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Liu Q, Zhu J, Sun M, Song L, Ke M, Ni Y, Fu Z, Qian H, Lu T. Multigenerational Adaptation Can Enhance the Pathogen Resistance of Plants via Changes in Rhizosphere Microbial Community Assembly. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14581-14591. [PMID: 38957087 DOI: 10.1021/acs.jafc.4c02200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Plants withstand pathogen attacks by recruiting beneficial bacteria to the rhizosphere and passing their legacy on to the next generation. However, the underlying mechanisms involved in this process remain unclear. In our study, we combined microbiomic and transcriptomic analyses to reveal how the rhizosphere microbiome assembled through multiple generations and defense-related genes expressed in Arabidopsis thaliana under pathogen attack stress. Our results showed that continuous exposure to the pathogen Pseudomonas syringae pv tomato DC3000 led to improved growth and increased disease resistance in a third generation of rps2 mutant Arabidopsis thaliana. It could be attributed to the enrichment of specific rhizosphere bacteria, such as Bacillus and Bacteroides. Pathways associated with plant immunity and growth in A. thaliana, such as MAPK signaling pathways, phytohormone signal transduction, ABC transporter proteins, and flavonoid biosynthesis, were activated under the influence of rhizosphere bacterial communities. Our findings provide a scientific basis for explaining the relationship between beneficial microbes and defense-related gene expression. Understanding microbial communities and the mechanisms involved in plant responses to disease can contribute to better plant management and reduction of pesticide use.
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Affiliation(s)
- Qiuyun Liu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jichao Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mengyan Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lin Song
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yinhua Ni
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
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2
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Fang X, Zhang M, Zheng P, Wang H, Wang K, Lv J, Shi F. Biochar-bacteria-plant combined potential for remediation of oil-contaminated soil. Front Microbiol 2024; 15:1343366. [PMID: 38835489 PMCID: PMC11148334 DOI: 10.3389/fmicb.2024.1343366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024] Open
Abstract
Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar-bacteria-plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.
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Affiliation(s)
- Xin Fang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Mei Zhang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Pufan Zheng
- Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Research Center of Agricultural Products Preservation Engineering and Technology (Tianjin)), Tianjin, China
| | - Haomin Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Kefan Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Juan Lv
- School of Environmental Science and Engineering, Tiangong University, Tianjin, China
| | - Fuchen Shi
- College of Life Sciences, Nankai University, Tianjin, China
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3
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Li P, Dini-Andreote F, Jiang J. Exploiting microbial competition to promote plant health. TRENDS IN PLANT SCIENCE 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] [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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Wang Y, Zhang Y, Yang Z, Fei J, Zhou X, Rong X, Peng J, Luo G. Intercropping improves maize yield and nitrogen uptake by regulating nitrogen transformation and functional microbial abundance in rhizosphere soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120886. [PMID: 38648726 DOI: 10.1016/j.jenvman.2024.120886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
Intercropping-driven changes in nitrogen (N)-acquiring microbial genomes and functional expression regulate soil N availability and plant N uptake. However, present data seem to be limited to a specific community, obscuring the viewpoint of entire N-acquiring microbiomes and functions. Taking maize intercropped with legumes (peanut and soybean) and non-legumes (gingelly and sweet potato) as models, we studied the effects of intercropping on N transformations and N-acquiring microbiomes in rhizosphere soil across four maize growth stages. Meanwhile, we compiled promising strategies such as random forest analysis and structural equation model for the exploitation of the associations between microbe-driven N dynamics and soil-plant N trade-offs and maize productivity. Compared with monoculture, maize intercropping significantly increased the denitrification rate of rhizosphere soils across four maize growth stages, net N mineralization in the elongation and flowering stages, and the nitrification rate in the seedling and mature stages. The abundance of most N-acquiring microbial populations was influenced significantly by intercropping patterns and maize growth stages. Soil available N components (NH4+-N, NO3--N, and dissolved organic N content) showed a highly direct effect on plant N uptake, which mainly mediated by N transformations (denitrification rate) and N-acquiring populations (amoB, nirK3, and hzsB genes). Overall, the adaptation of N-acquiring microbiomes to changing rhizosphere micro-environments caused by intercropping patterns and maize development could promote soil N transformations and dynamics to meet demand of maize for N nutrient. This would offer another unique perspective to manage the benefits of the highly N-effective and production-effective intercropping ecosystems.
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Affiliation(s)
- Yizhe Wang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Yuping Zhang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
| | - Ziyu Yang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jiangchi Fei
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
| | - Xuan Zhou
- Institute of Soil and Fertilizer, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Xiangmin Rong
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Jianwei Peng
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Gongwen Luo
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
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Jiang Y, Zhang Y, Liu Y, Zhang J, Jiang M, Nong C, Chen J, Hou K, Chen Y, Wu W. Plant Growth-Promoting Rhizobacteria Are Key to Promoting the Growth and Furanocoumarin Synthesis of Angelica dahurica var. formosana under Low-Nitrogen Conditions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6964-6978. [PMID: 38525888 DOI: 10.1021/acs.jafc.3c09655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Microbiomes are the most important members involved in the regulation of soil nitrogen metabolism. Beneficial interactions between plants and microbiomes contribute to improving the nitrogen utilization efficiency. In this study, we investigated the Apiaceae medicinal plant Angelica dahurica var. formosana. We found that under a low-nitrogen treatment, the abundance of carbon metabolites in the rhizosphere secretions of A. dahurica var. formosana significantly increased, thereby promoting the ratio of C to N in rhizosphere and nonrhizosphere soils, increasing carbon sequestration, and shaping the microbial community composition, thus promoting a higher yield and furanocoumarin synthesis. Confirmation through the construction of a synthetic microbial community and feedback experiments indicated that beneficial plant growth-promoting rhizobacteria play a crucial role in improving nitrogen utilization efficiency and selectively regulating the synthesis of target furanocoumarins under low nitrogen conditions. These findings may contribute additional theoretical evidence for understanding the mechanisms of interaction between medicinal plants and rhizosphere microorganisms.
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Affiliation(s)
- Yijie Jiang
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Yunxin Zhang
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Yanan Liu
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Jiaheng Zhang
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Meiyan Jiang
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Changguo Nong
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Jinsong Chen
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Kai Hou
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Yinyin Chen
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Wei Wu
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
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Li X, Wu J, Cheng X, Cai Z, Wang Z, Zhou J. Biodegradable microplastics reduce the effectiveness of biofertilizers by altering rhizospheric microecological functions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120071. [PMID: 38246103 DOI: 10.1016/j.jenvman.2024.120071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
The effectiveness of biofertilizers as a cost-effective crop yield enhancer can be compromised by residual soil pollutants. However, the impact of accumulated polyadipate/butylene terephthalate microplastics (PBAT-MPs) from biodegradable mulch films on biofertilizer application and the consequent growth of crop plants remains unclear. Here, the effects of different levels of PBAT-MPs in soil treated with Bacillus amyloliquefaciens biofertilizer were assessed in a four-week potted experiment. PBAT-MPs significantly decreased the growth-promoting effect of the biofertilizer on Brassica chinensis L., resulting in a notable reduction in both above- and belowground biomass (up to 52.91% and 57.53%, respectively), as well as nitrate and crude fiber contents (up to 12.18% and 13.64%, respectively). In the rhizosphere microenvironment, PBAT-MPs increased soil organic carbon by 2.63-fold and organic matter by 2.68-fold, while enhancing sucrase (from 67.55% to 108.89%) and cellulase (from 31.26% to 49.10%) activities. PBAT-MPs also altered the rhizospheric bacterial community composition/diversity, resulting in more complex microbial networks. With regard to microbial function, PBAT-MPs impacted carbon metabolic function by inhibiting the 3-hydroxypropionate/4-hydroxybutyrate fixation pathway and influencing chitin and lignin degradation processes. Overall, the rhizospheric microbial profiles (composition, function, and network interactions) were the main contributors to plant growth inhibition. This study provides a practical case and theoretical basis for rational use of biodegradable mulch films and indicates that the residue of biodegradable films needs pay attention.
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Affiliation(s)
- Xinyang Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Jialing Wu
- Ecological Fertilizer Research Institute, Shenzhen Batian Ecological Engineering Co., Ltd., Shenzhen, PR China
| | - Xueyu Cheng
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Zhonghua Cai
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Zongkang Wang
- Ecological Fertilizer Research Institute, Shenzhen Batian Ecological Engineering Co., Ltd., Shenzhen, PR China.
| | - Jin Zhou
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China.
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7
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Zhan Y, Zhou Y, Wang E, Miao X, Zhou T, Yan N, Chen C, Li Q. Effects of reductive soil disinfestation combined with different types of organic materials on the microbial community and functions. Microbiol Spectr 2024; 12:e0080223. [PMID: 38230941 PMCID: PMC10846035 DOI: 10.1128/spectrum.00802-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/23/2023] [Indexed: 01/18/2024] Open
Abstract
Reductive soil disinfestation (RSD) is an effective method to inhibit soilborne pathogens. However, it remains unclear how RSD combined with different types of organic materials affects the soil ecosystems of perennial plants. Pot experiments were conducted to investigate the effects of RSD incorporated with perilla (PF), alfalfa (MS), ethanol, and acetic acid on soil properties, enzyme activities, microbial communities and functions, and seedling growth. Results showed that RSD-related treatments improved soil properties and enzyme activities, changed microbial community composition and structure, enhanced microbial interactions and functions, and facilitated seedling growth. Compared with CK, RSD-related treatments increased soil pH, available nitrogen, and available potassium contents, sucrase and catalase activities, and decreased soil electric conductivity values. Meanwhile, RSD-related treatment also significantly reduced the relative abundance of Fusarium while increasing the relative abundance of Arthrobacter, Terrabacter, and Gemmatimonas. The reduction was more evident in PF and MS treatment, suggesting the potential for RSD combined with solid agricultural wastes to suppress pathogens. Furthermore, the microbial network of RSD-related treatment was more complex and interconnected, and the functions related to carbon, nitrogen, sulfur, and hydrogen cycling were significantly increased, while the functions of bacterial and fungal plant pathogens were decreased. Importantly, RSD-related treatments also significantly promoted seed germination and seedling growth. In summary, RSD combined with solid agricultural wastes is better than liquid easily degradable compounds by regulating the composition and function of microbial communities to improve soil quality and promote plant growth.IMPORTANCEReductive soil disinfestation (RSD) is an effective agricultural practice. We found that RSD combined with solid agricultural wastes is better than that of liquid easily degradable compounds, may improve soil quality and microbial community structure, inhibit the proliferation of pathogenic bacteria, and contribute to the growth of replanted crops. Thus, RSD combined with solid agricultural wastes is more effective than liquid easily degradable compounds.
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Affiliation(s)
- Yu Zhan
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Yi Zhou
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, China
| | - Ergang Wang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Xinyue Miao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Tingting Zhou
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Ning Yan
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Changbao Chen
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Qiong Li
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
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Luo X, Sun K, Li HR, Zhang XY, Pan YT, Luo DL, Wu YB, Jiang HJ, Wu XH, Ma CY, Dai CC, Zhang W. Depletion of protective microbiota promotes the incidence of fruit disease. THE ISME JOURNAL 2024; 18:wrae071. [PMID: 38691444 DOI: 10.1093/ismejo/wrae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data, and microbiological culturable approaches, we reported that roots and fruits (pods) of peanut, a typical plant that bears fruits underground, recruit different bacterial and fungal communities independently of cropping conditions and that the incidence of pod disease under monocropping conditions is attributed to the depletion of Bacillus genus and enrichment of Aspergillus genus in geocarposphere. On this basis, we constructed a synthetic community (SynCom) consisting of three Bacillus strains from geocarposphere soil under rotation conditions with high culturable abundance. Comparative transcriptome, microbiome profiling, and plant phytohormone signaling analysis reveal that the SynCom exhibited more effective Aspergillus growth inhibition and pod disease control than individual strain, which was underpinned by a combination of molecular mechanisms related to fungal cell proliferation interference, mycotoxins biosynthesis impairment, and jasmonic acid-mediated plant immunity activation. Overall, our results reveal the filter effect of plant organs on the microbiome and that depletion of key protective microbial community promotes the fruit disease incidence.
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Affiliation(s)
- Xue Luo
- 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, 210023, 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, Jiangsu Province, 210023, China
| | - Hao-Ran Li
- 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, 210023, China
| | - Xiang-Yu 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, 210023, 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, 210023, China
| | - De-Lin Luo
- 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, 210023, China
| | - Yi-Bo Wu
- 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, 210023, 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, 210023, China
| | - Xiao-Han Wu
- 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, 210023, 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, 210023, 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, 210023, 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, 210023, China
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Li T, Li P, Qin W, Wu M, Saleem M, Kuang L, Zhao S, Tian C, Li Z, Jiang J, Chen K, Wang B. Fertilization Weakens the Ecological Succession of Dissolved Organic Matter in Paddy Rice Rhizosphere Soil at the Molecular Level. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19782-19792. [PMID: 37966898 DOI: 10.1021/acs.est.3c05939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Dissolved organic matter (DOM) is involved in numerous biogeochemical processes, and understanding the ecological succession of DOM is crucial for predicting its response to farming (e.g., fertilization) practices. Although plentiful studies have examined how fertilization practice affects the content of soil DOM, it remains unknown how long-term fertilization drives the succession of soil DOM over temporal scales. Here, we investigated the succession of DOM in paddy rice rhizosphere soils subjected to different long-term fertilization treatments (CK: no fertilization; NPK: inorganic fertilization; OM: organic fertilization) along with plant growth. Our results demonstrated that long-term fertilization significantly promoted the molecular chemodiversity of DOM, but it weakened the correlation between DOM composition and plant development. Time-decay analysis indicated that the DOM composition had a shorter halving time under CK treatment (94.7 days), compared to NPK (337.4 days) and OM (223.8 days) treatments, reflecting a lower molecular turnover rate of DOM under fertilization. Moreover, plant development significantly affected the assembly process of DOM only under CK, not under NPK and OM treatments. Taken together, our results demonstrated that long-term fertilization, especially inorganic fertilization, greatly weakens the ecological succession of DOM in the plant rhizosphere, which has a profound implication for understanding the complex plant-DOM interactions.
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Affiliation(s)
- Ting Li
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengfa Li
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, Alabama 36104, United States
| | - Lu Kuang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Chen
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Baozhan Wang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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10
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Andargie YE, Lee G, Jeong M, Tagele SB, Shin JH. Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere. FRONTIERS IN PLANT SCIENCE 2023; 14:1301698. [PMID: 38116158 PMCID: PMC10728675 DOI: 10.3389/fpls.2023.1301698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.
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Affiliation(s)
- Yohannes Ebabuye Andargie
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
- Next Generation Sequencing (NGS) Core Facility, Kyungpook National University, Daegu, Republic of Korea
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Zhang T, Tang H, Peng P, Ge S, Liu Y, Feng Y, Wang J. Sugarcane/soybean intercropping with reduced nitrogen addition promotes photosynthesized carbon sequestration in the soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1282083. [PMID: 38107008 PMCID: PMC10722189 DOI: 10.3389/fpls.2023.1282083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/25/2023] [Indexed: 12/19/2023]
Abstract
Introduction Sugarcane/soybean intercropping with reduced nitrogen (N) addition has improved soil fertility and sustainable agricultural development in China. However, the effects of intercropping pattern and N fertilizer addition on the allocation of photosynthesized carbon (C) in plant-soil system were far less understood. Methods In this study, we performed an 13CO2 pulse labeling experiment to trace C footprints in plant-soil system under different cropping patterns [sugarcane monoculture (MS), sugarcane/soybean intercropping (SB)] and N addition levels [reduced N addition (N1) and conventional N addition (N2)]. Results and discussion Our results showed that compared to sugarcane monoculture, sugarcane/soybean intercropping with N reduced addition increased sugarcane biomass and root/shoot ratio, which in turn led to 23.48% increase in total root biomass. The higher root biomass facilitated the flow of shoot fixed 13C to the soil in the form of rhizodeposits. More than 40% of the retained 13C in the soil was incorporated into the labile C pool [microbial biomass C (MBC) and dissolved organic C (DOC)] on day 1 after labeling. On day 27 after labeling, sugarcane/soybean intercropping with N reduced addition showed the highest 13C content in the MBC as well as in the soil, 1.89 and 1.14 times higher than the sugarcane monoculture, respectively. Moreover, intercropping pattern increased the content of labile C and labile N (alkaline N, ammonium N and nitrate N) in the soil. The structural equation model indicated that the cropping pattern regulated 13C sequestration in the soil mainly by driving changes in labile C, labile N content and root biomass in the soil. Our findings demonstrate that sugarcane/soybean intercropping with reduced N addition increases photosynthesized C sequestration in the soil, enhances the C sink capacity of agroecosystems.
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Affiliation(s)
- Tantan Zhang
- Key Laboratory of Agro-Environments in Tropics, Ministry of Agriculture and Rural Affairs, South China Agriculture University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agriculture University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Hu Tang
- Key Laboratory of Agro-Environments in Tropics, Ministry of Agriculture and Rural Affairs, South China Agriculture University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agriculture University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Peng Peng
- Key Laboratory of Agro-Environments in Tropics, Ministry of Agriculture and Rural Affairs, South China Agriculture University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agriculture University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Shiqiang Ge
- Key Laboratory of Agro-Environments in Tropics, Ministry of Agriculture and Rural Affairs, South China Agriculture University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agriculture University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Yali Liu
- Key Laboratory of Agro-Environments in Tropics, Ministry of Agriculture and Rural Affairs, South China Agriculture University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agriculture University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Yuanjiao Feng
- Key Laboratory of Agro-Environments in Tropics, Ministry of Agriculture and Rural Affairs, South China Agriculture University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agriculture University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jianwu Wang
- Key Laboratory of Agro-Environments in Tropics, Ministry of Agriculture and Rural Affairs, South China Agriculture University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agriculture University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
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Yue L, Jiao L, Tao M, Xu L, Cao X, Chen F, Wang C, Cheng B, Wang Z. Dynamics of organic acid exudation and rhizobacteria in maize rhizosphere respond to N-CDs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166500. [PMID: 37619720 DOI: 10.1016/j.scitotenv.2023.166500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
To sustainably feed the growing global population, it is essential to increase crop yields on limited land while reducing the use of fertilizers and agrochemicals. The rhizosphere regulation shows significant potential to address this challenge. Here, foliar applied doping of nitrogen in carbon dots (N-CDs) entered maize leaves, and were transported to the stems and roots. The internalized N-CDs significantly increased the biomass (26.4-93.8%) and photosynthesis (17.0-20.3 %) of maize seedling during the three-week application of N-CDs, providing the substrate for tricarboxylic acid cycle (TCA) in shoots and roots. Correspondingly, more organic acids involved in TCA cycle, such as citric acid (14.0-fold), succinic acid (4.4-fold) and malic acid (3.4-fold), were synthesized and then secreted into rhizosphere after exposed to N-CDs for one day. As the exposure time increased, greater secretion of above organic acids by the roots was induced. However, no significant change was observed in the relative abundance of rhizobacteria after foliar application with N-CDs for one day. After one week, the relative abundances of Azotobacter, Bacillus, Lysobacter, Mucilaginibacter, and Sphingomonas increased by 0.8-3.8 folds. The relative abundance of more beneficial rhizobacteria (Sphingomonas, Lysobacter, Rhizobium, Azotobacter, Pseudomonas, Mucilaginibacter and Bacillus) enriched by 0.3-6.0 folds after two weeks, and Sphingomonas, Flavisolibacter and Bacillus improved by 0.6-3.2 folds after three weeks. These dynamic changes suggested that N-CDs initiate the synthesis and secretion of organic acids and then recruited beneficial rhizobacteria. The hierarchical partitioning analysis further indicated that N-CDs-induced secretion of organic acids from the roots was the main drivers of rhizobacteria community dynamics. The differential microbes altered by N-CDs were mainly involved in nitrogen (N) and phosphorus (P) cycles, which are beneficial for N and P uptake, and maize growth. These results provide insights into understanding the rhizosphere regulation of nanomaterials to improve plant productivity and nutrient-use efficiency.
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Affiliation(s)
- Le Yue
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Liya Jiao
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Mengna Tao
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Lanqing Xu
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Bingxu Cheng
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China.
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Wu L, Weston LA, Zhu S, Zhou X. Editorial: Rhizosphere interactions: root exudates and the rhizosphere microbiome. FRONTIERS IN PLANT SCIENCE 2023; 14:1281010. [PMID: 37736613 PMCID: PMC10509041 DOI: 10.3389/fpls.2023.1281010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023]
Affiliation(s)
- Linkun Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Leslie A. Weston
- Gulbali Institute for Agriculture, Water and the Environment, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xingang Zhou
- College of Horticulture, Northeast Agricultural University, Xiangfang, Harbin, China
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14
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Tie Z, Wang P, Chen W, Tang B, Yu Y, Liu Z, Zhao S, Khan FH, Zhang X, Xi H. Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars. Front Microbiol 2023; 14:1229454. [PMID: 37637103 PMCID: PMC10450913 DOI: 10.3389/fmicb.2023.1229454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.
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Affiliation(s)
- Zhanjiang Tie
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Peng Wang
- Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang, China
| | - Weijian Chen
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Binghui Tang
- Cotton Research Institute, Shihezi Academy of Agricultural Sciences, Shihezi, Xinjiang, China
| | - Yu Yu
- Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang, China
| | - Zheng Liu
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Sifeng Zhao
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Faisal Hayat Khan
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - XueKun Zhang
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Hui Xi
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
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Mazzio E, Barnes A, Badisa R, Fierros-Romero G, Williams H, Council S, Soliman K. Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae's. J Funct Foods 2023; 107:105687. [PMID: 37654434 PMCID: PMC10469438 DOI: 10.1016/j.jff.2023.105687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Background Humans have been consuming medicinal plants (as herbs/ spices) to combat illness for centuries while ascribing beneficial effects predominantly to the plant/phytochemical constituents, without recognizing the power of obligatory resident microorganism' communities (MOCs) (live/dead bacteria, fungus, yeast, molds etc.) which remain after industrial microbial reduction methods. Very little is known about the taxonomic identity of residual antigenic microbial associated molecular patterns (MAMPs) debris in our botanical over the counter (OTC) products, which if present would be recognized as foreign (non-self) antigenic matter by host pattern recognition receptors (PRRs) provoking a host immune response; this the basis of vaccine adjuvants. As of today, only few research groups have removed the herbal MAMP biomass from herbs, all suggesting that immune activation may not be from the plant but rather its microbial biomass; a hypothesis we corroborate. Purpose The purpose of this work was to conduct a high through put screening (HTPS) of over 2500 natural plants, OTC botanical supplements and phytochemicals to elucidate those with pro-inflammatory; toll like receptor 4 (TLR4) activating properties in macrophages. Study Design The HTPS was conducted on RAW 264.7 cells vs. lipopolysaccharide (LPS) E. coli 0111:B4, testing iNOS / nitric oxide production ( NO 2 - ) as a perimeter endpoint. The data show not a single drug/chemical/ phytochemical and approximately 98 % of botanicals to be immune idle (not effective) with only 65 pro-inflammatory (hits) in a potency range of LPS. Method validation studies eliminated the possibility of false artifact or contamination, and results were cross verified through multiple vendors/ manufacturers/lot numbers by botanical species. Lead botanicals were evaluated for plant concentration of LPS, 1,3:1,6-β-glucan, 1,3:1,4-β-D-glucan and α-glucans; where the former paralleled strength in vitro. LPS was then removed from plants using high-capacity endotoxin poly lysine columns, where bioactivity of LPS null "plant" extracts were lost. The stability of E.Coli 0111:B4 in an acid stomach mimetic model was confirmed. Last, we conducted a reverse culture on aerobic plate counts (APCs) from select hits, with subsequent isolation of gram-negative bacteria (MacConkey agar). Cultures were 1) heat destroyed (retested/ confirming bioactivity) and 2) subject to taxonomical identification by genetic sequencing 18S, ITS1, 5.8 s, ITS2 28S, and 16S. Conclusion The data show significant gram negative MAMP biomass dominance in A) roots (e.g. echinacea, yucca, burdock, stinging nettle, sarsaparilla, hydrangea, poke, madder, calamus, rhaponticum, pleurisy, aconite etc.) and B) oceanic plants / algae's (e.g. bladderwrack, chlorella, spirulina, kelp, and "OTC Seamoss-blends" (irish moss, bladderwrack, burdock root etc), as well as other random herbs (eg. corn silk, cleavers, watercress, cardamom seed, tribulus, duckweed, puffball, hordeum and pollen). The results show a dominance of gram negative microbes (e.g. Klebsilla aerogenes, Pantoae agglomerans, Cronobacter sakazakii), fungus (Glomeracaea, Ascomycota, Irpex lacteus, Aureobasidium pullulans, Fibroporia albicans, Chlorociboria clavula, Aspergillus_sp JUC-2), with black walnut hull, echinacea and burdock root also containing gram positive microbial strains (Fontibacillus, Paenibacillus, Enterococcus gallinarum, Bromate-reducing bacterium B6 and various strains of Clostridium). Conclusion This work brings attention to the existence of a functional immune bioactive herbal microbiome, independent from the plant. There is need to further this avenue of research, which should be carried out with consideration as to both positive or negative consequences arising from daily consumption of botanicals highly laden with bioactive MAMPS.
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Affiliation(s)
- E. Mazzio
- Florida Agricultural and Mechanical University, College of Pharmacy and Pharmaceutical Sciences, Tallahassee, FL 32307, United States
| | - A. Barnes
- Florida Agricultural and Mechanical University, College of Pharmacy and Pharmaceutical Sciences, Tallahassee, FL 32307, United States
| | - R. Badisa
- Florida Agricultural and Mechanical University, College of Pharmacy and Pharmaceutical Sciences, Tallahassee, FL 32307, United States
| | - G. Fierros-Romero
- Florida Agricultural and Mechanical University, School of Environment, Tallahassee, FL 32307, United States
| | - H. Williams
- Florida Agricultural and Mechanical University, School of Environment, Tallahassee, FL 32307, United States
| | - S. Council
- John Gnabre Science Research Institute, Baltimore, MD 21224, United States
| | - K.F.A. Soliman
- Florida Agricultural and Mechanical University, College of Pharmacy and Pharmaceutical Sciences, Tallahassee, FL 32307, United States
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16
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Nadarajah K, Abdul Rahman NSN. The Microbial Connection to Sustainable Agriculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:2307. [PMID: 37375932 DOI: 10.3390/plants12122307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.
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Affiliation(s)
- Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Nur Sabrina Natasha Abdul Rahman
- Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
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Liu J, Wu L, Gong L, Wu Y, Tanentzap AJ. Phototrophic Biofilms Transform Soil-Dissolved Organic Matter Similarly Despite Compositional and Environmental Differences. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4679-4689. [PMID: 36893311 DOI: 10.1021/acs.est.2c08541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Dissolved organic matter (DOM) is the most reactive pool of organic carbon in soil and one of the most important components of the global carbon cycle. Phototrophic biofilms growing at the soil-water interface in periodically flooding-drying soils like paddy fields consume and produce DOM during their growth and decomposition. However, the effects of phototrophic biofilms on DOM remain poorly understood in these settings. Here, we found that phototrophic biofilms transformed DOM similarly despite differences in soil types and initial DOM compositions, with stronger effects on DOM molecular composition than soil organic carbon and nutrient contents. Specifically, growth of phototrophic biofilms, especially those genera belonging to Proteobacteria and Cyanobacteria, increased the abundance of labile DOM compounds and richness of molecular formulae, while biofilm decomposition decreased the relative abundance of labile components. After a growth and decomposition cycle, phototrophic biofilms universally drove the accumulation of persistent DOM compounds in soil. Our results revealed how phototrophic biofilms shape the richness and changes in soil DOM at the molecular level and provide a reference for using phototrophic biofilms to increase DOM bioactivity and soil fertility in agricultural settings.
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Affiliation(s)
- Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
| | - Lirong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Gong
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, School of the Environment, Trent University, Peterborough, Ontario K9L 0G2, Canada
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, U.K
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Kuang L, Li T, Wang B, Peng J, Li J, Li P, Jiang J. Diseased-induced multifaceted variations in community assembly and functions of plant-associated microbiomes. Front Microbiol 2023; 14:1141585. [PMID: 37007500 PMCID: PMC10060855 DOI: 10.3389/fmicb.2023.1141585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Plant-associated microorganisms are believed to be part of the so-called extended plant phenotypes, affecting plant growth and health. Understanding how plant-associated microorganisms respond to pathogen invasion is crucial to controlling plant diseases through microbiome manipulation. In this study, healthy and diseased (bacterial wilt disease, BWD) tomato (Solanum lycopersicum L.) plants were harvested, and variations in the rhizosphere and root endosphere microbial communities were subsequently investigated using amplicon and shotgun metagenome sequencing. BWD led to a significant increase in rhizosphere bacterial diversity in the rhizosphere but reduced bacterial diversity in the root endosphere. The ecological null model indicated that BWD enhanced the bacterial deterministic processes in both the rhizosphere and root endosphere. Network analysis showed that microbial co-occurrence complexity was increased in BWD-infected plants. Moreover, higher universal ecological dynamics of microbial communities were observed in the diseased rhizosphere. Metagenomic analysis revealed the enrichment of more functional gene pathways in the infected rhizosphere. More importantly, when tomato plants were infected with BWD, some plant-harmful pathways such as quorum sensing were significantly enriched, while some plant-beneficial pathways such as streptomycin biosynthesis were depleted. These findings broaden the understanding of plant–microbiome interactions and provide new clues to the underlying mechanism behind the interaction between the plant microbiome and BWD.
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Affiliation(s)
- Lu Kuang
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ting Li
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baozhan Wang
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Junwei Peng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiangang Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Pengfa Li
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Pengfa Li
| | - Jiandong Jiang
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiandong Jiang
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Zhang L, Bai J, Zhang K, Wei Z, Wang Y, Liu H, Xiao R, Jorquera MA. Characterizing bacterial communities in Phragmites australis rhizosphere and non-rhizosphere sediments under pressure of antibiotics in a shallow lake. Front Microbiol 2022; 13:1092854. [PMID: 36560949 PMCID: PMC9763296 DOI: 10.3389/fmicb.2022.1092854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Antibiotics are ubiquitous pollutants and widely found in aquatic ecosystems, which of rhizosphere sediment and rhizosphere bacterial communities had certain correlation. However, the response of bacterial communities in Phragmites australis rhizosphere and non-rhizosphere sediments to antibiotics stress is still poorly understood. Methods To address this knowledge gap, the samples of rhizosphere (R) and non-rhizosphere (NR) sediments of P. australis were collected to investigate the differences of bacterial communities under the influence of antibiotics and key bacterial species and dominate environmental factors in Baiyangdian (BYD) Lake. Results The results showed that the contents of norfloxacin (NOR), ciprofloxacin (CIP) and total antibiotics in rhizosphere sediments were significantly higher than that in non-rhizosphere sediments, meanwhile, bacterial communities in non-rhizosphere sediments had significantly higher diversity (Sobs, Shannon, Simpsoneven and PD) than those in rhizosphere sediments. Furthermore, total antibiotics and CIP were found to be the most important factors in bacterial diversity. The majority of the phyla in rhizosphere sediments were Firmicutes, Proteobacteria and Campilobacterota, while Proteobacteria, Chloroflexi was the most abundant phyla followed by Bacteroidota, Actinobacteriota in non-rhizosphere sediments. The dominate factors of shaping the bacterial communities in rhizosphere were total antibiotics, pH, sediment organic matter (SOM), and NH4-N, while dissolved organic carbon (DOC), NO3-N, pH, and water contents (WC) in non-rhizosphere sediments. Discussion It is suggested that antibiotics may have a substantial effect on bacterial communities in P. australis rhizosphere sediment, which showed potential risk for ARGs selection pressure and dissemination in shallow lake ecosystems.
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Affiliation(s)
- Ling Zhang
- School of Environment, Beijing Normal University, Beijing, China,School of Chemistry and Chemical Engineering, Qinghai Normal University, Xining, China
| | - Junhong Bai
- School of Environment, Beijing Normal University, Beijing, China,*Correspondence: Junhong Bai,
| | - Kegang Zhang
- Department of Environmental Engineering and Science, North China Electric Power University, Baoding, China
| | - Zhuoqun Wei
- School of Environment, Beijing Normal University, Beijing, China
| | - Yaqi Wang
- School of Environment, Beijing Normal University, Beijing, China
| | - Haizhu Liu
- School of Environment, Beijing Normal University, Beijing, China
| | - Rong Xiao
- College of Environment and Safety Engineering, FuZhou University, Fuzhou, China
| | - Milko A. Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
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