CN111424104A - Method for rapidly judging degradation of pleurotus eryngii strain based on bacterial community composition and abundance and application of method - Google Patents
Method for rapidly judging degradation of pleurotus eryngii strain based on bacterial community composition and abundance and application of method Download PDFInfo
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Abstract
The invention discloses a method for rapidly judging the strain decline of pleurotus eryngii based on the composition and abundance of a bacterial community and application thereof, belonging to the technical field of edible fungi. The method comprises the following steps: 1) performing high-throughput sequencing on the hyphae of the pleurotus eryngii strain to be detected through an Illumina HiSeq 2500 sequencing platform; 2) filtering and removing impurities from high-throughput sequencing data, clustering according to the similarity of more than 97%, and filtering OTU by taking 0.005% of all sequencing numbers as a threshold value to obtain the bacterial composition of bacterial strain hyphae and the abundance of flora; 3) whether the pleurotus eryngii strains decline or not is quickly judged through the obtained bacterial diversity index and the flora abundance. The bacterial composition and the structural condition of the pleurotus eryngii strains are comprehensively known, whether the pleurotus eryngii strains decline or not is judged based on the diversity index and the flora abundance, and a new judgment index is provided for a factory to quickly judge whether the pleurotus eryngii strains decline or not.
Description
Technical Field
The invention belongs to the technical field of edible fungi, and particularly relates to a method for rapidly judging the strain decline of pleurotus eryngii based on the composition and abundance of a bacterial community and application thereof.
Background
Pleurotus eryngii (Pleurotus eryngii)Pleurotus eryngii) Belonging to the order Agaricales, the order Basidiomycetes, the family Pleurotaceae, the genus Pleurotus, the scientific name Pleurotus Citrinopileatus Sing. The pleurotus eryngii has fleshy flesh, dense and firm stipe tissue and delicious taste, and is vegetatively called as delicious bolete on grassland. The pleurotus eryngii is rich in nutrition, is rich in protein, carbohydrate, vitamins and mineral substances such as calcium, magnesium, copper, zinc and the like, and has the function of improving the immunity of a human body. The pleurotus eryngii has the functions of tonifying qi and killing insects, can promote the digestion and absorption of lipid substances and the dissolution of cholesterol by a human body, and also has the effects of resisting cancers, promoting gastrointestinal digestion, preventing cardiovascular diseases, beautifying and the like. The pleurotus eryngii is a new rare edible fungus variety which is successfully developed and cultivated and integrates edible, medicinal and dietary therapy.
The method is characterized in that the strain decline is a phenomenon that economic characters of edible mushroom populations are deteriorated, so that changes deviating from human needs occur in the aspects of yield, quality, resistance and the like, in the edible mushroom industry, the strain decline refers to a phenomenon that the economic characters of the edible mushroom populations are deteriorated, so that the strain decline is caused, the influence of ② adverse environment causes variation of microbial genes, the strain decline is caused due to excessive ③ generation times, the three reasons are ① virus or bacterial infection strains, so that the strain decline is caused, the influence of the ② adverse environment causes the strain decline is caused, the former two reasons can be controlled by means of enhancing environmental control, improving operating skills and the like, so that the influence of the pollution of bacteria, viruses or environmental conditions on the strain decline is reduced and eliminated, the influence of the 3 reason is difficult to avoid, in the actual production, most of the pleurotus eryngii production plants still adopt a method for separating strains, adding strains, preserving strains, using strains, carrying out secondary culture and using, and carrying out secondary culture preservation and use, but the main research on the growth promotion of edible mushrooms, the strain maturation of the strain, the growth of the edible mushrooms, the strain, the growth of the strain, the growth promotion of the growth of the strain, the growth of the strain, the edible mushrooms, the strain, the growth of the strain, the strain development of the strain, the strain development of the growth of the strain, the strain development of the strain.
According to the research, the pleurotus eryngii starting strain and the degenerated strain are subjected to high-throughput sequencing, the symbiotic bacteria composition and diversity in the pleurotus eryngii starting strain and the degenerated strain are measured, and a method for judging the degeneration of pleurotus eryngii strains based on the symbiotic bacteria composition and diversity is established through the change condition of the symbiotic bacteria composition and diversity and the corresponding degenerated strain. Although the high-throughput sequencing technology is widely applied, the method is not reported in the aspect of researching the strain decline of the edible fungi, so that the method for judging the strain decline by combining the high-throughput sequencing technology with the strain decline of the edible fungi is established for the first time. Meanwhile, due to the characteristics of high efficiency, rapidness, accuracy and economy of the high-throughput sequencing technology, the composition and diversity of symbiotic bacteria in the strain can be accurately and rapidly determined, and the method is economical and practical, and is very suitable for pleurotus eryngii factories to judge whether the strain is degenerated. In addition, the method can also be used for various pleurotus eryngii research units, and the change rule of the composition and the structure of the bacterial community in the processes of subculture and production decline of pleurotus eryngii strains is measured by a high-throughput sequencing technology, so that the strain decline is controlled by regulating and controlling the endogenous bacterial community, the technical barrier is broken, and the obstacle is cleared for the development of edible fungi.
Disclosure of Invention
The invention aims to solve the problem of strain decline in the edible fungus industry, and provides a method for rapidly judging the strain decline of pleurotus eryngii based on the composition and abundance of a bacterial community and application thereof.
In order to achieve the purpose, the invention adopts the following technical scheme:
a method for rapidly judging degradation of pleurotus eryngii strains based on bacterial community composition and abundance comprises the following steps:
(1) extracting total DNA from mycelium of pleurotus eryngii strains to be detected, taking the total DNA as a template, and using a 16S rDNA V3+ V4 region universal primer: 338F: 5'-ACTCCTACGGGAGGCAGCA-3' and 806R: 5'-GGACTACHVGGGTWTCTA AT-3' is used as a primer to carry out PCR amplification, and the recovered PCR product is subjected to high-throughput sequencing by an Illumina HiSeq 2500 sequencing platform;
(2) splicing and filtering the high-throughput sequencing data to remove chimeras, clustering according to similarity of more than 97 percent of USEARCH, and filtering OTU by taking 0.005 percent of all sequencing numbers as a threshold value to obtain bacterial composition of strain hyphae and flora abundance;
(3) whether the pleurotus eryngii strains decline or not is quickly judged through the obtained bacterial diversity index and the flora abundance.
The step (3) of determining whether the strain is decayed specifically includes:
(1) when Simpson in the pleurotus eryngii hyphae is within the range of 0.05-0.09 or is larger than the range, and when the Shannon value is within the range of 3.2-4.6 or is smaller than the range, the strain is proved to have recession to a certain degree and is not suitable for being used as a seed for factory cultivation and production; or
(2) At a phylum level, when the relative abundances of firmicutes and bacteroidetes in pleurotus eryngii hyphae are respectively in the range of 15% -27% and 3% -12% or less than the range, and the relative abundance of actinomycetes is in the range of 21% -28% or more than the range, the strain is shown to be degenerated to a certain degree and is not suitable for being used as a seed for factory cultivation and production; or
(3) At genus level, when the hyphae of Pleurotus eryngii have Rhodococcus, Xanthium and SphingomonasWhen the abundance ratio is respectively in the interval range of 10.00-18.00%, 1.00-13.00% and 1.39-2.72% or more than the range,Dubosiellawhen the relative abundance of the genera, the Klebsiella and the Pseudomonas is in the range of 0.05-3.80%, 0.50-1.50% and 0.30-0.60% or less than the range, the strain is proved to have declined to a certain degree and is not suitable for being used as a plant cultivation and production seed.
The method for rapidly judging the degradation of the pleurotus eryngii strains based on the bacterial community composition and abundance is applied to the industrial cultivation production of pleurotus eryngii.
The invention has the advantages that:
the invention firstly establishes a method for judging strain decline by combining a high-throughput sequencing technology and the strain decline of edible fungi. The method determines the change rule of the bacterial community composition and structure in the processes of subculture and production decline of the pleurotus eryngii strains by a high-throughput sequencing technology, and provides a new judgment index for strain degeneration, which is simple, convenient, rapid and accurate. The method is very suitable for pleurotus eryngii factories to judge whether strains decline or not, and can also be used for various pleurotus eryngii research units to control the strain decline by regulating endogenous floras, break technical barriers and clear obstacles for development of edible fungi.
Detailed Description
In order to make the present invention more comprehensible, the technical solutions of the present invention are further described below with reference to specific embodiments, but the following examples are only examples of the present invention and do not represent the scope of the present invention defined by the claims.
Example 1
1. Materials and methods
1.1 test strains: 8 target strains are obtained by separating pleurotus eryngii fruiting bodies, subculturing and collecting by enterprises, and the results of the determination of the characteristics, physiological and biochemical indexes and fruiting experiments of the 8 pleurotus eryngii hyphae show that the production performance of the strains with the numbers of 7, 9, 11, 13 and 15 is reduced, the strains are degraded, and the strains with the numbers of 1, 3 and 5 are normal in production performance. The pleurotus eryngii fruiting body comes from Zhangzhou green biological science and technology limited in Fujian province.
1.2 culture Medium
Standard PDA solid medium (1L) comprises potato 200g, glucose 20g, and agar 20 g.
1.3 Primary reagents
EasyPure Genomic DNA Kit extraction Kit, PCR related reagent and AxyPrepDNA gel recovery Kit.
1.3 Experimental instruments
A constant temperature incubator, a super clean bench, a PCR instrument and a gel electrophoresis instrument.
2 method of experiment
2.1 obtaining samples of different Pleurotus eryngii strains, namely inoculating the preserved Pleurotus eryngii strains to a PDA culture medium, culturing for a week at 25 ℃, activating strains, inoculating the activated different Pleurotus eryngii strains to the PDA culture medium, wherein the inoculation area is 5mm × 5mm, culturing at constant temperature of 25 ℃, and setting 10 times of repetition for each treatment.
2.2 extracting and measuring the microbial DNA in the pleurotus eryngii mycelium: after the pleurotus eryngii hyphae overgrow the PDA culture medium plates, selecting 3 plates for each culture medium, scraping the hyphae under aseptic conditions, extracting total DNA by using an easy pure Genomic DNA Kit extraction Kit, and carrying out PCR amplification on the extracted total DNA. The PCR primers used 16S rDNA V3+ V4 region universal primers: 338F: 5'-ACTCCTACGGGAGGCAGCA-3' and 806R: 5 '-GGACTACHVGGGTWTCTAAT-3' was subjected to PCR amplification. PCR products were recovered using AxyPrepDNA gel recovery kit. High-throughput sequencing was then performed using the Illumina HiSeq 2500 sequencing platform.
2.3 processing the sequencing data of the microorganisms in the pleurotus eryngii mycelium, namely splicing sequencing original data by adopting F L ASH, performing quality filtration on the spliced sequences by adopting Trimmomatic, removing chimeras by using UCHIME to obtain high-quality Tags sequences, clustering the sequences by adopting USEARCH at the level of 97% similarity, filtering OTU by taking 0.005% of all sequencing numbers as a threshold value, and analyzing diversity index and bacterial abundance by using the result of OTU clustering analysis.
3 results and analysis
3.1 bacterial diversity index analysis of different strains of Pleurotus eryngii
The results of the bacterial diversity index of different strains of pleurotus eryngii are shown in table 1. As shown in Table 1, the Shannon and Simpson indexes are used for measuring species diversity, and the Simpson values of strains 7, 9, 11, 13 and 15 are obviously increased compared with those of strains 1, 3 and 5 and are all more than 0.05; the Shannon values of No. 7, 9, 11, 13 and 15 strains are reduced to a certain extent compared with No. 1, No. 3 and No. 5 strains, and are all below 4.6, which indicates that the variety of the degenerated strain is obviously different from that of the strain with normal production performance. Therefore, when Simpson in the pleurotus eryngii hyphae is in the range of 0.05-0.09 or is larger than the range, and when the Shannon value is in the range of 3.2-4.6 or is smaller than the range, the strain is proved to have declined to a certain degree, and is not suitable for being used as a seed for factory cultivation and production.
TABLE 1 bacterial diversity index of different strains of Pleurotus eryngii
3.2 analysis of relative abundance of bacteria in different strains of Pleurotus eryngii
The results of the relative abundance analysis of Pleurotus eryngii at the phylum level of different strains are shown in Table 2. At the phylum level, it is clear from Table 2 that the relative abundance of the higher abundant bacterial phyla of class 3 varies significantly with strain No. 7, including the phylum Firmicutes, Actinomycetes and Bacteroides. The phylum firmicutes and bacteroidetes are main relatively beneficial phyla, and the abundance of the two phyla is obviously reduced in the degenerated strains; the actinomycete phylum is the main peculiar phylum of the degenerated strain, and compared with the strain with normal production performance, the abundance of the three phyla in the degenerated strain is obviously reduced. Therefore, when the relative abundances of firmicutes and bacteroidetes in the pleurotus eryngii hyphae are respectively in the range of 15% -27% and 3% -12% or less than the range, and the relative abundance of actinomycetes is in the range of 21% -28% or more than the range, the bacterial strain is declined to a certain degree, and is not suitable for being used as a seed for factory cultivation and production.
TABLE 2 relative abundance of bacteria of different strains of Pleurotus eryngii (phylum level)
The relative abundance of Pleurotus eryngii at the level of different bacterial strains is shown in Table 3. At the genus level, it is clear from Table 3 that the relative abundance of major bacterial species of group 8, including Rhodococcus (R) is significantly changed in strains numbered 7, 9, 11, 13, 15Rhodococcus) Genus Xanthium (A), (B), (C)Ochrobactrum)、DubosiellaBelong to、Klebsiella genus (A), (B), (C)Klebsiella) Pseudomonas bacteria (A), (B) and (C)Pseudomonas) Sphingomonas (A), (B), (C)Sphingomonas). WhereinDubosiellaGenera, Klebsiella and Pseudomonas are major relatively beneficial genera, and the abundance of these 3 bacterial genera is significantly reduced in the degenerate strain; the Rhodococcus, the Xanthium and the Sphingomonas are the main special genera of the degenerated strain, and the abundances of the three genera in the degenerated strain are obviously increased. Therefore, when the relative abundance of the rhodococcus, the ochrobactrum and the sphingomonas in the pleurotus eryngii hypha is respectively in the range of 10.00-18.00%, 1.00-13.00% and 1.39-2.72% or more than the range,Dubosiellawhen the relative abundance of the genera, the Klebsiella and the Pseudomonas is in the range of 0.05-3.80%, 0.50-1.50% and 0.30-0.55% or less than the range, the strain is proved to have declined to a certain degree and is not suitable for being used as a plant cultivation and production seed.
TABLE 3 relative abundance of bacteria of different strains of Pleurotus eryngii (genus level)
4 summary of the invention
The results of the determination of the symbiotic bacterial composition and diversity of the original and the degenerate strains show that the bacteria of the strains with normal production performance and the degenerate strains have Shannon and Simpson indexes and the indexes of the bacteria of the phylum firmicutes, Actinomycetes, Bacteroides, Rhodococcus, Ochrobactrum, Sphingomonas, Sphingomon,DubosiellaBelong to、Obvious differences exist in the relative abundance of the Klebsiella and the Pseudomonas, and the indexes can be used as indexes for characterizing the strain decline. Through the characteristics of high efficiency, rapidness, accuracy and economy of a high-throughput sequencing technology, the pleurotus eryngii factory or a related research unit can rapidly and accurately determine corresponding indexes for judging strain recession, so that manpower and material resources are greatly saved, and the economic loss of the factory can be reduced to a certain degree.
The above description is only a preferred embodiment of the present invention, and all equivalent changes and modifications made in accordance with the claims of the present invention should be covered by the present invention.
SEQUENCE LISTING
<110> Fujian agriculture and forestry university
<120> method for rapidly judging degradation of pleurotus eryngii strains based on bacterial community composition and abundance and application thereof
<130>2
<160>2
<170>PatentIn version 3.3
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<213> Artificial sequence
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actcctacgg gaggcagca 19
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ggactachvg ggtwtctaat 20
Claims (3)
1. A method for rapidly judging the degradation of pleurotus eryngii strains based on the composition and abundance of bacterial communities is characterized by comprising the following steps: the method comprises the following steps:
(1) extracting total DNA from mycelium of pleurotus eryngii strains to be detected, taking the total DNA as a template, and using a 16S rDNA V3+ V4 region universal primer: 338F: 5'-ACTCCTACGGGAGGCAGCA-3' and 806R: 5'-GGACTACHVGGGTWTCTA AT-3' is used as a primer to carry out PCR amplification, and the recovered PCR product is subjected to high-throughput sequencing by an Illumina HiSeq 2500 sequencing platform;
(2) splicing and filtering the high-throughput sequencing data to remove chimeras, clustering according to similarity of more than 97 percent of USEARCH, and filtering OTU by taking 0.005 percent of all sequencing numbers as a threshold value to obtain bacterial composition of strain hyphae and flora abundance;
(3) whether the pleurotus eryngii strains decline or not is quickly judged by analyzing the bacterial diversity index and the flora abundance.
2. The method for rapidly judging the degradation of pleurotus eryngii strains based on the composition and abundance of bacterial communities according to claim 1, which is characterized in that: the step (3) of judging whether the strains decline specifically comprises the following steps:
(1) when Simpson in the pleurotus eryngii hyphae is within the range of 0.05-0.09 or is larger than the range, and when the Shannon value is within the range of 3.2-4.6 or is smaller than the range, the strain is declined and is not suitable for being used as a seed for factory cultivation and production; or
(2) At a phylum level, when the relative abundances of firmicutes and bacteroidetes in pleurotus eryngii hyphae are respectively in the range of 15% -27% and 3% -12% or less than the range, and the relative abundance of actinomycetes is in the range of 21% -28% or more than the range, the strain is declined and is not suitable for being used as a seed for factory cultivation and production any more; or
(3) At the genus level, when the relative abundance of the rhodococcus, the ochrobactrum and the sphingomonas in the pleurotus eryngii hyphae is in the range of 10.00-18.00%, 1.00-13.00%, 1.39-2.72% or more,DubosiellaWhen the relative abundance of the genera, the Klebsiella and the Pseudomonas is in the range of 0.05-3.80%, 0.50-1.50% and 0.30-0.55% or less than the range, the strain is declined and is not suitable for being used as a plant cultivation and production seed.
3. The method for rapidly judging the degradation of pleurotus eryngii strains based on the composition and abundance of bacterial communities as claimed in claim 1, which is applied to industrial cultivation and production of pleurotus eryngii.
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