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DNA sequence and community structure diversity of multi-year soil fungi in Grape of Xinjiang

This study is designed to understand the community structure and diversity of fungi in the rhizosphere soil of grape. As the sample for this study, the rhizosphere soil of Crimson seedless grape with different planting years was collected from Shihezi in Xinjiang to carry out high-throughput sequencing, by which the complete sequence of soil fungi DNA was identified, and accordingly, the richness and diversity index of fungi were determined. The results showed that the dominant phyla of fungi in the grape rhizosphere soil with different planting years were Ascomycota and Basidiomycota, and the dominant classes of fungi were Sordariomycetes and Dothideomycetes. Soil organic matter, total potassium, total nitrogen and available phosphorus were the main soil fertility factors affecting the abundance and diversity of soil fungal communities, among which soil organic matter had the most significant influence. In addition, the fungal diversity and richness were highest in the middle layer (20–35 cm) of the grape rhizosphere soil with 12 planting years and lowest in the lower layer (35–50 cm) of the grape rhizosphere soil with 5 planting years. Linear discriminant analysis suggested that there were more biomarkers in the vineyard rhizosphere soil with 10 planting years, which meant there were more fungal communities with significant difference in the soil, especially in the middle layer (20–35). The results of this study can provide data reference and theoretical basis for improving vineyard soil quality, evaluating soil microecological effects and improving ecological environment of vineyard soil.

Sample collection. Grapes are perennial plants, and their absorption roots are mostly distributed within 50 cm horizontal distance from the trunk, so the sampling points were selected within 30-40 cm from the trunk. Grape root depth is usually distributed within 60 cm vertical distance below the surface, so the sampling depths were selected within 50 cm below the surface. From the same variety of grape plants with different ages (5,8,10,12 and 15 years, denoted as ZN, XZ, HY, WH and GM, respectively), three plants were randomly selected for each age group. Around 30-40 cm from each grape plant, three points were selected for taking soil samples. After removing debris about 5 cm from the surface, the upper layer (5-20 cm), middle layer (20-35 cm) and lower layer (35-50 cm) of soil were taken with earth boring augers at each point. With disposable sterilized rubber gloves, the soil was manually mixed, subpackaged and marked to make samples (about 500 g each) through quartering method. Each sample was divided into two parts, which were immediately put into two sterilized self-sealing bags with labels denoting the sampling time, place, soil depth and serial number. The samples were coded with a two-digit system, where the first digit indicated the depth (1, 2 and 3 denoted the depth of 20, 35 and 50 cm, respectively) and the second indicated the replicate number. There were 5 age groups, each group included 3 plants, and for each plant the soil was taken at three depths; so, in total there were 45 soil samples (5 × 3 × 3). The fresh soil was immediately screened by 20-mesh sieve and divided into two parts, in which one was stored with liquid nitrogen and sent to Beijing Compass Biotechnology Co., Ltd for high-throughput sequencing, and the other was air-dried and stored for determining the physicochemical properties of soil. (See Table 1 for sample coding information).
Determination of soil physicochemical properties. The air-dried soil samples were tested for the following physicochemical factors: organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), nitrate nitrogen (XN), ammonium nitrogen (AN), available phosphorus (SP), available potassium (SK), pH value (1:5) and electrical conductivity (EC). The soil properties were determined in accordance with the methods in the textbook Soil Agrochemical Analysis compiled by Bao Shidan 7-10 . Specifically, SOM was determined by potassium dichromate titration with external heating; TN was determined with FOSS 1035 fully automatic nitrogen determinator by perchloric acid-sulfuric acid digestion method; TP was determined with Agilent Cary 60 UV-Vis spectrophotometer by perchloric acid-sulfuric acid digestion-molybdenum antimony D-iso ascorbic acid colorimetry (MADAC); TK was determined with Thermo Fisher Scientific S series atomic absorption spectrometer by perchloric acid-sulfuric acid digestion-atomic absorption method; XN and AN were determined with BRAN + LUEBBE continuous flow analyzer after extracting by 0.01 M calcium chloride; SP was determined with MADAC after extracting by sodium bicarbonate; SK was determined by atomic absorption method after extracting by ammonium acetate; pH was determined by Mettler Toledo FiveEasy™ Plus pH meter; and EC was determined by HANNA H1 2315 conductivity meter.
The 3 samples taken from the same layer of soil around each grape plant were mixed into one sample to determine their physicochemical properties. There were 5 age groups, and for each group the soil involved 3 depths, Then, the purity and concentration of the DNA were detected with 1% agarose gel electrophoresis. A proper amount of sample DNA was taken into a centrifuge tube, where the sample was diluted to 1 ng/μl with sterile water. Using the diluted genomic DNA as template, specific primers with Barcode were selected according to the sequencing region to be used; Phusion® high-fidelity PCR master mixing with GC buffer (New England Biolabs) was used together with NEB high-efficiency and high-fidelity enzymes to ensure the amplification efficiency and accuracy for carrying out PCR. The internal transcription spacer (ITS) 36 technique was used to analyze the nucleic acid sequence, and the fungal primers were ITS1 primers (ITS5-1737F and ITS2-2043R). PCR products were detected by 2% agarose gel electrophoresis; according to the determined concentration, the samples were mixed up for isoconcentration, and then the PCR products were purified by electrophoresis with 1 × TAE buffer and 2% agarose gel. Finally, the target bands were recovered by tapping. GeneJET gel recovery kit (Thermo Scientific) was used for product purification. Ion plus Fragment Library Kit 48rxns (Thermo Fisher) was used to construct the library, which was then quantified and qualified by Qubit, and sequencing was carried out with Ion S5TMXL (Thermofisher).
Biological information analysis. Cutadapt(V1.9.1) 11 was used to cut off the low-quality part of the reads; then, based on the reads obtained by Barcode, the data for each sample were separated. After cutting off Barcode and the primer sequences, raw reads were obtained. The raw reads were then detected with UCHIME Algorithm 12 and compared with gene annotation database to remove chimeric sequences 13 , so as to obtain the final clean reads.
Sequence clustering was carried out to all clean reads of the samples by using Uparse v7.0.1001 14 at the default identity of 97% to obtain OTUs (Operational Taxonomic Units). The sequences with the highest frequency of occurrence were selected as the representative sequences according to the principle of algorithm. Specie annotation was done to the representative sequences by the Blast method of Qiime version 1.9.1 15 , and specie annotation analysis were conducted as per the Unit database 16 to calculate the community composition of each sample at each classification level. Using MUSCLE 17 (Version 3.8.31), the phylogenetic relationships of all OTUs' representative sequences were obtained. Finally, the data of each sample were homogenized.
Qiime (Version 1.9.1) was used to calculate OTU abundance, Alpha diversity and UniFrac distance. R software (Version 2.15.3) was used to plot PCA, PcoA and NMDS diagrams. LEfSe software was used for LDA Effect Size analysis at the default LDA score of 4. Subsequently, all OUT data was statistically assigned and compared in terms of soil depth and grape planting years of each sample, in order to understand OUTs distributions and variations at the grape lands.

Results and analysis
Soil physicochemical properties. The test results of physicochemical factors of the soil are shown in Table 2. In the soil with 15-year vines, the average contents of TK and SK were highest and the contents of SOM and TN were lowest. In the soil with 5-year vines, the contents of XN and SK were relatively higher, and the soil pH was between 7.86 and 7.98, thus it is alkaline soil.
The analysis of variance showed that grape planting year had significant effect on TK and SP (P < 0.05), and soil depth had significant effect on SOM and SK (P < 0.05). Among the physicochemical indices, organic matter Table 2. Determined results of soil physicochemical properties. The data in the same row with different lower case letters denote that there is significant difference between the groups (P < 0.05). SOM soil organic matter content, TN total nitrogen content in soil, TP total phosphorus content in soil, TK total potassium content in soil, XN nitrate nitrogen content in soil, AN ammonium nitrogen content in soil, SP available phosphorus content in soil, SK available potassium content in soil. www.nature.com/scientificreports/ had an extremely significant effect on TN and TK (P < 0.01), while TN had a significant effect on TK and XN (P < 0.05). AN was closely related to XN (P < 0.05), and XN had a significant effect on pH value (P < 0.05).
Basic analysis of sequencing data. From the 45 soil samples, we obtained 3,625,859 original sequences, in which 3,068,591 were valid ones; so, from each sample, 68,199 valid sequences were obtained on average, with the minimum number 59999 and the maximum number 76469. Based on the abundance of OTUs at 97% level, we used QIIME to process the OTUs for the valid sequences, and obtained a total of 31,533 OTUs, among which the highest number of OTUs from single sample were 871. Further, the highest number of OTUs was 11,144, occurring in the middle layer (25-35 cm) and the lowest number of OTUs was 9745, occurring in the lower layer (35-50 cm); and the 12-year vine group (WH) had the highest number of OTUs, which was 7251, while the 5-year vine group (ZN) had the lowest number of OTUs, which was 5382. See Table 3 for the sequence number and OTU number of each soil sample, and see Table 4 for the sequence number and OTU number of soil samples in the terms of soil depth and grape planting year. QIIME (Version 1.9.1) was used to generate rarefaction curves for the 45 samples ( Fig. 1). Rarefaction curves can reveal the representativeness of samples, and they can be used to evaluate whether the current sequencing depth is enough to reflect the microbial diversity contained in the community samples. It can be seen from Fig. 1 that when the sequencing amount exceeded 60,000 reads, there were still new OTUs appearing, but the curve had become flat, indicating that the sampling was basically reasonable, which meant the confidence of the bacterial community structure in the real environment was relatively high, in other words, the current sequencing depth was enough to reflect the diversity of fungal communities contained in the community sample.
Analysis of composition and abundance of soil fungi. Species composition analysis reflects the community structure of samples at different taxonomic levels. At the phylum level, as shown in Fig. 2, the main dominant fungi in soil were Ascomycota with an average relative abundance of 34.49%, Basidiomycota with an average relative abundance of 13.85%, Mortierellomycota with an average relative abundance of 2.89%, Glomeromycota with an average relative abundance of 1.39%, and Chytridiomycota with an average relative abundance of  www.nature.com/scientificreports/  At the class level, as shown in Fig. 3, the main dominant taxa were Sordariomycetes, Dothideomycetes, Tremellomycetes, Agaricomycetes, and Tremellomycetes, and their average relative abundance were 13.23%, 10.60%, 6.07%, 5.22%, and 2.43%, respectively. The undetermined taxa at class level accounted for 54.69%. ANOVA analysis showed that grape planting year had a significant effect on the abundance of Tremellomycetes (P < 0.05), and soil depth had a significant effect on the abundance of Agaricomycetes (P < 0.05).
The effect of soil physicochemical properties on fungal community. Redundancy analysis (RDA) at phylum level was carried out to reveal the relationship between soil physicochemical factors and fungal communities (Fig. 4). The first two axes of RDA analysis explained the 70.44% variations of fungal communities, in which the first axis explained 50.7% and the second axis explained 19.74%. SOM had the most significant effect on fungal communities, followed by TK, and the effects of soil physicochemical properties on fungal communities were in the order of SOM > TK > TN > TP > SK > pH > XN > SP > AN.
In this study, Spearman analysis was used to evaluate the correlation between the abundance of top 13 dominant fungal taxa at the phylum level and the soil physicochemical properties, as shown in Fig. 5. The results showed that the abundance of Basidiomycota was negatively significantly correlated with TP (P < 0.05) and extremely negatively correlated with SOM (P < 0.01); the abundance of Glomeromycota was negatively significantly correlated with AN (P < 0.05) and extremely positively correlated with XN (P < 0.01); the abundance of Kickxellomycota was positively significantly correlated to TK, SP and pH (P < 0.05); the abundance of Zoopagomycota was positively significantly correlated with SP (P < 0.05) and extremely positively correlated to AN (P < 0.01); the abundance of Chytridiomycota was positively significantly correlated to XN (P < 0.05); the abundance of Mortierellomycota was positively significantly correlated to pH (P < 0.05); and the abundance of Blastocladiomycota was negatively significantly correlated with TN (P < 0.05). For other dominant fungal phyla, the correlation between their abundance and soil physicochemical factors were not significant.
Analysis of soil fungi diversity. Alpha diversity represents the diversity of species in a specific ecosystem, and it is mainly related to two factors, one is the number of species, i.e., richness, and the other is diversity, i.e., the uniformity of individual distribution in the community. The community richness indices mainly include Chao index and Ace index. The larger Chao and Ace, the more OTUs in the community, and the higher the community richness. Community diversity indices mainly include Shannon index and Simpson index. The greater Shannon index, the higher community diversity; on the contrary, the higher Simpson index, the lower community diversity 16,17 .
The community richness indices Chao1 and ACE and diversity indices Shannon and Simpson of each sample are shown in Tables 5 and 6. different ages showed no significant difference; comparatively, the Shannon index of WH (12-year vines) was slightly higher than that of other groups, and the Shannon index of Zn (5-year vines) was the lowest, indicating that the fungal diversity of soil with 12-year vines was slightly higher than that of other groups, and the fungal diversity of the soil with 5-year vines was the lowest, In general, the fungal diversity and richness of soil with 12-year vines were higher than those of other groups, and the fungal diversity and richness of soil with 5-year vines were lower than those of other groups.
According to the analysis on Chao1 and ACE indices in the terms of soil root depth, the sample groups were in the order of 35 cm deep group > 20 cm deep group > 50 cm deep group, indicating that the fungal richness was highest in the middle layer of the soil, followed by the top layer, and lowest in the lower layer. Shannon indices of different groups showed no significant difference. Comparatively, the Shannon index of the middle layer of the soil was slightly higher than that of other layers, and the Shannon index of the lower layer was the lowest. Fungal diversity also showed the trend of highest in the middle layer, followed by the upper layer and lowest in the lower layer.
Through correlation analysis of soil physicochemical indicators on the Alpha diversity indices of fungal communities, the results showed that SP had a positively significant correlation with Shannon index, and SP had an extremely positive correlation with fungal community diversity, while other physicochemical indicators had no significant correlation with the Alpha diversity indices.
Analysis on the correlation of Alpha diversity index of fungal communities and soil physicochemical indices ( Table 6) showed that available phosphorus (SP) had an extremely significant positive correlation with both Shannon index and Alpha diversity index, while other physicochemical indices had no significant correlation with Alpha diversity index.
Nonmetric Multidimensional Scaling (NMDS) is often used to compare the differences between sample groups. In this study, NMDS analysis was applied to reflect the species information contained in samples into multi-dimensional space in the form of points. The degree of differences between different samples is reflected by the distance between points, which can reflect both the differences between and within sample groups. From  Fig. 6, it can be seen that samples ZN1 (the upper layer of soil with 5-year vines), ZN3 (the lower layer of soil with 5-year vines) and HY3 (the lower layer of soil with 10-year vines) are far away from other samples, indicating that the fungal community structure of those samples was quite different from that of other samples. The close distance between other samples indicates that their similarity of fungal community structure was higher. www.nature.com/scientificreports/ LEfSe (LDA Effect Size) analysis. LEfSe was used to identify fungal species with significant differences in the terms of grape planting years and soil depths. Here, only the cladogram is showed. Firstly, the LEfSe analysis was carried out for different samples from the same soil depth, and the LDA score of 4 was used to identify statistically significant difference between fungal taxa. In the middle layer (20-35 cm), there were 14 taxa with LDA scores higher than 4, including 5 taxa of GM2 (15-year vine), 7 taxa of HY2 (10-year vine), and 2 taxa of ZN2 (5-year vine) (Fig. 7a). In the upper layer (5-20 cm) and the lower layer (35-50 layer), no taxa with significant difference were observed.  www.nature.com/scientificreports/ Then, the LEfSe analysis was carried out for samples from different soil depths, the results found there were 7 fungal taxa whose LDA scores were higher than 4, indicating they had statistically significant difference. The 7 fungal taxa included 1 taxa in the lower layer (35-50 cm) of GM3 (15-year vine), 5 taxa in the middle layer (15-25 cm) of HY2 (10-year vine), and 1 taxon in the middle layer (20-35 cm) of ZN2 (10-year vine), as shown in Fig. 7b. Generally, HY (15-year vine) sample group had more biomarkers than the groups of other planting years, especially in the middle layer (20-35 cm) there were more fungal communities with significant difference.
In the cladograms, circles radiated from inside to outside represent the taxonomic ranks from phylum to genus (or species). Each circle at different taxonomic ranks represents a classification at that level, and the Table 6. Alpha diversity indices of fungal communities in different soil depths. The abbreviations ZN, XZ, HY, WH, GM represent the grape planting years of 5, 8, 10, 12 and 15, respectively. The data in the same column with different lower case letters denote that there is significant difference between the groups (P < 0.05).  Table 7. Correlation between soil fungal Alpha diversity index and soil physical and chemical properties. *Means 0.05 level has significant correlation (P < 0.05). **Means 0.01 level has extremely significant correlation (P < 0.01).

Discussion
In this study, 45 soil samples from vineyards were tested for ITS rRNA gene of fungi by high-throughput sequencing, obtaining 31,533 OTUs at 97% similarity. In the terms of soil depth, the number of OTUs was highest for the samples from the middle layer and lowest for the samples from the lower layer. In the terms of grape planting year, the number of OTUs was highest for the WH group (12-year vines) and lowest for the ZN group (5-year group). The results indicated that the distribution of fungal communities were different in different depth of soil with different planting years of grape. From the vertical direction of soil, the 10-30 cm layer was the cultivated layer as well as root distribution zone, and we found there were most microbial species living in that layer, and www.nature.com/scientificreports/ the finding is similar to the research of Luan Liying et al. 18 ; the reason may be that the cultivated layer has stable temperature and moisture, abundant organic matter, sufficient water and fertilizer, which are all beneficial for the reproduction of microorganisms 19 . In this study, the dominant fungal phyla in the soil samples were Ascomycota, Basidiomycota, Mortierellomycota, Glomeromycota, and Chytridiomycota, in which Ascomycota was the absolute dominant fungal phyla, followed by Basidiomycota. The result is consistent with the findings of Wang, Li and Fu et al. [20][21][22] , indicating that Ascomyota and Basidiomycota have wide adaptability and are distributed under different soil conditions. The two fungal phyla are the key florae for decomposing cellulose in soil organic matter 23 , and most Ascomycota are saprophytic fungi, which play an important role in degrading soil organic matter and are liable to decompose degradable components in organic materials 24 . Yelle et al. 25 reported that Basidiomycota can degrade lignocellulose greatly to form mycorrhiza with plants, thus promoting the absorption of water and mineral elements by roots and improving the physical properties of soil. In addition, Basidiomycota can secrete antibacterial substances to inhibit the growth of soil pathogenic bacteria to protect host plants 26 .
At the class level, the dominant taxa were Sordariomycetes, Dothideomycetes, Tremellomycetes, and Agaricomycetes, in which Sordariomycetes and Dothideomycetes were the most dominant fungal classes, having their relative abundance higher than 10%. Ascomycetes play a key role in decomposition of SOM as well as a dominant role in fungal communities through participating in the secretion, assimilation and SOM degradation of roots.
In order to understand the effect of soil physicochemical factors on soil fungal communities, redundancy analysis (RDA) was carried out to soil fungal communities at the class level. The result showed that SOM had the most significant effect on fungal communities, followed by soil TK and TN. Spearman analysis showed that the dominant Basidiomycota was negatively significantly correlated with TP and extremely negatively correlated with SOM. The Kickxellomycota were positively significantly correlated with TK, SP and pH. The correlation analysis between soil physicochemical properties and Alpha diversity of fungal communities showed that SP was positively significantly correlated with Shannon index. The above results indicated that SOM, TK, TN and SP were the main soil fertility factors affecting the abundance and diversity of soil fungal communities, suggesting that such soil factors played an important role in the genetic diversity of soil fungal communities in this study. The result is similar to the findings of Yang Junbo 27 and Wu Lisha et al. 28 .
Alpha diversity analysis showed that the diversity and richness of fungi was highest in the soil with 12-year vines and lowest in the soil with 5-year vines. The diversity and richness of fungi were highest in the middle layer and lowest in the lower layer (25-35 cm). Currently, most studies believe that, after continuous cropping, the number of bacteria and Actinomycetes in soil will decrease and the number of fungi will increase, which means continuous cropping can transform the soil from "bacterial type" with high fertilizer to "fungal type" with low fertilizer 29 . With the increase of grape planting years, the accumulation of toxic substances secreted by roots was beneficial to the reproduction of fungi in soil and increased the diversity and abundance of fungi. Xiao Hong et al. found that the number of bacteria in the soil of new orchard was higher than that in the soil of continuously cropped orchard, but the number of fungi in the former was lower than that in the latter, and the overall soil condition of new orchard was better than that of the continuously cropped orchard 30 ; meanwhile, the structure of microbial communities in the orchard soil also showed certain regularity with the changes of time and space. Wang Shutong et al. found that with the extension of apple tree life, the number of rhizosphere microorganisms first increased and then decreased 31 ; rhizosphere bacteria and other microorganisms in orchard mainly concentrate in the 0-40 cm layer of soil, showing a decreasing trend from top to bottom 32 .
LEfSe (LDA Effect Size) analysis showed that there were more Biomarks in the soil with 10-year vines than in the soil with other planting years, which means there were significant difference fungal taxa in that group, especially in the middle layer. With the increase of grape planting years, the number of biomarkers increased, indicating that continuous cropping of grapes changed the community structure of soil fungi. Some studies have pointed out that the microbial communities in plant rhizosphere are closely related to plant growth time and root exudates 33,34 . Root exudates not only provide the necessary energy for rhizosphere microorganisms, but also directly affect the quantity and community structure of rhizosphere microorganisms, and their effects sometimes are positive and sometimes negative. With the increase of vine planting years, rhizosphere exudates gradually increase, which is beneficial to the growth and reproduction of some fungi.

Conclusion
According to high-throughput sequencing, we found that in grape rhizosphere soil there was a large number of fungi that adapted to environmental changes, and the structure of fungal communities showed difference both in the soil with different planting years and in the different soil depths. Soil physicochemical properties, grape planting year and soil depth all have certain effects on fungal diversity and community structure. The fungal taxa showed more significant difference in the middle layer of soil with longer planting years, and the formation of those specific fungal groups may be closely related to the root exudates of grape plants.
In this study, the community structure and diversity of rhizosphere soil fungi in vineyards were analyzed by high-throughput sequencing , and more in-depth study needs to be done on the evaluation on microecological functions in soil caused by the change of fungal abundance and the interaction between rhizosphere exudates and fungi. www.nature.com/scientificreports/ Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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