- Dissection of plant microbiota and plant-microbiome interactions
-
Kihyuck Choi , Raees Khan , Seon-Woo Lee
-
J. Microbiol. 2021;59(3):281-291. Published online February 23, 2021
-
DOI: https://doi.org/10.1007/s12275-021-0619-5
-
-
1,139
View
-
4
Download
-
59
Web of Science
-
58
Crossref
-
Abstract
PDF
-
Plants rooted in soil have intimate associations with a diverse
array of soil microorganisms. While the microbial diversity
of soil is enormous, the predominant bacterial phyla
associated with plants include Actinobacteria, Bacteroidetes,
Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply
nutrient niches for microbes, and microbes support plant
functions such as plant growth, development, and stress tolerance.
The interdependent interaction between the host plant
and its microbes sculpts the plant microbiota. Plant and microbiome
interactions are a good model system for understanding
the traits in eukaryotic organisms from a holobiont
perspective. The holobiont concept of plants, as a consequence
of co-evolution of plant host and microbiota, treats
plants as a discrete ecological unit assembled with their microbiota.
Dissection of plant-microbiome interactions is highly
complicated; however, some reductionist approaches are useful,
such as the synthetic community method in a gnotobiotic
system. Deciphering the interactions between plant and microbiome
by this reductionist approach could lead to better
elucidation of the functions of microbiota in plants. In addition,
analysis of microbial communities’ interactions would
further enhance our understanding of coordinated plant microbiota
functions. Ultimately, better understanding of plantmicrobiome
interactions could be translated to improvements
in plant productivity.
-
Citations
Citations to this article as recorded by 
- Imaging diffusion of quorum sensing molecule using aptasensors
Nianyu Jiang, Marissa Roghair Stroud, Soma Banerjee, Nima Alimoradi, Marit Nilsen-Hamilton, Larry Halverson, Pranav Shrotriya Sensors and Actuators B: Chemical.2027; 471: 141049. CrossRef - Trichoderma asperellum FJ035 Restructure the Rhizosphere Microbiome to Control the Cucumber Fusarium Wilt
Manman Zhang, Rui Wang, Raja Asad Ali Khan, Xin Zhan, Sen Ren, Haonan Jiang, Chenyao Zheng, Yinggu Wu, Fanxing Yang, Xiaoli Yu, Tong Liu Plant, Cell & Environment.2026; 49(2): 858. CrossRef - Evaluating microbial community profiles of Chile peppers grown on the International Space Station provides implications for fruiting crops
Christina L. M. Khodadad, Anirudha R. Dixit, Mary E. Hummerick, LaShelle E. Spencer, Cory J. Spern, Jacob Torres, Oscar Monje, Jeffrey T. Richards, Jennifer Gooden, Aaron B. Curry, Gioia D. Massa, Nicole DuFour, Lucie Poulet, Matthew W. Romeyn, Raymond M. Scientific Reports.2026;[Epub] CrossRef - Decoding Plant–Microbe Interactions through the Kiwifruit Microbiome in Bacterial Canker Disease
Xu-Gang Yang, Ya-Wen Yan, Xin-Xin Zhang, Yu Su, Mo-Xian Chen, Xiang-Yang Li Journal of Agricultural and Food Chemistry.2026; 74(1): 171. CrossRef - Microbiome and metabolome dynamics in phloem and rhizosphere of Pinus tabuliformis against Dendroctonus valens infestation
Yiru Han, Hui Huang, Zhiwei Zhang, Xinyu Li, Tao Li, Shixiang Zong Frontiers in Microbiology.2026;[Epub] CrossRef - Functional and ecological characterization of Labrys methylaminiphilus subsp. lupini subsp. nov., associated with Lupinus luteus nodules in acidic soils of southern Chile
Grace Armijo-Godoy, Luis Cottet, Annally Rupayan, Makarena Carrasco, Daniela Levicoy, Haroldo Salvo-Garrido Frontiers in Microbiology.2026;[Epub] CrossRef - Soil microbiota of industrial hemp (Cannabis sativa L.) grown in a long-term monoculture
Zhanna Klishchova, Carlos Godinho de Abreu, Hanna Laiko, Oleh Primakov, Serhii Mishchenko, Eustáquio Souza Dias, Sergiy Kyrylenko, Victor Satler Pylro Biotechnology for the Environment.2026;[Epub] CrossRef - Microbiome‐Wide Association Studies of Host Beneficial Microbes and Their Functional Mechanisms and Promising Applications in Sustainable Crops
Xiao Cheng, Haitao Shi Plant, Cell & Environment.2026;[Epub] CrossRef - It takes a village: how plant-associated bacterial communities socialise to shape plant growth and health
Freya Harrison, Rachel Wheatley, Carmen Escudero-Martínez, Andrzej Tkacz, Marta Albareda, Carmen Sánchez-Cañizares Essays in Biochemistry.2026; 70(3): 417. CrossRef - Plant-microbe interactions: PGPM as microbial inoculants/biofertilizers for sustaining crop productivity and soil fertility
Bibek Laishram, Okram Ricky Devi, Rinjumoni Dutta, T. Senthilkumar, Girish Goyal, Dinesh Kumar Paliwal, Narinder Panotra, Akhtar Rasool Current Research in Microbial Sciences.2025; 8: 100333. CrossRef - The combined effects of tetracycline and glyphosate on growth and rhizosphere bacteria community in hulless barley over the whole growth period
Wenxiu Xue, Shuhao Zhang, Fazila Younas, Ruwen Ma, Xingxu Yu, Jie Li, Xiaocui Wu, Wenhan Liu, Huitian Duan, Kang Wang, Xiaowei Cui, Xiufeng Cao, Zhaojie Cui Journal of Hazardous Materials.2025; 484: 136706. CrossRef - Diversity Analysis of Rhizosphere Microorganisms in Helichrysum arenarium (L.) Moench and Screening of Growth-Promoting Bacteria in Xinjiang, China
Xiaoyan Xin, Wei He, Junhui Zhou, Yong Chen, Xin Huang, Jinyu Yang, Jianjun Xu, Suqin Song Microbiology Research.2025; 16(5): 89. CrossRef - Bacterial community in the hyphosphere of an arbuscular mycorrhizal fungus differs from that in the surrounding environment and is influenced by hyphal disruption
Zexing Jin, Shilong Duan, Stéphane Declerck, Lin Zhang Mycorrhiza.2025;[Epub] CrossRef - Enhanced complexity of interkingdom co-occurrence networks in blueberry rhizosphere microbial communities under soil pH stress
Jilu Che, Yaqiong Wu, Hao Yang, Ying Chang, Wenlong Wu, Lianfei Lyu, Xiaomin Wang, Fuliang Cao, Weilin Li Applied Soil Ecology.2025; 212: 106191. CrossRef - Strong Host Modulation of Rhizosphere‐to‐Endosphere Microbial Colonisation in Natural Populations of the Pan‐Palaeotropical Keystone Grass Species, Themeda triandra
Riley J. Hodgson, Christian Cando‐Dumancela, Craig Liddicoat, Sunita A. Ramesh, Robert A. Edwards, Martin F. Breed Ecology and Evolution.2025;[Epub] CrossRef - Exploring the Bacterial Microbiota of Seeds
Angel J. Matilla Microbial Biotechnology.2025;[Epub] CrossRef - Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia
Ichrak Hamdene, Cristina Bez, Iris Bertani, Jorge Rojas López-Menchero, Anissa Yahyaoui, Vittorio Venturi, Najla Sadfi-Zouaoui BMC Microbiology.2025;[Epub] CrossRef - High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons
Luzia Stalder, Monika Maurhofer, Daniel Croll Microbiome.2025;[Epub] CrossRef - Effects of preceding crops on potassium dynamics, bacterial communities in tobacco-planted soils, and potassium allocation in tobacco plants
Jie Zhao, Ming Liu, Kaiyuan Gu, Xianglu Liu, Juan Li, Shuyue Guan, Chengwei Yang, Haiping He, Zexian Yang, Yanxia Hu Scientific Reports.2025;[Epub] CrossRef - Plant Growth‐Promoting Rhizobacteria Isolated From Natural Habitats Promote the Growth of Elymus sibiricus and Enhance Its Resistance to Abiotic Stress
Ruiqi Liang, Li Zhong, Zeyao Huang, Weixia Wang, Guangxin Lu, Tingheng Zhu Plant-Environment Interactions.2025;[Epub] CrossRef - Novel Verrucomicrobiota strains associated with plant root tissue enhance plant growth and suppress bacterial wilt in tomato
Minseo Choi, Manigundan Kaari, Hyoung Ju Lee, Seon-Woo Lee Frontiers in Microbiology.2025;[Epub] CrossRef - Modeling Growth Kinetics of Escherichia coli and Background Microflora in Hydroponically Grown Lettuce
Xiaoyan You, Dongqun Yang, Yang Qu, Mingming Guo, Yangping Zhang, Xiaoyan Zhao, Yujuan Suo Foods.2024; 13(9): 1359. CrossRef - Influence and Role of Fungi, Bacteria, and Mixed Microbial Populations on Phosphorus Acquisition in Plants
Yu Luo, Lige Ma, Qirui Feng, Huan Luo, Chen Chen, Shuqi Wang, Yue Yuan, Can Liu, Xulv Cao, Nannan Li Agriculture.2024; 14(3): 358. CrossRef - Endophytic Pseudomonas fluorescens promotes changes in the phenotype and secondary metabolite profile of Houttuynia cordata Thunb.
Kaifeng Wang, Zhannan Yang, Shiqiong Luo, Wenxuan Quan Scientific Reports.2024;[Epub] CrossRef - Rhizosphere Microorganisms in Subsurface Flow Garden Constructed Wetland and their Influence on Nitrogen Removal Efficiency
Baishi Wang, Liping Wu, Ruoqiao Wang, Jiangbo Huo, Zhou Yi, Zexin Wang, Hongzhou Zhang Water, Air, & Soil Pollution.2024;[Epub] CrossRef - Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture
Mingfei Chen, Shwetha M. Acharya, Mon Oo Yee, Kristine Grace M. Cabugao, Romy Chakraborty Frontiers in Microbiology.2024;[Epub] CrossRef - Using biochar for environmental recovery and boosting the yield of valuable non-food crops: The case of hemp in a soil contaminated by potentially toxic elements (PTEs)
Matteo Garau, Mauro Lo Cascio, Sotirios Vasileiadis, Tom Sizmur, Maria Nieddu, Maria Vittoria Pinna, Costantino Sirca, Donatella Spano, Pier Paolo Roggero, Giovanni Garau, Paola Castaldi Heliyon.2024; 10(6): e28050. CrossRef -
Differences in autotoxic substances and microbial community in the root space of
Panax notoginseng
coinducing the occurrence of root rot
Jinmiao Chen, Zhidan Liu, Yuyan Liu, Xiuling Ji, Xiaoran Li, Yunlin Wei, Futing Zi, Yong Tan, Arpita Bose Applied and Environmental Microbiology.2024;[Epub] CrossRef - Root-associated microbial diversity and metabolomics in maize resistance to stalk rot
Liming Wang, Jiao Jia, Qianfu Su, Hongzhe Cao, Shiqi Jia, Helong Si, Zhiyan Cao, Shujie Ma, Jihong Xing, Kang Zhang, Jingao Dong Frontiers in Microbiology.2024;[Epub] CrossRef - Interplant communication increases aphid resistance and alters rhizospheric microbes in neighboring plants of aphid‐infested cucumbers
Xingchen Liu, Changxia Du, Yinqing Tan, Cong Yue, Huaifu Fan Pest Management Science.2024; 80(10): 5005. CrossRef - Phage-Dependent Alteration of Rhizosphere Microbiota in Tomato Plants
Seung Yeup Lee, Roniya Thapa Magar, Kihyuck Choi, Hyo Jeong Kim, Insoo Park, Seon-Woo Lee Phytobiomes Journal.2024; 8(2): 223. CrossRef - MAPK Cascades in Plant Microbiota Structure and Functioning
Thijs Van Gerrewey, Hoo Sun Chung Journal of Microbiology.2024; 62(3): 231. CrossRef - The structure and diversity of bacteria and fungi in the roots and rhizosphere soil of three different species of Geodorum
Jianxiu Liu, Danjuan Zeng, Yang Huang, Lisha Zhong, Jialin Liao, Yuxing Shi, Haidu Jiang, Yajin Luo, Yu Liang, Shengfeng Chai BMC Genomics.2024;[Epub] CrossRef - Irradiance level and elevation shape the soil microbiome communities of Coffea arabica L.
Inocência da Piedade E. Tapaça, Chinedu C. Obieze, Gilberto V. de Melo Pereira, David Fangueiro, João Coutinho, Irene Fraga, Fábio L. Partelli, José C. Ramalho, Isabel Marques, Ana I. Ribeiro-Barros Environmental Microbiome.2024;[Epub] CrossRef - Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition
Tomasz Grzyb, Justyna Szulc International Journal of Molecular Sciences.2024; 25(24): 13601. CrossRef - Correlation of microbiomes in “plant-insect-soil” ecosystem
Guomeng Li, Peng Liu, Jihan Zhao, Liangyinan Su, Mengyu Zhao, Zhengjie Jiang, Yang Zhao, Xiping Yang Frontiers in Microbiology.2023;[Epub] CrossRef - Distinctive Structure and Assembly of Phyllosphere Microbial Communities between Wild and Cultivated Rice
Yue Yin, Yi-Fei Wang, Hui-Ling Cui, Rui Zhou, Lv Li, Gui-Lan Duan, Yong-Guan Zhu, Kristen M. DeAngelis Microbiology Spectrum.2023;[Epub] CrossRef -
Ecological Processes of Bacterial and Fungal Communities Associated with
Typha orientalis
Roots in Wetlands Were Distinct during Plant Development
Lixiao Wang, Jinxian Liu, Meiting Zhang, Tiehang Wu, Baofeng Chai, Alison Sinclair Microbiology Spectrum.2023;[Epub] CrossRef - Existence of antibiotic pollutant in agricultural soil: Exploring the correlation between microbiome and pea yield
Wangjing Zhai, Wenqi Jiang, Qiqi Guo, Zhixuan Wang, Donghui Liu, Zhiqiang Zhou, Peng Wang Science of The Total Environment.2023; 871: 162152. CrossRef - Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau
Zhijia Cui, Ran Li, Fan Li, Ling Jin, Haixu Wu, Chunya Cheng, Yi Ma, Zhenheng Wang, Yuanyuan Wang Frontiers in Microbiology.2023;[Epub] CrossRef - Integrated metagenomics and metabolomics analysis reveals changes in the microbiome and metabolites in the rhizosphere soil of Fritillaria unibracteata
Chengcheng Liu, Jingsheng Yu, Jizhe Ying, Kai Zhang, Zhigang Hu, Zhixiang Liu, Shilin Chen Frontiers in Plant Science.2023;[Epub] CrossRef - Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors
Yanping Shen, Yibo Liu, Yutong Du, Xu Wang, Jiunian Guan, Xiaohui Jia, Fukai Xu, Ziwei Song, Hongjie Gao, Baiyu Zhang, Ping Guo Science of The Total Environment.2023; 905: 167279. CrossRef - Effects of different fertilization conditions and different geographical locations on the diversity and composition of the rhizosphere microbiota of Qingke (Hordeum vulgare L.) plants in different growth stages
Lei Wang, Handong Wang, Meijin Liu, Jinqing Xu, Haiyan Bian, Tongrui Chen, En You, Chao Deng, Youhai Wei, Tianyu Yang, Yuhu Shen Frontiers in Microbiology.2023;[Epub] CrossRef - Editorial: Women in plant pathogen interactions: 2022
Špela Baebler, Anna Coll, Giulia Malacarne Frontiers in Plant Science.2023;[Epub] CrossRef - The Co-Association of Enterobacteriaceae and Pseudomonas with Specific Resistant Cucumber against Fusarium Wilt Disease
Yu-Lu Zhang, Xiao-Jing Guo, Xin Huang, Rong-Jun Guo, Xiao-Hong Lu, Shi-Dong Li, Hao Zhang Biology.2023; 12(2): 143. CrossRef - Niche-dependent microbial assembly in salt-tolerant tall fescue and its contribution to plant biomass
Tianqi Zhu, Liang Zhang, Zizheng Yan, Bowen Liu, Youyue Li, Xiangkai You, Mo-Xian Chen, Tie-Yuan Liu, Yuefei Xu, Jianhua Zhang Industrial Crops and Products.2023; 206: 117736. CrossRef - Effects of time-space conversion on microflora structure, secondary metabolites composition and antioxidant capacity of Codonopsis pilosula root
Lili Fan, Jiangqin Wang, Feifan Leng, Shaowei Li, Xiang Ma, Xiaoli Wang, Yonggang Wang Plant Physiology and Biochemistry.2023; 198: 107659. CrossRef - The Root Microbiome: Techniques for Exploration and Agricultural Applications
Ashling Cannon BioTechniques.2023; 75(1): 1. CrossRef - Multi-omics approaches for deciphering the microbial modulation of plants' genetic potentials: What's known and what's next?
Febri Doni, Mia Miranti, Muhamad Shakirin Mispan, Zulqarnain Mohamed, Norman Uphoff Rhizosphere.2022; 24: 100613. CrossRef - Effects of Combined Abiotic Stresses Related to Climate Change on Root Growth in Crops
Maria Sánchez-Bermúdez, Juan C. del Pozo, Mónica Pernas Frontiers in Plant Science.2022;[Epub] CrossRef - Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome
Alice Mataigne, Nathan Vannier, Philippe Vandenkoornhuyse, Stéphane Hacquard Microbiome.2022;[Epub] CrossRef - Can moderate heavy metal soil contaminations due to cement production influence the surrounding soil bacterial communities?
Thiago Augusto da Costa Silva, Marcos de Paula, Washington Santos Silva, Gustavo Augusto Lacorte Ecotoxicology.2022; 31(1): 134. CrossRef - Mechanisms of plant cell wall surveillance in response to pathogens, cell wall-derived ligands and the effect of expansins to infection resistance or susceptibility
Delia A. Narváez-Barragán, Omar E. Tovar-Herrera, Arturo Guevara-García, Mario Serrano, Claudia Martinez-Anaya Frontiers in Plant Science.2022;[Epub] CrossRef - Fecal Microbiota Transplants for Inflammatory Bowel Disease Treatment: Synthetic- and Engineered Communities-Based Microbiota Transplants Are the Future
Raees Khan, Nazish Roy, Hussain Ali, Muhammad Naeem, Eiji Sakai Gastroenterology Research and Practice.2022; 2022: 1. CrossRef - The root microbiome: Community assembly and its contributions to plant fitness
Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang, Yang Bai Journal of Integrative Plant Biology.2022; 64(2): 230. CrossRef - The Role of Synthetic Microbial Communities (SynCom) in Sustainable Agriculture
Ambihai Shayanthan, Patricia Ann C. Ordoñez, Ivan John Oresnik Frontiers in Agronomy.2022;[Epub] CrossRef - Microbiome engineering and plant biostimulants for sustainable crop improvement and mitigation of biotic and abiotic stresses
Su-Ee Lau, Wee Fei Aaron Teo, Ee Yang Teoh, Boon Chin Tan Discover Food.2022;[Epub] CrossRef - Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho Journal of Microbiology.2021; 59(3): 229. CrossRef
|