it. For every 200-500mL of water sample, replace the filter membrane with disposable tweezers. Put the replaced filter membrane into a centrifuge tube filled with anhydrous alcohol at a low temperature of 5-10°C. Save, filter 1-2L water sample and complete the sampling. 2.根据权利要求1所述的一种溶洞水环境DNA样品的现场采集方法,其特征在于:第一步中,采样的具体操作方法为:若溶洞水深≤2米,取离水底0.5m水样1000mL即可;若溶洞水深超过2米且低于10米的,取水下0.5m和离底部0.5m的水样各1000mL混合待用;若溶洞水深≥10米的,取水下0.5m、水下10m、以及离底部0.5m水样各1000mL混合待用。2. the on-site collection method of a kind of karst cave water environment DNA sample according to claim 1, is characterized in that: in the first step, the concrete operation method of sampling is: if karst cave water depth≤2 meters, take 0.5m water from the bottom If the water depth of the cave is more than 2 meters and less than 10 meters, take 1000 mL of water samples 0.5 m under the water and 0.5 m from the bottom and mix them for use; if the water depth of the cave is ≥ 10 meters, take 0.5 m of water, Mix 1000mL of water samples 10m down and 0.5m from the bottom for use. 3.根据权利要求1或2所述的一种溶洞水环境DNA样品的现场采集方法,其特征在于:第二步中,所述纸漏斗是400目纸漏斗。3. The method for on-site collection of DNA samples in a cave water environment according to claim 1 or 2, wherein in the second step, the paper funnel is a 400-mesh paper funnel.
CN202111368669.2A 2021-11-18 2021-11-18 Site collection method of karst cave water environment DNA sample Pending CN114047036A (en)

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