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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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Liang D, Ning Y, Ji C, Zhang Y, Wu H, Ma H, Zhang J, Wang J. Biochar and Manure Co-Application Increases Rice Yield in Low Productive Acid Soil by Increasing Soil pH, Organic Carbon, and Nutrient Retention and Availability. PLANTS (BASEL, SWITZERLAND) 2024; 13:973. [PMID: 38611502 PMCID: PMC11013642 DOI: 10.3390/plants13070973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
In recent years, overuse of chemical fertilization has led to soil acidification and decreased rice yield productivity in southern China. Biochar and manure co-application remediation may have positive effects on rice yield and improve acid paddy soil fertility. This study was conducted to understand the effects of co-application of wood biochar and pig manure on rice yield and acid paddy soil quality (0-40 cm soil layers) in a 5-year field experiment. The experiment consisted of six treatments: no biochar and no fertilizer (CK); biochar only (BC); mineral fertilizer (N); mineral fertilizer combined with biochar (N + BC); manure (25% manure N replacing fertilizer N) combined with mineral fertilizer (MN); and manure combined with mineral fertilizer and biochar (MN + BC). Total nitrogen application for each treatment was the same at 270 kg nitrogen ha-1y-1, and 30 t ha-1 biochar was added to the soil only in the first year. After five years, compared with N treatments, N + BC, MN, and MN + BC treatments increased the rice yield rate to 2.8%, 4.3%, and 6.3%, respectively, by improving soil organic matter, total nitrogen, and available phosphate under a 0-40 cm soil layer. MN + BC had the strongest resistance to soil acidification among all the treatments. The interaction between fertilizers and biochar application was significant (p < 0.05) in rice yield, soil electrical conductivity (10-20 cm), and soil available phosphate (20-40 cm). Principal component analysis indicated that the effect of manure on soil property was stronger than that of biochar in the 0-40 cm soil layer. The overall rice yield and soil fertility decreased in the order of biochar + mineral fertilizer + manure > mineral fertilizer + manure > biochar + mineral fertilizer > mineral fertilizer > biochar > control. These results suggest that biochar and manure co-application is a long-term viable strategy for improving acid soil productivity due to its improvements in soil pH, organic carbon, nutrient retention, and availability.
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Affiliation(s)
- Dong Liang
- Scientific Observatory and Experimental Station of Arable Land Conservation of Jiangsu Province, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (D.L.)
- Key Laboratory of Saline-Alkali Soil improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Yunwang Ning
- Scientific Observatory and Experimental Station of Arable Land Conservation of Jiangsu Province, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (D.L.)
- Key Laboratory of Saline-Alkali Soil improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Cheng Ji
- Scientific Observatory and Experimental Station of Arable Land Conservation of Jiangsu Province, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (D.L.)
- Key Laboratory of Saline-Alkali Soil improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Yongchun Zhang
- Scientific Observatory and Experimental Station of Arable Land Conservation of Jiangsu Province, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (D.L.)
- Key Laboratory of Saline-Alkali Soil improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Huashan Wu
- Scientific Observatory and Experimental Station of Arable Land Conservation of Jiangsu Province, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (D.L.)
- Key Laboratory of Saline-Alkali Soil improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Hongbo Ma
- Scientific Observatory and Experimental Station of Arable Land Conservation of Jiangsu Province, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (D.L.)
- Key Laboratory of Saline-Alkali Soil improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Jianwei Zhang
- Scientific Observatory and Experimental Station of Arable Land Conservation of Jiangsu Province, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (D.L.)
- Key Laboratory of Saline-Alkali Soil improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Jidong Wang
- Scientific Observatory and Experimental Station of Arable Land Conservation of Jiangsu Province, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (D.L.)
- Key Laboratory of Saline-Alkali Soil improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
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Duarte RDC, Iannetta PPM, Gomes AM, Vasconcelos MW. More than a meat- or synthetic nitrogen fertiliser-substitute: a review of legume phytochemicals as drivers of 'One Health' via their influence on the functional diversity of soil- and gut-microbes. FRONTIERS IN PLANT SCIENCE 2024; 15:1337653. [PMID: 38450400 PMCID: PMC10915056 DOI: 10.3389/fpls.2024.1337653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Legumes are essential to healthy agroecosystems, with a rich phytochemical content that impacts overall human and animal well-being and environmental sustainability. While these phytochemicals can have both positive and negative effects, legumes have traditionally been bred to produce genotypes with lower levels of certain plant phytochemicals, specifically those commonly termed as 'antifeedants' including phenolic compounds, saponins, alkaloids, tannins, and raffinose family oligosaccharides (RFOs). However, when incorporated into a balanced diet, such legume phytochemicals can offer health benefits for both humans and animals. They can positively influence the human gut microbiome by promoting the growth of beneficial bacteria, contributing to gut health, and demonstrating anti-inflammatory and antioxidant properties. Beyond their nutritional value, legume phytochemicals also play a vital role in soil health. The phytochemical containing residues from their shoots and roots usually remain in-field to positively affect soil nutrient status and microbiome diversity, so enhancing soil functions and benefiting performance and yield of following crops. This review explores the role of legume phytochemicals from a 'one health' perspective, examining their on soil- and gut-microbial ecology, bridging the gap between human nutrition and agroecological science.
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Affiliation(s)
- Rafael D. C. Duarte
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Pietro P. M. Iannetta
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
- Ecological Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Ana M. Gomes
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Marta W. Vasconcelos
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
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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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Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [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: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
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Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
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Kashiwagi FM, Wendler Miranda B, Maltempi de Souza E, Müller-Santos M. The naringenin-dependent regulator FdeR can be applied as a NIMPLY gate controlled by naringenin and arabinose. Synth Biol (Oxf) 2024; 9:ysae001. [PMID: 38249314 PMCID: PMC10799723 DOI: 10.1093/synbio/ysae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/07/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
The FdeR regulator has been reported as a transcriptional activator dependent on the interaction with naringenin. Previously, FdeR and its cognate promoter were used to construct naringenin-sensitive sensors, though no correlation was associated between the FdeR level of expression and outputs. Therefore, to understand this correlation, we constructed a circuit with FdeR expression adjusted by the arabinose concentration through an AraC-PBAD system and the FdeR-regulated promoter controlling the expression of GFP. We observed a significant reduction in the activity of the target promoter by increasing FdeR expression, indicating that although FdeR has been primarily classified as a transcriptional activator, it also represses transcription. Leveraging the bifunctional feature of FdeR, acting as both transcriptional activator and repressor, we demonstrated that this genetic circuit, when previously switched on by naringenin, can be switched off by inducing an increased FdeR expression level. This engineered system functioned as a NIMPLY gate, effectively decreasing GFP expression by 50% when arabinose was added without removing naringenin from the medium. Exploiting FdeR versatility, this study demonstrates an innovative application of this transcriptional factor for developing novel NIMPLY gates activated by a molecule with low toxicity and nutraceutical properties that may be important for several applications. Graphical Abstract.
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Affiliation(s)
- Fernanda Miyuki Kashiwagi
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Brenno Wendler Miranda
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
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Kumar GA, Kumar S, Bhardwaj R, Swapnil P, Meena M, Seth CS, Yadav A. Recent advancements in multifaceted roles of flavonoids in plant-rhizomicrobiome interactions. FRONTIERS IN PLANT SCIENCE 2024; 14:1297706. [PMID: 38250451 PMCID: PMC10796613 DOI: 10.3389/fpls.2023.1297706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/24/2023] [Indexed: 01/23/2024]
Abstract
The rhizosphere consists of a plethora of microbes, interacting with each other as well as with the plants present in proximity. The root exudates consist of a variety of secondary metabolites such as strigolactones and other phenolic compounds such as coumarin that helps in facilitating communication and forming associations with beneficial microbes in the rhizosphere. Among different secondary metabolites flavonoids (natural polyphenolic compounds) continuously increasing attention in scientific fields for showing several slews of biological activities. Flavonoids possess a benzo-γ-pyrone skeleton and several classes of flavonoids have been reported on the basis of their basic structure such as flavanones, flavonols, anthocyanins, etc. The mutualistic association between plant growth-promoting rhizobacteria (PGPR) and plants have been reported to help the host plants in surviving various biotic and abiotic stresses such as low nitrogen and phosphorus, drought and salinity stress, pathogen attack, and herbivory. This review sheds light upon one such component of root exudate known as flavonoids, which is well known for nodulation in legume plants. Apart from the well-known role in inducing nodulation in legumes, this group of compounds has anti-microbial and antifungal properties helping in establishing defensive mechanisms and playing a major role in forming mycorrhizal associations for the enhanced acquisition of nutrients such as iron and phosphorus. Further, this review highlights the role of flavonoids in plants for recruiting non-mutualistic microbes under stress and other important aspects regarding recent findings on the functions of this secondary metabolite in guiding the plant-microbe interaction and how organic matter affects its functionality in soil.
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Affiliation(s)
- Gokul Anil Kumar
- School of Basic Science, Department of Botany, Central University of Punjab, Bhatinda, Punjab, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Department of Plant Pathology, B.M. College of Agriculture, Khandwa, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, India
| | - Rupesh Bhardwaj
- School of Basic Science, Department of Botany, Central University of Punjab, Bhatinda, Punjab, India
| | - Prashant Swapnil
- School of Basic Science, Department of Botany, Central University of Punjab, Bhatinda, Punjab, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | | | - Ankush Yadav
- School of Basic Science, Department of Botany, Central University of Punjab, Bhatinda, Punjab, India
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Kim J, Lu LC, Gao X, Hofmockel KS, Masiello CA, Silberg JJ. Using Methyl Bromide for Interspecies Cell-Cell Signaling and As a Reporter in a Model Soil Consortium. ACS Synth Biol 2023; 12:3743-3753. [PMID: 37991716 DOI: 10.1021/acssynbio.3c00559] [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] [Indexed: 11/23/2023]
Abstract
Soil microbial communities with reduced complexity are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five-membered MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that V. beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally relevant hydration conditions. We find that methyl halide production can report on an MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. These tools will be useful for future studies that investigate how MSC responds to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.
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Affiliation(s)
- Jiwoo Kim
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Caroline A Masiello
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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Jansson JK, McClure R, Egbert RG. Soil microbiome engineering for sustainability in a changing environment. Nat Biotechnol 2023; 41:1716-1728. [PMID: 37903921 DOI: 10.1038/s41587-023-01932-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/01/2023] [Indexed: 11/01/2023]
Abstract
Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.
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Affiliation(s)
- Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G Egbert
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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Qian X, Tang X, Tian W, Xiao X, Wang Y, Lv Q, Li H, Feng S. Climate factors and host chemical profiles jointly drives the bacterial community assembly in Mussaenda pubescens stems. ENVIRONMENTAL RESEARCH 2023; 235:116687. [PMID: 37467942 DOI: 10.1016/j.envres.2023.116687] [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: 05/15/2023] [Revised: 07/08/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Endophytic bacteria residing within host plants can significantly impact on the host's growth, health, and overall relationship with its surrounding environment. However, the process that shape the community assembly of stem bacterial endophytes (SBEs) remains poorly understood. This study explored the community structure, co-occurrence patterns, and ecological processes of the SBEs inhabiting the shrub host, Mussaenda pubescens, across seven locations in southeastern China. We found that the absolute abundances, alpha diversity, and community composition of SBE communities exhibited notable differences among various host populations. Stem chemical characteristics were the most important factors influencing SBE community distribution, followed by geographic distance and climatic factors. The beta diversity decomposition analyses indicated that SBE community dissimilarities between sites were nearly equally driven by similarity, replacement diversity, and richness difference. The co-occurrence network analysis revealed that the keystone taxa were mostly observed in rare species, which may be essential for preserving the ecosystem's functions. Conditionally abundant taxa (CAT) showcased the highest closeness centrality, while exhibiting the lowest degree centrality and betweenness centrality as opposed to rare taxa. In addition, stochastic processes also played an important role in structuring SBE communities, with ecological drift being the dominant factor for both abundant and rare taxa. This study would deepen our understanding of the ecological dynamics and microbial interactions within plant endophytic microbiomes.
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Affiliation(s)
- Xin Qian
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xinghao Tang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Academy of Forestry Sciences, Fuzhou, 350012, China
| | - Weiwei Tian
- Sichuan Academy of Chinese Medical Sciences, Chengdu, 610041, China
| | - Xiangxi Xiao
- Fujian Academy of Forestry Sciences, Fuzhou, 350012, China
| | - Yonglong Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, 014030, China
| | - Qixin Lv
- Nanjing Agricultural University, Nanjing, 210095, China
| | - Hanzhou Li
- Wuhan Benagen Technology Company, Wuhan, 430000, China
| | - Song Feng
- College of Civil Engineering, Fuzhou University, Fuzhou, 350108, China.
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11
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Chen X, Wang S, Farag MA, Han Z, Chen D, Zhang X, Si J, Wu L. Interactions between endophytic fungus Pestalotiopsis sp. DO14 and Dendrobium catenatum: Deciphering plant polysaccharide and flavonoid accumulation and underlying mechanisms by comparative transcriptome and metabolome analyses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107942. [PMID: 37562204 DOI: 10.1016/j.plaphy.2023.107942] [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: 02/22/2023] [Revised: 07/11/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
Dendrobium catenatum, which belongs to the Orchidaceae family, has been used as a traditional medicine and healthy food in China for over 2000 years, and is of enormous economic value. Polysaccharides and flavonoids are two major functional ingredients in D. catenatum stems that contribute to its health benefits. D. catenatum lives in close association with endophytic fungi, but the literature regarding the further relations between them, especially the fungal-induced accumulation of metabolites in the host plant, is sparse. Our previous study showed that Pestalotiopsis sp. DO14 isolated from D. catenatum improved the host plant growth and metabolite accumulation. This study was performed to investigate dynamic variations of the growth traits, key metabolites (polysaccharides and flavonoids), and expression of key genes of D. catenatum under conditions of the DO14 colonization. Colonization with DO14 promoted D. catenatum growth as indicated by increased leaf area, mid-stem thickness, and plant height. The content of polysaccharides, mannose, and sucrose increased even without DO14 entering the host cells or forming a mature symbiotic relationship concurrent with improved photosynthesis rate. Furthermore, DO14 induced upregulation of genes involved in sugar and flavonoid metabolism, especially phosphoenolpyruvate carboxykinase (PCKA), chalcone synthase (CHS) and UDP-glycose flavonoid glycosyltransferase (UFGT). These observations suggested that endophytic fungi induce the accumulation of polysaccharides and flavonoids by plants, increasing the efficiency of carbon assimilation and carbon turnover. The findings of this study provide insight into the mechanisms underlying Orchidaceae-endophyte interactions, and suggest potential novel applications of endophytic fungi in D. catenatum breeding to improved plant quality.
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Affiliation(s)
- Xueliang Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China
| | - Shuyuan Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China
| | - Mohamed A Farag
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, 11562, Egypt
| | - Zhigang Han
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China
| | - Donghong Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China
| | - Xinfeng Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China
| | - Jinping Si
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China
| | - Lingshang Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China.
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12
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Wang X, Shen C, Chen T, Zhou X, Li Y. Geographical equations of Swertia mussotii bioactivities: evidence from the western Sichuan region of China. FRONTIERS IN PLANT SCIENCE 2023; 14:1112164. [PMID: 37448873 PMCID: PMC10338117 DOI: 10.3389/fpls.2023.1112164] [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: 11/30/2022] [Accepted: 06/07/2023] [Indexed: 07/15/2023]
Abstract
Swertia mussotii is the most authentic raw material used in Tibetan medicine in China for its various bioactivities. This natural medicine resource is at risk of being exhausted due to the double interference of climate change and anthropogenic over-collection. Little is known about habitat characteristics and the crucial environmental factors that influence the levels of active ingredients. The goal of this study is to understand the variability in the bioactive compound content of a wide range of wild S. mussotii as it adapts to changing environmental conditions. The target compound content of the whole plant material was analyzed with the environmental explanatory variables of the field sample sites using a constrained ordination method for their correlation analysis. The results show that 16.3 percent of the sampled wild S. mussotii populations with the highest bioactive content can be grouped into the elite type. The most prominent environmental variables affecting the content of major bioactive products include altitude, aspect, soil TK content, Fe content, and C/N and N/P ratios. Altitude and aspect put indirect effects that are mediated by plant height and density, N/P ratio puts a direct effect, while soil TK content, Fe content and C/N ratio have both direct and indirect effects on the bioactivity of S. mussotii. In addition to the total negative effects of altitude and C/N ratio, the remaining factors play a driving role. These findings demonstrate variation by geographical conditions across S. mussotii accessions for physiologic responses and secondary compounds in wild populations. The knowledge gained from this study can be used for environmental and plant physiology research, efficient collection of naturally active compounds, and conservation strategies for rare natural plant resources.
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Affiliation(s)
- Xiaobo Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
| | - Cheng Shen
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences (CAS), Xining, China
| | - Tao Chen
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences (CAS), Xining, China
| | - Xiaodan Zhou
- Department of Pharmacy, Gansu Provincial Hospital, Lanzhou, China
| | - Yulin Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences (CAS), Xining, China
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13
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Pre-emergent bioherbicide potential of Schinus terebinthifolia Raddi essential oil nanoemulsion for Urochloa brizantha. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2022.102598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Wang L, Chen M, Lam PY, Dini-Andreote F, Dai L, Wei Z. Multifaceted roles of flavonoids mediating plant-microbe interactions. MICROBIOME 2022; 10:233. [PMID: 36527160 PMCID: PMC9756786 DOI: 10.1186/s40168-022-01420-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 11/09/2022] [Indexed: 05/07/2023]
Abstract
Plant-microbe interactions dynamically affect plant growth, health, and development. The mechanisms underpinning these associations are-to a large extent-mediated by specialized host-derived secondary metabolites. Flavonoids are one of the most studied classes of such metabolites, regulating both plant development and the interaction with commensal microbes. Here, we provide a comprehensive review of the multiple roles of flavonoids in mediating plant-microbe interactions. First, we briefly summarize the general aspects of flavonoid synthesis, transport, and exudation in plants. Then, we review the importance of flavonoids regulating plant-microbe interactions and dynamically influencing the overall community assembly of plant-root microbiomes. Last, we highlight potential knowledge gaps in our understanding of how flavonoids determine the interactions between plants and commensal microbes. Collectively, we advocate the importance of advancing research in this area toward innovative strategies to effectively manipulate plant-microbiome composition, in this case, via flavonoid production and exudation in plant roots. Video Abstract.
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Affiliation(s)
- Lanxiang Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Moxian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Pui-Ying Lam
- Center for Crossover Education, Graduate School of Engineering Science, Akita University, Tegata Gakuen-machi 1-1, Akita City, Akita, 010-8502, Japan
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China.
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15
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Ghitti E, Rolli E, Crotti E, Borin S. Flavonoids Are Intra- and Inter-Kingdom Modulator Signals. Microorganisms 2022; 10:microorganisms10122479. [PMID: 36557733 PMCID: PMC9781135 DOI: 10.3390/microorganisms10122479] [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: 10/07/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Flavonoids are a broad class of secondary metabolites with multifaceted functionalities for plant homeostasis and are involved in facing both biotic and abiotic stresses to sustain plant growth and health. Furthermore, they were discovered as mediators of plant networking with the surrounding environment, showing a surprising ability to perform as signaling compounds for a multitrophic inter-kingdom level of communication that influences the plant host at the phytobiome scale. Flavonoids orchestrate plant-neighboring plant allelopathic interactions, recruit beneficial bacteria and mycorrhizal fungi, counteract pathogen outbreak, influence soil microbiome and affect plant physiology to improve its resilience to fluctuating environmental conditions. This review focuses on the diversified spectrum of flavonoid functions in plants under a variety of stresses in the modulation of plant morphogenesis in response to environmental clues, as well as their role as inter-kingdom signaling molecules with micro- and macroorganisms. Regarding the latter, the review addresses flavonoids as key phytochemicals in the human diet, considering their abundance in fruits and edible plants. Recent evidence highlights their role as nutraceuticals, probiotics and as promising new drugs for the treatment of several pathologies.
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16
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Bhatt K, Suyal DC, Kumar S, Singh K, Goswami P. New insights into engineered plant-microbe interactions for pesticide removal. CHEMOSPHERE 2022; 309:136635. [PMID: 36183882 DOI: 10.1016/j.chemosphere.2022.136635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.
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Affiliation(s)
- Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA.
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
| | - Saurabh Kumar
- ICAR-Research Complex for Eastern Region, Patna, 800014, Bihar, India
| | - Kuldeep Singh
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004, India
| | - Priya Goswami
- Department of Biotechnology, Mangalayatan University, Uttar Pradesh, India
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17
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Sridhar S, Ajo-Franklin CM, Masiello CA. A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology. ACS Synth Biol 2022; 11:2909-2916. [PMID: 35961652 PMCID: PMC9486965 DOI: 10.1021/acssynbio.2c00079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microbial biosensors sense and report exposures to stimuli, thereby facilitating our understanding of environmental processes. Successful design and deployment of biosensors hinge on the persistence of the microbial host of the genetic circuit, termed the chassis. However, model chassis organisms may persist poorly in environmental conditions. In contrast, non-model organisms persist better in environmental conditions but are limited by other challenges, such as genetic intractability and part unavailability. Here we identify ecological, metabolic, and genetic constraints for chassis development and propose a conceptual framework for the systematic selection of environmental biosensor chassis. We identify key challenges with using current model chassis and delineate major points of conflict in choosing the most suitable organisms as chassis for environmental biosensing. This framework provides a way forward in the selection of biosensor chassis for environmental synthetic biology.
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Affiliation(s)
- Swetha Sridhar
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United
States,Tel: 713-348-2565.
| | - Caroline M. Ajo-Franklin
- Department
of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Caroline A. Masiello
- Department
of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States,Department
of Earth, Environmental, and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United
States
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18
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Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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19
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Hsu C, Tsai HY, Chang CF, Yang CC, Su NW. Discovery of a novel phosphotransferase from Bacillus subtilis that phosphorylates a broad spectrum of flavonoids. Food Chem 2022; 400:134001. [DOI: 10.1016/j.foodchem.2022.134001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022]
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20
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Zhou J, Huang PW, Li X, Vaistij FE, Dai CC. Generalist endophyte Phomopsis liquidambaris colonization of Oryza sativa L. promotes plant growth under nitrogen starvation. PLANT MOLECULAR BIOLOGY 2022; 109:703-715. [PMID: 35522401 DOI: 10.1007/s11103-022-01268-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Fungal endophytes establish symbiotic relationships with host plants, which results in a mutual growth benefit. However, little is known about the plant genetic response underpinning endophyte colonization. Phomopsis liquidambaris usually lives as an endophyte in a wide range of asymptomatic hosts and promotes biotic and abiotic stress resistance. In this study, we show that under low nitrogen conditions P. liquidambaris promotes rice growth in a hydroponic system, which is free of other microorganisms. In order to gain insights into the mechanisms of plant colonization by P. liquidambaris under low nitrogen conditions, we compared root and shoot transcriptome profiles of root-inoculated rice at different colonization stages. We determined that genes related to plant growth promotion, such as gibberellin and auxin related genes, were up-regulated at all developmental stages both locally and systemically. The largest group of up-regulated genes (in both roots and shoots) were related to flavonoid biosynthesis, which is involved in plant growth as well as antimicrobial compounds. Furthermore, genes encoding plant defense-related endopeptidase inhibitors were strongly up-regulated at the early stage of colonization. Together, these results provide new insights into the molecular mechanisms of plant-microbe mutualism and the promotion of plant growth by a fungal endophyte under nitrogen-deficient conditions.
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Affiliation(s)
- Jun Zhou
- Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
- Centre for Novel Agricultural Products, Department of Biology, University of York, YO10 5DD, York, United Kingdom
| | - Peng-Wei Huang
- Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Xin Li
- Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Fabián E Vaistij
- Centre for Novel Agricultural Products, Department of Biology, University of York, YO10 5DD, York, United Kingdom
| | - Chuan-Chao Dai
- Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
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21
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Abstract
Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil recipe and used these materials to study the abiotic mechanisms driving soil microbial growth and communication. When we used standardized matrices with varying textures to culture gas-reporting biosensors, we found that a Gram-negative bacterium (Escherichia coli) grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while a Gram-positive bacterium (Bacillus subtilis) preferred sandy soils, sporulating at low water potentials. Soil texture, mineralogy, and alkalinity all attenuated the bioavailability of an acyl-homoserine lactone (AHL) signaling molecule that controls community-level microbial behaviors. Texture controlled the timing of AHL sensing, while AHL bioavailability was decreased ~105-fold by mineralogy and ~103-fold by alkalinity. Finally, we built artificial soils with a range of complexities that converge on the properties of one Mollisol. As artificial soil complexity increased to more closely resemble the Mollisol, microbial behaviors approached those occurring in the natural soil, with the notable exception of organic matter. IMPORTANCE Understanding environmental controls on soil microbes is difficult because many abiotic parameters vary simultaneously and uncontrollably when different natural soils are compared, preventing mechanistic determination of any individual soil parameter's effect on microbial behaviors. We describe how soil texture, mineralogy, pH, and organic matter content can be varied individually within artificial soils to study their effects on soil microbes. Using microbial biosensors that report by producing a rare indicator gas, we identify soil properties that control microbial growth and attenuate the bioavailability of a diffusible chemical used to control community-level behaviors. We find that artificial soils differentially affect signal bioavailability and the growth of Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) microbes. These artificial soils are useful for studying the mechanisms that underlie soil controls on microbial fitness, signaling, and gene transfer.
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22
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Dai H, Wu B, Chen B, Ma B, Chu C. Diel Fluctuation of Extracellular Reactive Oxygen Species Production in the Rhizosphere of Rice. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9075-9082. [PMID: 35593708 DOI: 10.1021/acs.est.2c00005] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reactive oxygen species (ROS) are ubiquitous on earth and drive numerous redox-centered biogeochemical processes. The rhizosphere of wetland plants is a highly dynamic interface for the exchange of oxygen and electrons, presenting the basis of the precedent for ROS production, yet whether extracellular ROS are produced in the rhizosphere remains unknown. Here, we designed a microfluidic chip setup to detect in-situ ROS productions in the rhizosphere of rice with spatial and temporal resolutions. Fluorescence imaging clearly displayed the hot spots of ROS generation in the rhizosphere. The formation concentration of the hydroxyl radical (•OH, a representative ROS, 10-6 M) was comparable to those by the classical photochemical route (10-6-10-7 M) in aquatic systems, therefore highlighting the rhizosphere as an unrecognized hotspot for ROS production. Moreover, the rhizosphere ROS production exhibits diel fluctuation, which simultaneously fluctuated with dissolved oxygen, redox potential, and pH, all driven by radial oxygen loss near the root in the daytime. The production and diel fluctuation of ROS were confirmed in the rhizosphere of rice root incubated in natural soils. We demonstrated that the extracellular ROS production was triggered by the interplay between root-released oxygen and microbial respiration released extracellular electrons, while iron mineral and organic matter might play key roles in storing and shuttling electrons. Our results highlight the rhizosphere as a widespread but previously unappreciated hotspot for ROS production, which may affect pollutant redox dynamics and biogeochemical processes in soils.
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Affiliation(s)
- Hengyi Dai
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Binbin Wu
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baoliang Chen
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bin Ma
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Chiheng Chu
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
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23
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Fulk EM, Gao X, Lu LC, Redeker KR, Masiello CA, Silberg JJ. Nondestructive Chemical Sensing within Bulk Soil Using 1000 Biosensors Per Gram of Matrix. ACS Synth Biol 2022; 11:2372-2383. [PMID: 35715210 DOI: 10.1021/acssynbio.2c00083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene expression can be monitored in hard-to-image environmental materials using gas-reporting biosensors, but these outputs have only been applied in autoclaved matrices that are hydrated with rich medium. To better understand the compatibility of indicator gas reporting with environmental samples, we evaluated how matrix hydration affects the gas signal of an engineered microbe added to a sieved soil. A gas-reporting microbe presented a gas signal in a forest soil (Alfisol) when hydrated to an environmentally relevant osmotic pressure. When the gas signal was concentrated prior to analysis, a biosensor titer of 103 cells/gram of soil produced a significant signal when soil was supplemented with halides. A signal was also observed without halide amendment, but a higher cell titer (106 cells/gram of soil) was required. A sugar-regulated gas biosensor was able to report with a similar level of sensitivity when added to an unsterilized soil matrix, illustrating how gas concentration enables biosensing within a soil containing environmental microbes. These results establish conditions where engineered microbes can report on gene expression in living environmental matrices with decreased perturbation of the soil environment compared to previously reported approaches, using biosensor titers that are orders of magnitude lower than the number of cells typically observed in a gram of soil.
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Affiliation(s)
- Emily M Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Kelly R Redeker
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Caroline A Masiello
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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24
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Bag S, Mondal A, Majumder A, Mondal SK, Banik A. Flavonoid mediated selective cross-talk between plants and beneficial soil microbiome. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2022; 21:1739-1760. [PMID: 35221830 PMCID: PMC8860142 DOI: 10.1007/s11101-022-09806-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 01/17/2022] [Indexed: 05/14/2023]
Abstract
UNLABELLED Plants generate a wide variety of organic components during their different growth phases. The majority of those compounds have been classified as primary and secondary metabolites. Secondary metabolites are essential in plants' adaptation to new changing environments and in managing several biotic and abiotic stress. It also invests some of its photosynthesized carbon as secondary metabolites to establish a mutual relationship with soil microorganisms in that specific niche. As soil harbors both pathogenic and beneficial microorganisms, it is essential to identify some specific metabolites that can discriminate beneficial and pathogenic ones. Thus, a detailed understanding of metabolite's architectures that interact with beneficial microorganisms could open a new horizon of ecology and agricultural research. Flavonoids are used as classic examples of secondary metabolites in this study to demonstrate recent developments in understanding and realizing how these valuable metabolites can be controlled at different levels. Most of the research was focused on plant flavonoids, which shield the host plant against competitors or predators, as well as having other ecological implications. Thus, in the present review, our goal is to cover a wide range of functional and signalling activities of secondary metabolites especially, flavonoids mediated selective cross-talk between plant and its beneficial soil microbiome. Here, we have summarized recent advances in understanding the interactions between plant species and their rhizosphere microbiomes through root exudates (flavonoids), with a focus on how these exudates facilitate rhizospheric associations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11101-022-09806-3.
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Affiliation(s)
- Sagar Bag
- Laboratory of Microbial Interaction, School of Biotechnology, Presidency University, Canal Bank Road, DG Block (Newtown), Action Area 1D, Newtown, Kolkata, West Bengal 700156 India
| | - Anupam Mondal
- Laboratory of Microbial Interaction, School of Biotechnology, Presidency University, Canal Bank Road, DG Block (Newtown), Action Area 1D, Newtown, Kolkata, West Bengal 700156 India
| | - Anusha Majumder
- Laboratory of Microbial Interaction, School of Biotechnology, Presidency University, Canal Bank Road, DG Block (Newtown), Action Area 1D, Newtown, Kolkata, West Bengal 700156 India
| | - Sunil Kanti Mondal
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal India
| | - Avishek Banik
- Laboratory of Microbial Interaction, School of Biotechnology, Presidency University, Canal Bank Road, DG Block (Newtown), Action Area 1D, Newtown, Kolkata, West Bengal 700156 India
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Kashiwagi FM, Wendler Miranda B, de Oliveira Pedrosa F, de Souza EM, Müller-Santos M. Control of Gene Expression With Quercetin-Responsive Modular Circuits. Front Bioeng Biotechnol 2021; 9:730967. [PMID: 34604189 PMCID: PMC8481877 DOI: 10.3389/fbioe.2021.730967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Control of gene expression is crucial for several biotechnological applications, especially for implementing predictable and controllable genetic circuits. Such circuits are often implemented with a transcriptional regulator activated by a specific signal. These regulators should work independently of the host machinery, with low gratuitous induction or crosstalk with host components. Moreover, the signal should also be orthogonal, recognized only by the regulator with minimal interference with the host operation. In this context, transcriptional regulators activated by plant metabolites as flavonoids emerge as candidates to control gene expression in bacteria. However, engineering novel circuits requires the characterization of the genetic parts (e.g., genes, promoters, ribosome binding sites, and terminators) in the host of interest. Therefore, we decomposed the QdoR regulatory system of B. subtilis, responsive to the flavonoid quercetin, and reassembled its parts into genetic circuits programmed to have different levels of gene expression and noise dependent on the concentration of quercetin. We showed that only one of the promoters regulated by QdoR worked well in E. coli, enabling the construction of other circuits induced by quercetin. The QdoR expression was modulated with constitutive promoters of different transcriptional strengths, leading to low expression levels when QdoR was highly expressed and vice versa. E. coli strains expressing high and low levels of QdoR were mixed and induced with the same quercetin concentration, resulting in two stable populations expressing different levels of their gene reporters. Besides, we demonstrated that the level of QdoR repression generated different noise levels in gene expression dependent on the concentration of quercetin. The circuits presented here can be exploited in applications requiring adjustment of gene expression and noise using a highly available and natural inducer as quercetin.
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Affiliation(s)
- Fernanda Miyuki Kashiwagi
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Brenno Wendler Miranda
- Biological Sciences Undergraduate Course, Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Fabio de Oliveira Pedrosa
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
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Singh P, Arif Y, Bajguz A, Hayat S. The role of quercetin in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:10-19. [PMID: 34087741 DOI: 10.1016/j.plaphy.2021.05.023] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 05/20/2023]
Abstract
Flavonoids are a special category of hydroxylated phenolic compounds having an aromatic ring structure. Quercetin is aspecial subclass of flavonoid. It is a bioactive natural compound built upon the flavon structure nC6(ring A)-C3(ring C)-C6(ring B). Quercetin facilitates several plant physiological processes, such as seed germination, pollen growth, antioxidant machinery, and photosynthesis, as well as induces proper plant growth and development. Quercetin is a powerful antioxidant, so it potently provides plant tolerance against several biotic and abiotic stresses. This review highlights quercetin's role in increasing several physiological and biochemical processes under stress and non-stress environments. Additionally, this review briefly assesses quercetin's role in mitigating biotic and abiotic stresses (e.g., salt, heavy metal, and UV stress). The biosynthesis of flavonoids, their signaling pathways, and quercetin's role in plant signaling are also discussed.
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Affiliation(s)
- Priyanka Singh
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Yamshi Arif
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Andrzej Bajguz
- Department of Biology and Plant Ecology, Faculty of Biology, University of Bialystok, 1J Ciolkowskiego St., 15-245, Bialystok, Poland
| | - Shamsul Hayat
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
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Reis de Andrade da Silva MS, de Melo Silveira dos Santos B, Hidalgo Chávez DW, de Oliveira R, Barbosa Santos CH, Oliveira EC, Rigobelo EC. K-humate as an agricultural alternative to increase nodulation of soybeans inoculated with Bradyrhizobium. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zhang M, Cai Z, Zhang G, Zhang D, Pan X. Abiotic mechanism changing tetracycline resistance in root mucus layer of floating plant: The role of antibiotic-exudate complexation. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125728. [PMID: 33813291 DOI: 10.1016/j.jhazmat.2021.125728] [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: 11/04/2020] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic contamination and antibiotic resistance have caused growing concerns in different aquatic environments. This work investigated the complexation between tetracycline chloride (TCH) and the molecular weight (MW)-fractionated root exudates - the key abiotic mechanism impacting antibiotic fate and antibiotic resistance in rhizosphere. Results show that the affinity of TCH to the high MW exudates (≥10 kDa) facilitated the TCH deposition on roots and meanwhile reinforced the expression of certain tetracycline resistance genes (i.e. tetA) and the growth of tetracycline resistant bacteria. The interaction between TCH and the lower MW exudates (<10 kDa) completely inhibited the bacteria growth even below the minimum inhibitory concentration of TCH. In microcosms, the abiotic interaction between TCH and root exudates made effects along with biotic processes. Persistent TCH stimulation (≥50 µg/L, 7 d) induced the change of tet gene abundance and bacteria phyla composition though the mediation of root exudates made the rhizosphere less sensitive to the TCH stress. Summarily, the affinity of antibiotics to root exudates varied with MWs, which was closely related to (i) the antibiotic fate in the root mucus layer, (ii) the bacteria inhibition capacity of antibiotics, and (iii) the antibiotic resistance and bacterial community.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhongxia Cai
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Guofu Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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Barra Caracciolo A, Terenzi V. Rhizosphere Microbial Communities and Heavy Metals. Microorganisms 2021; 9:microorganisms9071462. [PMID: 34361898 PMCID: PMC8307176 DOI: 10.3390/microorganisms9071462] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
The rhizosphere is a microhabitat where there is an intense chemical dialogue between plants and microorganisms. The two coexist and develop synergistic actions, which can promote plants’ functions and productivity, but also their capacity to respond to stress conditions, including heavy metal (HM) contamination. If HMs are present in soils used for agriculture, there is a risk of metal uptake by edible plants with subsequent bioaccumulation in humans and animals and detrimental consequences for their health. Plant productivity can also be negatively affected. Many bacteria have defensive mechanisms for resisting heavy metals and, through various complex processes, can improve plant response to HM stress. Bacteria-plant synergic interactions in the rhizosphere, as a homeostatic ecosystem response to HM disturbance, are common in soil. However, this is hard to achieve in agroecosystems managed with traditional practices, because concentrating on maximizing crop yield does not make it possible to establish rhizosphere interactions. Improving knowledge of the complex interactions mediated by plant exudates and secondary metabolites can lead to nature-based solutions for plant health in HM contaminated soils. This paper reports the main ecotoxicological effects of HMs and the various compounds (including several secondary metabolites) produced by plant-microorganism holobionts for removing, immobilizing and containing toxic elements.
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Karst J, Franklin J, Simeon A, Light A, Bennett JA, Erbilgin N. Assessing the dual-mycorrhizal status of a widespread tree species as a model for studies on stand biogeochemistry. MYCORRHIZA 2021; 31:313-324. [PMID: 33829296 DOI: 10.1007/s00572-021-01029-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Viewing plant species by their mycorrhizal type has explained a range of ecosystem processes. However, mycorrhizal type is confounded with plant phylogeny and the environments in which mycorrhizal partners occur. To circumvent these confounding effects, "dual-mycorrhizal" plant species may be potential models for testing the influence of mycorrhizal type on stand biogeochemistry. To assess their use as models, duality in mycorrhizas within a single host species must be confirmed and factors underlying their variation understood. We surveyed roots, soils, and leaves of mature aspen (Populus tremuloides) across 27 stands in western Canada spanning two biomes: boreal forest and parklands. Aspen roots were mostly ectomycorrhizal with sporadic and rare occurrences of arbuscular mycorrhizas. We further tested whether a climate moisture index predicted abundance of ectomycorrhizal roots (number of ectomycorrhizal root tips m-1 root length) surveyed at two depths (0-20 cm and 20-40 cm) and found that ectomycorrhizal root abundance in subsoils (20-40 cm) was positively related to the index. We subsequently examined the relationships between ectomycorrhizal root abundance, leaf traits, and slow and fast pools of soil organic carbon and nitrogen. The ratio of leaf lignin:N, but not its components, increased along with ectomycorrhizal root abundance in subsoils. Soil carbon and nitrogen pools were independent of ectomycorrhizal root abundance. Our results suggest that (1) categorizing aspen as dual-mycorrhizal may overstate the functional importance of arbuscular mycorrhizas in this species and life stage, (2) water availability influences ectomycorrhizal root abundance, and (3) ectomycorrhizal root abundance coincides with leaf quality.
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Affiliation(s)
- Justine Karst
- Department of Renewable Resources, University of Alberta, Edmonton, Canada.
| | - James Franklin
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
| | - Andrea Simeon
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
| | - Ashley Light
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
| | - Jonathan A Bennett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
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31
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Del Valle I, Fulk EM, Kalvapalle P, Silberg JJ, Masiello CA, Stadler LB. Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences. Front Microbiol 2021; 11:618373. [PMID: 33633695 PMCID: PMC7901896 DOI: 10.3389/fmicb.2020.618373] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.
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Affiliation(s)
- Ilenne Del Valle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Emily M. Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Caroline A. Masiello
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, United States
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Akanmu AO, Babalola OO, Venturi V, Ayilara MS, Adeleke BS, Amoo AE, Sobowale AA, Fadiji AE, Glick BR. Plant Disease Management: Leveraging on the Plant-Microbe-Soil Interface in the Biorational Use of Organic Amendments. FRONTIERS IN PLANT SCIENCE 2021; 12:700507. [PMID: 34394153 PMCID: PMC8360880 DOI: 10.3389/fpls.2021.700507] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/07/2021] [Indexed: 05/04/2023]
Abstract
Agriculture is faced with many challenges including loss of biodiversity, chemical contamination of soils, and plant pests and diseases, all of which can directly compromise plant productivity and health. In addition, inadequate agricultural practices which characterize conventional farming play a contributory role in the disruption of the plant-microbe and soil-plant interactions. This review discusses the role of organic amendments in the restoration of soil health and plant disease management. While the use of organic amendments in agriculture is not new, there is a lack of knowledge regarding its safe and proper deployment. Hence, a biorational approach of organic amendment use to achieve sustainable agricultural practices entails the deployment of botanicals, microbial pesticides, and organic minerals as organic amendments for attaining plant fitness and disease suppression. Here, the focus is on the rhizosphere microbial communities. The role of organic amendments in stimulating beneficial microbe quorum formation related to the host-plant-pathogen interactions, and its role in facilitating induced systemic resistance and systemic-acquired resistance against diseases was evaluated. Organic amendments serve as soil conditioners, and their mechanism of action needs to be further elaborated to ensure food safety.
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Affiliation(s)
- Akinlolu Olalekan Akanmu
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- *Correspondence: Olubukola Oluranti Babalola,
| | - Vittorio Venturi
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, Trieste, Italy
| | - Modupe Stella Ayilara
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Bartholomew Saanu Adeleke
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Adenike Eunice Amoo
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | | | - Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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Fulk EM, Huh D, Atkinson JT, Lie M, Masiello CA, Silberg JJ. A Split Methyl Halide Transferase AND Gate That Reports by Synthesizing an Indicator Gas. ACS Synth Biol 2020; 9:3104-3113. [PMID: 33104325 DOI: 10.1021/acssynbio.0c00355] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Monitoring microbial reactions in highly opaque or autofluorescent environments like soils, seawater, and wastewater remains challenging. To develop a simple approach for observing post-translational reactions within microbes situated in environmental matrices, we designed a methyl halide transferase (MHT) fragment complementation assay that reports by synthesizing an indicator gas. We show that backbone fission within regions of high sequence variability in the Rossmann domain yields split MHT (sMHT) AND gates whose fragments cooperatively associate to synthesize CH3Br. Additionally, we identify a sMHT whose fragments require fusion to pairs of interacting partner proteins for maximal activity. We also show that sMHT fragments fused to FKBP12 and the FKBP-rapamycin binding domain of mTOR display significantly enhanced CH3Br production in the presence of rapamycin. This gas production is reversed in the presence of the competitive inhibitor of FKBP12/FKPB dimerization, indicating that sMHT is a reversible reporter of post-translational reactions. This sMHT represents the first genetic AND gate that reports on protein-protein interactions via an indicator gas. Because indicator gases can be measured in the headspaces of complex environmental samples, this assay should be useful for monitoring the dynamics of diverse molecular interactions within microbes situated in hard-to-image marine and terrestrial matrices.
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Affiliation(s)
- Emily M. Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United States
| | - Dongkuk Huh
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Joshua T. Atkinson
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Margaret Lie
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Caroline A. Masiello
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, MS 126, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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Application of biochar and inorganic phosphorus fertilizer influenced rhizosphere soil characteristics, nodule formation and phytoconstituents of cowpea grown on tropical soil. Heliyon 2020; 6:e05255. [PMID: 33088981 PMCID: PMC7566107 DOI: 10.1016/j.heliyon.2020.e05255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/27/2020] [Accepted: 10/09/2020] [Indexed: 11/23/2022] Open
Abstract
The effect of biochar alone or co-applied with triple superphosphate on rhizosphere soil characteristics, nodule formation, phytoconstituents and antioxidant property of cowpea (Vigna uguiculata) is yet to be adequately examined in sub Saharan Africa. A field experiment was conducted where cowpea (Vigna unguiculata) was grown in a tropical sandy loam soil amended with biochar at 1.5 t ha−1 and 2.5 t ha−1 solely or together with inorganic phosphate fertilizer (Triple superphosphate), applied at a rate of 60 kg P ha −1. At 50% flowering, changes in selected rhizosphere soil properties (pH, total nitrogen, available phosphorus, soil organic carbon, cation exchange capacity), nodule count, phytochemicals (phenols, flavonoids, alkaloids, tannins, saponins) and antioxidant property of cowpea roots and leaves were determined by standard laboratory procedures. Differences between means of the measured parameters were established using ANOVA, and relationships among the parameters were explored using Pearson correlation (p < 0.05). Addition of biochar solely or in combination with TSP significantly (p < 0.05) increased soil pH, total nitrogen, available phosphorus, soil organic carbon, cation exchange capacity and root nodule count. Flavonoids, phenols, alkaloids, saponin, tannin contents and antioxidant activity in the roots and leaves were significantly (p < 0.05) higher in the amended soils compared with the unamended soil. Similarly, soil flavonoids, phenols, alkaloids and antioxidant activity were significantly higher in amended soils compared with control. Significant, positive inter and intra correlation with varying strength was found between soil properties, nodule number and phytoconstituents. This is an indication that biochar can be co-applied with triple superphosphate to sustain soil fertility, improve nodulation and enhance concentrations of phytoconstituents in soil, cowpea roots and leaves.
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Flavonoids in Agriculture: Chemistry and Roles in, Biotic and Abiotic Stress Responses, and Microbial Associations. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10081209] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The current world of climate change, global warming and a constantly changing environment have made life very stressful for living entities, which has driven the evolution of biochemical processes to cope with stressed environmental and ecological conditions. As climate change conditions continue to develop, we anticipate more frequent occurrences of abiotic stresses such as drought, high temperature and salinity. Living plants, which are sessile beings, are more exposed to environmental extremes. However, plants are equipped with biosynthetic machinery operating to supply thousands of bio-compounds required for maintaining internal homeostasis. In addition to chemical coordination within a plant, these compounds have the potential to assist plants in tolerating, resisting and escaping biotic and abiotic stresses generated by the external environment. Among certain biosynthates, flavonoids are an important example of these stress mitigators. Flavonoids are secondary metabolites and biostimulants; they play a key role in plant growth by inducing resistance against certain biotic and abiotic stresses. In addition, the function of flavonoids as signal compounds to communicate with rhizosphere microbes is indispensable. In this review, the significance of flavonoids as biostimulants, stress mitigators, mediators of allelopathy and signaling compounds is discussed. The chemical nature and biosynthetic pathway of flavonoid production are also highlighted.
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