Please wait a minute...
Journal of Integrative Agriculture  2023, Vol. 22 Issue (2): 585-597    DOI: 10.1016/j.jia.2022.08.010
Agro-ecosystem & Environment Advanced Online Publication | Current Issue | Archive | Adv Search |
Different genotypes regulate the microbial community structure in the soybean rhizosphere
QU Zheng1, 2, LI Yue-han1, 2, XU Wei-hui1, 2, CHEN Wen-jing1, 2, HU Yun-long1, 2, WANG Zhi-gang1, 2 

1 School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161006, P.R.China

2 Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, P.R.China

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      



The soybean rhizosphere has a specific microbial community, but the differences in microbial community structure between different soybean genotypes have not been explained.  The present study analyzed the structure of the rhizosphere microbial community in three soybean genotypes.  Differences in rhizosphere microbial communities between different soybean genotypes were verified using diversity testing and community composition, and each genotype had a specific rhizosphere microbial community composition.  Co-occurrence network analysis found that different genotype plant hosts had different rhizosphere microbial networks.  The relationship between rhizobia and rhizosphere microorganisms in the network also exhibited significant differences between different genotype plant hosts.  The ecological function prediction found that different genotypes of soybean recruited the specific rhizosphere microbial community.  These results demonstrated that soybean genotype regulated rhizosphere microbial community structure differences.  The study provides a reference and theoretical support for developing soybean microbial inoculum in the future.

Keywords:  soybean       rhizosphere       genotype       microbial community       host plants  
Received: 09 December 2021   Accepted: 29 January 2023

This research was funded by the Key Research and Development Projects of Heilongjiang Province, China (GA21B007 and GZ20210014) and the Basic Research Fees of Universities in Heilongjiang Province, China (135409103).

About author:  QU Zheng, E-mail:; Correspondence WANG Zhi-gang, Tel/Fax: +86-452-2738781, E-mail:

Cite this article: 

QU Zheng, LI Yue-han, XU Wei-hui, CHEN Wen-jing, HU Yun-long, WANG Zhi-gang. 2023. Different genotypes regulate the microbial community structure in the soybean rhizosphere. Journal of Integrative Agriculture, 22(2): 585-597.

Abena M T B, Chen G Q, Chen Z Y, Zheng X C, Li S S, Li T T, Zhong W H. 2020. Microbial diversity changes and enrichment of potential petroleum hydrocarbon degraders in crude oil-, diesel-, and gasoline-contaminated soil. 3 Biotech, 10, 42.
Albareda M, Rodriguez-Navarro D N, Temprano F J. 2009. Use of Sinorhizobium (Ensifer) fredii for soybean inoculants in South Spain. European Journal of Agronomy, 30, 205–211.
Bao W N, Luo Z S, Liu S W, Wu Y F, Wei P L, Xiao G N, Liu Y. 2019. Cloning and characterization of an oxiranedicarboxylate hydrolase from Labrys sp. WH-1. Journal of Zhejiang University (Science B), 20, 995–1002.
Barillot C D C, Sarde C O, Bert V, Tarnaud E, Cochet N. 2013. A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system. Annals of Microbiology, 63, 471–476.
Berendsen R L, Pieterse C M J, Bakker P. 2012. The rhizosphere microbiome and plant health. Trends in Plant Science, 17, 478–486.
Berendsen R L, Vismans G, Yu K, Song Y, de Jonge R, Burgman W P, Burmolle M, Herschend J, Bakker P, Pieterse C M J. 2018. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME Journal, 12, 1496–1507.
Berg G, Smalla K. 2009. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiology Ecology, 68, 1–13.
Buendiaclaveria A M, Rodrigueznavarro D N, Santamarialinaza C, Ruizsainz J E, Tempranovera F. 1994. Systematic and Applied Microbiology, 17, 155–160.
Caldera E J, Chevrette M G, McDonald B R, Currie C R. 2019. Local adaptation of bacterial symbionts within a geographic mosaic of antibiotic coevolution. Applied and Environmental Microbiology, 85, e01580-19.
Challacombe J F, Hesse C N, Bramer L M, McCue L A, Lipton M, Purvine S, Nicora C, Gallegos-Graves L, Porras-Alfaro A, Kuske C R. 2019. Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis. BMC Genomics, 20, 976.
Chatellier S, Mugnier N, Allard F, Bonnaud B, Collin V, van Belkum A, Veyrieras J B, Emler S. 2014. Comparison of two approaches for the classification of 16S rRNA gene sequences. Journal of Medical Microbiology, 63, 1311–1315.
Chen S F, Zhou Y Q, Chen Y R, Gu J. 2018. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34, 884–890.
Chu H N, Lee S J, Wang X, Lee S H, Yoon H M, Hwang Y J, Jung E S, Kwon Y, Wee C D, Jang K A, Kim H R. 2021. A correlation study on in vitro physiological activities of soybean cultivars, 19 individual isoflavone derivatives, and genetic characteristics. Antioxidants (Basel), 10, 2027.
Edgar R C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10, 996–998.
Fan K K, Cardona C, Li Y T, Shi Y, Xiang X J, Shen C C, Wang H F, Gilbert J A, Chu H Y. 2017. Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields. Soil Biology & Biochemistry, 113, 275–284.
Fernandez-Gonzalez A J, Cardoni M, Cabanas C G L, Valverde-Corredor A, Villadas P J, Fernandez-Lopez M, Mercado-Blanco J. 2020. Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive. Microbiome, 8, 19.
Ferreira A C, Nobre M F, Moore E, Rainey F A, Battista J R, da Costa M S. 1999. Characterization and radiation resistance of new isolates of Rubrobacter radiotolerans and Rubrobacter xylanophilus. Extremophiles, 3, 235–238.
Fida T T, Palamuru S, Pandey G, Spain J C. 2014. Aerobic biodegradation of 2,4-dinitroanisole by Nocardioides sp strain JS1661. Applied and Environmental Microbiology, 80, 7725–7731.
Garrido-Oter R, Nakano R T, Dombrowski N, Ma K W, McHardy A C, Schulze-Lefert P, AgBiome T. 2018. Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia. Cell Host & Microbe, 24, 155.
Goh Y K, Zoqratt M, Goh Y K, Ayub Q, Ting A S Y. 2020. Determining soil microbial communities and their influence on Ganoderma disease incidences in oil palm (Elaeis guineensis) via high-throughput sequencing. Biology (Basel), 9, 424.
Hacquard S, Garrido-Oter R, Gonzalez A, Spaepen S, Ackermann G, Lebeis S, McHardy A C, Dangl J L, Knight R, Ley R, Schulze-Lefert P. 2015. Microbiota and host nutrition across plant and animal kingdoms. Cell Host & Microbe, 17, 603–616.
Han Q, Ma Q, Chen Y, Tian B, Xu L X, Bai Y, Chen W F, Li X. 2020. Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. ISME Journal, 14, 1915–1928.
Hartman K, van der Heijden M G A, Roussely-Provent V, Walser J C, Schlaeppi K. 2017. Deciphering composition and function of the root microbiome of a legume plant. Microbiome, 5, 13.
He Y B, Liu D M, Yao Y M, Huang Q, Li J P, Chen Y Q, Shi S Q, Wan L, Yu S K, Wang D Y. 2013. Spatializing growth suitability for spring soybean cultivation in Northeast China. Journal of Applied Meteorology and Climatology, 52, 773–783.
Ikeda S, Rallos L E E, Okubo T, Eda S, Inaba S, Mitsui H, Minamisawa K. 2008. Microbial community analysis of field-grown soybeans with different nodulation phenotypes. Applied and Environmental Microbiology, 74, 5704–5709.
Jain V, Nainawatee H S. 2002. Plant flavonoids: Signals to legume nodulation and soil microorganisms. Journal of Plant Biochemistry and Biotechnology, 11, 1–10.
Jiang R, Wang J G, Zhu T, Zou B, Wang D Q, Rhee S K, An D, Ji Z Y, Quan Z X. 2020. Use of newly designed primers for quantification of complete ammonia-oxidizing (Comammox) bacterial clades and strict nitrite oxidizers in the genus nitrospira. Applied and Environmental Microbiology, 86, e01775-20.
Joyner J L, Kerwin J, Deeb M, Lozefski G, Prithiviraj B, Paltseva A, McLaughlin J, Groffman P, Cheng Z Q, Muth T R. 2019. Green infrastructure design influences communities of urban soil bacteria. Frontiers in Microbiology, 10, 982.
Kemen E. 2014. Microbe-microbe interactions determine oomycete and fungal host colonization. Current Opinion in Plant Biology, 20, 75–81.
Kourilova X, Schwarzerova J, Pernicova I, Sedlar K, Mrazova K, Krzyzanek V, Nebesarova J, Obruca S. 2021. The first insight into polyhydroxyalkanoates accumulation in multi-extremophilic Rubrobacter xylanophilus and Rubrobacter spartanus. Microorganisms, 9, 909.
Ling N, Zhu C, Xue C, Chen H, Duan Y H, Peng C, Guo S W, Shen Q R. 2016. Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis. Soil Biology & Biochemistry, 99, 137–149.
Lu Z Y, Xu Z H, Shen Z M, Tian Y C, Shen H. 2019. Dietary energy level promotes rumen microbial protein synthesis by improving the energy productivity of the ruminal microbiome. Frontiers in Microbiology, 10, 847.
Magoc T, Salzberg S L. 2011. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27, 2957–2963.
Mendes L W, Kuramae E E, Navarrete A A, van Veen J A, Tsai S M. 2014. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME Journal, 8, 1577–1587.
Miranda-Sanchez F, Rivera J, Vinuesa P. 2016. Diversity patterns of rhizobiaceae communities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes. Environmental Microbiology, 18, 2375–2391.
Parveen G, Noreen R, Shafique H A, Sultana V, Ehteshamul-Haque S, Athar M. 2019. Role of rhizobia in suppressing the root diseases of soybean under soil amendment. Planta Daninha, 37, e019172336.
Philippot L, Raaijmakers J M, Lemanceau P, van der Putten W H. 2013. Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology, 11, 789–799.
Poole P, Ramachandran V, Terpolilli J. 2018. Rhizobia: from saprophytes to endosymbionts. Nature Reviews Microbiology, 16, 291–303.
Ray J D, Fritschi F B, Heatherly L G. 2006. Large applications of fertilizer N at planting affects seed protein and oil concentration and yield in the early soybean production system. Field Crops Research, 99, 67–74.
Rodriguez-Navarro D N, Bellogin R, Camacho M, Daza A, Medina C, Ollero F J, Santamaria C, Ruiz-Sainz J E, Vinardell J M, Temprano F J. 2003. Field assessment and genetic stability of Sinorhizobium fredii strain SMH12 for commercial soybean inoculants. European Journal of Agronomy, 19, 299–309.
Siebielec S, Siebielec G, Sugier P, Wozniak M, Grzadziel J, Galazka A, Stuczynski T. 2020. Activity and diversity of microorganisms in root zone of plant species spontaneously inhabiting smelter waste piles. Molecules, 25, 5638.
Skouri-Panet F, Benzerara K, Cosmidis J, Ferard C, Caumes G, De Luca G, Heulin T, Duprat E. 2018. In vitro and in silico evidence of phosphatase diversity in the biomineralizing bacterium Ramlibacter tataouinensis. Frontiers in Microbiology, 8, 2592.
Smoot M E, Ono K, Ruscheinski J, Wang P L, Ideker T. 2011. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431–432.
Sohn S I, Ahn J H, Pandian S, Oh Y J, Shin E K, Kang H J, Cho W S, Cho Y S, Shin K S. 2021. Dynamics of bacterial community structure in the rhizosphere and root nodule of soybean: impacts of growth stages and varieties. International Journal of Molecular Sciences, 22, 5577.
Sugiyama A. 2019. The soybean rhizosphere: Metabolites, microbes, and beyond - A review. Journal of Advanced Research, 19, 67–73.
Sun J H, Yang L, Wei J, Quan J N, Yang X T. 2020. The responses of soil bacterial communities and enzyme activities to the edaphic properties of coal mining areas in Central China. PLoS ONE, 15, e0231198.
Wang H, Wang S D, Jiang Y, Zhao S J, Chen W X. 2014. Diversity of rhizosphere bacteria associated with different soybean cultivars in two soil conditions. Soil Science and Plant Nutrition, 60, 630–639.
Wang Q, Garrity G M, Tiedje J M, Cole J R. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261–5267.
Wang S Q, Sun B L, Tu J, Lu Z H. 2016. Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions. Journal of Theoretical Biology, 398, 1–8.
Xiao X, Chen W M, Zong L, Yang J, Jiao S, Lin Y B, Wang E T, Wei G H. 2017. Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments. Molecular Ecology, 26, 1641–1651.
Xu L, Zhang Y, Li C Y, Wang X Q, Liu J R, Friman V P. 2018. Nocardioides astragali sp nov., isolated from a nodule of wild Astragalus chrysopterus in northwestern China. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 111, 1157–1163.
Yang T, Siddique K H M, Liu K. 2020. Cropping systems in agriculture and their impact on soil health - A review. Global Ecology and Conservation, 23, e01118.
Zhao R R, Chen G W, Liu L, Zhang W, Sun Y F, Li B G, Wang G. 2020. Bacterial foraging facilitates aggregation of Chlamydomonas microsphaera in an organic carbon source-limited aquatic environment. Environmental Pollution, 259, 113924.
Zhou L S, Li H, Zhang Y, Han S Q, Xu H. 2016. Sphingomonas from petroleum-contaminated soils in Shenfu, China and their PAHs degradation abilities. Brazilian Journal of Microbiology, 47, 271–278.

[1] WANG Yuan-zheng, Olusegun IDOWU, WANG Yun, HOMMA Koki, NAKAZAKI Tetsuya, ZHENG Wen-jing, XU Zheng-jin, SHIRAIWA Tatsuhiko. Interaction effect of erect panicle genotype and environment on rice yield and yield components[J]. >Journal of Integrative Agriculture, 2023, 22(3): 716-726.
[2] WANG Deng-feng, YANG Xue-yun, WEI Yu-rong, LI Jian-jun, BOLATI Hongduzi, MENG Xiao-xiao, TUERXUN Gunuer, NUERDAN Nuerbaiheti, WU Jian-yong. Genome characterization of the Caprine arthritis-encephalitis virus in China: A retrospective genomic analysis of the earliest Chinese isolates[J]. >Journal of Integrative Agriculture, 2023, 22(3): 872-880.
[3] XU Chun-mei, XIAO De-shun, CHEN Song, CHU Guang, LIU Yuan-hui, ZHANG Xiu-fu, WANG Dan-ying.

Changes in the activities of key enzymes and the abundance of functional genes involved in nitrogen transformation in rice rhizosphere soil under different aerated conditions [J]. >Journal of Integrative Agriculture, 2023, 22(3): 923-934.

[4] GAO Hua-wei, YANG Meng-yuan, YAN Long, HU Xian-zhong, HONG Hui-long, ZHANG Xiang, SUN Ru-jian, WANG Hao-rang, WANG Xiao-bo, LIU Li-ke, ZHANG Shu-zhen, QIU Li-juan. Identification of tolerance to high density and lodging in short petiolate germplasm M657 and the effect of density on yield-related phenotypes of soybean[J]. >Journal of Integrative Agriculture, 2023, 22(2): 434-446.
[5] GAO Hua-wei, SUN Ru-jian, YANG Meng-yuan, YAN Long, HU Xian-zhong, FU Guang-hui, HONG Hui-long, GUO Bing-fu, ZHANG Xiang, LIU Li-ke, ZHANG Shu-zhen, QIU Li-juan. Characterization of the petiole length in soybean compact architecture mutant M657 and the breeding of new lines[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2508-2520.
[6] ZHANG Hua, WU Hai-yan, TIAN Rui, KONG You-bin, CHU Jia-hao, XING Xin-zhu, DU Hui, JIN Yuan, LI Xi-huan, ZHANG Cai-ying. Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2521-2537.
[7] ZOU Jia-nan, ZHANG Zhan-guo, KANG Qing-lin, YU Si-yang, WANG Jie-qi, CHEN Lin, LIU Yan-ru, MA Chao, ZHU Rong-sheng, ZHU Yong-xu, DONG Xiao-hui, JIANG Hong-wei, WU Xiao-xia, WANG Nan-nan, HU Zhen-bang, QI Zhao-ming, LIU Chun-yan, CHEN Qing-shan, XIN Da-wei, WANG Jin-hui. Characterization of chromosome segment substitution lines reveals candidate genes associated with the nodule number in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2197-2210.
[8] ZHANG Yin-Jie, GAO Wei, LUAN Hao-an, TAND Ji-wei, LI Ruo-nan, LI Ming-Yue, ZHANG Huai-zhi, HUANG Shao-wen. Effects of a decade of organic fertilizer substitution on vegetable yield and soil phosphorus pools, phosphatase activities, and the microbial community in a greenhouse vegetable production system[J]. >Journal of Integrative Agriculture, 2022, 21(7): 2119-2133.
[9] PAN Wen-jing, HAN Xue, HUANG Shi-yu, YU Jing-yao, ZHAO Ying, QU Ke-xin, ZHANG Ze-xin, YIN Zhen-gong, QI Hui-dong, YU Guo-long, ZHANG Yong, XIN Da-wei, ZHU Rong-sheng, LIU Chun-yan, WU Xiao-xia, JIANG Hong-wei, HU Zhen-bang, ZUO Yu-hu, CHEN Qing-shan, QI Zhao-ming. Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1886-1902.
[10] LIU Chen, TIAN Yu, LIU Zhang-xiong, GU Yong-zhe, ZHANG Bo, LI Ying-hui, NA Jie, QIU Li-juan. Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean (Glycine max L. Merr.)[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1903-1912.
[11] Muhammad QASWAR, Waqas AHMED, HUANG Jing, LIU Kai-lou, ZHANG Lu, HAN Tian-fu, DU Jiang-xue, Sehrish ALI, Hafeez UR-RAHIM, HUANG Qing-hai, ZHANG Hui-min. Interaction of soil microbial communities and phosphorus fractions under long-term fertilization in paddy soil [J]. >Journal of Integrative Agriculture, 2022, 21(7): 2134-2144.
[12] HUI Fang, XIE Zi-wen, LI Hai-gang, GUO Yan, LI Bao-guo, LIU Yun-ling, MA Yun-tao. Image-based root phenotyping for field-grown crops: An example under maize/soybean intercropping[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1606-1619.
[13] TIAN Yu, YANG Lei, LU Hong-feng, ZHANG Bo, LI Yan-fei, LIU Chen, GE Tian-li, LIU Yu-lin, HAN Jia-nan, LI Ying-hui, QIU Li-juan. QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(4): 933-946.
[14] SHI Wen-jun, SHAO Hui, SHA Ye, SHI Rong, SHI Dong-feng, CHEN Ya-chao, BAN Xiang-ben, MI Guo-hua. Grain dehydration rate is related to post-silking thermal time and ear characters in different maize hybrids[J]. >Journal of Integrative Agriculture, 2022, 21(4): 964-976.
[15] TENG Jin-yan, YE Shao-pan, GAO Ning, CHEN Zi-tao, DIAO Shu-qi, LI Xiu-jin, YUAN Xiao-long, ZHANG Hao, LI Jia-qi, ZHANG Xi-quan, ZHANG Zhe. Incorporating genomic annotation into single-step genomic prediction with imputed whole-genome sequence data[J]. >Journal of Integrative Agriculture, 2022, 21(4): 1126-1136.
No Suggested Reading articles found!