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Yan Z, Wei H, Wang H, Ye H. Sediment contamination alters the submersed macrophyte Vallisneria natans and root-associated microbiome profiles during phytoremediation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:117012. [PMID: 39243668 DOI: 10.1016/j.ecoenv.2024.117012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
The submerged plant Vallisneria natans plays an important role in the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sediments. In this study, V. natans and sediments were collected from different V. natans natural vegetation zones, and sediment mesocosms were set up for phytoremediation tests. In addition, commercial-grade V. natans were obtained from the Fish-Bird-Flower market for comparison with phytoremediation. Phytoremediation using V. natans from natural growth significantly increased the degradation of PAHs in Dashui Harbor (0.0148±0.0015 d-1) and Taihu Lake bay sediments (0.0082±0.0010 d-1) but not in commercial-grade V. natans. Transplanted V. natans from natural growth had a significant (p=0.002) effect on PAH degradation, especially in highly PAH-contaminated sedimentary environments. The distinct bacterial communities were strongly affected by sediment type and V. natans type, which contributed to different phytoremediation patterns. Less complex but more stable microbial co-occurrence networks play key roles in improving PAH phytoremediation potential. In addition, V. natans from natural growth in highly PAH-contaminated sediment could adapt to PAH stress by exuding tryptophan metabolites to assemble health-promoting microbiomes. This study provides novel evidence that initial microbial and physicochemical characteristics of sediment and submerged plant types should be considered in the use of bioremediation management strategies for organic pollutant-contaminated sediments.
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Affiliation(s)
- Zaisheng Yan
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Haoming Wei
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hongyang Wang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin 150025, China
| | - Huaxiang Ye
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin 150025, China
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Fang K, Kou YP, Tang N, Liu J, Zhang XY, He HL, Xia RX, Zhao WQ, Li DD, Liu Q. Differential responses of soil bacteria, fungi and protists to root exudates and temperature. Microbiol Res 2024; 286:127829. [PMID: 39018940 DOI: 10.1016/j.micres.2024.127829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/30/2024] [Indexed: 07/19/2024]
Abstract
The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.
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Affiliation(s)
- Kai Fang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; College of Agriculture and Biological Sciences, Dali University, Dali 671003, China
| | - Yong-Ping Kou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
| | - Na Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Jia Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Xiao-Ying Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - He-Liang He
- College of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644007, China
| | - Rui-Xue Xia
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Wen-Qiang Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Dan-Dan Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
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Hao Q, Lyu X, Qin D, Du N, Wu S, Bai S, Chen Z, Wang P, Zhao X. Synergistic mechanisms of denitrification in FeS 2-based constructed wetlands: Effects of organic carbon availability under day-night alterations. BIORESOURCE TECHNOLOGY 2024; 406:131066. [PMID: 38969240 DOI: 10.1016/j.biortech.2024.131066] [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: 05/22/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
In constructed wetlands (CWs), carbon source availability profoundly affected microbial metabolic activities engaged in both iron cycle and nitrogen metabolism. However, research gaps existed in understanding the biotransformation of nitrogen and iron in response to fluctuations in organic carbon content under day-night alterations. Results demonstrated increased removal efficiency of NO3--N (95.7 %) and NH4+-N (75.70 %) under light conditions, attributed to increased total organic carbon (TOC). This enhancement promoted the relative abundance of bacteria involved in nitrogen and iron processes, establishing a more stable microbial network. Elevated TOC content also upregulated genes for iron metabolism and glycolysis, facilitating denitrification. Spearman correlation analysis supported the synergistic mechanisms between FeS2-based autotrophic denitrification and TOC-mediated heterotrophic denitrification under light conditions. The significant impact of carbon sources on microbial activities underscores the critical role of organic carbon availability in enhancing nitrogen removal efficiency, providing valuable insights for optimizing FeS2-based CWs design and operation strategies.
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Affiliation(s)
- Qirui Hao
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiaonan Lyu
- Beijing Aquatic Technology Extension Station, Beijing 100021, China
| | - Dongli Qin
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Ningning Du
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Song Wu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Shuyan Bai
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Zhongxiang Chen
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Peng Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China.
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Griffin C, Oz MT, Demirer GS. Engineering plant-microbe communication for plant nutrient use efficiency. Curr Opin Biotechnol 2024; 88:103150. [PMID: 38810302 DOI: 10.1016/j.copbio.2024.103150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Nutrient availability and efficient use are critical for crop productivity. Current agricultural practices rely on excessive chemical fertilizers, contributing to greenhouse gas emissions and environmental pollution. Rhizosphere microbes facilitate plant nutrient acquisition and contribute to nutrient use efficiency. Thus, engineering plant-microbe communication within the rhizosphere emerges as a promising and sustainable strategy to enhance agricultural productivity. Recent advances in plant engineering have enabled the development of plants capable of selectively enriching beneficial microbes through root exudates. At the same time, synthetic biology techniques have produced microbes capable of improving nutrient availability and uptake by plants. By engineering plant-microbe communication, researchers aim to harness beneficial soil microbes, thereby offering a targeted and efficient approach to optimizing plant nutrient use efficiency.
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Affiliation(s)
- Catherine Griffin
- Department of Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - M Tufan Oz
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Mathieu L, Ballini E, Morel JB, Méteignier LV. The root of plant-plant interactions: Belowground special cocktails. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102547. [PMID: 38749206 DOI: 10.1016/j.pbi.2024.102547] [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: 03/13/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 06/14/2024]
Abstract
Plants interact with each other via a multitude of processes among which belowground communication facilitated by specialized metabolites plays an important but overlooked role. Until now, the exact targets, modes of action, and resulting phenotypes that these metabolites induce in neighboring plants have remained largely unknown. Moreover, positive interactions driven by the release of root exudates are prevalent in both natural field conditions and controlled laboratory environments. In particular, intraspecific positive interactions suggest a genotypic recognition mechanism in addition to non-self perception in plant roots. This review concentrates on recent discoveries regarding how plants interact with one another through belowground signals in intra- and interspecific mixtures. Furthermore, we elaborate on how an enhanced understanding of these interactions can propel the field of agroecology forward.
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Affiliation(s)
- Laura Mathieu
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Elsa Ballini
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Jean-Benoit Morel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Louis-Valentin Méteignier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France.
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Jiang P, Wang Y, Zhang Y, Fei J, Rong X, Peng J, Yin L, Luo G. Intercropping enhances maize growth and nutrient uptake by driving the link between rhizosphere metabolites and microbiomes. THE NEW PHYTOLOGIST 2024; 243:1506-1521. [PMID: 38874414 DOI: 10.1111/nph.19906] [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: 10/24/2023] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields and resource utilization. However, the precise mechanisms through which the interactions between rhizosphere metabolites and the microbiome contribute to plant production remain ambiguous, thus impeding the understanding of the yield-enhancing advantages of intercropping. This study conducted field experiments (initiated in 2013) and pot experiments, coupled with multi-omics analysis, to investigate plant-metabolite-microbiome interactions in the rhizosphere of maize. Field-based data revealed significant differences in metabolite and microbiome profiles between the rhizosphere soils of maize monoculture and intercropping. In particular, intercropping soils exhibited higher microbial diversity and metabolite chemodiversity. The chemodiversity and composition of rhizosphere metabolites were significantly related to the diversity, community composition, and network complexity of soil microbiomes, and this relationship further impacted plant nutrient uptake. Pot-based findings demonstrated that the exogenous application of a metabolic mixture comprising key components enriched by intercropping (soyasapogenol B, 6-hydroxynicotinic acid, lycorine, shikimic acid, and phosphocreatine) significantly enhanced root activity, nutrient content, and biomass of maize in natural soil, but not in sterilized soil. Overall, this study emphasized the significance of rhizosphere metabolite-microbe interactions in enhancing yields in intercropping systems. It can provide new insights into rhizosphere controls within intensive agroecosystems, aiming to enhance crop production and ecosystem services.
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Affiliation(s)
- Pan Jiang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
| | - Yizhe Wang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
| | - Yuping Zhang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jiangchi Fei
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Xiangmin Rong
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jianwei Peng
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Lichu Yin
- College of Resources, Hunan Agricultural University, 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, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
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Rolli E, Ghitti E, Mapelli F, Borin S. Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity. FRONTIERS IN PLANT SCIENCE 2024; 15:1429096. [PMID: 39036359 PMCID: PMC11258928 DOI: 10.3389/fpls.2024.1429096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/13/2024] [Indexed: 07/23/2024]
Abstract
Introduction The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized. Methods Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms. Results Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation. Discussion These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.
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Affiliation(s)
| | | | | | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Trevisan F, Waschgler F, Tiziani R, Cesco S, Mimmo T. Exploring glycine root uptake dynamics in phosphorus and iron deficient tomato plants during the initial stages of plant development. BMC PLANT BIOLOGY 2024; 24:495. [PMID: 38831411 PMCID: PMC11145798 DOI: 10.1186/s12870-024-05120-6] [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: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Phosphorus (P) and iron (Fe) deficiencies are relevant plants nutritional disorders, prompting responses such as increased root exudation to aid nutrient uptake, albeit at an energy cost. Reacquiring and reusing exudates could represent an efficient energy and nitrogen saving strategy. Hence, we investigated the impact of plant development, Fe and P deficiencies on this process. Tomato seedlings were grown hydroponically for 3 weeks in Control, -Fe, and -P conditions and sampled twice a week. We used Isotope Ratio Mass-Spectrometry to measure δ13C in roots and shoots after a 2-h exposure to 13C-labeled glycine (0, 50, or 500 μmol L-1). Plant physiology was assessed with an InfraRed Gas Analyzer and ionome with an Inductively Coupled Plasma Mass-Spectrometry. RESULTS Glycine uptake varied with concentration, suggesting an involvement of root transporters with different substrate affinities. The uptake decreased over time, with -Fe and -P showing significantly higher values as compared to the Control. This highlights its importance during germination and in nutrient-deficient plants. Translocation to shoots declined over time in -P and Control but increased in -Fe plants, suggesting a role of Gly in the Fe xylem transport. CONCLUSIONS Root exudates, i.e. glycine, acquisition and their subsequent shoot translocation depend on Fe and P deficiency. The present findings highlight the importance of this adaptation to nutrient deficiencies, that can potentially enhance plants fitness. A thorough comprehension of this trait holds potential significance for selecting cultivars that can better withstand abiotic stresses.
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Affiliation(s)
- F Trevisan
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Bolzano, 39100, Italy.
| | - F Waschgler
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Bolzano, 39100, Italy
| | - R Tiziani
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Bolzano, 39100, Italy
| | - S Cesco
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Bolzano, 39100, Italy
| | - T Mimmo
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Bolzano, 39100, Italy.
- Competence Centre for Plant Health, Free University of Bolzano, Bolzano, 39100, Italy.
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Du J, Xu B, Ma G, Ma L, Liang J, Li K, Jiao H, Tian B, Li B, Ma L. The impact of benzoic acid and lactic acid on the treatment efficiency and microbial community in the sulfur autotrophic denitrification process. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e11056. [PMID: 38825347 DOI: 10.1002/wer.11056] [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: 03/04/2024] [Revised: 04/26/2024] [Accepted: 05/11/2024] [Indexed: 06/04/2024]
Abstract
Nitrate poses a potential threat to aquatic ecosystems. This study focuses on the sulfur autotrophic denitrification mechanism in the process of water culture wastewater treatment, which has been successfully applied to the degradation of nitrogen in water culture farm effluents. However, the coexistence of organic acids in the treatment process is a common environmental challenge, significantly affecting the activity of denitrifying bacteria. This paper aims to explore the effects of adding benzoic acid and lactic acid on denitrification performance, organic acid removal rate, and microbial population abundance in sulfur autotrophic denitrification systems under optimal operating conditions, sulfur deficiency, and high hydraulic load. In experiments with 50 mg·L-1 of benzoic acid or lactic acid alone, the results show that benzoic acid and lactic acid have a stimulating effect on denitrification activity, with the stimulating effect significantly greater than the inhibitory effect. Under optimal operating conditions, the average denitrification rate of the system remained above 99%; under S/N = 1.5 conditions, the average denitrification rate increased from 88.34% to 91.93% and 85.91%; under HRT = 6 h conditions, the average denitrification rate increased from 75.25% to 97.79% and 96.58%. In addition, the addition of organic acids led to a decrease in microbial population abundance. At the phylum level, Proteobacteria has always been the dominant bacterial genus, and its relative abundance significantly increased after the addition of benzoic acid, from 40.2% to 61.5% and 62.4%. At the genus level, Thiobacillus, Sulfurimonas, Chryseobacterium, and Thermomonas maintained high population abundances under different conditions. PRACTITIONER POINTS: Employing autotrophic denitrification process for treating high-nitrate wastewater. Utilizing organic acids as external carbon sources. Denitrifying bacteria demonstrate high utilization efficiency towards organic acids. Organic acids promote denitrification more than they inhibit it. The promotion is manifested in the enhancement of activity and microbial abundance.
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Affiliation(s)
- Jiancheng Du
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Bing Xu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
- Institute of Resources and Environment, Shandong Jianzhu University, Jinan, China
| | - Guangxiang Ma
- Shandong Environmental Science Society, Jinan, China
| | - Liang Ma
- Shandong Guochen Industrial Group Co., Ltd., Jinan, China
| | - Jinhao Liang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Ke Li
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Hui Jiao
- Shandong Guochen Industrial Group Co., Ltd., Jinan, China
| | - Binbin Tian
- Shandong Guochen Industrial Group Co., Ltd., Jinan, China
| | - Bingxu Li
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Linfeng Ma
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
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Keren G, Yehezkel G, Satish L, Adamov Z, Barak Z, Ben-Shabat S, Kagan-Zur V, Sitrit Y. Root-secreted nucleosides: signaling chemoattractants of rhizosphere bacteria. FRONTIERS IN PLANT SCIENCE 2024; 15:1388384. [PMID: 38799096 PMCID: PMC11120975 DOI: 10.3389/fpls.2024.1388384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/09/2024] [Indexed: 05/29/2024]
Abstract
The rhizosphere is a complex ecosystem, consisting of a narrow soil zone influenced by plant roots and inhabited by soil-borne microorganisms. Plants actively shape the rhizosphere microbiome through root exudates. Some metabolites are signaling molecules specifically functioning as chemoattractants rather than nutrients. These elusive signaling molecules have been sought for several decades, and yet little progress has been made. Root-secreted nucleosides and deoxynucleosides were detected in exudates of various plants by targeted ultra-performance liquid chromatography-mass spectrometry/mass spectrometry. Rhizobacteria were isolated from the roots of Helianthemum sessiliflorum carrying the mycorrhizal desert truffle Terfezia boudieri. Chemotaxis was determined by a glass capillary assay or plate assays on semisolid agar and through a soil plate assay. Nucleosides were identified in root exudates of plants that inhabit diverse ecological niches. Nucleosides induced positive chemotaxis in plant beneficial bacteria Bacillus pumilus, Bacillus subtilis, Pseudomonas turukhanskensis spp., Serratia marcescens, and the pathogenic rhizobacterium Xanthomonas campestris and E coli. In a soil plate assay, nucleosides diffused to substantial distances and evoked chemotaxis under conditions as close as possible to natural environments. This study implies that root-secreted nucleosides are involved in the assembly of the rhizosphere bacterial community by inducing chemotaxis toward plant roots. In animals, nucleoside secretion known as "purinergic signaling" is involved in communication between cells, physiological processes, diseases, phagocytic cell migration, and bacterial activity. The coliform bacterium E. coli that inhabits the lower intestine of warm-blooded organisms also attracted to nucleosides, implying that nucleosides may serve as a common signal for bacterial species inhabiting distinct habitats. Taken together, all these may indicate that chemotaxis signaling by nucleosides is a conserved universal mechanism that encompasses living kingdoms and environments and should be given further attention in plant rhizosphere microbiome research.
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Affiliation(s)
- Guy Keren
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Galit Yehezkel
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lakkakula Satish
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Zahar Adamov
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ze’ev Barak
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shimon Ben-Shabat
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Varda Kagan-Zur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yaron Sitrit
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Katif Research Center for Research & Development, Netivot, Israel
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11
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Zhang G, Bai J, Zhai Y, Jia J, Zhao Q, Wang W, Hu X. Microbial diversity and functions in saline soils: A review from a biogeochemical perspective. J Adv Res 2024; 59:129-140. [PMID: 37392974 PMCID: PMC11081963 DOI: 10.1016/j.jare.2023.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Soil salinization threatens food security and ecosystem health, and is one of the important drivers to the degradation of many ecosystems around the world. Soil microorganisms have extremely high diversity and participate in a variety of key ecological processes. They are important guarantees for soil health and sustainable ecosystem development. However, our understanding of the diversity and function of soil microorganisms under the change of increased soil salinization is fragmented. AIM OF REVIEW Here, we summarize the changes in soil microbial diversity and function under the influence of soil salinization in diverse natural ecosystems. We particularly focus on the diversity of soil bacteria and fungi under salt stress and the changes in their emerging functions (such as their mediated biogeochemical processes). This study also discusses how to use the soil microbiome in saline soils to deal with soil salinization for supporting sustainable ecosystems, and puts forward the knowledge gaps and the research directions that need to be strengthened in the future. KEY SCIENTIFIC CONCEPTS OF REVIEW Due to the rapid development of molecular-based biotechnology (especially high-throughput sequencing technology), the diversity and community composition and functional genes of soil microorganisms have been extensively characterized in different habitats. Clarifying the responding pattern of microbial-mediated nutrient cycling under salt stress and developing and utilizing microorganisms to weaken the adverse effects of salt stress on plants and soil, which are of guiding significance for agricultural production and ecosystem management in saline lands.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China; Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, PR China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China.
| | - Yujia Zhai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou 45003, PR China
| | - Qingqing Zhao
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, PR China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Xingyun Hu
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350007, PR China
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12
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Zhuang Y, Wang H, Tan F, Wu B, Liu L, Qin H, Yang Z, He M. Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108619. [PMID: 38604013 DOI: 10.1016/j.plaphy.2024.108619] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.
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Affiliation(s)
- Yong Zhuang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
| | - Hao Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Furong Tan
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Linpei Liu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Han Qin
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - ZhiJuan Yang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Mingxiong He
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
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13
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Huang F, Lei M, Li W. The rhizosphere and root selections intensify fungi-bacteria interaction in abiotic stress-resistant plants. PeerJ 2024; 12:e17225. [PMID: 38638154 PMCID: PMC11025542 DOI: 10.7717/peerj.17225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024] Open
Abstract
The microbial communities, inhabiting around and in plant roots, are largely influenced by the compartment effect, and in turn, promote the growth and stress resistance of the plant. However, how soil microbes are selected to the rhizosphere, and further into the roots is still not well understood. Here, we profiled the fungal, bacterial communities and their interactions in the bulk soils, rhizosphere soils and roots of eleven stress-resistant plant species after six months of growth. The results showed that the root selection (from the rhizosphere soils to the roots) was stronger than the rhizosphere selection (from the bulk soils to the rhizosphere soils) in: (1) filtering stricter on the fungal (28.5% to 40.1%) and bacterial (48.9% to 68.1%) amplicon sequence variants (ASVs), (2) depleting more shared fungal (290 to 56) and bacterial (691 to 2) ASVs measured by relative abundance, and (3) increasing the significant fungi-bacteria crosskingdom correlations (142 to 110). In addition, the root selection, but not the rhizosphere selection, significantly increased the fungi to bacteria ratios (f:b) of the observed species and shannon diversity index, indicating unbalanced effects to the fungal and bacteria communities exerted by the root selection. Based on the results of network analysis, the unbalanced root selection effects were associated with increased numbers of negative interaction (140 to 99) and crosskingdom interaction (123 to 92), suggesting the root selection intensifies the negative fungi-bacteria interactions in the roots. Our findings provide insights into the complexity of crosskingdom interactions and improve the understanding of microbiome assembly in the rhizosphere and roots.
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Affiliation(s)
- Feng Huang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, Guangdong, China
| | - Mengying Lei
- Guangdong Eco-Engineering Polytechnic, Guangzhou, Guangdong, China
| | - Wen Li
- Key Laboratory of Plant Development and City College of Vocational Technology·Utilization of Ningbo, Ningbo, Zhejiang, China
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14
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Eroğlu ÇG, Bennett AA, Steininger-Mairinger T, Hann S, Puschenreiter M, Wirth J, Gfeller A. Neighbour-induced changes in root exudation patterns of buckwheat results in altered root architecture of redroot pigweed. Sci Rep 2024; 14:8679. [PMID: 38622223 PMCID: PMC11018816 DOI: 10.1038/s41598-024-58687-3] [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: 11/29/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Roots are crucial in plant adaptation through the exudation of various compounds which are influenced and modified by environmental factors. Buckwheat root exudate and root system response to neighbouring plants (buckwheat or redroot pigweed) and how these exudates affect redroot pigweed was investigated. Characterising root exudates in plant-plant interactions presents challenges, therefore a split-root system which enabled the application of differential treatments to parts of a single root system and non-destructive sampling was developed. Non-targeted metabolome profiling revealed that neighbour presence and identity induces systemic changes. Buckwheat and redroot pigweed neighbour presence upregulated 64 and 46 metabolites, respectively, with an overlap of only 7 metabolites. Root morphology analysis showed that, while the presence of redroot pigweed decreased the number of root tips in buckwheat, buckwheat decreased total root length and volume, surface area, number of root tips, and forks of redroot pigweed. Treatment with exudates (from the roots of buckwheat and redroot pigweed closely interacting) on redroot pigweed decreased the total root length and number of forks of redroot pigweed seedlings when compared to controls. These findings provide understanding of how plants modify their root exudate composition in the presence of neighbours and how this impacts each other's root systems.
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Affiliation(s)
- Çağla Görkem Eroğlu
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland
| | - Alexandra A Bennett
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Markus Puschenreiter
- Department of Forest and Soil Sciences, Institute of Soil Research, Rhizosphere Ecology & Biogeochemistry Group, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Judith Wirth
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland
| | - Aurélie Gfeller
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland.
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15
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Fan X, Ge AH, Wang E. Spatially distributed metabolites SWEETen the root for microbes. Cell Host Microbe 2024; 32:445-447. [PMID: 38604122 DOI: 10.1016/j.chom.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024]
Abstract
Limited understanding exists on the spatial configuration of underground plant-microbe interactions. In this issue of Cell Host & Microbe, Loo et al. illustrate the sugar transporter-involved interdependent interaction between root metabolites and microbial spatial colonization, providing insights into metabolic-associated organization of plant-microbe interactions.
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Affiliation(s)
- Xiaoyan Fan
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - An-Hui Ge
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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16
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Sun K, Dai LZ, Chen MH, Si YB, Fang GD, Li SY, Yu HQ. Laccase-induced decontamination and humification mechanisms of estrogen in water-crop matrices. PNAS NEXUS 2024; 3:pgae118. [PMID: 38595803 PMCID: PMC11002785 DOI: 10.1093/pnasnexus/pgae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Enzymatic humification plays a crucial biogeochemical role in eliminating steroidal estrogens and expanding organic carbon stocks. Estrogenic contaminants in agroecosystems can be taken up and acropetally translocated by crops, but the roles of laccase-triggered rhizospheric humification (L-TRH) in pollutant dissipation and plant uptake remain poorly understood. In this study, the laccase-induced decontamination and humification mechanisms of 17β-estradiol (E2) in water-crop media were investigated by performing greenhouse pot experiments with maize seedlings (Zea mays L.). The results demonstrated that L-TRH effectively dissipated E2 in the rhizosphere solution and achieved the kinetic constants of E2 dissipation at 10 and 50 μM by 8.05 and 2.75 times as much as the treatments without laccase addition, respectively. The copolymerization of E2 and root exudates (i.e. phenols and amino acids) consolidated by L-TRH produced a larger amount of humified precipitates with the richly functional carbon architectures. The growth parameters and photosynthetic pigment levels of maize seedlings were greatly impeded after a 120-h exposure to 50 μM E2, but L-TRH motivated the detoxication process and thus mitigated the phytotoxicity and bioavailability of E2. The tested E2 contents in the maize tissues initially increased sharply with the cultivation time but decreased steadily. Compared with the treatment without laccase addition, the uptake and accumulation of E2 in the maize tissues were obviously diminished by L-TRH. E2 oligomers such as dimer, trimer, and tetramer recognized in the rhizosphere solution were also detected in the root tissues but not in the shoots, demonstrating that the acropetal translocation of E2 oligomers was interrupted. These results highlight a promising strategy for decontaminating estrogenic pollutants, boosting rhizospheric humification, and realizing low-carbon emissions, which would be beneficial for agroenvironmental bioremediation and sustainability.
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Affiliation(s)
- Kai Sun
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Ling-Zhi Dai
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Mei-Hua Chen
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - You-Bin Si
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Guo-Dong Fang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shun-Yao Li
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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17
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Saati-Santamaría Z, Flores-Félix JD, Igual JM, Velázquez E, García-Fraile P, Martínez-Molina E. Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host. J Mol Evol 2024; 92:169-180. [PMID: 38502221 PMCID: PMC10978704 DOI: 10.1007/s00239-024-10164-1] [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: 02/15/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
The bacterial strain SECRCQ15T was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15T, we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15T genome. We also found that singletons of F. quinoae SECRCQ15T are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | | | - José M Igual
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain.
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain.
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
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18
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Azri R, Lamine M, Bensalem-Fnayou A, Hamdi Z, Mliki A, Ruiz-Lozano JM, Aroca R. Genotype-Dependent Response of Root Microbiota and Leaf Metabolism in Olive Seedlings Subjected to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:857. [PMID: 38592857 PMCID: PMC10974243 DOI: 10.3390/plants13060857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Under stress or in optimum conditions, plants foster a specific guild of symbiotic microbes to strengthen pivotal functions including metabolic regulation. Despite that the role of the plant genotype in microbial selection is well documented, the potential of this genotype-specific microbial assembly in maintaining the host homeostasis remains insufficiently investigated. In this study, we aimed to assess the specificity of the foliar metabolic response of contrasting olive genotypes to microbial inoculation with wet-adapted consortia of plant-growth-promoting rhizobacteria (PGPR), to see if previously inoculated plants with indigenous or exogenous microbes would display any change in their leaf metabolome once being subjected to drought stress. Two Tunisian elite varieties, Chetoui (drought-sensitive) and Chemleli (drought-tolerant), were tested under controlled and stressed conditions. Leaf samples were analyzed by gas chromatography-mass spectrometry (GC-TOFMS) to identify untargeted metabolites. Root and soil samples were used to extract microbial genomic DNA destined for bacterial community profiling using 16S rRNA amplicon sequencing. Respectively, the score plot analysis, cluster analysis, heat map, Venn diagrams, and Krona charts were applied to metabolic and microbial data. Results demonstrated dynamic changes in the leaf metabolome of the Chetoui variety in both stress and inoculation conditions. Under the optimum state, the PGPR consortia induced noteworthy alterations in metabolic patterns of the sensitive variety, aligning with the phytochemistry observed in drought-tolerant cultivars. These variations involved fatty acids, tocopherols, phenols, methoxyphenols, stilbenoids, triterpenes, and sugars. On the other hand, the Chemleli variety displaying comparable metabolic profiles appeared unaffected by stress and inoculation probably owing to its tolerance capacity. The distribution of microbial species among treatments was distinctly uneven. The tested seedlings followed variety-specific strategies in selecting beneficial soil bacteria to alleviate stress. A highly abundant species of the wet-adapted inoculum was detected only under optimum conditions for both cultivars, which makes the moisture history of the plant genotype a selective driver shaping microbial community and thereby a useful tool to predict microbial activity in large ecosystems.
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Affiliation(s)
- Rahma Azri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
- National Insitute of Applied Science and Technology, University of Carthage, Centre Urbain Nord, BP 676, Charguia Cedex 1080, Tunisia
| | - Myriam Lamine
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Asma Bensalem-Fnayou
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Zohra Hamdi
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Juan Manuel Ruiz-Lozano
- Departament of Microbiology, Soil System and Symbiosis, Zaidín Experimental Station, Spanish Reaserch Council (CSIC), Prof. Albareda 1, 18008 Granada, Spain
| | - Ricardo Aroca
- Departament of Microbiology, Soil System and Symbiosis, Zaidín Experimental Station, Spanish Reaserch Council (CSIC), Prof. Albareda 1, 18008 Granada, Spain
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19
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Yang SH, Shan L, Chu KH. Root exudates enhanced 6:2 FTOH defluorination, altered metabolite profiles and shifted soil microbiome dynamics. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133651. [PMID: 38309165 DOI: 10.1016/j.jhazmat.2024.133651] [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: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
6:2 Fluorotelomer alcohol (FTOH), one of per- and polyfluoroalkyl substances (PFAS), is widely used as a raw material in synthesizing surfactants and fluorinated polymers. However, little is known about the role of root exudates on 6:2 FTOH biodegradation in the rhizosphere. This study examined the effects of root exudates produced from dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) grown under different nutrient conditions (nutrient-rich, sulfur-free, and potassium-free) on 6:2 FTOH biotransformation with or without bioaugmentating agent Rhodococcus jostii RHA1. All the exudates enhanced defluorination of 6:2 FTOH by glucose-grown RHA1. Amendment of dicot or monocot root exudates, regardless of the plant growth conditions, also enhanced 6:2 FTOH biotransformation in soil microcosms. Interestingly, high levels of humic-like substances in the root exudates are linked to high extents of 6:2 FTOH defluorination. Bioaugmenting strain RHA1 along with root exudates facilitated 6:2 FTOH transformation with a production of more diverse metabolites. Microbial community analysis revealed that Rhodococcus was predominant in all strain RHA1 spiked treatments. Different root exudates changed the soil microbiome dynamics. This study provided new insight into 6:2 FTOH biotransformation with different root exudates, suggesting that root exudates amendment and bioaugmentation are promising approaches to promote rhizoremediation for PFAS-contaminated soil.
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Affiliation(s)
- Shih-Hung Yang
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Libo Shan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1085, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, USA.
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20
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Ragland CJ, Shih KY, Dinneny JR. Choreographing root architecture and rhizosphere interactions through synthetic biology. Nat Commun 2024; 15:1370. [PMID: 38355570 PMCID: PMC10866969 DOI: 10.1038/s41467-024-45272-5] [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: 07/17/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.
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Affiliation(s)
- Carin J Ragland
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Y Shih
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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21
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Ghitti E, Rolli E, Vergani L, Borin S. Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400. FRONTIERS IN PLANT SCIENCE 2024; 15:1325048. [PMID: 38371405 PMCID: PMC10869545 DOI: 10.3389/fpls.2024.1325048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Introduction Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress. Methods By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400. Results Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern. Discussions This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.
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Affiliation(s)
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Marschmann GL, Tang J, Zhalnina K, Karaoz U, Cho H, Le B, Pett-Ridge J, Brodie EL. Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model. Nat Microbiol 2024; 9:421-433. [PMID: 38316928 PMCID: PMC10847045 DOI: 10.1038/s41564-023-01582-w] [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: 04/20/2023] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
Abstract
Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.
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Affiliation(s)
- Gianna L Marschmann
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jinyun Tang
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kateryna Zhalnina
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Heejung Cho
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Beatrice Le
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
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Qu M, Cheng X, Xu Q, Zeng Z, Zheng M, Mei Y, Zhao J, Liu G. Fate of glyphosate in lakes with varying trophic levels and its modification by root exudates of submerged macrophytes. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132757. [PMID: 37865072 DOI: 10.1016/j.jhazmat.2023.132757] [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: 06/28/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023]
Abstract
Accelerated eutrophication in lakes reduces the number of submerged macrophytes and alters the residues of glyphosate and its degradation products. However, the effects of submerged macrophytes on the fate of glyphosate remain unclear. We investigated eight lakes with varying trophic levels along the middle and lower reaches of the Yangtze River in China, of which five lakes contained either glyphosate or aminomethylphosphate (AMPA). Glyphosate and AMPA residues were significantly positively correlated with the trophic levels of lakes (P < 0.01). In lakes, glyphosate is degraded through the AMPA and sarcosine pathways. Eight shared glyphosate-degrading enzymes and genes were observed in different lake sediments, corresponding to 44 degrading microorganisms. Glyphosate concentrations in sediments were significantly higher in lakes with lower abundances of soxA (sarcosine oxidase) and soxB (sarcosine oxidase) (P < 0.05). In the presence of submerged macrophytes, oxalic and malonic acids secreted by the roots of submerged macrophytes increased the abundance of glyphosate-degrading microorganisms containing soxA or soxB (P < 0.05). These results revealed that a decrease in the number of submerged macrophytes in eutrophic lakes may inhibit glyphosate degradation via the sarcosine pathway, leading to a decrease in glyphosate degradation and an increase in glyphosate residues.
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Affiliation(s)
- Mengjie Qu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China; State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuan Cheng
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qiang Xu
- School of Management and Economics, Beijing Institute of Technology, Beijing 100081, China
| | - Ziming Zeng
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Mingming Zheng
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yunjun Mei
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jianwei Zhao
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guanglong Liu
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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Novak V, Andeer PF, Bowen BP, Ding Y, Zhalnina K, Hofmockel KS, Tomaka C, Harwood TV, van Winden MCM, Golini AN, Kosina SM, Northen TR. Reproducible growth of Brachypodium in EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation. SCIENCE ADVANCES 2024; 10:eadg7888. [PMID: 38170767 PMCID: PMC10776018 DOI: 10.1126/sciadv.adg7888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew Brachypodium distachyon hydroponically in fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (nitrate, ammonium, and ammonium nitrate), followed by nitrogen starvation. Analyses of exudates with liquid chromatography-tandem mass spectrometry, biomass, medium pH, and nitrogen uptake showed EcoFAB 2.0's low intratreatment data variability. Furthermore, the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids-peptides and alkaloids. Comparatively, nitrogen deficiency decreased nitrogen-containing compounds but increased shikimates-phenylpropanoids. Subsequent bioassays with two shikimates-phenylpropanoids (shikimic and p-coumaric acids) on soil bacteria or Brachypodium seedlings revealed their distinct capacity to regulate both bacterial and plant growth. Our results suggest that (i) Brachypodium alters exudation in response to nitrogen status, which can affect rhizobacterial growth, and (ii) EcoFAB 2.0 is a valuable standardized plant research tool.
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Affiliation(s)
- Vlastimil Novak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter F. Andeer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yezhang Ding
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kirsten S. Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Connor Tomaka
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas V. Harwood
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Amber N. Golini
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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25
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Wang YX, Liu XY, Di HH, He XS, Sun Y, Xiang S, Huang ZB. The mechanism of microbial community succession and microbial co-occurrence network in soil with compost application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167409. [PMID: 37769744 DOI: 10.1016/j.scitotenv.2023.167409] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
The application of organic and chemical fertilizer into soil can regulate microbial communities. However, the response mechanism of microbial communities in soil to compost and chemical fertilizer application remain unclear. In this study, compost made of tobacco leaves individually and combined with chemical fertilizer was applied, respectively, to investigate their effect on soil microorganisms during the pot-culture process. High-throughput sequence, neutral community model and null model were employed to clarify how soil microbial community respond to the application of compost and chemical fertilizer. Furthermore, random forest model was applied to predict the relationships between the plant agronomical traits and the soil microorganism during the pot-culture process. The results demonstrated that the simultaneous application of compost and chemical fertilizer increased significantly the richness and diversity of the microorganisms in soil (p < 0.05), groups C and D led to a significant reduction in the number of nodes and edges in the microbial network (77.78 %-96.57 %). The dominant bacteria in the application of 50 g fertilizer accounted for the highest proportion (40 %) and organic matter was the main factors driving the change in bacterial communities. Compared to the tilled soil, the microbial communities of the soil with the simultaneous application of compost and chemical fertilizer were more susceptible to stochastic processes, and soil microorganisms had less influence on the growth of crops during pot-culture. In conclusion, the simultaneous application of compost and fertilizer altered the ecological functions of soil microbial communities, leading to an enhanced stochastic process of community formation.
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Affiliation(s)
- Yu-Xin Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xie-Yang Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Hui-Hui Di
- Enshi Tobacco Company of Hubei Province Corporation, Enshi 445000, China
| | - Xiao-Song He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yue Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Song Xiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Zhan-Bin Huang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
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26
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Weigh KV, Batista BD, Hoang H, Dennis PG. Characterisation of Soil Bacterial Communities That Exhibit Chemotaxis to Root Exudates from Phosphorus-Limited Plants. Microorganisms 2023; 11:2984. [PMID: 38138128 PMCID: PMC10745596 DOI: 10.3390/microorganisms11122984] [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] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The ability to sense and direct movement along chemical gradients is known as 'chemotaxis' and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change and may recruit symbionts that enhance host stress tolerance. Decoding this language of attraction could support the development of microbiome management strategies that would enhance agricultural production and sustainability. In this study, we employ a culture-independent bait-trap chemotaxis assay to capture microbial communities attracted to root exudates from phosphorus (P)-sufficient and P-deficient Arabidopsis thaliana Col-0 plants. The captured populations were then enumerated and characterised using flow cytometry and phylogenetic marker gene sequencing, respectively. Exudates attracted significantly more cells than the control but did not differ between P treatments. Relative to exudates from P-sufficient plants, those collected from P-deficient plants attracted a significantly less diverse bacterial community that was dominated by members of the Paenibacillus, which is a genus known to include powerful phosphate solubilisers and plant growth promoters. These results suggest that in response to P deficiency, Arabidopsis exudates attract organisms that could help to alleviate nutrient stress.
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Affiliation(s)
| | | | | | - Paul G. Dennis
- School of the Environment, The University of Queensland, Brisbane, QLD 4072, Australia (B.D.B.)
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27
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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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Pena R, Bluhm SL, Ammerschubert S, Agüi-Gonzalez P, Rizzoli SO, Scheu S, Polle A. Mycorrhizal C/N ratio determines plant-derived carbon and nitrogen allocation to symbiosis. Commun Biol 2023; 6:1230. [PMID: 38053000 PMCID: PMC10698078 DOI: 10.1038/s42003-023-05591-7] [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: 06/03/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
Carbon allocation of trees to ectomycorrhizas is thought to shape forest nutrient cycling, but the sink activities of different fungal taxa for host resources are unknown. Here, we investigate fungal taxon-specific differences in naturally composed ectomycorrhizal (EM) communities for plant-derived carbon and nitrogen. After aboveground dual labeling of young beech with 15N and 13C, ectomycorrhizas formed with different fungal taxa exhibit strong differences in label enrichment. Secondary Ion Mass Spectrometry (SIMS) imaging of nitrogen in cross sections of ectomycorrhizas demonstrates plant-derived 15N in both root and fungal structures. Isotope enrichment in ectomycorrhizas correlates with that in the corresponding ectomycorrhiza-attached lateral root, supporting fungal taxon-specific N and C fluxes in ectomycorrhizas. The enrichments with 13C and 15N in the symbiosis decrease with increasing C/N ratio of ectomycorrhizas, converging to zero at high C/N. The relative abundances of EM fungal species on roots are positively correlated with 13C enrichment, demonstrating higher fitness of stronger than of less C-demanding symbioses. Overall, our results support that differences among the C/N ratios in ectomycorrhizas formed with different fungal species regulate the supply of the symbioses with host-derived carbon and provide insights on functional traits of ectomycorrhizas, which are important for major ecosystem processes.
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Affiliation(s)
- Rodica Pena
- Forest Botany and Tree Physiology, University of Göttingen, Göttingen, Germany
- Department of Sustainable Land Management, School of Agriculture Policy and Development, University of Reading, Reading, UK
| | - Sarah L Bluhm
- J.F. Blumenbach Institute of Zoology and Anthropology, Animal Ecology, University of Göttingen, Göttingen, Germany
| | - Silke Ammerschubert
- Forest Botany and Tree Physiology, University of Göttingen, Göttingen, Germany
| | - Paola Agüi-Gonzalez
- Department of Neuro- and Sensory Physiology and Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology and Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, Animal Ecology, University of Göttingen, Göttingen, Germany
- Centre for Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Göttingen, Göttingen, Germany.
- Centre for Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany.
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Adedayo AA, Babalola OO. Genomic mechanisms of plant growth-promoting bacteria in the production of leguminous crops. Front Genet 2023; 14:1276003. [PMID: 38028595 PMCID: PMC10654986 DOI: 10.3389/fgene.2023.1276003] [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: 08/11/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Legumes are highly nutritious in proteins and are good food for humans and animals because of their nutritional values. Plant growth-promoting bacteria (PGPR) are microbes dwelling in the rhizosphere soil of a plant contributing to the healthy status, growth promotion of crops, and preventing the invasion of diseases. Root exudates produced from the leguminous plants' roots can lure microbes to migrate to the rhizosphere region in other to carry out their potential activities which reveals the symbiotic association of the leguminous plant and the PGPR (rhizobia). To have a better cognition of the PGPR in the rhizosphere of leguminous plants, genomic analyses would be conducted employing various genomic sequences to observe the microbial community and their functions in the soil. Comparative genomic mechanism of plant growth-promoting rhizobacteria (PGPR) was discussed in this review which reveals the activities including plant growth promotion, phosphate solubilization, production of hormones, and plant growth-promoting genes required for plant development. Progress in genomics to improve the collection of genotyping data was revealed in this review. Furthermore, the review also revealed the significance of plant breeding and other analyses involving transcriptomics in bioeconomy promotion. This technological innovation improves abundant yield and nutritional requirements of the crops in unfavorable environmental conditions.
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de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
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Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
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31
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Subrahmaniam HJ, Lind Salomonsen C, Radutoiu S, Ehlers BK, Glasius M. Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana. OPEN RESEARCH EUROPE 2023; 3:12. [PMID: 37645513 PMCID: PMC10445920 DOI: 10.12688/openreseurope.15377.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 08/31/2023]
Abstract
Background Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant Arabidopsis thaliana. We highlight key challenges associated with sampling strategies and develop a framework for analyzing both narrow- and broad-scale patterns of root exudate composition in a large set of natural A. thaliana accessions. Methods Our method involves cultivating individual seedlings in vitro inside a plastic mesh, followed by a short hydroponic sampling period in small quantities of ultrapure water. The mesh makes it easy to handle plants of different sizes and allows for large-scale characterization of individual plant root exudates under axenic conditions. This setup can also be easily extended for prolonged temporal exudate collection experiments. Furthermore, the short sampling time minimizes the duration of the experiment while still providing sufficient signal even with small volume of the sampling solution. We used ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for untargeted metabolic profiling, followed by tentative compound identification using MZmine3 and SIRIUS 5 software, to capture a broad overview of root exudate composition in A. thaliana accessions. Results Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software. Conclusions The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.
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Affiliation(s)
- Harihar Jaishree Subrahmaniam
- Department of Ecoscience, Aarhus University, 8000 Aarhus C, Denmark
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics - Plant Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Simona Radutoiu
- Department of Molecular Biology and Genetics - Plant Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Bodil K. Ehlers
- Department of Ecoscience, Aarhus University, 8000 Aarhus C, Denmark
| | - Marianne Glasius
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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Matilla MA, Gavira JA, Krell T. Accessing nutrients as the primary benefit arising from chemotaxis. Curr Opin Microbiol 2023; 75:102358. [PMID: 37459734 DOI: 10.1016/j.mib.2023.102358] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 09/17/2023]
Abstract
About half of the known bacterial species perform chemotaxis that gains them access to sites that are optimal for growth and survival. The motility apparatus and chemotaxis signaling pathway impose a large energetic and metabolic burden on the cell. There is almost no limit to the type of chemoeffectors that are recognized by bacterial chemoreceptors. For example, they include hormones, neurotransmitters, quorum-sensing molecules, and inorganic ions. However, the vast majority of chemoeffectors appear to be of metabolic value. We review here the experimental evidence indicating that accessing nutrients is the main selective force that led to the evolution of chemotaxis.
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Affiliation(s)
- Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José A Gavira
- Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Armilla, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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Wang Z, Liu J, Xu H, Liu J, Zhao Z, Gong X. Core Microbiome and Microbial Community Structure in Coralloid Roots of Cycas in Ex Situ Collection of Kunming Botanical Garden in China. Microorganisms 2023; 11:2144. [PMID: 37763988 PMCID: PMC10537389 DOI: 10.3390/microorganisms11092144] [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] [Received: 07/14/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.
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Affiliation(s)
- Zhaochun Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
| | - Haiyan Xu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhiwei Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
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Yuan T, Ren W, Wang Z, Fry EL, Tang S, Yin J, Zhang J, Jia Z. How does the pattern of root metabolites regulating beneficial microorganisms change with different grazing pressures? FRONTIERS IN PLANT SCIENCE 2023; 14:1180576. [PMID: 37484473 PMCID: PMC10361787 DOI: 10.3389/fpls.2023.1180576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023]
Abstract
Grazing disturbance can change the structure of plant rhizosphere microbial communities and thereby alter the feedback to promote plant growth or induce plant defenses. However, little is known about how such changes occur and vary under different grazing pressures or the roles of root metabolites in altering the composition of rhizosphere microbial communities. In this study, the effects of different grazing pressures on the composition of microbial communities were investigated, and the mechanisms by which different grazing pressures changed rhizosphere microbiomes were explored with metabolomics. Grazing changed composition, functions, and co-expression networks of microbial communities. Under light grazing (LG), some saprophytic fungi, such as Lentinus sp., Ramichloridium sp., Ascobolus sp. and Hyphoderma sp., were significantly enriched, whereas under heavy grazing (HG), potentially beneficial rhizobacteria, such as Stenotrophomonas sp., Microbacterium sp., and Lysobacter sp., were significantly enriched. The beneficial mycorrhizal fungus Schizothecium sp. was significantly enriched in both LG and HG. Moreover, all enriched beneficial microorganisms were positively correlated with root metabolites, including amino acids (AAs), short-chain organic acids (SCOAs), and alkaloids. This suggests that these significantly enriched rhizosphere microbial changes may be caused by these differential root metabolites. Under LG, it is inferred that root metabolites, especially AAs such as L-Histidine, may regulate specific saprophytic fungi to participate in material transformations and the energy cycle and promote plant growth. Furthermore, to help alleviate the stress of HG and improve plant defenses, it is inferred that the root system actively regulates the synthesis of these root metabolites such as AAs, SCOAs, and alkaloids under grazing interference, and then secretes them to promote the growth of some specific plant growth-promoting rhizobacteria and fungi. To summarize, grasses can regulate beneficial microorganisms by changing root metabolites composition, and the response strategies vary under different grazing pressure in typical grassland ecosystems.
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Affiliation(s)
- Ting Yuan
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Weibo Ren
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zhaoming Wang
- Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd., Hohhot, China
| | - Ellen L. Fry
- Department of Biology, Edge Hill University, Ormskirk, United Kingdom
| | - Shiming Tang
- Key Laboratory of Model Innovation in Forage Production Efficiency, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jingjing Yin
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiatao Zhang
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zhenyu Jia
- Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd., Hohhot, China
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Abbas S, Basit F, Tanwir K, Zhu X, Hu J, Guan Y, Hu W, Sheteiwy MS, Yang H, El-Keblawy A, El-Tarabily KA, AbuQamar SF, Lou J. Exogenously applied sodium nitroprusside alleviates nickel toxicity in maize by regulating antioxidant activities and defense-related gene expression. PHYSIOLOGIA PLANTARUM 2023; 175:e13985. [PMID: 37616000 DOI: 10.1111/ppl.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/17/2023] [Accepted: 07/27/2023] [Indexed: 08/25/2023]
Abstract
Nickel (Ni) stress adversely affects plant growth and biomass accumulation, posturing severe menace to crop production and food security. The current study aimed to determine the putative role of sodium nitroprusside (SNP) in mitigating Ni-induced phytotoxicity and identify the underlying defense mechanisms in maize, which are poorly understood. Our findings showed that SNP significantly augmented plant growth, biomass, and photosynthesis-related attributes (Fv/Fm, Fm, qP ETR, and ΦPSII) through diminishing Ni uptake and translocation in root and shoot tissues of maize under Ni stress conditions. In parallel, exogenous SNP substantially relieved maize seedlings from Ni-induced stress by enhancing enzymatic (SOD, CAT, and GPX) and non-enzymatic (phenol and flavonoids) antioxidant defenses and reducing oxidative stress indicators (MDA and H2 O2 ). The results revealed that SNP treatment increased the content of organic osmolyte glycine betaine and the activity of GST, concomitantly with ATP and ionic exchange capacity (including Ca2+ -ATPase and Mg2+ -ATPase), advocating its sufficiency to promote plant growth and avert Ni-induced stress in maize plants. The only exception was the production of organic acids (citric, oxalic, malic, and formic acids), which was reduced as SNP treatment relieved maize seedlings from Ni-induced oxidative damage. The application of SNP also displayed higher expression of defense- and detoxifying-related genes than in control treatments. Together, our data highlighted the mechanism involved in the amelioration of Ni toxicity by SNP; thus, suggesting a potential role of SNP in mitigating the adverse effects of Ni-contaminated soils to boost growth and yield of crop plants, that is, maize.
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Affiliation(s)
- Saghir Abbas
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Farwa Basit
- Hainan Research Institute, Zhejiang University, Sanya, China
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kashif Tanwir
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Xiaobo Zhu
- Hainan Research Institute, Zhejiang University, Sanya, China
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jin Hu
- Hainan Research Institute, Zhejiang University, Sanya, China
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yajing Guan
- Hainan Research Institute, Zhejiang University, Sanya, China
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Weimin Hu
- Hainan Research Institute, Zhejiang University, Sanya, China
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mohamed S Sheteiwy
- Department of Applied Biology, Faculty of Science, University of Sharjah, Sharjah, United Arab Emirates
- Department of Agronomy, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Haishui Yang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ali El-Keblawy
- Department of Applied Biology, Faculty of Science, University of Sharjah, Sharjah, United Arab Emirates
| | - Khaled A El-Tarabily
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Jianfeng Lou
- Shanghai Agro-Technology Extension Service Center, Shanghai, China
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Muhamadali H, Winder CL, Dunn WB, Goodacre R. Unlocking the secrets of the microbiome: exploring the dynamic microbial interplay with humans through metabolomics and their manipulation for synthetic biology applications. Biochem J 2023; 480:891-908. [PMID: 37378961 PMCID: PMC10317162 DOI: 10.1042/bcj20210534] [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: 04/06/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Metabolomics is a powerful research discovery tool with the potential to measure hundreds to low thousands of metabolites. In this review, we discuss the application of GC-MS and LC-MS in discovery-based metabolomics research, we define metabolomics workflows and we highlight considerations that need to be addressed in order to generate robust and reproducible data. We stress that metabolomics is now routinely applied across the biological sciences to study microbiomes from relatively simple microbial systems to their complex interactions within consortia in the host and the environment and highlight this in a range of biological species and mammalian systems including humans. However, challenges do still exist that need to be overcome to maximise the potential for metabolomics to help us understanding biological systems. To demonstrate the potential of the approach we discuss the application of metabolomics in two broad research areas: (1) synthetic biology to increase the production of high-value fine chemicals and reduction in secondary by-products and (2) gut microbial interaction with the human host. While burgeoning in importance, the latter is still in its infancy and will benefit from the development of tools to detangle host-gut-microbial interactions and their impact on human health and diseases.
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Affiliation(s)
- Howbeer Muhamadali
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Catherine L. Winder
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Warwick B. Dunn
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Royston Goodacre
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
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