不同紫云英品种根瘤内生细菌的类群和多样性分析

方宇; 刘彩玲; 林陈强; 陈济琛; 贾宪波

doi:10.19303/j.issn.1008-0384.2024.06.012

不同紫云英品种根瘤内生细菌的类群和多样性分析

doi: 10.19303/j.issn.1008-0384.2024.06.012

福建省农业科学院资源环境与土壤肥料研究所，福建　福州　350003

基金项目: 福建省科技计划公益类专项（2022R1025006）；福建省自然科学基金项目（2023J01360、2021J01480）；福建省农业科学院科技创新团队建设项目（CXTD2021002-3）；福建省农业科学院农业高质量发展超越“5511”协同创新工程项目（XTCXGC2021009）；福建省农业科学院科技创新平台专项（CXPT2023007）；现代农业产业技术体系建设专项（CARS-22）；福建省对外合作项目（DWHZ2023-5）

详细信息

作者简介:
方宇（1979 —），女，博士，副研究员，主要从事农业微生物研究，E-mail：fangyu1106@163.com

通讯作者:
贾宪波（1986 —），男，博士，副研究员，主要从事农业微生物研究，E-mail: xbj2011@163.com

中图分类号: Q939.96
计量
- 文章访问数: 146
- HTML全文浏览量: 68
- PDF下载量: 50
- 被引次数: 0
出版历程
- 收稿日期: 2024-03-14
- 修回日期: 2024-05-07
- 网络出版日期: 2024-07-10
- 刊出日期: 2024-06-28

Endophytic Microbes in Root Nodules of Different Cultivars of Astragalus Sinicus L.

Institute of Resources, Environment and Soil Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian　350003, China

摘要

摘要: 目的阐释紫云英根瘤内生菌的群落结构，为研发根瘤菌菌剂及了解固氮机制提供依据。方法以福建省种植的不同紫云英品种的根瘤为材料，借助Illumina Miseq PE300测序平台，以16S rRNA基因为靶标，研究不同紫云英品种的根瘤内生细菌的多样性。结果不同品种会影响紫云英根瘤内生细菌的类群和多样性。浙紫5号（ZZ5）的优势属为假单胞菌属（Pseudomonas），其余品种根瘤内生细菌的优势属均为中慢生根瘤菌属（Mesorhizobium）。闽紫8号（MZ8）、信阳（XY）和浙紫5号的根瘤内生细菌的多样性指数（Shannon）较高，除了共生固氮的中慢生根瘤菌外，还包括丰富的非根瘤菌，如假单胞菌属、寡养单胞菌属（Stenotrophomonas）、杜擀氏菌属（Duganella）、泛菌属（Pantoea）、欧文氏菌属（Erwinia）等。闽紫8号、信阳和浙紫5号这3个品种根瘤中含有较高丰度的致病菌大黄欧文氏菌（Erwinia rhapontici）和菠萝泛菌PA13（ Pantoea ananatis PA13）。结论紫云英品种对根瘤内生细菌的群落结构有一定影响，浙紫5号的根瘤内生细菌主要为具促生作用的非根瘤菌假单胞菌，而其余品种为具固氮能力的根瘤菌，在生产实际中可以采用紫云英混种的方式达到固氮促生的双重功效。
- 紫云英 /
- 品种 /
- 根瘤 /
- 内生细菌 /
- 多样性
Abstract: Objective Being crucial to the development of rhizobium inoculants and the understanding on the associated mechanisms of soil nitrogen fixation, community structure of the endophytic microorganisms in root nodules of Astragalus sinicus L. was investigated. Method Endophytic microbial community in the root nodules of 7 cultivars of A. sinicus planted in Fujian was analyzed with the Illumina Miseq PE300 sequencing platform using 16S rRNA as the target gene. Result The microbial composition of endophytic community in the nodules of the different cultivars varied. For instance, the predominant genus in ZZ5 root nodules was Pseudomonas, but it was Mesorhizobium in other cultivars. Furthermore, high Shannon indices were found in the root nodules of MZ8, XY, and ZZ5 with diverse non-rhizobial endophytes like Pseudomonas, Stenotrophomonas, Duganella, Erwinia, etc. In contrast, high relative abundances of pathogens, such as Erwinia rhapontici and Pantoea ananatis PA13 existed in the root nodules of MZ8, XY, and ZZ5. Conclusions Significant microbial variations in the endophytic communities were evident among the different varieties of A. sinicus planted in Fujian. The predominant genus in the root nodules of ZZ5 was non-rhizobial, growth-promoting Pesudomonas, while it was rhizobia for the other cultivars.
- Astragalus sinicus /
- cultivar /
- root nodule /
- endophytic bacteria /
- diversity

HTML全文

图 1 不同紫云英品种根瘤内生细菌门水平的相对丰度

MZ7：闽紫7号；MZ8：闽紫8号；GZ：光泽；XY：信阳；XZ：湘紫；YJZ：弋江籽；ZZ5：浙紫5号；下同。

Figure 1. Relative abundance of endophytic microbes at phylum level in root nodules of different cultivars of A. sinicus

MZ7: Minzi No. 7; MZ8: Minzi No.8; GZ: Guangze; XY: Xinyang; XZ: Xiangzi; YJZ: Yijiangzi; ZZ5: Zhezi No. 5. Same for below.

下载: 全尺寸图片幻灯片

图 2 不同紫云英品种根瘤内生细菌目水平的相对丰度

Figure 2. Relative abundance of endophytic microbes at order level in root nodules of different cultivars of A. sinicus

下载: 全尺寸图片幻灯片

图 3 不同紫云英品种根瘤内生细菌属水平的相对丰度

Figure 3. Relative abundance of endophytic microbes at genus level in root nodules of different cultivars of A. sinicus

下载: 全尺寸图片幻灯片

图 4 不同紫云英品种根瘤内生细菌种水平的相对丰度

Figure 4. Relative abundance of endophytic microbes at species level in root nodules of different cultivars of A. sinicus

下载: 全尺寸图片幻灯片

图 5 基于OTU水平紫云英根瘤内生细菌群落组成主坐标分析

Figure 5. Principal coordinates analysis on endophytic microbes at OTU level in root nodules of different cultivars of A. sinicus

下载: 全尺寸图片幻灯片

表 1 不同紫云英品种根瘤内生细菌的Alpha多样性指数

Table 1. Alpha diversity index of endophytic microbes at genus level in root nodules of different cultivars of A. sinicus

样本 Sample	Ace指数 Ace index	Chao1 指数 Chao1 index	Shannon指数 Shannon index	Simpson指数 Simpson index	覆盖度 Coverage/%
闽紫7号 MZ7	26.26	24.25	0.07	0.98	99.98
闽紫8号 MZ8	104.42	90.11	1.58	0.30	99.93
光泽 GZ	25.86	23.67	0.08	0.98	99.98
信阳 XY	191.81	191.50	1.73	0.40	99.92
湘紫 XZ	97.85	68.60	0.14	0.96	99.94
弋江紫 YJZ	23.60	23.00	0.11	0.96	99.98
浙紫5号 ZZ5	72.45	84.50	1.13	0.53	99.95

下载: 导出CSV

参考文献(30)

[1]	曹卫东, 黄鸿翔. 关于我国恢复和发展绿肥若干问题的思考 [J]. 中国土壤与肥料, 2009, (4):1−3. doi: 10.3969/j.issn.1673-6257.2009.04.001 CAO W D, HUANG H X. Ideas on restoration and development of green manures in China [J]. Soil and Fertilizer Sciences in China, 2009(4): 1−3. (in Chinese) doi: 10.3969/j.issn.1673-6257.2009.04.001
[2]	谢志坚, 周春火, 贺亚琴, 等. 21世纪我国稻区种植紫云英的研究现状及展望[J]. 草业学报, 2018, 27(8): 185-196. XIE Z J, ZHOU C H, HE Y Q, et al. A review of Astragalus sinicus in paddy fields in South China since 2000s[J]. Acta Prataculturae Sinica, 2018, 27(8): 185-196. (in Chinese)
[3]	BREWIN N J. Development of the legume root nodule[J]. Annual Review of Cell Biology, 1991, 7: 191-226.
[4]	MARTÍNEZ-HIDALGO P, HIRSCH A M. The nodule microbiome: N₂-fixing rhizobia do not live alone [J]. Phytobiomes Journal, 2017, 1(2): 70−82. doi: 10.1094/PBIOMES-12-16-0019-RVW
[5]	PREYANGA R, ANANDHAM R, KRISHNAMOORTHY R, et al. Groundnut (Arachis hypogaea) nodule Rhizobium and passenger endophytic bacterial cultivable diversity and their impact on plant growth promotion[J]. Rhizosphere, 2021, 17: 100309.
[6]	WILSON D. Endophyte: The evolution of a term, and clarification of its use and definition [J]. Oikos, 1995, 73(2): 274. doi: 10.2307/3545919
[7]	MIRANDA-SÁNCHEZ F, RIVERA J, VINUESA P. Diversity patterns of Rhizobiaceae communities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes [J]. Environmental Microbiology, 2016, 18(8): 2375−2391. doi: 10.1111/1462-2920.13061
[8]	张爱梅, 殷一然, 孔维宝, 等. 基于高通量测序分析西藏沙棘根瘤内生菌的多样性 [J]. 生态学报, 2021, 41(20):8212−8221. ZHANG A M, YIN Y R, KONG W B, et al. Diversity of endophytes associated with Hippophae tibetana root nodules based on high-throughput sequencing [J]. Acta Ecologica Sinica, 2021, 41(20): 8212−8221. (in Chinese)
[9]	魏继华, 李佳益, 刘宏, 等. 沙棘根瘤内生菌株库构建与微生物多样性分析 [J]. 浙江农林大学学报, 2022, 39(2):356−363. doi: 10.11833/j.issn.2095-0756.20210246 WEI J H, LI J Y, LIU H, et al. Construction of endophytic strain bank of seabuckthorn nodule and an analysis of microbial diversity [J]. Journal of Zhejiang A & F University, 2022, 39(2): 356−363. (in Chinese) doi: 10.11833/j.issn.2095-0756.20210246
[10]	肖潇. 豆科植物根际和根瘤内生细菌群落结构、变化规律及其影响因素研究[D]. 杨凌: 西北农林科技大学, 2017. XIAO X. The structure, variation and influence factors of leguminous plant rhizosphere and nodule endosphere microbiome[D]. Yangling: Northwest A & F University, 2017. (in Chinese)
[11]	李静. 陕北地区白刺花根瘤内生菌遗传多样性及其促生特性研究[D]. 延安: 延安大学, 2022. LI J. Genetic diversity and growth promoting characteristics of endophytic bacteria from Sophora davidii (franch. ) skeels root nodules in northern shaanxi[D]. Yan’an: Yan’an University, 2022. (in Chinese)
[12]	BULGARELLI D, ROTT M, SCHLAEPPI K, et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota [J]. Nature, 2012, 488(7409): 91−95. doi: 10.1038/nature11336
[13]	LUNDBERG D S, LEBEIS S L, PAREDES S H, et al. Defining the core Arabidopsis thaliana root microbiome [J]. Nature, 2012, 488(7409): 86−90. doi: 10.1038/nature11237
[14]	BULGARELLI D, GARRIDO-OTER R, MÜNCH P C, et al. Structure and function of the bacterial root microbiota in wild and domesticated barley [J]. Cell Host & Microbe, 2015, 17(3): 392−403.
[15]	CHEN S F, ZHOU Y Q, CHEN Y R, et al. Fastp: An ultra-fast all-in-one FASTQ preprocessor[J]. Bioinformatics, 2018, 34(17): i884-i890.
[16]	MAGOČ T, SALZBERG S L. FLASH: Fast length adjustment of short reads to improve genome assemblies[J]. Bioinformatics, 2011, 27(21): 2957-2963.
[17]	EDGAR R C. UPARSE: Highly accurate OTU sequences from microbial amplicon reads[J]. Nature Methods, 2013, 10: 996-998.
[18]	COLE J R, WANG Q, FISH J A, et al. Ribosomal Database Project: Data and tools for high throughput rRNA analysis[J]. Nucleic Acids Research, 2014, 42(Database issue): D633-D642.
[19]	曹卫东, 高嵩涓. 到2025年中国绿肥发展策略 [J]. 中国农业资源与区划, 2023, 44(12):1−9. CAO W D, GAO S J. Chinese green manure development strategy by 2025 [J]. Chinese Journal of Agricultural Resources and Regional Planning, 2023, 44(12): 1−9. (in Chinese)
[20]	RAHIMLOU S, BAHRAM M, TEDERSOO L. Phylogenomics reveals the evolution of root nodulating alpha- and beta-Proteobacteria (rhizobia)[J]. Microbiological Research, 2021, 250: 126788.
[21]	PANG J F, PALMER M, SUN H J, et al. Diversity of root nodule-associated bacteria of diverse legumes along an elevation gradient in the Kunlun Mountains, China[J]. Frontiers in Microbiology, 2021, 12: 633141.
[22]	ZHANG J J, SHANG Y M, LIU C Z, et al. Mesorhizobium jarvisii is a dominant and widespread species symbiotically efficient on Astragalus sinicus L. in the Southwest of China[J]. Systematic and Applied Microbiology, 2020, 43(5): 126102.
[23]	尚益民. 我国豆科绿肥共生根瘤菌多样性分析与优势菌种资源挖掘[D]. 郑州: 郑州轻工业大学, 2020 SHANG Y M. The diversity analysis of legume green manure symbiotic rhizobia and mining of dominant species resources in china[D]. Zhengzhou: Zhengzhou University of Light Industry, 2020. (in Chinese)
[24]	TAPIA-GARCÍA E Y, HERNÁNDEZ-TREJO V, GUEVARA-LUNA J, et al. Plant growth-promoting bacteria isolated from wild legume nodules and nodules of Phaseolus vulgaris L. trap plants in central and southern Mexico[J]. Microbiological Research, 2020, 239: 126522.
[25]	SANTOYO G, DEL CARMEN OROZCO-MOSQUEDA M, GOVINDAPPA M. Mechanisms of biocontrol and plant growth-promoting activity in soil bacterial species ofBacillusandPseudomonas: A review[J]. Biocontrol Science and Technology, 2012, 22(8): 855-872.
[26]	BIESSY A, FILION M. Phenazines in plant-beneficial Pseudomonas spp. : Biosynthesis, regulation, function and genomics[J]. Environmental Microbiology, 2018, 20(11): 3905-3917.
[27]	张学贤, 李阜棣, 曹燕珍, 等. 紫云英根瘤菌分子遗传学研究进展 [J]. 华中农业大学学报, 2003, 22(1):77−83. doi: 10.3321/j.issn:1000-2421.2003.01.018 ZHANG X X, LI F D, CAO Y Z, et al. Molecular genetics of Astragalus sincus rhizobia [J]. Journal of Huazhong Agricultural, 2003, 22(1): 77−83. (in Chinese) doi: 10.3321/j.issn:1000-2421.2003.01.018
[28]	张俊杰, 彭姗姗, 尚益民, 等. 湖南益阳地区紫云英根瘤菌的遗传多样性研究 [J]. 河南农业大学学报, 2020, 54(3):480−487. ZHANG J J, PENG S S, SHANG Y M, et al. Study on genetic diversity of rhizobia associated with Astragalus sinicus L. from Yiyang, Hunan Province [J]. Journal of Henan Agricultural University, 2020, 54(3): 480−487. (in Chinese)
[29]	HUANG H C, HSIEH T F, ERICKSON R S. Biology and epidemiology of Erwinia rhapontici, causal agent of pink seed and crown rot of plants [J]. Plant Pathology Bulletin, 2003, 12: 69−76.
[30]	COTHER E J, NOBLE D H, VAN DE VEN R J, et al. Bacterial pathogens of rice in the Kingdom of Cambodia and description of a new pathogen causing a serious sheath rot disease[J]. Plant Pathology, 2010, 59(5): 944-953.