Study on Bacterial Diversity and Community Structure in Grape Rhizosphere Soil Based on High-throughput Sequencing

Volume 6, Issue 6, December 2021     |     PP. 129-153      |     PDF (1265 K)    |     Pub. Date: December 28, 2021
DOI: 10.54647/biology18195    80 Downloads     3157 Views  

Author(s)

FengXue, College of Life Sciences, Shihezi University, Shihezi,832003, China; Guilin Tourism University,Guilin Guangxi 541000, China
TongLiu, Guilin Tourism University,Guilin Guangxi 541000, China

Abstract
In this study, we used the rhizosphere soil of Crimson seedless grape vines with large planting area in Shihezi, Xinjiang as research material, sequenced the bacterial 16S rRNA gene (V4) in different depths of the soil with the grape vines planted for 5, 8, 10, 12 and 15 years by using Illumina MiSeq sequencing platform, and analyzed the diversity and community structure of soil bacteria through bioinformatics related methods. The results showed that 196,690 OTUs were obtained from 45 grape vine rhizosphere soil samples, and the dominant bacterial phyla in the rhizosphere soil were Proteobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes and Actinobacteria, and the main dominant bacterial genera were Bacteroides, Sphingomonas, Prevotella_9, Lactobacillus and Enterococcus. Redundancy analysis (RDA) showed that soil total potassium and total phosphorus had the greatest influence on bacterial community structure. Correlation analysis showed that all dominant bacterial communities, except for Actinobacteria, were significantly related to soil physicochemical properties. Alpha diversity analysis showed that in 15-25cm deep soil, Shannon index, Chao1 and ACE indices were the highest, indicating that layer had the highest bacterial diversity and community richness; Chao1 and ACE indices of 8-year-old vine group were the highest, indicating that group had the highest bacterial community richness; so, grape vine planting years and soil depth had some influence on the diversity and richness of bacterial communities. Beta diversity and PCoA (principal coordinates analysis) analysis showed that bacterial community structure presented significant difference between different samples. Clustering results also showed that soil depth had some influence on bacterial community structure. Linear discriminant analysis suggested that the 15-year-old vine group had the highest level of biomarkers and classification, and the 15-year-old vine group also had more unique bacterial community (biomarkers) than other age groups, especially in the lower soil layer (25-35cm).

Keywords
grape; rhizosphere soil; high-throughput sequencing; bacterial diversity.

Cite this paper
FengXue, TongLiu, Study on Bacterial Diversity and Community Structure in Grape Rhizosphere Soil Based on High-throughput Sequencing , SCIREA Journal of Biology. Volume 6, Issue 6, December 2021 | PP. 129-153. 10.54647/biology18195

References

[ 1 ] He Jizheng, Li Jing, Zheng Yuanming. Thoughts on the microbial diversity-stability relationship in soil ecosystems [J]. Biodiversity Science, 2013, 21(4): 411-420 (in Chinese)
[ 2 ] Yang Haijun, Xiao qiming, Liu Anyuan. Soil Microbial Diversity and Its Action [J]. Journal of Nanhua University (Science And Technology), 2005, 19(4):21-27. (in Chinese)
[ 3 ] Liu Lingzhi, Lu Deguo, Qin Sijun. Research progress on functional microbial diversity of orchard soil ecosystem [J]. Northern Fruits, 2014(6):1-4. (in Chinese)
[ 4 ] Wang Baoli, Cen Jian, Wu Chuandong, et al. Effects of Nitrogen Form on Bacterium Diversity in Excessive Fertilization Dryland Soil [J]. Journal of Agro-Environment Science, 2011, 30(7):1351-1356. (in Chinese)
[ 5 ] Bao SD. Soil Agricultural Chemistry Analysis[M]. Beijing: China Agriculture Press, 2000: 1-114 (in Chinese)
[ 6 ] Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads[J]. Embnet Journal, 2011, 17(1) .
[ 7 ] Edgar, Robert C., et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27.16 (2011): 2194-2200.
[ 8 ] Haas, Brian J., et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome research 21.3 (2011): 494-504.
[ 9 ] Edgar, Robert C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature methods 10.10 (2013): 996-998.
[ 10 ] Wang, Qiong, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and environmental microbiology 73.16 (2007): 5261-5267.
[ 11 ] Quast C, Pruesse E, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. (2013) : D590-D596.
[ 12 ] MUSCLE: multiple sequence alignment with high accuracy and high throughputEdgar, 2004.
[ 13 ] Pitta DW, Pinchak E, Dowd SE, et al. Rumen bacterial diversity dynamics associated with changing from bermudagrass hay to grazed winter wheat diets. Microbial ecology 2010,59(3):511-522.
[ 14 ] Shannon CE. The mathematical theory of communication. 1963. MD computing :computers in medical practice 1997, 14(4):306-317.
[ 15 ] Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities[J]. Applied and environmental microbiology, 2005, 71(12):8228-8235.
[ 16 ] Zhao Aihua, Du Xiaojun, Zang Jing, et al. Soil bacterial diversity in the Baotianman deciduous broad-leaved forest [J]. Biodiversity Science, 2015,23 (5): 649-657. (in Chinese)
[ 17 ] Peiffer J A, Spor A, Koren O, et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions[J]. Proceedings of the National Academy of Sciences, 2013, 110(16): 6548–6553
[ 18 ] Fierer N, Bradford M A, Jackson R B. Toward an ecological classification of soil bacteria[J]. Ecology, 2007, 88(6): 1354–1364
[ 19 ] Na Xiaofan, Zheng Guoqi, Peng Li, et al. Microbial Biodiversity in Rhizosphere of Lycium Barbarum Relative to Cultivation History [J]. Acta Soda Sinica, 2016,53 (1): 241–252. (in Chinese)
[ 20 ] Zhao Fan, Zhao Mizhen, et al. Microbial Community Structures and Diversities in Strawberry Rhizosphere Soils Based on High-throughput [J]. Soils, 2019,51 (1): 51–60. (in Chinese)
[ 21 ] Yang Meiling, Zhang Xia, Wang Shaoming et al. Analysis of bacterial community characteristics in rhizosphere soil of Yumin safflower based on high-throughput sequencing [J]. Microbiology, 2018,45 (11): 2429-2438 (in Chinese)
[ 22 ] Zhao Xiang, Liu Hongling et al. Effects of drip irrigation on bacterial diversity and community structure in rhizosphere soil of alfalfa [J]. Microbiology, 2019, 46(10): 2579-2590 (in Chinese)
[ 23 ] Chang Anran, Li Jia et al. Analysis of Bacterial Community Structure in Rhizosphere Soil of Tobacco based on the Metagenomics 16S rDNA Sequencing Technology [J]. Journal of Agricultural Science and Technology, 2017,19 (2): 43-50 (in Chinese)
[ 24 ] Doumbou CL, Salove MKH, Crawford DL, et al. Actinomycetes, promising tools to control plant diseases and to promote plant growth[J]. Phytoprotection, 2001, 82(3): 85-144
[ 25 ] Tokala RK, Strap JL, Jung CM, et al. Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum)[J]. Applied and Environmental Microbiology, 2002, 68(5): 2161-2171
[ 26 ] Zhang PP, Qin S, Yuan B, et al. Diversity and bioactivity of actinomycetes isolated from medicinal plant Taxus chinensis and rhizospheric soil[J]. Acta Microbiologica Sinica, 2016, 56(2): 241-254 (in Chinese)
[ 27 ] Shan Nana, Lai Bo. Study Progresses and Prospect on the Ecological Characteristics of Soil-inhabiting Microorganism in Soil Forming Process of Aeolian Sand Soil [J]. Environmental Protection of Xinjiang, 2004, 26(S1): 79-82. (in Chinese)
[ 28 ] Zhu D, Zhang L, Wei ZX, et al. Effects of Bacterial manure on soil Physicochemical Properties and Microbial community diversity in Rhizosphere of Highland barley [J]. Acta Pedologica Sinica, 2014, 51(3): 627-635 (in Chinese)
[ 29 ] Lauber CL, Hamady M, Knight R, et al. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale[J]. Applied Environmental Microbiology, 2009, 75(15): 5111-5120
[ 30 ] Rousk J, Bååth E, Brookes PC, et al. Soil bacterial and fungal communities across a pH gradient in an arable soil[J]. The ISME Journal, 2010, 4(10): 1340-1351
[ 31 ] Lauber CL, Hamady M, Knight R, et al. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale[J]. Applied and Environmental Microbiology, 2009, 75(15): 5111-5120
[ 32 ] Wang JC, Xue C, Song Y, et al. Wheat and rice growth stages and fertilization regimes alter soil bacterial community structure, but not diversity[J]. Frontiers in Microbiology, 2016, 7: 1207
[ 33 ] Dunfield KE, Germida JJ. Diversity of bacterial communities in the rhizosphere and root interior of field-grown genetically modified Brassica napus[J]. FEMS Microbiology Ecology, 2001, 38(1): 1-9
[ 34 ] Nardi S, Concheri G, Pizzeghello D, et al. Soil organic matter mobilization by root exudates[J]. Chemosphere, 2000, 41(5): 653-658