CN110305942B - Method and device for testing DNA (deoxyribonucleic acid) dynamic water return-drive characteristic of fish environment - Google Patents
Method and device for testing DNA (deoxyribonucleic acid) dynamic water return-drive characteristic of fish environment Download PDFInfo
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Abstract
The invention provides a method and a device for testing DNA dynamic water returning and trending characteristics of a fish environment, and relates to the field of water environment and water ecology protection, wherein the testing method comprises the following steps: step (1): collecting a living biological sample of a target test fish; step (2): developing a fish environment DNA shedding characteristic experiment in a fish environment DNA kinetic water returning characteristic testing device; and (3): developing a fish environment DNA degradation characteristic experiment on the basis of the step (2); and (4): carrying out a fish environment DNA adsorption characteristic test on the basis of the step (2); and (5): testing and analyzing the time-varying process of the environmental DNA concentration, and analyzing the characteristic of the fish environmental DNA trend. The invention can accurately and quantitatively test the water movement tendency and trend characteristics of the environmental DNA of fishes of different types and in the life history stage, and has important scientific application value.
Description
Technical Field
The invention relates to the field of water environment and water ecology protection, in particular to a method and a device for testing DNA dynamic water returning and trending characteristics of a fish environment.
Background
Water conservancy projects are widely concerned about the influence of fish breeding habitat, and monitoring and evaluation are important foundations of protection. Environmental DNA monitoring is widely used as a non-invasive, high-aging emerging method to assess the presence of rare or invasive species. Researches find that the environmental DNA concentration has a correlation with the biological characteristics of fishes and the environmental characteristics of water bodies, but the bottleneck problem of how to test the environmental DNA flowing water tendency characteristics needs to be solved by applying the environmental DNA concentration to the aspects of predicting and evaluating the distribution of fishes and breeding habitats, life history behaviors, biomass and the like.
Disclosure of Invention
The invention aims to overcome the defects of the background art and provides a method and a device for testing the water moving tendency characteristics of the DNA of a fish environment.
In order to achieve the purpose, the invention provides a method for testing the DNA kinetic water tendency characteristics of a fish environment, which is characterized by comprising the following steps of:
a method for testing the DNA water movement tendency characteristics of fish environment comprises the following steps:
step (1): collecting a living biological sample of a target test fish;
step (2): developing a fish environment DNA shedding characteristic experiment in a fish environment DNA kinetic water returning characteristic testing device;
and (3): developing a fish environment DNA degradation characteristic experiment on the basis of the step (2);
and (4): carrying out a fish environment DNA adsorption characteristic test on the basis of the step (2);
and (5): testing and analyzing the time-varying process of the environmental DNA concentration, and analyzing the characteristic of the fish environmental DNA trend.
Further, the step (1) collects the living organism samples of the target test fishes from the field or breeding field, including adult fishes, juvenile fishes and fish eggs, and simultaneously tests the basic biological characteristics of the fishes, including weight, size and developmental stage, and adapts in the domestication pond for 24h, during which the fish is fasted.
Further, the step (2) is to put the living biological sample of the target test fish into a device for testing the DNA dynamic water regression characteristics of the fish environment, and set working conditions of different flow rates (u, m/s), water temperatures (T, DEG C), dissolved oxygen (DO, mg/L) factors and different time intervals (T) within 2-4 d respectively i S) taking a quantitative water sample (V) i mL) in 24 hours respectively, and performing vacuum filtration through a filter membrane with the pore diameter of 0.22 mu m, and storing the filtered filter membrane at-20 ℃ for later use for testing the environmental DNA concentration in the step (5).
Further, the step (3) is that on the basis of the step (2), the living biological samples of the target test fishes are taken out from the device for testing the DNA dynamic water homing and homing characteristics of the fish environment for different time intervals (t) within 4-8 d i S) taking a quantitative water sample (V) i mL) in 24 hours respectively, and performing vacuum filtration through a filter membrane with the pore diameter of 0.22 mu m, and storing the filtered filter membrane at-20 ℃ for later use for testing the environmental DNA concentration in the step (5).
Further, in the step (4), on the basis of the step (2), the living biological sample of the target test fish is taken out from the device for testing the DNA kinetic water regression characteristics of the fish environment, a certain amount of suspended sediment particles are added, and the working conditions of different turbidity water flows are created within 1-2 d at different time intervals (t) i S) taking a quantitative water sample (V) i mL) and respectively performing vacuum filtration through a filter membrane with the aperture of 0.22 mu m within 24h, and storing the filtered filter membrane at-20 ℃ for later use for testing the environmental DNA concentration in the step 5.
Further, the step (5) adopts a quantitative real-time qPCR (real-time qPCR) technology to test the quantity (N) of the environmental DNA fragments in the filter membranes filtered in the steps (2), (3) and (4) i Copies), calculating the environmental DNA concentration (C) i ,copies/mL):
C i =N i /V i
The device for testing the characteristic of returning to the trend of the DNA flowing water of the fish environment can be considered as a completely mixed water body, and the time change process of the characteristic of returning to the trend of the DNA flowing water of the fish environment adopts a one-dimensional model for representation:
wherein C is i copies/mL, which is the ambient DNA concentration; t is time, s; s is the shedding rate of the environmental DNA, copies/(mL. D); k is a radical of 1 The degradation rate of environmental DNA is 1/d; k is a radical of 2 As the environmental DNA adsorption rate, 1/d.
thus, formula (1) can be characterized as,
S=(k 1 +k 2 )C 0 (2)
when the living biological sample of the target test fish is taken out from the device for testing the behavior of the fish environment DNA flowing water returning characteristic in the step (3), S =0, then the formula (1) can be characterized as,
thus, the process of degradation of the DNA in the fish environment by the time of flowing water can be characterized by the following exponential model
When the living biological sample of the target test fish is taken out from the device for testing the DNA dynamic water returning and trending characteristics of the fish environment in the step (4), S =0, then the formula (1) can be represented as,
therefore, the DNA water movement time adsorption process of the fish environment can be characterized as an exponential model
Above, C 0 In order to take out a living biological sample of a target test fish from a fish environment DNA flowing water returning characteristic test device, the initial steady environment DNA concentration is copies/mL;
plotting the time intervals (t) in steps (2), (3) and (4) separately i S) ambient DNA concentration (C) i copies/mL) is analyzed, the time-varying rule of the water environment DNA concentration in the regression process of shedding, degradation, adsorption and the like is analyzed, an index model shown in the formulas (4) and (6) is fitted by adopting a regression method such as weighted least squares and the like, and the shedding rate (S) and the degradation rate (k) of the fish environment DNA are determined 1 ) And adsorption ratio (k) 2 ) And the like.
The utility model provides a fish environment DNA moves water and returns to trend characteristic test device, includes that the annular flow way that supplies fish to perch, the frequency conversion disc that is located annular flow way one side make the stream system, set up in upstream barricade and the low reaches barricade of frequency conversion disc system upper and lower reaches, be located the water environmental factor monitoring system of annular flow way opposite side, ADV velocity of flow appearance and sampling system, the frequency conversion disc makes the stream system and includes inverter motor, drive belt, axis of rotation and disc piece, inverter motor passes through the drive axis of rotation of drive belt and then drives the disc piece rotatory.
Furthermore, the arrangement width of the disc sheets is close to the width of the annular flow channel, and the distance between the disc sheets is set to be 0.5-2 cm.
Furthermore, the annular flow channel is made of organic glass, the upstream fish blocking grid is made of a circular tube with the diameter of 0.5-2 cm and is made into a honeycomb structure, the downstream fish blocking grid is made of a chemical fiber net piece, and the mesh size can prevent the tested object fish from passing through.
Furthermore, the upper end of the annular flow channel is provided with a positioning support, the water environment factor monitoring system and the ADV flow velocity meter are erected on the positioning support, and the water environment factor monitoring system comprises a water temperature sensor, a dissolved oxygen sensor, a pH value sensor, a conductivity sensor and a turbidity sensor.
The invention has the following beneficial effects:
1. the method divides a fish environment DNA returning mechanism into three typical processes of falling, degradation and adsorption, respectively develops an experiment in a special test device for the fish environment DNA dynamic water returning characteristic, tests the fish environment DNA concentration at different time nodes based on a qPCR technology, draws a scatter diagram of the environment DNA concentration at different time intervals, regresses and fits an environment DNA concentration time process line, and quantitatively analyzes the change rule of the fish environment DNA concentration along with time under the influence of hydrodynamic force and environmental factors.
2. The invention is based on a special testing device with controllable hydrodynamic force and other environmental factors, and can theoretically analyze the influence of the environmental factors on the DNA trend characteristic of the fish environment.
3. According to the invention, based on the test and regression analysis of the time process data of the DNA concentration of the fish environment, the key regression characteristic parameters such as the shedding rate, the degradation rate and the adsorption rate of the DNA of the fish environment are calculated quantitatively.
Drawings
FIG. 1 is a flowchart of one embodiment of a method for testing the DNA kinetic water homing characteristics of a fish environment according to the invention;
FIG. 2 is a schematic plan view of an embodiment of the apparatus for testing environment DNA hydrodynamic homing characteristics of fish according to the present invention;
FIG. 3 isbase:Sub>A cross-sectional view taken along line A-A of FIG. 2;
FIG. 4 is a schematic view of the cross-sectional structure B-B in FIG. 2;
FIG. 5 is a schematic diagram of the DNA concentration time course of a fish shedding environment;
FIG. 6 is a schematic diagram of the time course of the degradation or adsorption of the environmental DNA concentration of fish.
In the figure: 1-an annular flow channel, 2-a variable frequency motor, 3-a transmission belt, 4-a rotating shaft, 5-a disc, 6-an upstream fish barrage, 7-a downstream fish barrage, 8-a positioning bracket, 9-an environmental factor monitoring system, 10-an ADV flow meter, 11-a sampling system, 12-a sampling port and 13-a sampling valve.
Detailed Description
The following detailed description of the preferred embodiments of the present invention will be given with reference to the accompanying drawings, which are not intended to limit the present invention, but are given by way of illustration only, so as to enable those skilled in the art to more clearly understand the contents and advantages of the present invention.
As shown in fig. 1, an embodiment of the present invention provides a method for testing a fish environmental DNA hydrodynamic tendency characteristic, which is characterized by comprising the following steps:
step (1): collecting a living biological sample of a target test fish;
specifically, living biological samples of target test fishes, including adult fishes, juvenile fishes, fish eggs and the like, are collected from the field or breeding field; meanwhile, the basic biological characteristics of the fish, including weight, size, development stage and the like, are tested. Acclimatization is carried out in a domesticated pond for 24 hours, and fasting is carried out in the period.
Step (2): carrying out a fish environment DNA shedding characteristic experiment;
specifically, biological samples of living fish to be tested are respectively placed into a plurality of devices for testing the DNA dynamic water regression characteristics of the fish environment, and working conditions of different flow rates (u, m/s) are set, such as 0.2, 0.4, 0.8, 1.2m/s and the like, and water temperature (T, DEG C) and dissolved oxygen (DO, mg/L) factors are tested. Different time intervals (t) within 2-4 d i ) Taking a quantitative water sample (V) i mL) 50mL, e.g., 0h, 2h, 6h, 12h, 18h, 24h, 1.5d, 2d, 3d, 4d, etc. Will quantify the amount of the water sample (V) i mL) are respectively filtered in vacuum in 24 hours through filter membranes with the pore diameter of 0.22 mu m, and the filter membranes after filtration are stored at the temperature of minus 20 ℃ for later use for testing the environmental DNA concentration in the step (5)
And (3): developing a fish environment DNA degradation characteristic experiment on the basis of the step (2);
specifically, on the basis of the step (2), taking out the living biological samples of the target test fishes from the device for testing the DNA kinetic water homing and homing characteristics of the fish environment for 4-8 d at different time intervals (t) i S) taking a quantitative water sample (V) i mL) 50mL, e.g., 0h, 2h, 6h, 12h, 24h, 1.5d, 2d, 4d, 6d, 8d, etc. Will quantify the water sample (V) i ) Vacuum filtering with filter membrane with pore diameter of 0.22 μm within 24 hr, and storing at-20 deg.C for use in step (5) for testing environmental DNA concentrationThe preparation method is used.
And (4): carrying out a fish environment DNA adsorption characteristic test on the basis of the step (2);
specifically, on the basis of the step (2), taking out a living biological sample of the target test fish from a device for testing the DNA kinetic water tendency and tendency characteristics of the fish environment, adding a certain amount of suspended sediment particles, creating water flow conditions with different turbidities (Tur, NTU) and different time intervals (t) within 1-2 d i S) taking a quantitative water sample (V) i mL) 50mL, for example, 0min, 2min, 5min, 10min, 20min, 30min, 1h, 2h, 6h, 1d, 2d, etc. Will quantify the water sample (V) i mL) are respectively filtered in vacuum through a filter membrane with the aperture of 0.22 mu m within 24h, and the filtered filter membrane is stored at the temperature of minus 20 ℃ for later use for testing the environmental DNA concentration in the step (5).
Referring to fig. 2, 3 and 4, the device for testing the homing and homing characteristics of DNA flowing water in fish environment adopted in the steps (2), (3) and (4) comprises an annular flow channel 1 for fish to inhabit, a variable frequency disc flow generating system positioned on one side of the annular flow channel 1, an upstream fish grating 6 and a downstream fish grating 7 which are arranged on the upstream and downstream of the variable frequency disc flow generating system, a water environment factor monitoring system 9, an ADV flow velocity meter 10 and a sampling system 11 which are positioned on the other side of the annular flow channel 1, wherein the variable frequency disc flow generating system comprises a variable frequency motor 2, a transmission belt 3, a rotating shaft 4 and disc plates 5, the variable frequency motor 2 drives the rotating shaft 4 through the transmission belt 3 to further drive the disc plates 5 to rotate, the disc plates 5 are formed by vertically overlapping a plurality of disc plates, the arrangement width of the disc plates 5 is equal to the width of the annular flow channel 1, and the distance between the disc plates can be set to be 0.5-2 cm according to the flow generating strength requirement, so that the mechanical damage to the DNA fragment of the environment can be avoided. The water environment factor monitoring system 9 comprises a water temperature (T, DEG C) sensor, a dissolved oxygen (DO, mg/L) sensor, a turbidity (Tur, NTU) sensor and the like, the ADV flow meter 10 is used for measuring the flow rate (u, m/s) and the turbulence characteristics of the water body, and the sampling system 11 is used for sampling water samples at different time intervals.
The annular flow channel 1 can be made of transparent materials such as organic glass and the like, so that the activity state of fishes can be observed conveniently, and environmental factors can be regulated and controlled conveniently; the shape of the test piece can be circular or oval according to the test requirement.
The upstream fish barrier 6 can be made into a honeycomb structure by adopting a circular pipe with the diameter of 0.5-2 cm and has the function of adjusting the flow state of water flow; the downstream fish barrier 7 is made of chemical fiber net sheets, and the mesh size can prevent the tested fishes from passing through.
As shown in fig. 3, a positioning support 8 is arranged at the upper end of the annular flow channel 1, and the water environment factor monitoring system 9 is erected on the positioning support 8, and includes water environment factor sensors for monitoring the change process of water environment factors, such as water temperature, dissolved oxygen, pH value, conductivity, turbidity, and the like.
The ADV flow meter 10 is also erected on the positioning bracket 8, so that the flow velocity and the turbulence characteristics of different spatial positions of the water body can be conveniently measured.
And (5): testing and analyzing the time-varying process of the environmental DNA concentration, and analyzing the water movement characteristics of the environmental DNA of the fish.
The step (5) adopts a real-time quantitative instant polymerase chain reaction (real-time qPCR) technology to test the quantity (N) of the environmental DNA fragments in the filtered filter membrane in the steps (2), (3) and (4) i ) And calculating the environmental DNA concentration.
C i =N i /V i
The device for testing the characteristic of returning to the trend of the DNA flowing water in the fish environment can be considered as a completely mixed water body, and the time change process of the characteristic of returning to the trend of the DNA flowing water in the fish environment is represented by a one-dimensional model.
Wherein C is i copies/mL, which is the ambient DNA concentration; t is time, s; s is the shedding rate of the environmental DNA, copies/(mL. D); k is a radical of 1 The degradation rate of environmental DNA is 1/d; k is a radical of 2 For environmental DNA aspirationAttachment ratio, 1/d.
therefore, the temperature of the molten metal is controlled,
S=(k 1 +k 2 )C 0
when the living biological sample of the target test fish is taken out from the device for testing the characteristic of returning to the trend of the DNA flowing water of the fish environment in the step (3), S =0, the one-dimensional model can be characterized as,
therefore, the degradation process of the DNA flowing water time of the fish environment can be characterized as an exponential model
When S =0 after the living biological sample of the target test fish is taken out from the device for testing the DNA flowing water returning characteristic of the fish environment in the step (4), the one-dimensional model can be characterized as,
therefore, the DNA water movement time adsorption process of the fish environment can be characterized as an exponential model
Above, C 0 In order to take out the living biological sample of the target test fish from the device for testing the DNA dynamic water returning and trend characteristics of the fish environment, the initial steady-state environment DNA concentration is copies/mL.
Referring to FIG. 5, the different time intervals (t) of step (2) are plotted i S) shedding of fishAmbient DNA concentration (C) i copies/mL) to analyze the time variation rule of the water environment DNA concentration in the shedding process.
Referring to FIG. 6, the different time intervals (t) of steps (3) or (4) are plotted i S) DNA concentration (C) in fish shedding environment i copies/mL) to analyze the change rule of the DNA concentration of the water environment along with time in the fate process of degradation or adsorption and the like. Determining the shedding rate (S) and the degradation rate (k) of the fish environmental DNA by adopting a weighted least square equal regression method to simulate a fish environmental DNA degradation and adsorption index model 1 ) Or adsorption ratio (k) 2 ) Equal key regression characteristic parameter, i.e. k 1 Or k 1 +k 2 =0.8011 1/d,C 0 =1.8751×10 4 copies/mL,S=1.5021×10 4 copies/(mL·d)。
The method divides a fish environment DNA returning mechanism into three typical processes of falling, degradation and adsorption, respectively develops an experiment in a special test device for the fish environment DNA dynamic water returning characteristic, tests the fish environment DNA concentration at different time nodes based on a qPCR technology, draws a scatter diagram of the environment DNA concentration at different time intervals, regresses and fits an environment DNA concentration time process line, and quantitatively analyzes the change rule of the fish environment DNA concentration along with time under the influence of hydrodynamic force and environmental factors.
The above description is only for the specific embodiments of the present invention, but the scope of the present invention is not limited thereto, and any changes or substitutions that can be easily conceived by those skilled in the art within the technical scope of the present invention are also within the scope of the present invention.
Claims (6)
1. A method for testing the characteristic of returning to home of DNA (deoxyribonucleic acid) of fish environment in water movement is characterized by comprising the following steps of: the method comprises the following steps:
step (1): collecting a living biological sample of a target test fish;
step (2): developing a fish environment DNA shedding characteristic experiment in a fish environment DNA flowing water converging and diverging characteristic testing device;
and (3): developing a fish environment DNA degradation characteristic experiment on the basis of the step (2);
and (4): carrying out a fish environment DNA adsorption characteristic test on the basis of the step (2);
and (5): testing and analyzing the time-varying process of the environmental DNA concentration, and analyzing the water moving attribute and trend characteristic of the environmental DNA of the fish;
putting a living biological sample of the target test fish into a device for testing the DNA kinetic water homing and homing characteristics of the fish environment, respectively setting working conditions of different flow rates, water temperatures and dissolved oxygen factors, taking quantitative water samples at different time intervals within 2-4 d, respectively performing vacuum filtration through filter membranes with the aperture of 0.22 mu m within 24h, and storing the filtered filter membranes at the temperature of-20 ℃ for later use for testing the DNA concentration of the environment in the step (5);
taking out a living biological sample of the target test fish from the device for testing the characteristic of returning to trend of DNA flowing water of the fish environment on the basis of the step (2), taking quantitative water samples at different time intervals within 4-8 d, respectively carrying out vacuum filtration through filter membranes with the aperture of 0.22 mu m within 24h, and storing the filtered filter membranes at the temperature of-20 ℃ for later use for testing the concentration of the DNA of the environment in the step (5);
taking out a living biological sample of the target test fish from a device for testing the DNA tendency characteristics of the running water of the fish environment on the basis of the step (2), adding a certain amount of suspended sediment particles to create working conditions of water flows with different turbidities, taking quantitative water samples at different time intervals within 1-2 d, respectively performing vacuum filtration through filter membranes with the aperture of 0.22 mu m within 24h, and storing the filtered filter membranes at the temperature of-20 ℃ for later use for testing the DNA concentration of the environment in the step (5);
and (5) testing the quantity of the environmental DNA fragments in the filter membranes filtered in the steps (2), (3) and (4) by adopting a quantitative instant polymerase chain reaction qPCR technology, and calculating the environmental DNA concentration:
C i =N i /V i
the device for testing the DNA kinetic water returning and driving characteristics of the fish environment is considered to be a completely mixed water body, and the time change process of the DNA kinetic water returning and driving characteristics of the fish environment is characterized by adopting a one-dimensional model:
wherein C is i Is the ambient DNA concentration, copies/mL; t is time, d; s is the shedding rate of environmental DNA, copies/(mL. D); k is a radical of formula 1 The degradation rate of environmental DNA is 1/d; k is a radical of formula 2 The adsorption rate of environmental DNA is 1/d,
thus, the formula (1) is characterized in that,
S=(k 1 +k 2 )C 0 (2)
when the living biological sample of the target test fish is taken out from the device for testing the behavior of the fish environment DNA flowing water returning characteristic in the step (3), S =0, the expression (1) is characterized in that,
therefore, the degradation process of the DNA in the fish environment in the flowing water time is characterized by the following exponential model
When the living biological sample of the target test fish is taken out from the device for testing the DNA kinetic water homing and homing characteristics of the fish environment in the step (4), S =0, the expression (1) is characterized in that,
therefore, the DNA water movement time adsorption process of the fish environment is characterized by the following exponential model
Above, C 0 In order to take out a living biological sample of a target test fish from a fish environment DNA flowing water returning characteristic test device, the initial steady environment DNA concentration is copies/mL;
respectively drawing scatter diagrams of the environmental DNA concentrations at different time intervals in the steps (2), (3) and (4), analyzing the time-varying rule of the water body environmental DNA concentration in the falling, degradation and adsorption regression processes, fitting index models shown in the formulas (4) and (6) by adopting a weighted least square regression method, and determining the fish environmental DNA falling rate S and the degradation rate k 1 And adsorption ratio k 2 The key is to get the characteristic parameter.
2. The method for testing the DNA kinetic water homing characteristics of the fish environment according to claim 1, wherein the method comprises the following steps: the step (1) collects living biological samples of target test fishes from the field or a breeding field, including adult fishes, juvenile fishes and fish eggs, simultaneously tests basic biological characteristics of the fishes, including weight, size and developmental stage, adapts for 24h in a domestication pond, and fasts the period.
3. The utility model provides a fish environment DNA moves water and returns to trend characteristic test device which characterized in that: the device comprises an annular flow channel for fish to inhabit, a variable frequency disc flow making system positioned on one side of the annular flow channel, an upstream fish barricade and a downstream fish barricade which are arranged on the upstream and downstream of the variable frequency disc flow making system, a water environment factor monitoring system positioned on the other side of the annular flow channel, an ADV (adaptive differential pressure) flow velocity meter and a sampling system, wherein the variable frequency disc flow making system comprises a variable frequency motor, a transmission belt, a rotating shaft and a disc, and the variable frequency motor drives the rotating shaft through the transmission belt so as to drive the disc to rotate.
4. The device for testing the DNA kinetic water fate characteristics of fish environment according to claim 3, wherein: the arrangement width of the disc sheets is close to the width of the annular flow channel, and the distance between the disc sheets is set to be 0.5-2 cm.
5. The device for testing the DNA kinetic water homing characteristics of the fish environment of claim 3, wherein: the annular flow channel is made of organic glass, the upstream fish blocking fence is made of a circular tube with the diameter of 0.5-2 cm and is of a honeycomb structure, the downstream fish blocking fence is made of chemical fiber net sheets, and the size of the mesh is capable of preventing the tested fishes from passing through.
6. The device for testing the DNA kinetic water homing characteristics of the fish environment of claim 3, wherein: the upper end of the annular flow channel is provided with a positioning support, the water environment factor monitoring system and the ADV flow velocity meter are erected on the positioning support, and the water environment factor monitoring system comprises a water temperature sensor, a dissolved oxygen sensor, a pH value sensor, a conductivity sensor or a turbidity sensor.
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