CN106048077A - Gene chip for detecting beta-proteobacteria communities in marine environment - Google Patents
Gene chip for detecting beta-proteobacteria communities in marine environment Download PDFInfo
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- CN106048077A CN106048077A CN201610708997.5A CN201610708997A CN106048077A CN 106048077 A CN106048077 A CN 106048077A CN 201610708997 A CN201610708997 A CN 201610708997A CN 106048077 A CN106048077 A CN 106048077A
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- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
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Abstract
The invention provides a gene chip for detecting beta-proteobacteria communities in a marine environment. The gene chip comprises a chip carrier and a probe which is fixed on the chip carrier and used for detecting Alcaligenaceae bacteria, Burkholderiaceae bacteria, Comamonadaceae bacteria, Hydrogenophilaceae bacteria, Methylophilaceae bacteria, Neisseriaceae bacteria, Nitrosomonadaceae bacteria, Oxalobacteraceae bacteria and Rhodocyclaceae bacteria in seawater. The probe used for the chip can realize rapid and high-throughput detection of beta-proteobacteria communities in seawater, and can detect up to 9 beta-proteobacteria families' information. Therefore, the invention provides powerful technical support for monitoring bacterial communities in the marine environment and has laid a solid foundation for establishing and improving an offshore and marine environmental quality comprehensive assessment system.
Description
Technical field
The invention belongs to field of molecular detection, be specifically related to a kind of γ in marine environment-mycetozoan group detected
Gene chip.
Background technology
β-mycetozoan and α, γ, δ, ε-mycetozoan subclass belong to Proteobacteria.Wherein α-mycetozoan, γ-mycetozoan exist
In marine environment most commonly seen, β-mycetozoan report is relatively fewer, but its function should not be underestimated.Lee et al. is utilizing Fish/
During MAR technical research poly-phosphorus microorganism, determine that polyP bacteria is mainly under the jurisdiction of β-deformation Gammaproteobacteria;β-change is thought in the research of Kong et al.
Shape bacterium subclass quasi-microorganism is the most relevant with the removal efficiency of phosphorus;Also there are some researches show that the microorganism of β-mycetozoan subclass possesses more
Degradation capability, is common in polluted water body.Such as, Rhodocyclaceae section therein microorganism more comprise for aerobic
Denitrification bacillus class, occupy in water environment, possesses stronger metabolism diversity, plays the work of key in bioremediation of waters
With.Nitrosomonadaceae is then typical Nitrobacteriaceae.Therefore, β-mycetozoan occupies very important in the environment
Status, strengthens its detection Research Significance great.
At present, marine environment biological monitoring is with plankton, benthon, intertidal organism, necton, escherichia coli
It is main project Deng biological species composition and Monitoring of Quantity, lacks the monitoring to marine bacteria community diversity.Antibacterial complexity
Structure of community, function, interaction and the dynamic change maintenance important in inhibiting to marine ecology function.Microbiologic population pair
Environmental change response is quick, and pollution is had indicative function.Therefore, increase each bacterial species of marine environment composition and quantity
The monitoring of distribution, to setting up, to perfect immediate offshore area marine environmental quality overall evaluation system the most necessary.β-mycetozoan is as one
Class metabolism diversity is complicated, has the microorganism of stronger repair to water pollution, includes marine environment biological monitoring in and have
The most urgent necessity.
The most traditional microorganism monitoring is mainly by isolated culture method.This monitoring method is loaded down with trivial details, time-consuming, uncomfortable
Close and various bacteria is monitored simultaneously.Need development high flux, efficient, convenient, the marine bacteria community monitoring skill of low cost badly
Art.Biochip technology is to use fabricated in situ or micro-deposition techniques to be solidified in an orderly manner on holder by a large amount of DNA probes,
Then with the sample hybridization of labelling, by the detection analysis to hybridization signal, it is thus achieved that the gene order of sample, gene expression information
Etc. hereditary information.There is high flux, concurrency;Using fluorescent labeling, the accuracy of detection is high, the detection time is short, can be the most real
Show automatization and quickly detect.Chip preparation and result detection and signal analysis, processing procedure are adopted and computerized control,
Analyze, testing result the most objective, accurate.
Summary of the invention
The technical problem to be solved is to provide a kind of gene core detecting marine environment γ-mycetozoan group
Sheet, can detection marine environment γ-mycetozoan group parallel, quick, high-throughout, make biochip technology preferably be applied to
Marine environmental monitoring, to make up the deficiency of existing detection technique.
The gene chip of the present invention, includes chip carrier, and is fixed on chip carrier, be used for detecting in sea water
Alcaligenaceae bacterium, Burkholderiaceae bacterium, Comamonadaceae bacterium, Hydrogenophilaceae bacterium,
Methylophilaceae bacterium, Neisseriaceae bacterium, Nitrosomonadaceae bacterium, Oxalobacteraceae bacterium,
The probe of Rhodocyclaceae bacterium.
Wherein for detecting the nucleic probe of Alcaligenaceae bacterium, its nucleotides sequence is classified as in SEQ ID NO:1-3
Any one or several;
Wherein for detecting the nucleic probe of Alcanivoracaceae bacterium, its nucleotides sequence is classified as SEQ ID NO:4-6
In any one or several;
Wherein for detecting the nucleic probe of Comamonadaceae bacterium, its nucleotides sequence is classified as in SEQ ID NO:7-9
Any one or several;
Wherein for detecting the nucleic probe of Hydrogenophilaceae bacterium, its nucleotides sequence is classified as SEQ ID NO:
Any one or several in 10-12;
Wherein for detecting the nucleic probe of Methylophilaceae bacterium, its nucleotides sequence is classified as SEQ ID NO:13-
Any one or several in 15;
Wherein for detecting the nucleic probe of Neisseriaceae bacterium, its nucleotides sequence is classified as in SEQ ID NO:16-18
Any one or several;
Wherein for detecting the nucleic probe of Nitrosomonadaceae bacterium, its nucleotides sequence is classified as SEQ ID NO:19-
Any one or several in 21;
Wherein for detecting the nucleic probe of Oxalobacteraceae bacterium, its nucleotides sequence is classified as SEQ ID NO:22-
Any one or several in 23;
Wherein for detecting the nucleic probe of Rhodocyclaceae bacterium, its nucleotides sequence is classified as SEQ ID NO:24-26
In any one or several;
Be further fixed on hybridizing positive control Quality Control probe on the gene chip of the present invention, hybridization negative control Quality Control is visited
Any one or several in pin, surface chemistry Quality Control probe,
Wherein the nucleotides sequence of hybridization positive control Quality Control probe (PC) is classified as SEQ ID NO:27;
The nucleotides sequence of hybridization negative control Quality Control probe (NC) is classified as SEQ ID NO:28;
The nucleotides sequence of surface chemistry Quality Control probe (CK) is classified as SEQ ID NO:29, is one and uses HEX dye marker
The oligonucleotide sequence of 40 T.The position of these fluorescent probe points can be as DNA microarray coordinate on chip, in chip detection
During play location probe location effect.
The probe that chip of the present invention is used can quickly, with high throughput to the β in sea water-mycetozoan group be examined
Surveying, maximum can detect the β-mycetozoan information of 9 sections, thus the monitoring for marine environment bacterial community provides strong skill
Art is supported, has established solid foundation for setting up, perfecting immediate offshore area marine environmental quality overall evaluation system.
Accompanying drawing explanation
Fig. 1: β of the present invention-Proteobacteria group gene chip layout.
Specific detection (Comamonadaceae) the section detection knot of Fig. 2: β of the present invention-Proteobacteria group gene chip
Fruit figure.
Detailed description of the invention
Below in conjunction with embodiment, the present invention is described in detail, the experiment of unreceipted actual conditions in the following example
Method, generally can condition routinely, such as institute in " Molecular Cloning: A Laboratory guide " that J. Pehanorm Brooker (Sambrook) etc. writes
The condition stated, or run according to the condition proposed by manufacturer.
The probe design of embodiment 1: β-mycetozoan group detection gene chip
High throughput sequencing technologies and clone library technology is used to obtain β-mycetozoan group information in In The East China Sea.According to β-
Mycetozoan group 16S rRNA gene sequence information, in In The East China Sea 31 main β-deformation Cordycepps
(Alcaligenaceae、Burkholderiaceae、Comamonadaceae、Hydrogenophilaceae、
Methylophilaceae、Neisseriaceae、Nitrosomonadaceae、Oxalobacteraceae、
Rhodocyclaceae) carry out probe design, and verify in BLAST, it is thus achieved that be used for preparing the probe sequence of gene chip
Row.
The above-mentioned sequence possibly as probe, from detecting specific angle, is screened, the most really by applicant
Determine following probe sequence:
Wherein for detecting the nucleic probe of Alcaligenaceae microorganism, its nucleotides sequence is classified as SEQ ID NO:1-
Any one or several in 3;
Wherein for detecting the nucleic probe of Burkholderiaceae microorganism, its nucleotides sequence is classified as SEQ ID NO:
Any one or several in 4-6;
Wherein for detecting the nucleic probe of Comamonadaceae microorganism, its nucleotides sequence is classified as SEQ ID NO:7-
Any one or several in 9;
Wherein for detecting the nucleic probe of Hydrogenophilaceae microorganism, its nucleotides sequence is classified as SEQ ID
Any one or several in NO:10-12;
Wherein for detecting the nucleic probe of Methylophilaceae microorganism, its nucleotides sequence is classified as SEQ ID NO:
Any one or several in 13-15;
Wherein for detecting the nucleic probe of Neisseriaceae microorganism, its nucleotides sequence is classified as SEQ ID NO:16-
Any one or several in 18;
Wherein for detecting the nucleic probe of Nitrosomonadaceae microorganism, its nucleotides sequence is classified as SEQ ID
Any one or several in NO:19-21;
Wherein for detecting the nucleic probe of Oxalobacteraceae microorganism, its nucleotides sequence is classified as SEQ ID NO:
Any one or several in 22-23;
Wherein for detecting the nucleic probe of Rhodocyclaceae microorganism, its nucleotides sequence is classified as SEQ ID NO:
Any one or several in 24-26;
Make a little on chip:
Hybridization positive control Quality Control probe (PC), uses the conservative fragment of bacterial 16 S rRNA gene.It is main
Function be with PCR amplification procedure in expand out label based on 16S rRNA gene hybridization, thus to amplification, labelling and
The correctness of the detection processes such as hybridization control effectively, and its nucleotides sequence is classified as SEQ ID NO:27;
Hybridization negative control Quality Control probe (NC), uses the oligonucleotide sequence of one section of 40 T.This probe will not be with
Any amplification and marked product combine, and therefore this probe can monitor the reliability of crossover process, its nucleotide sequence from the negative
For SEQ ID NO:28;
Surface chemistry Quality Control probe (CK) is an oligonucleotide sequence with 40 T of HEX dye marker, can monitoring point
The reliability of sample process, additionally the position of fluorescent probe point can be as DNA microarray coordinate on chip, during chip detection
Playing the effect of location probe location, its nucleotides sequence is classified as SEQ ID NO:29 (Fig. 1).
Embodiment 2: the specific detection of the β of the present invention-mycetozoan group detection gene chip
The representative of the sea water advantage family Comamonadaceae in β-mycetozoan is selected to clone Uncultured
The specificity of β-mycetozoan group detection gene chip is detected by Comamonadaceae bacterium clone 2-8.
1. the extraction of DNA: extract plasmid DNA with plasmid extraction kit.
2. the amplification of 16S rRNA gene: utilize cloning vehicle pEASY-T1 universal primer M13F (GTA AAA CGA
CGG CCA GT) and M13R (GTC CTT TGT CGA TAC TG) 16S rRNA gene is carried out linear amplification.Amplification program
It is 94 DEG C of 5min, 25 circulations (94 DEG C of 30s, 55 DEG C of 30s, 72 DEG C of 1min 30s), 72 DEG C of 10min.
3. fluorescent labeling: utilize fluorescently-labeled random primer (Cy3-NNN NNN NNN) and Klenow enzyme to 16S
RRNA gene amplification product is marked.37 DEG C of 1.5h, 70 DEG C of 10min.
4. hybridization: 15 μ L fluorescent mark products and 5 μ L hybridization solutions are mixed miscellaneous with α mycetozoan group gene chip 50 DEG C
Hand over 12h.Chip cleans, and uses scanner testing result after drying.
Result shows (Fig. 2), clones Uncultured Comamonadaceae bacterium clone 2-8 and this
The probe of Comamonadaceae section corresponding on bright gene chip has an obvious hybridization signal, and with the probe of other section
Amixia signal, illustrates that the ocean β-mycetozoan group detection gene chip of the present invention has high specificity.
Embodiment 3: utilize the β in chip detection seawater sample-mycetozoan kind
Ocean β-mycetozoan group detection the gene chip of seawater sample 22A with the present invention is hybridized, concrete grammar
Such as embodiment 2.And compare with the result of high-flux sequence.Result is as shown in table 1.
β-mycetozoan species detection result in table 1 seawater sample 22A
Genechip detection result shows that the β mycetozoan subclass contained in seawater sample 22A comprises
Burkholderiaceae、Comamonadaceae、Methylophilaceae、Nitrosomonadaceae、
Oxalobacteraceae;High-flux sequence result shows to comprise containing β mycetozoan subclass in seawater sample 22A
Comamonadaceae、Methylophilaceae、Neisseriaceae、Nitrosomonadaceae、
Rhodocyclaceae.The testing result of the gene chip of the present invention is unanimous on the whole with high-flux sequence result, and this gene is described
Chip can accurately identify the kind of marine environment β-mycetozoan.
Embodiment 4: utilize the β in chip detection seawater sample-mycetozoan structure of community
Ocean by seawater sample 22A, 151A, Y1MB601, Y1P404, PE104, HSPI104,203,602 and the present invention
β-mycetozoan group detection gene chip hybridizes, concrete grammar such as embodiment 2.Wherein, 22A Yu 151A was from east in 2013
Sea sea water sample;203 and 602 from 2012 shrimp pool water samples;Y1MB601 and Y1P404 is from big pool shrimp intestinal summer in 2014;
PE104 and HSPI104 be 2013 autumn big pool sample.Kind and the abundance of each β-mycetozoan chip detection gone out are carried out
PCoA analyzes, and analyzes with the PCoA of high-flux sequence result and compare.Chip detection result show seawater sample 22A with
The β of 151A-mycetozoan structure of community similarity is higher, gets together;203,602 to be all from shrimp to Y1MB601, Y1P404 relevant
Sample, β therein-mycetozoan structure of community similarity is higher, gets together;The β of PE104, HSP104-mycetozoan structure of community
Similarity is higher, gets together.High-flux sequence result again shows that seawater sample 22A with 151A gets together, 203,602,
Y1MB601, Y1P404 get together, and other two environmental sample is got together.The gene chip of this explanation present invention can be accurate
Really, quickly sea water β-mycetozoan group is identified, and substantially reduce the detection time.Therefore, for marine environment antibacterial
The monitoring of group provides strong technical support, establishes for setting up, perfecting immediate offshore area marine environmental quality overall evaluation system
Determine solid foundation.
Claims (7)
1. a gene chip, it is characterised in that described gene chip includes chip carrier, and is fixed on chip carrier
On, for detect Alcaligenaceae bacterium in sea water, Burkholderiaceae bacterium, Comamonadaceae bacterium,
Hydrogenophilaceae bacterium, Methylophilaceae bacterium, Neisseriaceae bacterium, Nitrosomonadaceae bacterium,
The probe of any one in Oxalobacteraceae bacterium, Rhodocyclaceae bacterium,
Wherein for detecting the nucleic probe of Alcaligenaceae bacterium, what its nucleotides sequence was classified as in SEQ ID NO:1-3 appoints
One or more;
For detecting the nucleic probe of Alcanivoracaceae bacterium, it is arbitrary that its nucleotides sequence is classified as in SEQ ID NO:4-6
Plant or several;
For detecting the nucleic probe of Comamonadaceae bacterium, its nucleotides sequence is classified as any one in SEQ ID NO:7-9
Or it is several;
For detecting the nucleic probe of Hydrogenophilaceae bacterium, what its nucleotides sequence was classified as in SEQ IDNO:10-12 appoints
One or more;
For detecting the nucleic probe of Methylophilaceae bacterium, it is arbitrary that its nucleotides sequence is classified as in SEQ IDNO:13-15
Plant or several;
For detecting the nucleic probe of Neisseriaceae bacterium, its nucleotides sequence is classified as any one in SEQ ID NO:16-18
Or it is several;
For detecting the nucleic probe of Nitrosomonadaceae bacterium, what its nucleotides sequence was classified as in SEQ IDNO:19-21 appoints
One or more;
For detecting the nucleic probe of Oxalobacteraceae bacterium, it is arbitrary that its nucleotides sequence is classified as in SEQ IDNO:22-23
Plant or several;
For detecting the nucleic probe of Rhodocyclaceae bacterium, it is arbitrary that its nucleotides sequence is classified as in SEQ ID NO:24-26
Plant or several.
2. gene chip as claimed in claim 1, it is characterised in that described chip carrier is further fixed on hybridizing positive control
Any one or several in Quality Control probe, hybridization negative control Quality Control probe, surface chemistry Quality Control probe.
3. gene chip as claimed in claim 2, it is characterised in that the nucleotide of described hybridization positive control Quality Control probe
Sequence is SEQ ID NO:27.
4. gene chip as claimed in claim 2, it is characterised in that the nucleotide of described hybridization negative control Quality Control probe
Sequence is SEQ ID NO:28.
5. gene chip as claimed in claim 2, it is characterised in that the nucleotide sequence of described surface chemistry Quality Control probe
For SEQ ID NO:29.
6. gene chip as claimed in claim 5, it is characterised in that surface chemistry Quality Control probe HEX dyestuff is marked.
7. the application in detection marine environment γ-mycetozoan group of the gene chip described in any one of claim 1-6.
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Cited By (1)
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CN112063695A (en) * | 2020-09-10 | 2020-12-11 | 中国科学院天津工业生物技术研究所 | Bacterial community gene chip for detecting marine oil spill environment |
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