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Kumar N, Jaitak V. Recent Advancement in NMR Based Plant Metabolomics: Techniques, Tools, and Analytical Approaches. Crit Rev Anal Chem 2024:1-25. [PMID: 38990786 DOI: 10.1080/10408347.2024.2375314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Plant metabolomics, a rapidly advancing field within plant biology, is dedicated to comprehensively exploring the intricate array of small molecules in plant systems. This entails precisely gathering comprehensive chemical data, detecting numerous metabolites, and ensuring accurate molecular identification. Nuclear magnetic resonance (NMR) spectroscopy, with its detailed chemical insights, is crucial in obtaining metabolite profiles. Its widespread application spans various research disciplines, aiding in comprehending chemical reactions, kinetics, and molecule characterization. Biotechnological advancements have further expanded NMR's utility in metabolomics, particularly in identifying disease biomarkers across diverse fields such as agriculture, medicine, and pharmacology. This review covers the stages of NMR-based metabolomics, including historical aspects and limitations, with sample preparation, data acquisition, spectral processing, analysis, and their application parts.
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Affiliation(s)
- Nitish Kumar
- Department of Pharmaceutical Science and Natural Products, Central University of Punjab, Bathinda, India
| | - Vikas Jaitak
- Department of Pharmaceutical Science and Natural Products, Central University of Punjab, Bathinda, India
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Liu X, Laipan M, Zhang C, Zhang M, Wang Z, Yuan M, Guo J. Microbial weathering of montmorillonite and its implication for Cd(II) immobilization. CHEMOSPHERE 2024; 349:140850. [PMID: 38043615 DOI: 10.1016/j.chemosphere.2023.140850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
Interactions between silicate bacteria and silicates are very common in nature and hold great potential in altering their mutual physicochemical properties. But their interactions in regulating contaminants remediation involving performance and mechanisms are often overlooked. Here, we focused on the interactions between silicate bacteria (Paenibacillus polymyxa, PP; Bacillus circulans, BC) and a soil silicate montmorillonite (Mt), and their impact on Cd(II) immobilization. The obtained results showed that Mt greatly promoted the growth of the bacteria, resulting in a maximum 10.31 times increase in biomass production. In return, the bacteria strongly enhanced the Cd(II) adsorption on Mt, with adsorption capacities increased by 80.61%-104.45% in comparison to the raw Mt. Additionally, the bacteria-Mt interaction changed Cd(II) to a more stabilized state with a maximum reduction of 38.90%/g Mt in bioavailability. The enhancement of Cd(II) adsorption and immobilization on the bacterial modified Mt was caused by the following aspects: (1) the bacteria activities altered the aggregation state of Mt and made it better dispersed, thus more active sites were exposed; (2) the microbial activities brought about more rough and crumpled surface, as well as smaller Mt fragments; (3) a variety of microbial-derived functional groups were introduced onto the Mt surface, increasing its affinity for heavy metals; (4) the main Cd(II) immobilization mechanism was changed from ion exchange to the combination of ion exchange and functional groups induced adsorption. This work elucidates the potential ecological and evolutionary processes of silicate bacteria-soil clay mineral interactions, and bears direct implications for the clay-mediated bioremediation of heavy metals in natural environments.
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Affiliation(s)
- Xun Liu
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Minwang Laipan
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
| | - Chao Zhang
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Min Zhang
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Ziyu Wang
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Mengyao Yuan
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Junkang Guo
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
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Wu S, Bougoure J, Wang J, Thomsen L, Chan TS, Yi Q, Li Z, Southam G, Huang L. Nitrogen-Rich Organic Matter Formation and Stabilization in Iron Ore Tailings: A Submicrometer Investigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12325-12338. [PMID: 37574860 DOI: 10.1021/acs.est.3c03011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Organic matter (OM) formation and stabilization are critical processes in the eco-engineered pedogenesis of Fe ore tailings, but the underlying mechanisms are unclear. The present 12 month microcosm study has adopted nanoscale secondary ion mass spectrometry (NanoSIMS) and synchrotron-based scanning transmission X-ray microscopy (STXM) techniques to investigate OM formation, molecular signature, and stabilization in tailings at micro- and nanometer scales. In this system, microbial processing of exogenous isotopically labeled OM demonstrated that 13C labeled glucose and 13C/15N labeled plant biomass were decomposed, regenerated, and associated with Fe-rich minerals in a heterogeneous pattern in tailings. Particularly, when tailings were amended with plant biomass, the 15N-rich microbially derived OM was generated and bound to minerals to form an internal organo-mineral association, facilitating further OM stabilization. The organo-mineral associations were primarily underpinned by interactions of carboxyl, amide, aromatic, and/or aliphatic groups with weathered mineral products derived from biotite-like minerals in fresh tailings (i.e., with Fe2+ and Fe3+) or with Fe3+ oxyhydroxides in aged tailings. The study revealed microbial OM generation and subsequent organo-mineral association in Fe ore tailings at the submicrometer scale during early stages of eco-engineered pedogenesis, providing a basis for the development of microbial based technologies toward tailings' ecological rehabilitation.
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Affiliation(s)
- Songlin Wu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia
| | - Jian Wang
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - Lars Thomsen
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Ting-Shan Chan
- National Synchrotron Radiation Research Centre, Hsinchu Science Park, Hsinchu 30092, Taiwan
| | - Qing Yi
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Zhen Li
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gordon Southam
- School of Earth & Environmental Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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Ghio AJ, Pavlisko EN, Roggli VL, Todd NW, Sangani RG. Cigarette Smoke Particle-Induced Lung Injury and Iron Homeostasis. Int J Chron Obstruct Pulmon Dis 2022; 17:117-140. [PMID: 35046648 PMCID: PMC8763205 DOI: 10.2147/copd.s337354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022] Open
Abstract
It is proposed that the mechanistic basis for non-neoplastic lung injury with cigarette smoking is a disruption of iron homeostasis in cells after exposure to cigarette smoke particle (CSP). Following the complexation and sequestration of intracellular iron by CSP, the host response (eg, inflammation, mucus production, and fibrosis) attempts to reverse a functional metal deficiency. Clinical manifestations of this response can present as respiratory bronchiolitis, desquamative interstitial pneumonitis, pulmonary Langerhans’ cell histiocytosis, asthma, pulmonary hypertension, chronic bronchitis, and pulmonary fibrosis. If the response is unsuccessful, the functional deficiency of iron progresses to irreversible cell death evident in emphysema and bronchiectasis. The subsequent clinical and pathological presentation is a continuum of lung injuries, which overlap and coexist with one another. Designating these non-neoplastic lung injuries after smoking as distinct disease processes fails to recognize shared relationships to each other and ultimately to CSP, as well as the common mechanistic pathway (ie, disruption of iron homeostasis).
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Affiliation(s)
- Andrew J Ghio
- Human Studies Facility, US Environmental Protection Agency, Chapel Hill, NC, 27514, USA
- Correspondence: Andrew J Ghio Human Studies Facility, US Environmental Protection Agency, 104 Mason Farm Road, Chapel Hill, NC, USA Email
| | | | | | - Nevins W Todd
- Department of Medicine, University of Maryland, Baltimore, MD, 21201, USA
| | - Rahul G Sangani
- Department of Medicine, West Virginia University, Morgantown, WV, USA
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Lybrand RA, Austin JC, Fedenko J, Gallery RE, Rooney E, Schroeder PA, Zaharescu DG, Qafoku O. A coupled microscopy approach to assess the nano-landscape of weathering. Sci Rep 2019; 9:5377. [PMID: 30926847 PMCID: PMC6441011 DOI: 10.1038/s41598-019-41357-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/04/2019] [Indexed: 11/08/2022] Open
Abstract
Mineral weathering is a balanced interplay among physical, chemical, and biological processes. Fundamental knowledge gaps exist in characterizing the biogeochemical mechanisms that transform microbe-mineral interfaces at submicron scales, particularly in complex field systems. Our objective was to develop methods targeting the nanoscale by using high-resolution microscopy to assess biological and geochemical drivers of weathering in natural settings. Basalt, granite, and quartz (53-250 µm) were deployed in surface soils (10 cm) of three ecosystems (semiarid, subhumid, humid) for one year. We successfully developed a reference grid method to analyze individual grains using: (1) helium ion microscopy to capture micron to sub-nanometer imagery of mineral-organic interactions; and (2) scanning electron microscopy to quantify elemental distribution on the same surfaces via element mapping and point analyses. We detected locations of biomechanical weathering, secondary mineral precipitation, biofilm formation, and grain coatings across the three contrasting climates. To our knowledge, this is the first time these coupled microscopy techniques were applied in the earth and ecosystem sciences to assess microbe-mineral interfaces and in situ biological contributors to incipient weathering.
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Affiliation(s)
- Rebecca A Lybrand
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Jason C Austin
- Department of Geology, University of Georgia, Athens, GA, 30602, USA
| | - Jennifer Fedenko
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Rachel E Gallery
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, 85721, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Erin Rooney
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Paul A Schroeder
- Department of Geology, University of Georgia, Athens, GA, 30602, USA
| | - Dragos G Zaharescu
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Odeta Qafoku
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
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Kim YC, Anderson AJ. Rhizosphere pseudomonads as probiotics improving plant health. MOLECULAR PLANT PATHOLOGY 2018; 19:2349-2359. [PMID: 29676842 PMCID: PMC6638116 DOI: 10.1111/mpp.12693] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/08/2018] [Accepted: 04/18/2018] [Indexed: 05/25/2023]
Abstract
Many root-colonizing microbes are multifaceted in traits that improve plant health. Although isolates designated as biological control agents directly reduce pathogen growth, many exert additional beneficial features that parallel changes induced in animal and other hosts by health-promoting microbes termed probiotics. Both animal and plant probiotics cause direct antagonism of pathogens and induce systemic immunity in the host to pathogens and other stresses. They also alter host development and improve host nutrition. The probiotic root-colonizing pseudomonads are generalists in terms of plant hosts, soil habitats and the array of stress responses that are ameliorated in the plant. This article illustrates how the probiotic pseudomonads, nurtured by the carbon (C) and nitrogen (N) sources released by the plant in root exudates, form protective biofilms on the root surface and produce the metabolites or enzymes to boost plant health. The findings reveal the multifunctional nature of many of the microbial metabolites in the plant-probiotic interplay. The beneficial effects of probiotics on plant function can contribute to sustainable yield and quality in agricultural production.
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Affiliation(s)
- Young Cheol Kim
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangju 61186South Korea
| | - Anne J. Anderson
- Department of Biological EngineeringUtah State UniversityLoganUT 84322‐4105USA
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Anderson AJ, McLean JE, Jacobson AR, Britt DW. CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6513-6524. [PMID: 28481096 DOI: 10.1021/acs.jafc.7b01302] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
As the world population increases, strategies for sustainable agriculture are needed to fulfill the global need for plants for food and other commercial products. Nanoparticle formulations are likely to be part of the developing strategies. CuO and ZnO nanoparticles (NPs) offer potential as fertilizers, as they provide bioavailable essential metals, and as pesticides, because of dose-dependent toxicity. Effects of these metal oxide NPs on rhizosphere functions are the focus of this review. These NPs at doses of ≥10 mg metal/kg change the production of key metabolites involved in plant protection in a root-associated microbe, Pseudomonas chlororaphis O6. Altered synthesis occurs in the microbe for phenazines, which function in plant resistance to pathogens, the pyoverdine-like siderophore that enhances Fe bioavailability in the rhizosphere and indole-3-acetic acid affecting plant growth. In wheat seedlings, reprogramming of root morphology involves increases in root hair proliferation (CuO NPs) and lateral root formation (ZnO NPs). Systemic changes in wheat shoot gene expression point to altered regulation for metal stress resilience as well as the potential for enhanced survival under stress commonly encountered in the field. These responses to the NPs cross kingdoms involving the bacteria, fungi, and plants in the rhizosphere. Our challenge is to learn how to understand the value of these potential changes and successfully formulate the NPs for optimal activity in the rhizosphere of crop plants. These formulations may be integrated into developing practices to ensure the sustainability of crop production.
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Affiliation(s)
- Anne J Anderson
- Department of Biology , Utah State University , Logan , Utah 84322-5305 , United States
| | - Joan E McLean
- Department of Civil and Environmental Engineering, Utah Water Research Laboratory , Utah State University , Logan , Utah 84322-8200 , United States
| | - Astrid R Jacobson
- Department of Plants, Soils and Climate , Utah State University , Logan , Utah 84322-4820 , United States
| | - David W Britt
- Department of Bioengineering , Utah State University , Logan , Utah 84322-4105 , United States
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