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Journal of Integrative Agriculture  2023, Vol. 22 Issue (8): 2412-2425    DOI: 10.1016/j.jia.2023.01.006
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Host niche, genotype, and field location shape the diversity and composition of the soybean microbiome

YANG Hong-jun1, 2, 3, YE Wen-wu1, 2#, YU Ze1, 2, SHEN Wei-liang4, LI Su-zhen5, WANG Xing6, CHEN Jia-jia1, 2, 7, WANG Yuan-chao1, 2, ZHENG Xiao-bo1, 2

1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, P.R.China

2 Key Laboratory of Soybean Disease and Pest Control of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, P.R.China

3 College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, P.R.China

4 Suzhou Academy of Agricultural Sciences, Suzhou 234000, P.R.China

5 Jining Academy of Agricultural Sciences, Jining 272131, P.R.China

6 Xuzhou Academy of Agricultural Sciences, Xuzhou 221131, P.R.China

7 College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, P.R.China

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摘要  内生微生物可以帮助植物获得营养物质,抑制病原菌等生物和非生物胁迫,是影响植物生长、营养和健康的关键因素之一;然而,对于田间条件下存在于大豆不同组织中的细菌和真菌微生物群落的组成及影响因素,仍缺乏足够的了解。本研究以大豆为研究对象,对16S rRNA和ITS特定区段的PCR扩增子进行高通量测序,探究不同组织(根、茎、叶和荚)、不同品种(安豆203、荷豆12、山宁16和中黄13)以及不同地理位置(济宁、宿州和徐州)对大豆内生细菌和真菌群落组成及多样性的影响。结果表明,不同组织之间的内生微生物群落差异明显,根部内生细菌和真菌群落的组成及多样性显著区分于地上部的茎、叶和荚;供试品种间茎部的细菌群落和叶部的真菌群落组成差异最大;试验地点显著影响各个器官中的细菌群落组成,其中对根茎部的影响比叶荚部更强,而对于真菌群落组成,茎叶部所受影响比根荚部更明显。此外,与大豆病害相关的微生物丰度在不同组织和品种间存在差异(如:镰刀菌在根部丰度更高,而链格孢菌在叶部丰度更高),可能与这些微生物在寄主中的生态位以及寄主的抗感性有关。微生物群落组成与多样性的系统分析将有助于植物保护技术的发展,从而有益于大豆健康。

Abstract  Plant-associated microbes represent a key determinant of plant fitness through acquiring nutrients, promoting growth, and resisting to abiotic and biotic stresses.  However, an extensive characterization of the bacterial and fungal microbiomes present in different plant compartments of soybean in field conditions has remained elusive.  In this study, we investigated the effects of four niches (roots, stems, leaves, and pods), four genotypes (Andou 203, Hedou 12, Sanning 16, and Zhonghuang 13), and three field locations (Jining, Suzhou, and Xuzhou) on the diversity and composition of bacterial and fungal communities in soybean using 16S and internal transcribed spacer rRNA amplicon sequencing, respectively.  The soybean microbiome significantly differed across organs.  Host genotypes explained more variation in stem bacterial community composition and leaf fungal community composition.  Field location significantly affected the composition of bacterial communities in all compartments and the effects were stronger in the root and stem than in the leaf and pod, whereas field location explained more variation in stem and leaf fungal community composition than in the root and pod.  The relative abundances of potential soybean fungal pathogens also differed among host organs and genotypes, reflecting the niches of these microbes in the host and probably their compatibility to the host genotypes.  Systematic profiling of the microbiome composition and diversity will aid the development of plant protection technologies to benefit soybean health.  
Keywords:  microbiome soybean        plant pathogen       endophytes       host niche       genotype       field  
Received: 18 August 2022   Accepted: 05 December 2022
Fund: This work was supported by grants from the earmarked fund for China Agriculture Research System (CARS-004-PS14), the National Key R&D Program of China (2018YFD0201000), and the Special Fund for Agro-scientific Research in the Public Interest, China (201303018).
About author:  YANG Hong-jun, E-mail:; #Correspondence YE Wen-wu, E-mail:

Cite this article: 

YANG Hong-jun, YE Wen-wu, YU Ze, SHEN Wei-liang, LI Su-zhen, WANG Xing, CHEN Jia-jia, WANG Yuan-chao, ZHENG Xiao-bo. 2023. Host niche, genotype, and field location shape the diversity and composition of the soybean microbiome. Journal of Integrative Agriculture, 22(8): 2412-2425.

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