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Sun K, Pan YT, Jiang HJ, Xu JY, Ma CY, Zhou J, Liu Y, Shabala S, Zhang W, Dai CC. Root endophyte-mediated alteration in plant H2O2 homeostasis regulates symbiosis outcome and reshapes the rhizosphere microbiota. J Exp Bot 2024; 75:3153-3170. [PMID: 38394357 DOI: 10.1093/jxb/erae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/22/2024] [Indexed: 02/25/2024]
Abstract
Endophytic symbioses between plants and fungi are a dominant feature of many terrestrial ecosystems, yet little is known about the signaling that defines these symbiotic associations. Hydrogen peroxide (H2O2) is recognized as a key signal mediating the plant adaptive response to both biotic and abiotic stresses. However, the role of H2O2 in plant-fungal symbiosis remains elusive. Using a combination of physiological analysis, plant and fungal deletion mutants, and comparative transcriptomics, we reported that various environmental conditions differentially affect the interaction between Arabidopsis and the root endophyte Phomopsis liquidambaris, and link this process to alterations in H2O2 levels and H2O2 fluxes across root tips. We found that enhanced H2O2 efflux leading to a moderate increase in H2O2 levels at the plant-fungal interface is required for maintaining plant-fungal symbiosis. Disturbance of plant H2O2 homeostasis compromises the symbiotic ability of plant roots. Moreover, the fungus-regulated H2O2 dynamics modulate the rhizosphere microbiome by selectively enriching for the phylum Cyanobacteria, with strong antioxidant defenses. Our results demonstrated that the regulation of H2O2 dynamics at the plant-fungal interface affects the symbiotic outcome in response to external conditions and highlight the importance of the root endophyte in reshaping the rhizosphere microbiota.
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Affiliation(s)
- Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Yi-Tong Pan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Jia-Yan Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Jiayu Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Yunqi Liu
- Zhongguancun Xuyue Non-invasive Micro-test Technology Industrial Alliance, Beijing 10080, China
| | - Sergey Shabala
- School of Biological Science, University of Western Australia, Crawley, WA 60909, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
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Li P, Dini-Andreote F, Jiang J. Exploiting microbial competition to promote plant health. Trends Plant Sci 2024:S1360-1385(24)00121-3. [PMID: 38760241 DOI: 10.1016/j.tplants.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
The host-associated microbiota can promote colonization resistance against pathogens via a mechanism termed 'nutrient blocking', as highlighted in a recent article by Spragge et al. This implies that greater metabolic overlap between commensal taxa and pathogens leads to disease suppression. Here, we discuss future avenues for how this principle can be exploited in the rhizosphere microbiota to promote plant health.
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Affiliation(s)
- Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA; The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China.
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Yang Y, Xu N, Zhang Z, Lei C, Chen B, Qin G, Qiu D, Lu T, Qian H. Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere. J Agric Food Chem 2024; 72:5659-5670. [PMID: 38442360 DOI: 10.1021/acs.jafc.3c09160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.
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Affiliation(s)
- Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
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Zhang LN, Jiang CH, Si F, Song N, Yang W, Zhu Y, Luo Y, Guo JH. Long-Term Field Application of a Plant Growth-Promoting Rhizobacterial Consortium Suppressed Root-Knot Disease by Shaping the Rhizosphere Microbiota. Plant Dis 2024; 108:94-103. [PMID: 37467122 DOI: 10.1094/pdis-09-22-2196-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) are one of the most economically important plant parasitic nematodes, infecting almost all cultivated plants and resulting in severe yield losses every year. Plant growth-promoting rhizobacteria (PGPR) have been extensively used to prevent and control root-knot diseases and increase yield. In this study, the effect of a consortium of three PGPR strains (Bacillus cereus AR156, B. subtilis SM21, and Serratia sp. XY21; hereafter "BBS") on root-knot disease of cucumber was evaluated. The application of BBS significantly reduced the severity of root-knot disease by 56 to 72%, increased yield by 36 to 55%, and improved fruit quality by 14 to 90% and soil properties by 1 to 90% relative to the control in the cucumber fields of the Nanjing suburb, Jiangsu Province, from 2015 to 2018. BBS altered the rhizosphere bacterial community. Compared with the control group, it significantly (false discovery rate, P < 0.05) increased the abundance of 14 bacterial genera that were negatively correlated with disease severity. Additionally, the redundancy analysis suggested that BBS-treated rhizosphere soil samples were dominated by disease-suppressive bacteria, including the genera Iamia, Kutzneria, Salinibacterium, Mycobacterium, Kribbella, Pseudonocardia, Sporichthya, Sphaerisporangium, Actinomadura, Flavisolibacter, Phenylobacterium, Bosea, Hyphomicrobium, Agrobacterium, Sphingomonas, and Nannocystis, which were positively related to total organic carbon, total nitrogen, total organic matter, dissolved organic carbon, [Formula: see text]-N, and available phosphorus contents. This suggests that BBS suppresses root-knot nematodes and improves the soil chemical properties of cucumber by altering the rhizosphere microbial community.
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Affiliation(s)
- Li-Na Zhang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, School of Life Science, Huaiyin Normal University, Huaian 223300, China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Engineering Center of Bioresource Pesticide in Jiangsu Province, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng 224002, China
| | - Chun-Hao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Engineering Center of Bioresource Pesticide in Jiangsu Province, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
| | - Fangjie Si
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Engineering Center of Bioresource Pesticide in Jiangsu Province, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
| | - Ning Song
- Nanjing Planck Technology and Trade Co., Ltd., Nanjing 210095, China
| | - Wei Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, School of Life Science, Huaiyin Normal University, Huaian 223300, China
| | - Yanze Zhu
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, School of Life Science, Huaiyin Normal University, Huaian 223300, China
| | - Jian-Hua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Engineering Center of Bioresource Pesticide in Jiangsu Province, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
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Wang L, Wang H, Liu M, Xu J, Bian H, Chen T, You E, Deng C, Wei Y, Yang T, Shen Y. Corrigendum: 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. Front Microbiol 2023; 14:1268063. [PMID: 37614594 PMCID: PMC10443637 DOI: 10.3389/fmicb.2023.1268063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/25/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1094034.].
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Affiliation(s)
- Lei Wang
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Handong Wang
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Meijin Liu
- Gannan Institute of Agricultural Sciences, Hezuo, China
| | - Jinqing Xu
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Haiyan Bian
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tongrui Chen
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - En You
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Deng
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Youhai Wei
- Academy of Agriculture and Forestry Science, Qinghai University, Xining, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Yuhu Shen
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
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Paries M, Gutjahr C. The good, the bad, and the phosphate: regulation of beneficial and detrimental plant-microbe interactions by the plant phosphate status. New Phytol 2023. [PMID: 37145847 DOI: 10.1111/nph.18933] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/21/2023] [Indexed: 05/06/2023]
Abstract
Phosphate (Pi ) is indispensable for life on this planet. However, for sessile land plants it is poorly accessible. Therefore, plants have developed a variety of strategies for enhanced acquisition and recycling of Pi . The mechanisms to cope with Pi limitation as well as direct uptake of Pi from the substrate via the root epidermis are regulated by a conserved Pi starvation response (PSR) system based on a family of key transcription factors (TFs) and their inhibitors. Furthermore, plants obtain Pi indirectly through symbiosis with mycorrhiza fungi, which employ their extensive hyphal network to drastically increase the soil volume that can be explored by plants for Pi . Besides mycorrhizal symbiosis, there is also a variety of other interactions with epiphytic, endophytic, and rhizospheric microbes that can indirectly or directly influence plant Pi uptake. It was recently discovered that the PSR pathway is involved in the regulation of genes that promote formation and maintenance of AM symbiosis. Furthermore, the PSR system influences plant immunity and can also be a target of microbial manipulation. It is known for decades that the nutritional status of plants influences the outcome of plant-microbe interactions. The first molecular explanations for these observations are now emerging.
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Affiliation(s)
- Michael Paries
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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Wang L, Wang H, Liu M, Xu J, Bian H, Chen T, You E, Deng C, Wei Y, Yang T, Shen Y. 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. Front Microbiol 2023; 14:1094034. [PMID: 37213511 PMCID: PMC10192736 DOI: 10.3389/fmicb.2023.1094034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/12/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction The excessive use of chemical fertilizer causes increasing environmental and food security crisis. Organic fertilizer improves physical and biological activities of soil. Rhizosphere microbiota, which consist of highly diverse microorganisms, play an important role in soil quality. However, there is limited information about the effects of different fertilization conditions on the growth of Qingke plants and composition of the rhizosphere microbiota of the plants. Methods In this study, we characterized the rhizosphere microbiota of Qingke plants grown in three main Qingke-producing areas (Tibet, Qinghai, and Gansu). In each of the three areas, seven different fertilization conditions (m1-m7, m1: Unfertilized; m2: Farmer Practice; m3: 75% Farmer Practice; m4: 75% Farmer Practice +25% Organic manure; m5: 50% Farmer Practice; m6: 50% Farmer Practice +50% Organic manure; m7: 100% Organic manure) were applied. The growth and yields of the Qingke plants were also compared under the seven fertilization conditions. Results There were significant differences in alpha diversity indices among the three areas. In each area, differences in fertilization conditions and differences in the growth stages of Qingke plants resulted in differences in the beta diversity of the rhizosphere microbiota. Meanwhile, in each area, fertilization conditions, soil depths, and the growth stages of Qingke plants significantly affected the relative abundance of the top 10 phyla and the top 20 bacterial genera. For most of microbial pairs established through network analysis, the significance of their correlations in each of the microbial co-occurrence networks of the three experimental sites was different. Moreover, in each of the three networks, there were significant differences in relative abundance and genera among most nodes (i.e., the genera Pseudonocardia, Skermanella, Pseudonocardia, Skermanella, Aridibacter, and Illumatobacter). The soil chemical properties (i.e., TN, TP, SOM, AN, AK, CEC, Ca, and K) were positively or negatively correlated with the relative abundance of the top 30 genera derived from the three main Qingke-producing areas (p < 0.05). Fertilization conditions markedly influenced the height of a Qingke plant, the number of spikes in a Qingke plant, the number of kernels in a spike, and the fresh weight of a Qingke plant. Considering the yield, the most effective fertilization conditions for Qingke is combining application 50% chemical fertilizer and 50% organic manure. Conclusion The results of the present study can provide theoretical basis for practice of reducing the use of chemical fertilizer in agriculture.
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Affiliation(s)
- Lei Wang
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Handong Wang
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Meijin Liu
- Gannan Institute of Agricultural Sciences, Hezuo, China
| | - Jinqing Xu
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Haiyan Bian
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tongrui Chen
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - En You
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Deng
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Youhai Wei
- Academy of Agriculture and Forestry Science, Qinghai University, Xining, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Yuhu Shen
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
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Zhao L, He Y, Zheng Y, Xu Y, Shi S, Fan M, Gu S, Li G, Tianli W, Wang J, Li J, Deng X, Liao X, Du J, Nian F. Differences in soil physicochemical properties and rhizosphere microbial communities of flue-cured tobacco at different transplantation stages and locations. Front Microbiol 2023; 14:1141720. [PMID: 37152740 PMCID: PMC10157256 DOI: 10.3389/fmicb.2023.1141720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/03/2023] [Indexed: 05/09/2023] Open
Abstract
Rhizosphere microbiota play an important role in regulating soil physical and chemical properties and improving crop production performance. This study analyzed the relationship between the diversity of rhizosphere microbiota and the yield and quality of flue-cured tobacco at different transplant times (D30 group, D60 group and D90 group) and in different regions [Linxiang Boshang (BS) and Linxiang ZhangDuo (ZD)] by high-throughput sequencing technology. The results showed that there were significant differences in the physicochemical properties and rhizosphere microbiota of flue-cured tobacco rhizosphere soil at different transplanting times, and that the relative abundance of Bacillus in the rhizosphere microbiota of the D60 group was significantly increased. RDA and Pearson correlation analysis showed that Bacillus, Streptomyces and Sphingomonas were significantly correlated with soil physical and chemical properties. PIGRUSt2 function prediction results showed that compared with the D30 group, the D60 group had significantly increased metabolic pathways such as the superpathway of pyrimidine deoxyribonucleoside salvage, allantoin degradation to glyoxylate III and pyrimidine deoxyribonucleotides de novo biosynthesis III metabolic pathways. The D90 group had significantly increased metabolic pathways such as ubiquitol-8 biosynthesis (prokaryotic), ubiquitol-7 biosynthesis (prokaryotic) and ubiquitol-10 biosynthesis (prokaryotic) compared with the D60 group. In addition, the yield and quality of flue-cured tobacco in the BS region were significantly higher than those in the ZD region, and the relative abundance of Firmicutes and Bacillus in the rhizosphere microbiota of flue-cured tobacco in the BS region at the D60 transplant stage was significantly higher than that in the ZD region. In addition, the results of the hierarchical sample metabolic pathway abundance map showed that the PWY-6572 metabolic pathway was mainly realized by Paenibacillus, and that the relative abundance of flue-cured tobacco rhizosphere microbiota (Paenibacillus) participating in PWY-6572 in the D60 transplant period in the BS region was significantly higher than that in the ZD region. In conclusion, different transplanting periods of flue-cured tobacco have important effects on soil physical and chemical properties and rhizosphere microbial communities. There were significant differences in the rhizosphere microbiota and function of flue-cured tobacco in different regions, which may affect the performance and quality of this type of tobacco.
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Affiliation(s)
- Leifeng Zhao
- College of Tobacco Science, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuansheng He
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Yuanxian Zheng
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Yinlian Xu
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Shoujie Shi
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Meixun Fan
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Shaolong Gu
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Guohong Li
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Wajie Tianli
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Jiming Wang
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Junying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Xiaopeng Deng
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Xiaolin Liao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jun Du
- Institute of Plant Nutrition, Agricultural Resources and Environmental Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Jun Du,
| | - Fuzhao Nian
- College of Tobacco Science, Yunnan Agricultural University, Kunming, Yunnan, China
- Fuzhao Nian,
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9
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Xiao Z, Fan N, Wang X, Ji H, Yue L, He F, Wang Z. Earthworms Drive the Effect of La 2O 3 Nanoparticles on Radish Taproot Metabolite Profiles and Rhizosphere Microbial Communities. Environ Sci Technol 2022; 56:17385-17395. [PMID: 36351052 DOI: 10.1021/acs.est.2c05828] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To promote the sustainable and safe application of nanotechnology employing engineered nanoparticles (NPs) in agroecosystems, it is crucial to pay more attention to the NP-mediated biological response process and environmental impact assessment simultaneously. Herein, 50 mg kg-1 La2O3 NPs were added to soils without and with earthworms for cherry radish growth for 50 days to investigate the response changes of metabolites in radish above- and below-ground organs and rhizosphere bacterial communities. We found that La2O3 NP exposure, especially with earthworms, notably increased the La bioavailability and uptake by taproots and eventually increased radish leaf sucrose content and plant biomass. The La2O3 NP exposure significantly altered metabolite profiles in taproot flesh and peel tissues, and particularly La2O3 NP exposure combined with earthworms was more conducive to La2O3 NPs to promote radish taproot peel to synthesize more secondary antioxidant metabolites. Moreover, compared with the control, the La2O3 NP exposure resulted in weaker and fewer correlations between rhizosphere bacteria and taproot metabolites, but this was recovered somewhat after the inoculation of earthworms. Altogether, our results provide novel insights into the soil-fauna-driven biological and biochemical impact of La2O3 NP exposure on edible root crops and the long-term environmental risks to the rhizosphere microbiota in agroecosystems.
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Affiliation(s)
- Zhenggao Xiao
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Ningke Fan
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Xie Wang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Haihua Ji
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Feng He
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
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10
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Chen JM, Feng WM, Yan H, Liu P, Zhou GS, Guo S, Yu G, Duan JA. Explore the interaction between root metabolism and rhizosphere microbiota during the growth of Angelica sinensis. Front Plant Sci 2022; 13:1005711. [PMID: 36420035 PMCID: PMC9676459 DOI: 10.3389/fpls.2022.1005711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Angelica sinensis is a medicinal plant widely used to treat multiple diseases in Asia and Europe, which contains numerous active components with therapeutic value. The interaction between root and rhizosphere microorganisms is crucial for the growth and quality formation of medicinal plants. But the micro-plant-metabolite regulation patterns for A. sinensis remain largely undetermined. Here, we collected roots and rhizosphere soils from A. sinensis in seedling stage (M) and picking stage (G), respectively cultivated for one year and two years, generated metabolite for roots, microbiota data for rhizospheres, and conducted a comprehensive analysis. Changes in metabolic and microbial communities of A.sinensis over growth were distinct. The composition of rhizosphere microbes in G was dominated by proteobacteria, which had a strong correlation with the synthesis of organic acids, while in M was dominated by Actinobacteria, which had a strong correlation with the synthesis of phthalide and other organoheterocyclic compounds, flavonoids, amines, and fatty acid. Additionally, co-occurrence network analysis identified that Arthrobacter was found to be strongly correlated with the accumulation of senkyunolide A and n-butylidenephthalide. JGI 0001001.H03 was found to be strongly correlated with the accumulation of chlorogenic acid. Based on rhizosphere microorganisms, this study investigated the correlation between root metabolism and rhizosphere microbiota of A. sinensis at different growth stages in traditional geoherb region, which could provide references for exploring the quality formation mechanism of A. sinensis in the future.
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Affiliation(s)
| | | | - Hui Yan
- *Correspondence: Hui Yan, ; Pei Liu, ; Jin-Ao Duan,
| | - Pei Liu
- *Correspondence: Hui Yan, ; Pei Liu, ; Jin-Ao Duan,
| | | | | | | | - Jin-Ao Duan
- *Correspondence: Hui Yan, ; Pei Liu, ; Jin-Ao Duan,
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11
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Luo W, Zai X, Sun J, Li D, Li Y, Li G, Wei G, Chen W. Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean. Front Microbiol 2021; 12:783563. [PMID: 34925288 PMCID: PMC8678505 DOI: 10.3389/fmicb.2021.783563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022] Open
Abstract
Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and>2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.
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Affiliation(s)
- Wen Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Xiaoyu Zai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Jieyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Da Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Yuanli Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Guoqiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
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12
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Shang XC, Cai X, Zhou Y, Han X, Zhang CS, Ilyas N, Li Y, Zheng Y. Pseudomonas Inoculation Stimulates Endophytic Azospira Population and Induces Systemic Resistance to Bacterial Wilt. Front Plant Sci 2021; 12:738611. [PMID: 36406638 PMCID: PMC9673043 DOI: 10.3389/fpls.2021.738611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/19/2021] [Indexed: 06/04/2023]
Abstract
Bacterial communities in the rhizosphere play an important role in sustaining plant growth and the health of diverse soils. Recent studies have demonstrated that microbial keystone taxa in the rhizosphere microbial community are extremely critical for the suppression of diseases. However, the mechanisms involved in disease suppression by keystone species remain unclear. The present study assessed the effects of three Pseudomonas strains, which were identified as keystone species in our previous study, on the growth performance and root-associated bacterial community of tobacco plants. A high relative abundance of Ralstonia was found in the non-inoculated group, while a large Azospira population was observed in all groups inoculated with the three Pseudomonas strains. Correspondingly, the activities of the defense-related enzymes and the expression levels of the defense signaling marker genes of the plant were increased after inoculation with the Pseudomonas strains. Moreover, the correlation analyses showed that the relative abundance of Azospira, the activity of superoxide dismutase, catalase, and polyphenol oxidase, and the expression of H1N1, ACC Oxidase, and PR1 a/c had a significantly negative (p<0.05) relationship with the abundance of Ralstonia. This further revealed that the keystone species, such as Pseudomonas spp., can suppress bacterial wilt disease by enhancing the systemic resistance of tobacco plants.
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Affiliation(s)
- Xian-chao Shang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianjie Cai
- Shanghai Tobacco Group Co., Ltd., Shanghai, China
| | - Yanan Zhou
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xiaobin Han
- Biological Organic Fertilizer Engineering Technology Center of China Tobacco, Zunyi Branch of Guizhou Tobacco Company, Zunyi, China
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Naila Ilyas
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yanfen Zheng
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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13
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Deng Q, Zhang T, Xie D, Yang Y. Rhizosphere Microbial Communities Are Significantly Affected by Optimized Phosphorus Management in a Slope Farming System. Front Microbiol 2021; 12:739844. [PMID: 34589078 PMCID: PMC8473901 DOI: 10.3389/fmicb.2021.739844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022] Open
Abstract
Soil rhizosphere microorganisms play crucial roles in promoting plant nutrient absorption and maintaining soil health. However, the effects of different phosphorus (P) managements on soil microbial communities in a slope farming system are poorly understood. Here, rhizosphere microbial communities under two P fertilization levels-conventional (125 kg P2O5 ha-1, P125) and optimal (90 kg P2O5 ha-1, P90)-were compared at four growth stages of maize in a typical sloped farming system. The richness and diversity of rhizosphere bacterial communities showed significant dynamic changes throughout the growth period of maize, while different results were observed in fungal communities. However, both the P fertilization levels and the growth stages influenced the structure and composition of the maize rhizosphere microbiota. Notably, compared to P125, Pseudomonas, Conexibacter, Mycobacterium, Acidothermus, Glomeromycota, and Talaromyces were significantly enriched in the different growth stages of maize under P90, while the relative abundance of Fusarium was significantly decreased during maize harvest. Soil total nitrogen (TN) and pH are the first environmental drivers of change in bacterial and fungal community structures, respectively. The abundance of Gemmatimonadota, Proteobacteria, and Cyanobacteria showed significant correlations with soil TN, while that of Basidiomycota and Mortierellomycota was significantly related to pH. Additionally, P90 strengthened the connection between bacteria, but reduced the links between fungi at the genus level. Our work helps in understanding the role of P fertilization levels in shaping the rhizosphere microbiota and may manipulate beneficial microorganisms for better P use efficiency.
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Affiliation(s)
- Qianxin Deng
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Tong Zhang
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Deti Xie
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Yuheng Yang
- College of Plant Protection, Southwest University, Chongqing, China
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14
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Zhang G, Wei G, Wei F, Chen Z, He M, Jiao S, Wang Y, Dong L, Chen S. Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant. Front Microbiol 2021; 12:713523. [PMID: 34484152 PMCID: PMC8415459 DOI: 10.3389/fmicb.2021.713523] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/30/2021] [Indexed: 12/20/2022] Open
Abstract
Understanding the ecological patterns of rhizosphere microbial communities is critical for propelling sustainable agriculture and managing ecosystem functions by exploiting microorganisms. However, this knowledge is still unclear, especially under host-associated large-scale and regarding the comparison between bacteria and fungi. We examined community assembly processes and community characters including environmental thresholds and co-occurrence patterns across the cultivatable area of Panax notoginseng for bacteria and fungi. Both are vital members of the rhizosphere but differ considerably in their life history and dispersal potentiality. Edaphic factors drove the parallel variations of bacterial and fungal communities. Although bacterial and fungal communities exhibited similar biogeographic patterns, the assembly of fungi was more driven by dispersal limitation than selection compared with bacteria. This finding supported the 'size-dispersal' hypothesis. pH and total nitrogen respectively mediated the relative importance of deterministic and stochastic processes in shaping bacterial and fungal communities. In addition, fungal communities exhibited potentially broader environmental thresholds and more modular co-occurrence patterns than bacteria (bacteria: 0.67; fungi: 0.78). These results emphasized the importance of dispersal limitation in structuring rhizosphere microbiota and shaping community features of ecologically distinct microorganisms. This study provides insights into the improved prediction and management of the key functions of rhizosphere microbiota.
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Affiliation(s)
- Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd., Wenshan, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - Mingjun He
- Hainan Branch Institute of Medicinal Plant, Chinese Academy of Medical Sciences and Peking Union Medical College, Wanning, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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15
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Chang HX, Noel ZA, Chilvers MI. A β-lactamase gene of Fusarium oxysporum alters the rhizosphere microbiota of soybean. Plant J 2021; 106:1588-1604. [PMID: 33788336 DOI: 10.1111/tpj.15257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
The rhizosphere is a multitrophic environment, and for soilborne pathogens such as Fusarium oxysporum, microbial competition in the rhizosphere is inevitable before reaching and infecting roots. This study established a tritrophic interaction among the plant growth-promoting rhizobacterium Burkholderia ambifaria, F. oxysporum and Glycine max (soybean) to study the effects of F. oxysporum genes on shaping the soybean microbiota. Although B. ambifaria inhibited mycelial growth and increased bacterial propagation in the presence of F. oxysporum, F. oxysporum still managed to infect soybean in the presence of B. ambifaria. RNA-Seq identified a putative F. oxysporum secretory β-lactamase-coding gene, FOXG_18438 (abbreviated as Fo18438), that is upregulated during soybean infection in the presence of B. ambifaria. The ∆Fo18438 mutants displayed reduced mycelial growth towards B. ambifaria, and the complementation of full Fo18438 and the Fo18438 β-lactamase domain restored mycelial growth. Using the F. oxysporum wild type, ∆Fo18438 mutants and complemented strains with full Fo18438, Fo18438 β-lactamase domain or Fo18438 RTA1-like domain for soil inoculation, 16S rRNA amplicon sequencing revealed that the abundance of a Burkholderia operational taxonomic unit (OTU) was increased in the rhizosphere microbiota infested by the strains with Fo18438 β-lactamase domain. Non-metric multidimensional scaling and PICRUSt2 functional analysis revealed differential abundance for the bacterial β-lactam-related functions when contrasting the genotypes of F. oxysporum. These results indicated that the Fo18438 β-lactamase domain provides F. oxysporum with the advantage of growing into the soybean rhizosphere, where β-lactam antibiosis is involved in microbial competition. Accordingly, this study highlights the capability of an F. oxysporum gene for altering the soybean rhizosphere and taproot microbiota.
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Affiliation(s)
- Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan
| | - Zachary A Noel
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
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16
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Han G, Mannaa M, Kim N, Jeon HW, Jung H, Lee HH, Kim J, Park J, Park AR, Kim JC, Seo YS. Response of Pine Rhizosphere Microbiota to Foliar Treatment with Resistance-Inducing Bacteria against Pine Wilt Disease. Microorganisms 2021; 9:microorganisms9040688. [PMID: 33810444 PMCID: PMC8065550 DOI: 10.3390/microorganisms9040688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 11/19/2022] Open
Abstract
In this study, two bacterial strains, IRP7 and IRP8, were selected to induce resistance against pine wilt disease (PWD). Foliar application with these strains to nematode-inoculated pine seedlings significantly reduced PWD severity. The effect of nematode inoculation and bacterial treatment on the rhizosphere bacterial community was investigated. The results indicated that the rhizosphere of nematode-inoculated seedlings contained a lower relative abundance of beneficial microbes such as Paraburkholderia, Bradyrhizobium, Rhizobacter, Lysobacter, and Caballeronia. Bacterial treatment resulted in significant changes in the microbes that were represented in relatively low relative abundance. Treatment with IRP7 resulted in an increase in the relative abundance of Nitrospirillum, Bacillus, and Luteibacter, which might be useful for protection against infection. Treatment with IRP8 resulted in an increase in the relative abundance of obligate bacterial predators of the Bdellovibrio genus that were previously shown to control several bacterial phytopathogens and may have a role in the management of nematode-carried bacteria. The selected bacteria were identified as Pseudomonas koreensis IRP7 and Lysobacter enzymogenes IRP8 and are suggested as a potential treatment for induced resistance against PWD. To our knowledge, this is the first report on the effect of foliar treatment with resistance-inducing bacteria on the rhizosphere microbiota.
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Affiliation(s)
- Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Department of Plant Pathology, Cairo University, Giza 12613, Egypt
| | - Namgyu Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Hee Won Jeon
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Junheon Kim
- Forest Insect Pests and Diseases Division, National Institute of Forest Science, Seoul 02455, Korea;
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Ae Ran Park
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
| | - Jin-Cheol Kim
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
- Correspondence: (J.-C.K.); (Y.-S.S.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Correspondence: (J.-C.K.); (Y.-S.S.)
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17
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Hernández-Terán A, Navarro-Díaz M, Benítez M, Lira R, Wegier A, Escalante AE. Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico. FEMS Microbiol Ecol 2021; 96:5850751. [PMID: 32490512 DOI: 10.1093/femsec/fiaa109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial community assemblages, using genetically distinct wild cotton populations as a model of study. We followed a common garden experiment including five wild cotton populations, controlling for plant genotypes, environmental conditions and soil microbial community inoculum, to test for microbial differences associated with genetic variation of the plant hosts. Microbial communities of the treatments were characterized by culture-independent 16S rRNA gene amplicon sequencing with Illumina MiSeq platform. We analyzed microbial community diversity (alpha and beta), and diversity structure of such communities, determined by co-occurrence networks. Results show that different plant genotypes select for different and specific microbial communities from a common inoculum. Although we found common amplicon sequence variants (ASVs) to all plant populations (235), we also found unique ASVs for different populations that could be related to potential functional role of such ASVs in the rhizosphere.
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Affiliation(s)
- Alejandra Hernández-Terán
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcelo Navarro-Díaz
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Rafael Lira
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54090, Mexico City, Mexico
| | - Ana Wegier
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
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18
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Wang X, Feng H, Wang Y, Wang M, Xie X, Chang H, Wang L, Qu J, Sun K, He W, Wang C, Dai C, Chu Z, Tian C, Yu N, Zhang X, Liu H, Wang E. Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia-legume symbiosis. Mol Plant 2021; 14:503-516. [PMID: 33309942 DOI: 10.1016/j.molp.2020.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/02/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. Plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume-rhizobia symbiosis, in their roots. Nevertheless, the relationship between the AM and rhizobial symbioses in native soil is poorly understood. Here, we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula by performing quantitative microbiota profiling (QMP) of 16S rRNA genes. We found that M. truncatula mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load (quantitative abundance) in the rhizosphere and roots, and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native soil. Moreover, quantitative microbial co-abundance network analyses revealed that AM symbiosis affects Rhizobiales hubs among plant microbiota and benefits the plant holobiont. Through QMP of rhizobial rpoB and AM fungal SSU rRNA genes, we revealed a new layer of interaction whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of M. truncatula. We further showed that AM symbiosis-conditioned microbial communities within the M. truncatula rhizosphere could promote nodulation in different legume plants in native soil. Given that the AM and rhizobial symbioses are critical for crop growth, our findings might inform strategies to improve agricultural management. Moreover, our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.
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Affiliation(s)
- Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Huan Feng
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mingxing Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xingguang Xie
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Huizhong Chang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Like Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jicheng Qu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wei He
- Shanghai Hanyubio Co., Ltd, Shanghai 201201, China
| | - Chunyan Wang
- College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Changfu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Nan Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xuebin Zhang
- Center for Multi-Omics Research, Collaborative Innovation Center of Crop Stress Biology, Henan Province, Kaifeng 475001, China; Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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19
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Windisch S, Sommermann L, Babin D, Chowdhury SP, Grosch R, Moradtalab N, Walker F, Höglinger B, El-Hasan A, Armbruster W, Nesme J, Sørensen SJ, Schellenberg I, Geistlinger J, Smalla K, Rothballer M, Ludewig U, Neumann G. Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root-Microbial Interactions and Plant Health of Lettuce. Front Microbiol 2021; 11:597745. [PMID: 33519736 PMCID: PMC7838544 DOI: 10.3389/fmicb.2020.597745] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/18/2020] [Indexed: 11/13/2022] Open
Abstract
Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen Olpidium sp. (76-90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting Olpidium infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and Olpidium infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87-97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (Pseudomonadaceae, Mortierella elongata) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of Pseudomonas spp. In contrast, high relative abundance of Pseudomonadaceae (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61-74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.
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Affiliation(s)
- Saskia Windisch
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Loreen Sommermann
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Doreen Babin
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | | | - Rita Grosch
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Narges Moradtalab
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Frank Walker
- Central Chemical-Analytical Laboratory, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Birgit Höglinger
- Central Chemical-Analytical Laboratory, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Abbas El-Hasan
- Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Wolfgang Armbruster
- Department of Food Chemistry and Analytical Chemistry, Institute of Food Chemistry, University of Hohenheim, Stuttgart, Germany
| | - Joseph Nesme
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ingo Schellenberg
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Jörg Geistlinger
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Günter Neumann
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
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20
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Frindte K, Zoche SA, Knief C. Development of a Distinct Microbial Community Upon First Season Crop Change in Soils of Long-Term Managed Maize and Rice Fields. Front Microbiol 2020; 11:588198. [PMID: 33240244 PMCID: PMC7680734 DOI: 10.3389/fmicb.2020.588198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/12/2020] [Indexed: 11/24/2022] Open
Abstract
The introduction of crop rotation regimes in paddy soils, for example, rice in combination with maize, implements the establishment of new paddy fields to compensate for reduced rice production on existing fields. To study responses of the soil and rhizosphere microbiota upon introduction of a new crop species into continuous cropping agroecosystems, we conducted experiments with soils from adjacent fields where rice and maize were grown successively for more than 30 years. In microcosm experiments, rice and maize plants were cultivated in both soils under the respective plant-required management regime, i.e., rice cultivation under flooded conditions and maize under non-flooded conditions. 16S rRNA gene and fungal ITS region amplicon analysis showed that the soil and rhizosphere microbiota was clearly distinct between soils after long-term rice/maize management. Upon change of the management regime, the bulk soil microbiota became different to both, the former microbial community in the soil and the community being characteristic for the respective type of long-term cropping. Nevertheless, the influence of the soil management history remained clearly visible besides the impact of the new management regime. Similar results were observed for the rhizosphere, though the combined effect of plant species and altered management was even more effective in this compartment compared to the bulk soil. The newly introduced crop plant did not take over characteristic members of the rhizosphere microbiota of the previously cultivated crop; instead, some previously rare taxa became enriched. Thus, the formerly grown crop species did not directly affect the recruitment of microorganisms in the rhizosphere of the following crop species. Further, the results show that the rhizosphere and bulk soil microbiota do not develop straight toward the specific microbiota that is characteristic for a continuous cropping system, but reach a distinct stage upon introduction of a new crop species and new management practices.
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Affiliation(s)
- Katharina Frindte
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Sarah A Zoche
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
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21
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Liu N, Lewis C, Zheng W, Fu ZQ. Phage Cocktail Therapy: Multiple Ways to Suppress Pathogenicity. Trends Plant Sci 2020; 25:315-317. [PMID: 32191865 DOI: 10.1016/j.tplants.2020.01.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Phage cocktails have emerged as precision tools for controlling plant bacterial diseases. Wang et al. now report that phage cocktails decreased the occurrence of tomato bacterial wilt disease efficiently by infecting and destroying bacterial pathogens, selecting phage-resistant but slow-growing pathogen strains, and fostering bacterial species that are antagonistic to the pathogens.
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Affiliation(s)
- Na Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, People's Republic of China
| | - Connor Lewis
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Wenming Zheng
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, People's Republic of China.
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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22
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Cheng Z, Lei S, Li Y, Huang W, Ma R, Xiong J, Zhang T, Jin L, Haq HU, Xu X, Tian B. Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota. Microorganisms 2020; 8:E170. [PMID: 31991727 DOI: 10.3390/microorganisms8020170] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/18/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Microorganisms that colonize the plant rhizosphere can contribute to plant health, growth and productivity. Although the importance of the rhizosphere microbiome is known, we know little about the underlying mechanisms that drive microbiome assembly and composition. In this study, the variation, assembly and composition of rhizobacterial communities in 11 tomato cultivars, combined with one cultivar in seven different sources of soil and growing substrate, were systematically investigated. The tomato rhizosphere microbiota was dominated by bacteria from the phyla Proteobacteria, Bacteroidetes, and Acidobacteria, mainly comprising Rhizobiales, Xanthomonadales, Burkholderiales, Nitrosomonadales, Myxococcales, Sphingobacteriales, Cytophagales and Acidobacteria subgroups. The bacterial community in the rhizosphere microbiota of the samples in the cultivar experiment mostly overlapped with that of tomato cultivar MG, which was grown in five natural field soils, DM, JX, HQ, QS and XC. The results supported the hypothesis that tomato harbors largely conserved communities and compositions of rhizosphere microbiota that remains consistent in different cultivars of tomato and even in tomato cultivar grown in five natural field soils. However, significant differences in OTU richness (p < 0.0001) and bacterial diversity (p = 0.0014 < 0.01) were observed among the 7 different sources of soil and growing substrate. Two artificial commercial nutrient soils, HF and CF, resulted in a distinct tomato rhizosphere microbiota in terms of assembly and core community compared with that observed in natural field soils. PERMANOVA of beta diversity based on the combined data from the cultivar and soil experiments demonstrated that soil (growing substrate) and plant genotype (cultivar) had significant impacts on the rhizosphere microbial communities of tomato plants (soil, F = 22.29, R2 = 0.7399, p < 0.001; cultivar, F = 2.04, R2 = 0.3223, p = 0.008). Of these two factors, soil explained a larger proportion of the compositional variance in the tomato rhizosphere microbiota. The results demonstrated that the assembly process of rhizosphere bacterial communities was collectively influenced by soil, including the available bacterial sources and biochemical properties of the rhizosphere soils, and plant genotype.
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23
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Honeker LK, Gullo CF, Neilson JW, Chorover J, Maier RM. Effect of Re-acidification on Buffalo Grass Rhizosphere and Bulk Microbial Communities During Phytostabilization of Metalliferous Mine Tailings. Front Microbiol 2019; 10:1209. [PMID: 31214146 PMCID: PMC6554433 DOI: 10.3389/fmicb.2019.01209] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/13/2019] [Indexed: 02/01/2023] Open
Abstract
Phytostabilized highly acidic, pyritic mine tailings are susceptible to re-acidification over time despite initial addition of neutralizing amendments. Studies examining plant-associated microbial dynamics during re-acidification of phytostabilized regions are sparse. To address this, we characterized the rhizosphere and bulk bacterial communities of buffalo grass used in the phytostabilization of metalliferous, pyritic mine tailings undergoing re-acidification at the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, AZ. Plant-associated substrates representing a broad pH range (2.35-7.76) were sampled to (1) compare the microbial diversity and community composition of rhizosphere and bulk compartments across a pH gradient, and (2) characterize how re-acidification affects the abundance and activity of the most abundant plant growth-promoting bacteria (PGPB; including N2-fixing) versus acid-generating bacteria (AGB; including Fe-cycling/S-oxidizing). Results indicated that a shift in microbial diversity and community composition occurred at around pH 4. At higher pH (>4) the species richness and community composition of the rhizosphere and bulk compartments were similar, and PGPB, such as Pseudomonas, Arthrobacter, Devosia, Phyllobacterium, Sinorhizobium, and Hyphomicrobium, were present and active in both compartments with minimal presence of AGB. In comparison, at lower pH (<4) the rhizosphere had a significantly higher number of species than the bulk (p < 0.05) and the compartments had significantly different community composition (unweighted UniFrac; PERMANOVA, p < 0.05). Whereas some PGPB persisted in the rhizosphere at lower pH, including Arthrobacter and Devosia, they were absent from the bulk. Meanwhile, AGB dominated in both compartments; the most abundant were the Fe-oxidizer Leptospirillum and Fe-reducers Acidibacter and Acidiphilium, and the most active was the Fe-reducer Aciditerrimonas. This predominance of AGB at lower pH, and even their minimal presence at higher pH, contributes to acidifying conditions and poses a significant threat to sustainable plant establishment. These findings have implications for phytostabilization field site management and suggest re-application of compost or an alternate buffering material may be required in regions susceptible to re-acidification to maintain a beneficial bacterial community conducive to long-term plant establishment.
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Affiliation(s)
| | | | - Julia W. Neilson
- Department of Soil, Water, and Environmental Science, The University of Arizona, Tucson, AZ, United States
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24
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Abstract
Iron is an essential nutrient for most life on Earth because it functions as a crucial redox catalyst in many cellular processes. However, when present in excess iron can lead to the formation of harmful hydroxyl radicals. Hence, the cellular iron balance must be tightly controlled. Perturbation of iron homeostasis is a major strategy in host-pathogen interactions. Plants use iron-withholding strategies to reduce pathogen virulence or to locally increase iron levels to activate a toxic oxidative burst. Some plant pathogens counteract such defenses by secreting iron-scavenging siderophores that promote iron uptake and alleviate iron-regulated host immune responses. Mutualistic root microbiota can also influence plant disease via iron. They compete for iron with soil-borne pathogens or induce a systemic resistance that shares early signaling components with the root iron-uptake machinery. This review describes the progress in our understanding of the role of iron homeostasis in both pathogenic and beneficial plant-microbe interactions.
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Affiliation(s)
- Eline H Verbon
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3508 TB Utrecht, The Netherlands;
| | - Pauline L Trapet
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3508 TB Utrecht, The Netherlands;
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3508 TB Utrecht, The Netherlands;
| | - Sophie Kruijs
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3508 TB Utrecht, The Netherlands;
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3508 TB Utrecht, The Netherlands;
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3508 TB Utrecht, The Netherlands;
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25
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Shelby N, Hulme PE, van der Putten WH, McGinn KJ, Weser C, Duncan RP. No difference in the competitive ability of introduced and native Trifolium provenances when grown with soil biota from their introduced and native ranges. AoB Plants 2016; 8:plw016. [PMID: 26969431 PMCID: PMC4833883 DOI: 10.1093/aobpla/plw016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
The evolution of increased competitive ability (EICA) hypothesis could explain why some introduced plant species perform better outside their native ranges. The EICA hypothesis proposes that introduced plants escape specialist pathogens or herbivores leading to selection for resources to be reallocated away from defence and towards greater competitive ability. We tested the hypothesis that escape from soil-borne enemies has led to increased competitive ability in three non-agriculturalTrifolium(Fabaceae) species native to Europe that were introduced to New Zealand in the 19th century.Trifoliumperformance is intimately tied to rhizosphere biota. Thus, we grew plants from one introduced (New Zealand) and two native (Spain and the UK) provenances for each of three species in pots inoculated with soil microbiota collected from the rhizosphere beneath conspecifics in the introduced and native ranges. Plants were grown singly and in competition with conspecifics from a different provenance in order to compare competitive ability in the presence of different microbial communities. In contrast to the predictions of the EICA hypothesis, we found no difference in the competitive ability of introduced and native provenances when grown with soil microbiota from either the native or introduced range. Although plants from introduced provenances of two species grew more slowly than native provenances in native-range soils, as predicted by the EICA hypothesis, plants from the introduced provenance were no less competitive than native conspecifics. Overall, the growth rate of plants grown singly was a poor predictor of their competitive ability, highlighting the importance of directly quantifying plant performance in competitive scenarios, rather than relying on surrogate measures such as growth rate.
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Affiliation(s)
- Natasha Shelby
- Bio-Protection Research Centre, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - Philip E Hulme
- Bio-Protection Research Centre, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands Laboratory of Nematology, Wageningen University, PO Box 8123, 6700 ES Wageningen, The Netherlands
| | - Kevin J McGinn
- Bio-Protection Research Centre, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - Carolin Weser
- Bio-Protection Research Centre, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
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