Microbial Communities in Rhizosphere and Root-Endosphere of Wild Cymbidium ensifolium
-
摘要:
目的 比较野生建兰根际和根内细菌的种群结构差异，为研究根共生细菌与建兰的营养关系奠定理论基础。 方法 采用高通量测序技术鉴定福州鼓山野生建兰根际和根内共生细菌，分析其种类多样性和种群结构。 结果 建兰根际、根内拥有种类多样的细菌，辛普森指数分别为0.99、0.95；香农指数比较显示建兰根际细菌种类多样性显著高于根内。建兰根际拥有10门细菌，优势门为变形菌门（60.5%）、酸杆菌门（20.5%）、放线菌门（15.3%），根内优势细菌门分别为变形菌门（75.3%）、酸杆菌门（7.3%）、放线菌门（14.6%）。根际与根内丰度最高的10个细菌属中，Solibacter、Acidipila仅在根际中，戴氏菌、新鞘氨醇菌和Granulicella仅存在于根内。根际中酸杆菌门酸杆菌纲的丰度显著高于根内，11个差异显著的目，仅肠杆菌目在根内的丰度大于根际，根际有12个属的丰度显著高于根内。 结论 建兰根际与根内细菌种类丰富度存在显著性差异，其原因可能是不同生态位的细菌对建兰的生物学功能存在较大差异。 Abstract:Objective Community diversity and structures of the bacteria in the rhizosphere and endosphere of wild Cymbidium ensifolium were studied to understand the symbiotic relationship between them. Method The high-throughput sequencing method was applied to identify the bacteria in the rhizosphere soil and the root-endosphere of C. ensifolium at locations in Mt. Gushan, Fuzhou where the wild orchids were found. Species diversity and community structures of the spheres were compared. Result Numerous species of bacteria were found in the specimens. The Simpson index in the rhizosphere soil was determined to be of 0.99, and that in the root-endosphere 0.95. The Shannon indices indicated that the rhizosphere was significantly more diverse on species than the root-endosphere. There were 10 phyla of bacteria in the rhizosphere with the dominant ones being Proteobacteria (60.5%), Acidobacteria (20.5%), and Actinobacteria (15.3%). In the root-endosphere, the prevailing phyla were Proteobacteria (75.3%), Acidobacteria (7.3%), and Actinobacteria (14.6%). Among the 10 bacterial genera in the highest abundance, Solibacter and Acidipila existed only in the rhizosphere, while Dyella, Novosphingobium, and Granulicella only in the root-endosphere. The abundance of Acidobacteria Acidobacteriia bacteria in the rhizosphere were significantly higher than those in the root-endosphere. Of the 11 significantly different orders, only Enterobacteriales showed a greater abundance in the root-endosphere than in the rhizosphere. There were 12 genera significantly more abundant in the rhizosphere than in the root-endosphere. Conclusion The significantly different microbial community diversity and structures in the field rhizosphere and root-endosphere of wild C. ensifolium grown at the same area might reflect a highly complex synergism between the environment and the plants. -
图 1 建兰根际与根内细菌16S rDNA高通量测序结果稀释曲线
Figure 1. Rarefaction curve of 16S rDNA high-throughput sequencing of bacteria in C. ensifolium rhizosphere soil and C. ensifolium root-endosphere
图 2 建兰根际与根内细菌优势类群
注：图中细菌无中文名称用黑线代替（图3～6同）。
Figure 2. Dominant groups of bacteria in rhizosphere soil and C. ensifolium roots
Note: Bacteria absent Chinese names are shown by black lines (same for Figs. 3～6).
图 3 建兰根际与根内细菌丰度最大的10个目
Figure 3. Dominant bacterial orders in in rhizosphere soil and C. ensifolium roots
图 4 建兰根际与根内细菌丰度最大的10个属
Figure 4. Dominant bacterial genera in rhizosphere soil and C. ensifolium roots
图 5 建兰根际与根内细菌不同分类单元下差异显著的类群
Figure 5. Significantly different bacterial groups of different taxa unit in rhizosphere soil and C. ensifolium roots
图 6 建兰根际、根内共有的细菌OUT数量
Figure 6. Number of OUTs on bacteria commonly found in rhizosphere soil and C. ensifolium roots
表 1 建兰根际土壤及根内部样品细菌OUTs丰度和α多样性指数
Table 1. OUTs richness and alpha diversity indices of bacteria in rhizosphere soil and C. ensifolium root-endosphere
样品
Sample有效序列
Clean reads可操作分类单位
OTUsα多样性指数 alphy diversity indices 香农指数
Shannon辛普森指数
Simpson超1指数
Chao1测序深度
Good’s coverage根际 Rhiz 74 878±6 490 817±42 7.56±0.09* 0.99±0.00 865.43±36.11* 0.998±0.00 根内 Endo 68 600±10 198 654±78 6.10±1.05* 0.95±0.04 700.99±67.30* 0.998±0.00 注：*在P=0.05水平下，该指标根际与根内细菌存在显著性差异。
Note: *at the level of P=0.05, there is a significant difference between this indicator rhizosphere and endosphere bacteria.
下载: 导出CSV
-
[1] 罗毅波, 贾建生, 王春玲. 中国兰科植物保育的现状和展望 [J]. 生物多样性, 2003, 11(1):70−77. doi: 10.3321/j.issn:1005-0094.2003.01.010LUO Y B, JIA J S, WANG C L. A general review of the conservation status of Chinese orchids [J]. Chinese Biodiversity, 2003, 11(1): 70−77.(in Chinese) doi: 10.3321/j.issn:1005-0094.2003.01.010 [2] 陈瑞蕊, 林先贵, 施亚琴. 兰科菌根的研究进展 [J]. 应用与环境生物学报, 2003, 9(1):97−101. doi: 10.3321/j.issn:1006-687X.2003.01.023CHEN R R, LIN X G, SHI Y Q. Research advances of orchid mycorrhizae [J]. Chinese Journal of Applied and Environmental Biology, 2003, 9(1): 97−101.(in Chinese) doi: 10.3321/j.issn:1006-687X.2003.01.023 [3] PETERSON R L, MASSICOTTE H B, Melville LH. Mycorrhizas: anatomy and cell biology[M]. Ottawa: NRC Research Press, 2004: 123－145. [4] BAYMAN P, GONZALEZ E J, FUMERO J J, et al. Are fungi necessary? How fungicides affect growth and survival of the orchid Lepanthes rupestris in the field [J]. Journal of Ecology, 2002, 90(6): 1002−1008. doi: 10.1046/j.1365-2745.2002.00733.x [5] WILKINSON K G, DIXON K W, SIVASITHAMPARAM K. Interaction of soil bacteria, mycorrhizal fungi and orchid seed in relation to germination of Australian orchids [J]. New Phytologist, 1989, 112(3): 429−435. doi: 10.1111/j.1469-8137.1989.tb00334.x [6] DEARNALEY J D W, MARTOS F, SELOSSE M A. 12 orchid mycorrhizas: molecular ecology, physiology, evolution and conservation aspects[M]//Fungal Associations. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012: 207－230. [7] 贾勇炯, 曹有龙, 王水, 等. 彩心建兰花枝茎节离体培养的研究 [J]. 四川大学学报(自然科学版), 2000, 37(1):94−97.JIA Y J, CAO Y L, WANG S, et al. Studies on the culture of internode of flower branch of China orchid [J]. Journal of Sichuan University (Natural Science Edition), 2000, 37(1): 94−97.(in Chinese) [8] 李丽, 罗君琴, 聂振鹏, 等. 线艺建兰的组织培养和快速繁殖(简报) [J]. 亚热带植物科学, 2008, 37(2):69−70. doi: 10.3969/j.issn.1009-7791.2008.02.018LI L, LUO J Q, NIE Z P, et al. Tissue cultrue and rapid propagation of Cymbidium ensifolium with verge line pattern leaves [J]. Subtropical Plant Science, 2008, 37(2): 69−70.(in Chinese) doi: 10.3969/j.issn.1009-7791.2008.02.018 [9] 张萍, 宋希强. 兰科植物内生细菌物种多样性及其促生机理研究进展 [J]. 热带亚热带植物学报, 2012, 20(1):92−98. doi: 10.3969/j.issn.1005-3395.2012.01.017ZHANG P, SONG X Q. Advances in diversity and promotion mechanism of endophytic bacteria associated with orchids [J]. Journal of Tropical and Subtropical Botany, 2012, 20(1): 92−98.(in Chinese) doi: 10.3969/j.issn.1005-3395.2012.01.017 [10] 吴庆珊, 雷珣, 雷友梅, 等. 金钗石斛内生细菌的组成及多样性分析 [J]. 植物资源与环境学报, 2018, 27(1):79−90. doi: 10.3969/j.issn.1674-7895.2018.01.10WU Q S, LEI X, LEI Y M, et al. Analyses on composition and diversity of endophytic bacteria in Dendrobium nobile [J]. Journal of Plant Resources and Environment, 2018, 27(1): 79−90.(in Chinese) doi: 10.3969/j.issn.1674-7895.2018.01.10 [11] TEIXEIRA DA SILVA J A, TSAVKELOVA E A, ZENG S J, et al. Symbiotic in vitro seed propagation of Dendrobium: fungal and bacterial partners and their influence on plant growth and development [J]. Planta, 2015, 242(1): 1−22. doi: 10.1007/s00425-015-2301-9 [12] 张辑. 中国兰属植物内生菌多样性研究[D]. 北京: 中国林业科学研究院, 2012.ZHANG J. Research on diversity of endosymbiotic fungi in roots of Cymbidium[D]. Chinese Academy of Forestry. 2012. (in Chinese) [13] 李杰, 王芝娜, 匡萍, 等. 野生兰属植物菌根真菌的分离和表型鉴定 [J]. 亚热带农业研究, 2013, 9(4):254−257.LI J, WANG Z N, KUANG P, et al. Isolation and phenotype identification of mycorrhizal fungi associated with wild Cymbidium plants [J]. Subtropical Agriculture Research, 2013, 9(4): 254−257.(in Chinese) [14] EDWARDS J, JOHNSON C, SANTOS-MEDELLÍN C, et al. Structure, variation, and assembly of the root-associated microbiomes of rice [J]. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(8): E911−E920. doi: 10.1073/pnas.1414592112 [15] EDGAR R C. UPARSE: highly accurate OTU sequences from microbial amplicon reads [J]. Nature Methods, 2013, 10(10): 996−998. doi: 10.1038/nmeth.2604 [16] WANG Q, GARRITY G M, TIEDJE J M, et al. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy [J]. Applied and Environmental Microbiology, 2007, 73(16): 5261−5267. doi: 10.1128/AEM.00062-07 [17] QUAST C, PRUESSE E, YILMAZ P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools [J]. Nucleic Acids Research, 2012, 41(D1): D590−D596. doi: 10.1093/nar/gks1219 [18] SPELLERBERG I F, FEDOR P J. A tribute to Claude Shannon (1916-2001) and a Plea for more rigorous use of species richness, species diversity and the ‘Shannon-Wiener’ Index [J]. Global Ecology and Biogeography, 2003, 12(3): 177−179. doi: 10.1046/j.1466-822X.2003.00015.x [19] PUIG P, KOKONENDJI C C. Non-parametric estimation of the number of Zeros in truncated count distributions [J]. Scandinavian Journal of Statistics, 2018, 45(2): 347−365. doi: 10.1111/sjos.12293 [20] JOST L. Entropy and diversity [J]. Oikos, 2006, 113(2): 363−375. doi: 10.1111/j.2006.0030-1299.14714.x [21] LACKNER G, MOEBIUS N, HERTWECK C. Endofungal bacterium controls its host by an hrp type III secretion system [J]. The ISME Journal, 2011, 5(2): 252−261. doi: 10.1038/ismej.2010.126 [22] BONFANTE P, DESIRÒ A. Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota [J]. The ISME Journal, 2017, 11(8): 1727−1735. doi: 10.1038/ismej.2017.21 [23] LUMINI E, BIANCIOTTO V, JARGEAT P, et al. Presymbiotic growth and sporal morphology are affected in the arbuscular mycorrhizal fungus Gigaspora margarita cured of its endobacteria [J]. Cellular Microbiology, 2007, 9(7): 1716−1729. doi: 10.1111/j.1462-5822.2007.00907.x [24] SALVIOLI A, GHIGNONE S, NOVERO M, et al. Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential [J]. The ISME Journal, 2016, 10(1): 130−144. doi: 10.1038/ismej.2015.91 [25] 李骜, 宋希强. 海南岛华石斛根部可培养的共生细菌的多样性 [J]. 热带生物学报, 2015, 6(3):279−284.LI A, SONG X Q. Diversity of culturable endophytic bacteria isolated from the roots of Dendrobium sinense(Orchidaceae) inhabiting Hainan island [J]. Journal of Tropical Biology, 2015, 6(3): 279−284.(in Chinese) [26] CHEN W F, GUAN S H, ZHAO C T, et al. Different Mesorhizobium species associated with Caragana carry similar symbiotic genes and have common host Ranges [J]. FEMS Microbiology Letters, 2008, 283(2): 203−209. doi: 10.1111/j.1574-6968.2008.01167.x [27] AMPOMAH O Y, HUSS-DANELL K. Genetic diversity of root nodule bacteria nodulating Lotus corniculatus and Anthyllis vulneraria in Sweden [J]. Systematic and Applied Microbiology, 2011, 34(4): 267−275. doi: 10.1016/j.syapm.2011.01.006 [28] TAN H W, WEIR B S, CARTER N, et al. Rhizobia with 16S rRNA and nifH Similar to Mesorhizobium huakuii but Novel recA, glnII, nodA and nodC Genes Are Symbionts of New Zealand Carmichaelinae [J]. PLoS One, 2012, 7(10): e47677. doi: 10.1371/journal.pone.0047677 [29] LUO D X, LANGENDRIES S, MENDEZ S G, et al. Plant growth promotion driven by a novel Caulobacter strain [J]. Molecular Plant-Microbe Interactions, 2019, 32(9): 1162−1174. doi: 10.1094/MPMI-12-18-0347-R -
点击查看大图
图(6) / 表(1)
计量
- 文章访问数: 1340
- HTML全文浏览量: 459
- PDF下载量: 25
- 被引次数: 0
