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Nguyen LTT, Park AR, Van Le V, Hwang I, Kim JC. Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight. Appl Microbiol Biotechnol 2024; 108:49. [PMID: 38183485 DOI: 10.1007/s00253-023-12874-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/17/2023] [Accepted: 11/05/2023] [Indexed: 01/08/2024]
Abstract
Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.
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Affiliation(s)
- Loan Thi Thanh Nguyen
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Inmin Hwang
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea.
- JAN153 Biotech Incorporated, Gwangju, 61186, Republic of Korea.
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Lin X, Xu G, Li Y, Yu Y. Chemical fertilizers promote dissemination of ARGs in maize rhizosphere: An overlooked risk revealed after 37-year traditional agriculture practice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173737. [PMID: 38844214 DOI: 10.1016/j.scitotenv.2024.173737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/01/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Bacterial communities in soil and rhizosphere maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs and antibiotic resistant bacteria (ARB) are well-characterized under traditional farming practices. Here we compared the ARG profiles of maize rhizosphere and their bulk soils using metagenomic analysis to identify the ARG dissemination and explored the potential impact of chemical fertilization on ARB. Results showed a relatively lower abundance but higher diversity of ARGs under fertilization than straw-return. Moreover, the abundance and diversity of MGEs were significantly promoted by chemical fertilizer inputs in the rhizosphere compared to bulk soil. Machine learning and bipartite networks identified three bacterial genera (Pseudomonas, Bacillus and Streptomyces) as biomarkers for ARG accumulation. Thus we cultured 509 isolates belonging to these three genera from the rhizosphere and tested their antimicrobial susceptibility, and found that multi-resistance was frequently observed among Pseudomonas isolates. Assembly-based tracking explained that ARGs and four class I integrons (LR134330, LS998783, CP065848, LT883143) were co-occurred among contigs from Pseudomonas sp. Chemical fertilizers may shape the resistomes of maize rhizosphere, highlighting that rhizosphere carried multidrug-resistant Pseudomonas isolates, which may pose a risk to animal and human health. This study adds knowledge of long-term chemical fertilization on ARG dissemination in farmland systems and provides information for decision-making in agricultural production and monitoring.
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Affiliation(s)
- Xiaolong Lin
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; School of Agriculture, Sun Yat-sen University, Guangzhou 510275, China
| | - Guanghui Xu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yanjun Li
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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Benmrid B, Ghoulam C, Ammar I, Nkir D, Saidi R, Staropoli A, Iacomino G, ELhajjami E, Cheto S, Geistlinger J, Idbella M, Bargaz A. Drought-tolerant rhizobacteria with predicted functional traits enhanced wheat growth and P uptake under moderate drought and low P-availability. Microbiol Res 2024; 285:127795. [PMID: 38824819 DOI: 10.1016/j.micres.2024.127795] [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: 03/13/2024] [Revised: 05/06/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
This study aims to investigate the effect of isolated drought-tolerant rhizobacteria, spanning various groups, such as nitrogen-fixing bacteria (NFB), phosphate solubilizing bacteria (PSB), and other plant growth promoting rhizobacteria (PGPR), on the growth of wheat (Triticum durum) plants, focusing on various morphological and physiological responses under moderate drought and low-P availability. Among 343 rhizobacterial morphotypes, 16 exhibited tolerance to NaCl and PEG-6000. These included 8 PSB, 4 NFB, and 4 osmotolerant-PGPR groups, distributed across 14 different genera. Biochemical characterization showcased diverse PGP capabilities, particularly in P solubilization. The dynamic responses of drought-tolerant PSB to salt and PEG-6000-induced drought stress involved variations in organic acid (OA) secretion, with specific acids, including palmitic, lactic, and stearic, playing crucial roles in enhancing available P fractions. Inoculation with rhizobacteria significantly increased both shoot (SDW) and root (RDW) dry weights of wheat plants, as well as rhizosphere available P. PSB11 (Arthrobacter oryzae) emerged as the most effective strain, plausibly due to its positive impact on root morphological traits (length, surface, and volume). Other isolates, PSB10 (Priestia flexa), PSB13 (Bacillus haynesii), and particularly PGPR2 (Arthrobacter pascens) significantly increased shoot P content (up to 68.91 %), with a 2-fold increase in chlorophyll content. The correlation analysis highlighted positive associations between SDW, shoot P content, chlorophyll content index (CCI), and leaf area. Additionally, a negative correlation emerged between microbial biomass P and root morphophysiological parameters. This pattern could be explained by reduced competition between plants and rhizobacteria for accessible P, as indicated by low microbial biomass P and strong plant growth. Our investigation reveals the potential of drought-tolerant rhizobacteria in enhancing wheat resilience to moderate drought and low-P conditions. This is demonstrated through exceptional performance in influencing root architecture, P utilization efficiency, and overall plant physiological parameters. Beyond these outcomes, the innovative isolation procedure employed, targeting rhizobacteria from diverse groups, opens new avenues for targeted isolation techniques. This unique approach contributes to the novelty of our study, offering promising prospects for targeted bioinoculants in mitigating the challenges of drought and P deficiency in wheat cultivation.
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Affiliation(s)
- Bouchra Benmrid
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco.
| | - Cherki Ghoulam
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco; Agrobiotechnology & Bioengineering Center, Research Unit CNRST labeled, Cadi Ayyad University, Faculty of Sciences and Techniques, Marrakech 40000, Morocco
| | - Ibnyasser Ammar
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco
| | - Dounia Nkir
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco
| | - Rym Saidi
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco
| | - Alessia Staropoli
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy; Institute for Sustainable Plant Protection, National Research Council, Naples 80055, Italy
| | - Giuseppina Iacomino
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy
| | - Ezzoubair ELhajjami
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco
| | - Said Cheto
- Agrobiotechnology & Bioengineering Center, Research Unit CNRST labeled, Cadi Ayyad University, Faculty of Sciences and Techniques, Marrakech 40000, Morocco
| | | | - Mohamed Idbella
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco; Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy
| | - Adnane Bargaz
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco.
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Sangeetha S, Krishna PH. Inclusion of Pseudomonas fluorescens into soil-like fraction from municipal solid waste management park to enhance plastic biodegradation. Biodegradation 2024; 35:789-802. [PMID: 38687420 DOI: 10.1007/s10532-024-10085-2] [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: 11/21/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024]
Abstract
Single-use facial masks which are predominantly made out of polypropylene is being used and littered in large quantities during post COVID-19 situation. Extensive researches on bioremediation of plastic pollution on soil led to the identification of numerous plastic degrading microorganisms. These organisms assimilate plastic polymers as their carbon source for synthesizing energy. Pseudomonas fluorescens (PF) is one among such microorganism which is being identified to biodegrade plastic polymers in controlled environment. The natural biodegradation of facial mask in soil-like fraction collected from municipal waste management site, bioaugmentation of the degradation process with Pseudomonas fluorescens, biostimulation of the soil with carbonless nutritional supplements and combined bioaugmentation with biostimulation process were studied in the present work. The study has been conducted both in controlled and in natural condition for a period of 12 months. The efficiency of the degradation was verified through FTIR analyses using carbonyl index, bond energy change, Loss in ignition (LOI) measurement along with CHNS analyses of residual substances. The analysis of results reported that carbonyl index (in terms of transmittance) was reduced to 46% of the control batch through the inclusion of PF in natural condition. The bioaugmented batch maintained in natural condition showed 33% reduction of LOI with respect to the control batch. The unburnt carbon content of the residual matter obtained from the furnace were analysed using CHNS analyser and indicated the lowest carbon content in the same bioaugmented batch. In this study, an attempt is made to verify the feasibility of enhancing biodegradation of single-use facial mask by bioaugmentation of soil-like fraction available in solid waste management park with Pseudomonas fluorescens under natural condition. CHNS and FTIR analysis assures the biodegradation of plastic waste in the soil-like fraction using Pseudomonas fluorescens under both controlled and natural environmental condition.
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Affiliation(s)
- S Sangeetha
- National Institute of Technology, Warangal, Telangana, 506 004, India.
| | - P Hari Krishna
- National Institute of Technology, Warangal, Telangana, 506 004, India
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Núñez-Muñoz LA, Sánchez-García ME, Calderón-Pérez B, De la Torre-Almaraz R, Ruiz-Medrano R, Xoconostle-Cázares B. Metagenomic Analysis of Rhizospheric Bacterial Community of Citrus Trees Expressing Phloem-Directed Antimicrobials. MICROBIAL ECOLOGY 2024; 87:93. [PMID: 39008123 PMCID: PMC11249458 DOI: 10.1007/s00248-024-02408-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024]
Abstract
Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota.
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Affiliation(s)
- Leandro Alberto Núñez-Muñoz
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico
| | - Martín Eduardo Sánchez-García
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico
| | - Berenice Calderón-Pérez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico
| | - Rodolfo De la Torre-Almaraz
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54090, Mexico City, Estado de México, Mexico
| | - Roberto Ruiz-Medrano
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico
- Centro de Investigación y de Estudios Avanzados, Programa de Doctorado Transdisciplinario en Desarrollo Científico y Tecnológico Para La Sociedad, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico
| | - Beatriz Xoconostle-Cázares
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico.
- Centro de Investigación y de Estudios Avanzados, Programa de Doctorado Transdisciplinario en Desarrollo Científico y Tecnológico Para La Sociedad, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico.
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Oubohssaine M, Sbabou L, Aurag J. Potential of the plant growth-promoting rhizobacterium Rhodococcus qingshengii LMR356 in mitigating lead stress impact on Sulla spinosissima L. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34150-8. [PMID: 38980484 DOI: 10.1007/s11356-024-34150-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024]
Abstract
Mining-related lead (Pb) pollution of the soil poses serious hazards to ecosystems and living organisms, including humans. Improved heavy metal phytoremediation efficacy, achieved by using phytostabilizing plants assisted by plant-growth-promoting (PGP) microorganisms, has been presented as an effective strategy for remediating polluted soils. The objective of this research was to examine the response and potential of the plant-growth-promoting bacterium LMR356, a Rhodococcus qingshengii strain isolated from an abandoned mining soil, under lead stress conditions. Compared to non-contaminated culture media, the presence of lead induced a significant decrease in auxin production (from 21.17 to 2.65 μg mL-1) and phosphate solubilization (from 33.60 to 8.22 mg L-1), whereas other PGP traits increased drastically, such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity (from 38.17 to 71.37 nmol mg-1 h-1 α-ketobutyrate), siderophore production (from 69 to 83%), exopolysaccharide production (from 1952.28 to 3637.72 mg mL-1), biofilm formation, and motility. We, therefore, investigated the behavior of Sulla spinosissima L. in the presence or absence of this strain under a variety of experimental conditions. Under hydroponic conditions, Sulla plants showed endurance to varying lead concentrations (500-1000 μM). Inoculation of plants with Rhodococcus qingshengii strain LMR356 enhanced plant tolerance, as demonstrated by the increase in plant biomass (ranging from 14.41 to 79.12%) compared to non-inoculated Pb-stressed and non-stressed control plants. Antioxidant enzyme activities (increasing by -42.71 to 126.8%) and chlorophyll (383.33%) and carotenoid (613.04%) content were also augmented. In addition to its impact on plant lead tolerance, strain LMR356 showed a growth-promoting effect on Sulla plants when cultivated in sterilized non-contaminated sand. Parameters such as plant biomass (16.57%), chlorophyll (24.14%), and carotenoid (30%) contents, as well as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) activities, were all elevated compared to non-inoculated plants. Furthermore, when the same plant species was cultivated in highly polluted soil, inoculation increased plant biomass and improved its physiological properties. These findings demonstrate that LMR356 is a phytobeneficial bacterial strain capable of enhancing Sulla growth under normal conditions and improving its heavy metal tolerance in multi-polluted soils. Thus, it can be considered a promising biofertilizer candidate for growing Sulla spinosissima L. or other selected plants intended for application in restoration and stabilization initiatives aimed at reviving and safeguarding environmentally compromised and polluted soils after mining activities.
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Affiliation(s)
- Malika Oubohssaine
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000, Rabat, Morocco.
| | - Laila Sbabou
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000, Rabat, Morocco
| | - Jamal Aurag
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000, Rabat, Morocco
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Liu C, Tian J, Chen L, He Q, Liu X, Bian R, Zheng J, Cheng K, Xia S, Zhang X, Wu J, Li L, Joseph S, Pan G. Biochar boosted high oleic peanut production with enhanced root development and biological N fixation by diazotrophs in a sand-loamy Primisol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:173061. [PMID: 38723970 DOI: 10.1016/j.scitotenv.2024.173061] [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: 11/02/2023] [Revised: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Peanut yield and quality face significant threats due to climate change and soil degradation. The potential of biochar technology to address this challenge remains unanswered, though biochar is acknowledged for its capacity to enhance the soil microbial community and plant nitrogen (N) supply. A field study was conducted in 2021 on oil peanuts grown in a sand-loamy Primisol that received organic amendments at 20 Mg ha-1. The treatments consisted of biochar amendments derived from poultry manure (PB), rice husk (RB), and maize residue (MB), as well as manure compost (OM) amendment, compared to no organic amendment (CK). In 2022, during the second year after amendment, samples of bulk topsoil, rooted soil, and plants were collected at the peanut harvest. The analysis included the assessment of soil quality, peanut growth traits, microbial community, nifH gene abundance, and biological N fixation (BNF) rate. Compared to the CK, the OM treatment led to an 8 % increase in peanut kernel yield, but had no effect on kernel quality in terms of oil production. Conversely, both PB and MB treatments increased kernel yield by 10 %, whereas RB treatment showed no change in yield. Moreover, all biochar amendments significantly improved oilseed quality by 10-25 %, notably increasing the proportion of oleic acid by up to 70 %. Similarly, while OM amendment slightly decreased root development, all biochar treatments significantly enhanced root development by over 80 %. Furthermore, nodule number, fresh weight per plant, and the nifH gene abundance in rooted soil remained unchanged under OM and PB treatments but was significantly enhanced under RB and MB treatments compared to CK. Notably, all biochar amendments, excluding OM, increased the BNF rate and N-acetyl-glucosaminidase activity. These changes were attributed to alterations in soil aggregation, moisture retention, and phosphorus availability, which were influenced by the diverse physical and chemical properties of biochars. Overall, maize residue biochar contributed synergistically to enhancing soil fertility, peanut yield, and quality while also promoting increased root development, a shift in the diazotrophic community and BNF.
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Affiliation(s)
- Cheng Liu
- Institute of Eco-environmental Research, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China; Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Hangzhou 310023, Zhejiang, China; Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Jing Tian
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Lei Chen
- Institute of Cash Crop, Shangqiu Academy of Agriculture and Forest Sciences, Shangqiu 476002, Henan, China
| | - Qunling He
- Institute of Cash Crop, Shangqiu Academy of Agriculture and Forest Sciences, Shangqiu 476002, Henan, China
| | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Rongjun Bian
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Jufeng Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Kun Cheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Shaopan Xia
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xuhui Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Jihua Wu
- Institute of Cash Crop, Shangqiu Academy of Agriculture and Forest Sciences, Shangqiu 476002, Henan, China
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Stephen Joseph
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; School of Materials Science and Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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Hussain A, Faizan S, Kumari R, Pandey E. Morphological and biochemical responses of Vicia faba (faba beans) grown on fly ash amended soil in the presence of Rhizobium leguminosarum and arbuscular mycorrhizal fungus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:44361-44373. [PMID: 38949734 DOI: 10.1007/s11356-024-34154-4] [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: 02/15/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
An experiment was conducted in the greenhouse to investigate the feasibility of Vicia faba grown on different fly ash concentrations (0-30%) and dual inoculation with Rhizobium and arbuscular mycorrhizal fungi (AMF). Sampling was done 45 days after sowing to analyse the plant growth parameters, photosynthetic attributes (total chlorophyll and carotenoids content), protein content, nitrogen (N) and phosphorus (P) content, defensive factors (antioxidant activity and proline content) and damage markers (lipid peroxidation, reactive oxygen species and cell viability). The results revealed that the application of fly ash (FA) alone did not result in any significant improvement in growth, biochemical and physiological parameters. However, dual inoculation showed a synergistic impact on legume growth, photosynthetic pigments, protein, proline, and cell viability. Rhizobium, AMF and 10% FA showed maximum enhancement in all attributes mentioned. 20% and 30% fly doses showed a reduction in growth, photosynthesis and antioxidants and caused oxidative stress via lipid peroxidation. The results showed that the synergistic or combined interactions between all three variables of the symbiotic relationship (Rhizobium-legume-AMF) boosted plant productivity.
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Affiliation(s)
- Alisha Hussain
- Environmental Physiology Laboratory, Department of Botany, Aligarh Muslim University, U.P, Aligarh, 202002, India
| | - Shahla Faizan
- Environmental Physiology Laboratory, Department of Botany, Aligarh Muslim University, U.P, Aligarh, 202002, India.
| | - Rinkee Kumari
- Environmental Physiology Laboratory, Department of Botany, Aligarh Muslim University, U.P, Aligarh, 202002, India
| | - Ekta Pandey
- Environmental Physiology Laboratory, Department of Botany, Aligarh Muslim University, U.P, Aligarh, 202002, India
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Negi R, Sharma B, Jan T, Kaur T, Chowdhury S, Kapoor M, Singh S, Kumar A, Rai AK, Rustagi S, Shreaz S, Kour D, Ahmed N, Kumar K, Yadav AN. Microbial Consortia: Promising Tool as Plant Bioinoculants for Agricultural Sustainability. Curr Microbiol 2024; 81:222. [PMID: 38874817 DOI: 10.1007/s00284-024-03755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/31/2024] [Indexed: 06/15/2024]
Abstract
In the present scenario, growing population demands more food, resulting in the need for sustainable agriculture. Numerous approaches are explored in response to dangers and obstacles to sustainable agriculture. A viable approach is to be exploiting microbial consortium, which generate diverse biostimulants with growth-promoting characteristics for plants. These bioinoculants play an indispensable role in optimizing nutrient uptake efficiency mitigating environmental stress. Plant productivity is mostly determined by the microbial associations that exist at the rhizospheric region of plants. The engineered consortium with multifunctional attributes can be effectively employed to improve crop growth efficacy. A number of approaches have been employed to identify the efficient consortia for plant growth and enhanced crop productivity. Various plant growth-promoting (PGP) microbes with host growth-supporting characteristics were investigated to see if they might work cohesively and provide a cumulative effect for improved growth and crop yield. The effective microbial consortia should be assessed using compatibility tests, pot experimentation techniques, generation time, a novel and quick plant bioassay, and sensitivity to external stimuli (temperature, pH). The mixture of two or more microbial strains found in the root microbiome stimulates plant growth and development. The present review deals with mechanism, formulation, inoculation process, commercialization, and applications of microbial consortia as plant bioinoculants for agricultural sustainability.
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Affiliation(s)
- Rajeshwari Negi
- Department of Genetics, Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India
| | - Babita Sharma
- Department of Microbiology, Akal College of Basic Science, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India
| | - Tawseefa Jan
- Department of Food Technology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India
| | - Tanvir Kaur
- Department of Genetics, Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India
| | - Sohini Chowdhury
- Chitkara Center for Research and Development, Chitkara University, Baddi, Himachal Pradesh, India
| | - Monit Kapoor
- Centre of Research Impact and Outcome, Chitkara University, Rajpura, Punjab, India
| | - Sangram Singh
- Department of Biochemistry, Dr. Ram Manohar Lohia Avadh University, Faizabad, Uttar Pradesh, India
| | - Anu Kumar
- University Institute of Biotechnology, Chandigarh University, Mohali, 140413, Punjab, India
| | - Ashutosh Kumar Rai
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
| | - Sarvesh Rustagi
- Department of Food Technology, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Sheikh Shreaz
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, PO Box 24885, 13109, Safat, Kuwait
| | - Divjot Kour
- Department of Microbiology, Akal College of Basic Science, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India
| | - Naseer Ahmed
- Department of Food Technology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India
| | - Krishan Kumar
- Department of Food Technology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India
| | - Ajar Nath Yadav
- Department of Genetics, Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India.
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10
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Gamalero E, Glick BR. Use of plant growth-promoting bacteria to facilitate phytoremediation. AIMS Microbiol 2024; 10:415-448. [PMID: 38919713 PMCID: PMC11194615 DOI: 10.3934/microbiol.2024021] [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: 03/08/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Here, phytoremediation studies of toxic metal and organic compounds using plants augmented with plant growth-promoting bacteria, published in the past few years, were summarized and reviewed. These studies complemented and extended the many earlier studies in this area of research. The studies summarized here employed a wide range of non-agricultural plants including various grasses indigenous to regions of the world. The plant growth-promoting bacteria used a range of different known mechanisms to promote plant growth in the presence of metallic and/or organic toxicants and thereby improve the phytoremediation ability of most plants. Both rhizosphere and endophyte PGPB strains have been found to be effective within various phytoremediation schemes. Consortia consisting of several PGPB were often more effective than individual PGPB in assisting phytoremediation in the presence of metallic and/or organic environmental contaminants.
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Affiliation(s)
- Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada N2L 3G1
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11
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Sharma P, Chandra R. Phytoremediation mechanism and role of plant growth promoting rhizobacteria in weed plants for eco-restoration of hazardous industrial waste polluted site: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:42495-42520. [PMID: 38872037 DOI: 10.1007/s11356-024-33910-w] [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] [Accepted: 06/01/2024] [Indexed: 06/15/2024]
Abstract
Plants have numerous strategies for phytoremediation depending upon the characteristic of pollutants. Plant growth promoting rhizobacteria (PGPR) are essential to the process of phytoremediation and play a key part in it. The mechanism of PGPR for phytoremediation is mediated by two methods; under the direct method there is phytohormone production, nitrogen fixation, nutrient mineral solubilization, and siderophore production while the indirect method includes quorum quenching, antibiosis, production of lytic enzyme, biofilm formation, and hydrogen cyanide production. Due to their economic and environmental viability, most researchers have recently concentrated on the potential of weed plants for phytoremediation. Although weed plants are considered unwanted and noxious, they have a high growth rate and adaptability which opens a high scope for its role in phytoremediation of contaminated site. The interaction of plant with rhizobacteria starts from root exudates containing various organic acids and peptides which act as nutrients essential for colonization and siderophore production by the rhizospheric bacteria. The rhizobacteria, while colonizing, tend to promote plant growth and health either directly by providing phytohormones and minerals or indirectly by suppressing growth of possible phytopathogens. Recently, several weed plants have been reported for phytoextraction of heavy metals (Ni, Pb, Zn, Hg, Cd, Cu, As, Fe, and Cr) contaminants from various agro-based industries. These potential native weed plants have high prospect of eco-restoration of polluted site with complex organo-metallic waste for sustainable development.
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Affiliation(s)
- Pratishtha Sharma
- Department of Environmental Microbiology, School of Earth and Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh, 226025, India
| | - Ram Chandra
- Department of Environmental Microbiology, School of Earth and Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh, 226025, India.
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12
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Arunrat N, Sansupa C, Sereenonchai S, Hatano R, Lal R. Fire-Induced Changes in Soil Properties and Bacterial Communities in Rotational Shifting Cultivation Fields in Northern Thailand. BIOLOGY 2024; 13:383. [PMID: 38927263 PMCID: PMC11200764 DOI: 10.3390/biology13060383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
Fire is a common practice in rotational shifting cultivation (RSC), but little is known about the dynamics of bacterial populations and the impact of fire disturbance in northern Thailand. To fill the research gap, this study aims to investigate the dynamics of soil bacterial communities and examine how the soil's physicochemical properties influence the bacterial communities in RSC fields over a period of one year following a fire. Surface soil samples (0-2 cm depth) were collected from sites with 6 (RSC-6Y) and 12 (RSC-12Y) years of fallow in Chiang Mai Province, northern Thailand at six different time points: before burning, 5 min after burning (summer), 3 months after burning (rainy season), 6 months after burning (rainy season), 9 months after burning (winter), and 12 months after burning (summer). The results revealed a reduction in the soil bacterial communities' diversity and an increase in soil nutrient levels immediately after the fire. The fire significantly influenced the abundance of Firmicutes, Proteobacteria, Acidobacteria, and Planctomycetes, but not that of Actinobacteria. At the genus level, Bacillus, Conexibacter, and Chthoniobacter showed increased abundance following the fire. During the rainy season, a recovery in the abundance of the soil bacterial communities was observed, although soil nutrient availability declined. Soil physicochemical properties such as pH, organic matter, organic carbon, electrical conductivity, cation exchange capacity, nitrate-nitrogen, available phosphorus, exchangeable potassium, total nitrogen, bulk density, sand, and silt contents significantly influenced the composition of bacterial communities. Alpha diversity indices indicated a decrease in diversity immediately after burning, followed by an increase from the early rainy season until the summer season, indicating that seasonal variation affected the composition of the soil bacterial communities. After one year of burning, an increase in bacterial richness was observed, while the diversity of the bacterial communities reverted to pre-burning levels.
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Affiliation(s)
- Noppol Arunrat
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Chakriya Sansupa
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Sukanya Sereenonchai
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Ryusuke Hatano
- Laboratory of Soil Science, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan;
| | - Rattan Lal
- CFAES Rattan Lal Center for Carbon Management and Sequestration, The Ohio State University, 2021 Coffey Rd, Columbus, OH 43210, USA;
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13
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Jung SY, Kim HS, Moon WK, Hong EM. Comparison and analysis of soil microbial communities in organic and conventional paddy fields by farming season. ENVIRONMENTAL RESEARCH 2024; 249:118341. [PMID: 38320718 DOI: 10.1016/j.envres.2024.118341] [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: 11/16/2023] [Revised: 01/19/2024] [Accepted: 01/27/2024] [Indexed: 02/13/2024]
Abstract
Interest in soil health and biodiversity conservation has become increasingly important. Consequently, studies comparing the chemical and biological characteristics of organic and traditional paddy soils have been increasing. Soil microorganisms are essential in nutrient cycling; however, their diversity is challenging to ascertain because of their environmental sensitivity and complex interactions. Particularly, in domestic rice cultivation, the soil undergoes multiple irrigation and drainage processes during crop growth, providing a diverse ecological environment for soil microorganisms. The objective of this study is to compare the microbial community and diversity between paddy soils in two agricultural systems. We selected organic and conventional paddy fields in Yangpyeong, Gyeonggi Province, and collected monthly samples from August to November 2022 for analysis. Bacteria and fungi were amplified from the 16S rRNA V3V4 region, ITS 3-4 region respectively, For the comparison of microbial diversity, Alpha diversity indices (Chao1, Shannon, Gini-Simpson indices) were analyzed. The results indicated genus-level differences in microbial communities, with the genera Mucor and Sirastachys exclusively present in organic paddy soils, while the genus Ustilaginoidea was exclusively found in conventional paddy soils. Among them, Ustilaginoidea is reported to be a fungus causing false smut disease, causing damage to crop growth and quality. Additionally, the comparison of microbial diversity between the two farming showed no significant differences (p>0.05). In conclusion, When the microbial communities present in both farming systems were examined, organic farming appeared to be more advantageous than conventional farming regarding crop disease and health. This study provides essential soil chemical and microbiological data for understanding the fundamental characteristics of paddy soils in South Korea.
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Affiliation(s)
- Se Yoon Jung
- Department of Environment Science, Kangwon National University, Chuncheon, Kangwon-do, 24341, Republic of Korea.
| | - Hyuck Soo Kim
- School of Natural Resources and Environmental Science, Kangwon National University, Chuncheon, Kangwon-do, 24341, Republic of Korea.
| | - Woon-Ki Moon
- Environment Solution Eco, GwangMyeong, Gyeonggi-do, 14348, Republic of Korea.
| | - Eun-Mi Hong
- Department of Environment Science, Kangwon National University, Chuncheon, Kangwon-do, 24341, Republic of Korea; School of Natural Resources and Environmental Science, Kangwon National University, Chuncheon, Kangwon-do, 24341, Republic of Korea.
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14
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Tan J, Wei N, Turcotte MM. Trophic interactions in microbiomes influence plant host population size and ecosystem function. Proc Biol Sci 2024; 291:20240612. [PMID: 38772419 DOI: 10.1098/rspb.2024.0612] [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: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 05/23/2024] Open
Abstract
Plant microbiomes that comprise diverse microorganisms, including prokaryotes, eukaryotes and viruses, are the key determinants of plant population dynamics and ecosystem function. Despite their importance, little is known about how species interactions (especially trophic interactions) between microbes from different domains modify the importance of microbiomes for plant hosts and ecosystems. Using the common duckweed Lemna minor, we experimentally examined the effects of predation (by bacterivorous protists) and parasitism (by bacteriophages) within microbiomes on plant population size and ecosystem phosphorus removal. Our results revealed that the addition of predators increased plant population size and phosphorus removal, whereas the addition of parasites showed the opposite pattern. The structural equation modelling further pointed out that predation and parasitism affected plant population size and ecosystem function via distinct mechanisms that were both mediated by microbiomes. Our results highlight the importance of understanding microbial trophic interactions for predicting the outcomes and ecosystem impacts of plant-microbiome symbiosis.
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Affiliation(s)
- Jiaqi Tan
- Department of Biological Sciences, Louisianan State University, Baton Rouge, LA 70803, USA
| | - Na Wei
- The Holden Arboretum, Kirtland, OH 44094, USA
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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15
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Remenyik J, Csige L, Dávid P, Fauszt P, Szilágyi-Rácz AA, Szőllősi E, Bacsó ZR, Szepsy Jnr I, Molnár K, Rácz C, Fidler G, Kállai Z, Stündl L, Dobos AC, Paholcsek M. Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region. PLoS One 2024; 19:e0300563. [PMID: 38626236 PMCID: PMC11020696 DOI: 10.1371/journal.pone.0300563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/29/2024] [Indexed: 04/18/2024] Open
Abstract
A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.
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Affiliation(s)
- Judit Remenyik
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - László Csige
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - Péter Dávid
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Péter Fauszt
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Anna Anita Szilágyi-Rácz
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Erzsébet Szőllősi
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Zsófia Réka Bacsó
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - István Szepsy Jnr
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - Krisztina Molnár
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Csaba Rácz
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Gábor Fidler
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Zoltán Kállai
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - László Stündl
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Attila Csaba Dobos
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Melinda Paholcsek
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
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16
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Zhang X, Li X, Chen F, Cao X, Wang C, Jiao L, Yue L, Wang Z. Selenium Nanomaterials Enhance the Nutrients and Functional Components of Fuding Dabai Tea. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:681. [PMID: 38668175 PMCID: PMC11053761 DOI: 10.3390/nano14080681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
Theanine, polyphenols, and caffeine not only affect the flavor of tea, but also play an important role in human health benefits. However, the specific regulatory mechanism of Se NMs on fat-reducing components is still unclear. In this study, the synthesis of fat-reducing components in Fuding Dabai (FDDB) tea was investigated. The results indicated that the 100-bud weight, theanine, EGCG, total catechin, and caffeine contents of tea buds were optimally promoted by 10 mg·L-1 Se NMs in the range of 24.3%, 36.2%, 53.9%, 67.1%, and 30.9%, respectively. Mechanically, Se NMs promoted photosynthesis in tea plants, increased the soluble sugar content in tea leaves (30.3%), and provided energy for the metabolic processes, including the TCA cycle, pyruvate metabolism, amino acid metabolism, and the glutamine/glutamic acid cycle, ultimately increasing the content of amino acids and antioxidant substances (catechins) in tea buds; the relative expressions of key genes for catechin synthesis, CsPAL, CsC4H, CsCHI, CsDFR, CsANS, CsANR, CsLAR, and UGGT, were significantly upregulated by 45.1-619.1%. The expressions of theanine synthesis genes CsTs, CsGs, and CsGOGAT were upregulated by 138.8-693.7%. Moreover, Se NMs promoted more sucrose transfer to the roots, with the upregulations of CsSUT1, CsSUT2, CsSUT3, and CsSWEET1a by 125.8-560.5%. Correspondingly, Se NMs enriched the beneficial rhizosphere microbiota (Roseiarcus, Acidothermus, Acidibacter, Conexicter, and Pedosphaeraceae), enhancing the absorption and utilization of ammonium nitrogen by tea plants, contributing to the accumulation of theanine. This study provides compelling evidence supporting the application of Se NMs in promoting the lipid-reducing components of tea by enhancing its nitrogen metabolism.
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Affiliation(s)
- Xiaoli Zhang
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Xiaona Li
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Liya Jiao
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
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17
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Kovács B, Andreolli M, Lampis S, Biró B, Kotroczó Z. Bacterial Community Structure Responds to Soil Management in the Rhizosphere of Vine Grape Vineyards. BIOLOGY 2024; 13:254. [PMID: 38666866 PMCID: PMC11048173 DOI: 10.3390/biology13040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
The microbial communities of the rhizospheres of vineyards have been subject to a considerable body of research, but it is still unclear how the applied soil cultivation methods are able to change the structure, composition, and level of diversity of their communities. Rhizosphere samples were collected from three neighbouring vineyards with the same time of planting and planting material (rootstock: Teleki 5C; Vitis vinifera: Müller Thurgau). Our objective was to examine the diversity occurring in bacterial community structures in vineyards that differ only in the methods of tillage procedure applied, namely intensive (INT), extensive (EXT), and abandoned (AB). For that we took samples from two depths (10-30 cm (shallow = S) and 30-50 cm (deep = D) of the grape rhizosphere in each vineyard and the laboratory and immediately prepared the slices of the roots for DNA-based analysis of the bacterial communities. Bacterial community structure was assessed by means of PCR-DGGE analysis carried out on the v3 region of 16S rRNA gene. Based on the band composition of the DGGE profiles thus obtained, the diversity of the microbial communities was evaluated and determined by the Shannon-Weaver index (H'). Between the AB and EXT vineyards at the S depth, the similarity of the community structure was 55%; however, the similarity of the D samples was more than 80%, while the difference between the INT samples and the other two was also higher than 80%. Based on our results, we can conclude that intensive cultivation strongly affects the structure and diversity of the bacterial community.
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Affiliation(s)
- Barnabás Kovács
- Institute of Viticulture and Enology, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary
| | - Marco Andreolli
- Department of Biotechnology & Verona University Culture Collection-Department of Biotechnology (VUCC-DBT), University of Verona, 37134 Verona, Italy; (M.A.); (S.L.)
| | - Silvia Lampis
- Department of Biotechnology & Verona University Culture Collection-Department of Biotechnology (VUCC-DBT), University of Verona, 37134 Verona, Italy; (M.A.); (S.L.)
| | - Borbála Biró
- Department of Agro-Environmental Studies, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary; (B.B.); (Z.K.)
| | - Zsolt Kotroczó
- Department of Agro-Environmental Studies, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary; (B.B.); (Z.K.)
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18
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Li X, Zheng X, Yadav N, Saha S, Salama ES, Li X, Wang L, Jeon BH. Rational management of the plant microbiome for the Second Green Revolution. PLANT COMMUNICATIONS 2024; 5:100812. [PMID: 38213028 PMCID: PMC11009158 DOI: 10.1016/j.xplc.2024.100812] [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: 08/02/2023] [Revised: 11/06/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.
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Affiliation(s)
- Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Nikita Yadav
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Shouvik Saha
- Natural Resources Research Institute, University of Minnesota Duluth, Hermantown, MN 55811, USA; Department of Biotechnology, Brainware University, Barasat, Kolkata 700125, West Bengal, India
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Likun Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea.
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19
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Su H, Lai H, Gao F, Zhang R, Wu S, Ge F, Li Y, Yao H. The proliferation of beneficial bacteria influences the soil C, N, and P cycling in the soybean-maize intercropping system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:25688-25705. [PMID: 38483720 DOI: 10.1007/s11356-024-32851-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 03/06/2024] [Indexed: 04/19/2024]
Abstract
Soybean-maize intercropping system can improve the utilization rate of farmland and the sustainability of crop production systems. However, there is a significant gap in understanding the interaction mechanisms between soil carbon (C), nitrogen (N), and phosphorus (P) cycling functional genes, rhizosphere microorganisms, and nutrient availability. To reveal the key microorganisms associated with soil nutrient utilization and C, N, and P cycling function in the soybean-maize intercropping system, we investigated the changes in soil properties, microbial community structure, and abundance of functional genes for C, N, and P cycling under soybean-maize intercropping and monocropping at different fertility stages in a pot experiment. We found that there was no significant difference in the rhizosphere microbial community between soybean-maize intercropping and monocropping at the seeding stage. As the reproductive period progressed, differences in microbial community structure between intercropping and monocropping gradually became significant, manifesting the advantages of intercropping. During the intercropping process of soybean and maize, the relative abundance of beneficial bacteria in soil rhizosphere significantly increased, particularly Streptomycetaceae and Pseudomonadaceae. Moreover, the abundances of C, N, and P cycling functional genes, such as abfA, mnp, rbcL, pmoA (C cycling), nifH, nirS-3, nosZ-2, amoB (N cycling), phoD, and ppx (P cycling), also increased significantly. Redundancy analysis and correlation analysis showed that Streptomycetaceae and Pseudomonadaceae were significantly correlated with soil properties and C, N, and P cycling functional genes. In brief, soybean and maize intercropping can change the structure of microbial community and promote the proliferation of beneficial bacteria in the soil rhizosphere. The accumulation of these beneficial bacteria increased the abundance of C, N, and P cycling functional genes in soil and enhanced the ability of plants to fully utilize environmental nutrients and promoted growth.
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Affiliation(s)
- Hao Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiling Lai
- Lianhe Equator Environmental Impact Assessment Co., Ltd, Tianjin, 300042, China
| | - Fuyun Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruipeng Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sixuan Wu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Furong Ge
- Beilun District Agriculture and Rural Bureau, Ningbo, 315800, Zhejiang Province, China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China.
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China.
| | - Huaiying Yao
- Wuhan Institute of Technology, Wuhan, 430074, China
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20
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Qin H, Wang Z, Sha W, Song S, Qin F, Zhang W. Role of Plant-Growth-Promoting Rhizobacteria in Plant Machinery for Soil Heavy Metal Detoxification. Microorganisms 2024; 12:700. [PMID: 38674644 PMCID: PMC11052264 DOI: 10.3390/microorganisms12040700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Heavy metals migrate easily and are difficult to degrade in the soil environment, which causes serious harm to the ecological environment and human health. Thus, soil heavy metal pollution has become one of the main environmental issues of global concern. Plant-growth-promoting rhizobacteria (PGPR) is a kind of microorganism that grows around the rhizosphere and can promote plant growth and increase crop yield. PGPR can change the bioavailability of heavy metals in the rhizosphere microenvironment, increase heavy metal uptake by phytoremediation plants, and enhance the phytoremediation efficiency of heavy-metal-contaminated soils. In recent years, the number of studies on the phytoremediation efficiency of heavy-metal-contaminated soil enhanced by PGPR has increased rapidly. This paper systematically reviews the mechanisms of PGPR that promote plant growth (including nitrogen fixation, phosphorus solubilization, potassium solubilization, iron solubilization, and plant hormone secretion) and the mechanisms of PGPR that enhance plant-heavy metal interactions (including chelation, the induction of systemic resistance, and the improvement of bioavailability). Future research on PGPR should address the challenges in heavy metal removal by PGPR-assisted phytoremediation.
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Affiliation(s)
| | | | | | | | - Fenju Qin
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Wenchao Zhang
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, China
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21
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Wang X, Chi Y, Song S. Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review. Front Microbiol 2024; 15:1347745. [PMID: 38591030 PMCID: PMC10999704 DOI: 10.3389/fmicb.2024.1347745] [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: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.
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Affiliation(s)
| | - Yongkuan Chi
- School of Karst Science, State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
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22
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Li X, Xu L, Demaree B, Noecker C, Bisanz JE, Weisgerber DW, Modavi C, Turnbaugh PJ, Abate AR. Microbiome single cell atlases generated with a commercial instrument. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.08.551713. [PMID: 37609281 PMCID: PMC10441329 DOI: 10.1101/2023.08.08.551713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes' genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.
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23
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Vido JJ, Wang X, Sale PWG, Celestina C, Shindler AE, Hayden HL, Tang C, Wood JL, Franks AE. Bacterial community shifts occur primarily through rhizosphere expansion in response to subsoil amendments. Environ Microbiol 2024; 26:e16587. [PMID: 38454741 DOI: 10.1111/1462-2920.16587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 01/22/2024] [Indexed: 03/09/2024]
Abstract
To comprehensively evaluate the impact of agricultural management practices on soil productivity, it is imperative to conduct a thorough analysis of soil bacterial ecology. Deep-banding nutrient-rich amendments is a soil management practice that aims to improve plant growth and soil structure by addressing the plant-growth constraints posed by dense-clay subsoils. However, the response of bacterial communities to deep-banded amendments has not been thoroughly studied. To address this knowledge gap, we conducted a controlled-environment column experiment to examine the effects of different types of soil amendments (poultry litter, wheat straw + chemical fertiliser and chemical fertiliser alone) on bacterial taxonomic composition in simulated dense-clay subsoils. We evaluated the bacterial taxonomic and ecological group composition in soils beside and below the amendment using 16S rRNA amplicon sequencing and robust statistical methods. Our results indicate that deep-banded amendments alter bacterial communities through direct and indirect mechanisms. All amendments directly facilitated a shift in bacterial communities in the absence of growing wheat. However, a combination of amendments with growing wheat led to a more pronounced bacterial community shift which was distinct from and eclipsed the direct impact of the amendments and plants alone. This indirect mechanism was evidenced to be mediated primarily by plant growth and hypothesised to result from an enhancement in wheat root distribution, density and rhizodeposition changes. Therefore, we propose that subsoil amendments regardless of type facilitated an expansion in the rhizosphere which engineered a substantial plant-mediated bacterial community response within the simulated dense-clay subsoils. Overall, our findings highlight the importance of considering the complex and synergistic interactions between soil physicochemical properties, plant growth and bacterial communities when assessing agricultural management strategies for improving soil and plant productivity.
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Affiliation(s)
- Joshua J Vido
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
| | - Xiaojuan Wang
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, Australia
- School of Agriculture Food, and Ecosystem Sciences, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Peter W G Sale
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, Australia
| | - Corinne Celestina
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, Australia
- School of Agriculture Food, and Ecosystem Sciences, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Anya E Shindler
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
| | - Helen L Hayden
- School of Agriculture Food, and Ecosystem Sciences, Faculty of Science, University of Melbourne, Melbourne, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Bundoora, Australia
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, Australia
| | - Jennifer L Wood
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
- Centre for Future Landscapes, La Trobe University, Bundoora, Australia
| | - Ashley E Franks
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
- Centre for Future Landscapes, La Trobe University, Bundoora, Australia
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24
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Hathurusinghe SHK, Azizoglu U, Shin JH. Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health. PLANTS (BASEL, SWITZERLAND) 2024; 13:695. [PMID: 38475541 DOI: 10.3390/plants13050695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.
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Affiliation(s)
| | - Ugur Azizoglu
- Department of Crop and Animal Production, Safiye Cikrikcioglu Vocational College, Kayseri University, Kayseri 38039, Turkey
- Genome and Stem Cell Research Center, Erciyes University, Kayseri 38039, Turkey
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
- NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of Korea
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25
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Sakauchi K, Otaki JM. Soil Microbes and Plant-Associated Microbes in Response to Radioactive Pollution May Indirectly Affect Plants and Insect Herbivores: Evidence for Indirect Field Effects from Chernobyl and Fukushima. Microorganisms 2024; 12:364. [PMID: 38399767 PMCID: PMC10892324 DOI: 10.3390/microorganisms12020364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The biological impacts of the nuclear accidents in Chernobyl (1986) and Fukushima (2011) on wildlife have been studied in many organisms over decades, mainly from dosimetric perspectives based on laboratory experiments using indicator species. However, ecological perspectives are required to understand indirect field-specific effects among species, which are difficult to evaluate under dosimetric laboratory conditions. From the viewpoint that microbes play a fundamental role in ecosystem function as decomposers and symbionts for plants, we reviewed studies on microbes inhabiting soil and plants in Chernobyl and Fukushima in an attempt to find supporting evidence for indirect field-specific effects on plants and insect herbivores. Compositional changes in soil microbes associated with decreases in abundance and species diversity were reported, especially in heavily contaminated areas of both Chernobyl and Fukushima, which may accompany explosions of radioresistant species. In Chernobyl, the population size of soil microbes remained low for at least 20 years after the accident, and the abundance of plant-associated microbes, which are related to the growth and defense systems of plants, possibly decreased. These reported changes in microbes likely affect soil conditions and alter plant physiology. These microbe-mediated effects may then indirectly affect insect herbivores through food-mass-mediated, pollen-mediated, and metabolite-mediated interactions. Metabolite-mediated interactions may be a major pathway for ecological impacts at low pollution levels and could explain the decreases in insect herbivores in Fukushima. The present review highlights the importance of the indirect field effects of long-term low-dose radiation exposure under complex field circumstances.
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Affiliation(s)
| | - Joji M. Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara 903-0213, Okinawa, Japan;
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26
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Ducousso-Détrez A, Lahrach Z, Fontaine J, Lounès-Hadj Sahraoui A, Hijri M. Cultural techniques capture diverse phosphate-solubilizing bacteria in rock phosphate-enriched habitats. Front Microbiol 2024; 15:1280848. [PMID: 38384267 PMCID: PMC10879417 DOI: 10.3389/fmicb.2024.1280848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024] Open
Abstract
Phosphorus (P) deficiency is a common problem in croplands where phosphate-based fertilizers are regularly used to maintain bioavailable P for plants. However, due to their limited mobility in the soil, there has been an increased interest in microorganisms that can convert insoluble P into a bioavailable form, and their use to develop phosphate-solubilizing bioinoculants as an alternative to the conventional use of P fertilizers. In this study, we proposed two independent experiments and explored two entirely different habitats to trap phosphate-solubilizing bacteria (PSBs). In the first experiment, PSBs were isolated from the rhizoplane of native plant species grown in a rock-phosphate (RP) mining area. A subset of 24 bacterial isolates from 210 rhizoplane morphotypes was selected for the inorganic phosphate solubilizing activities using tricalcium phosphate (TCP) as the sole P source. In the second experiment, we proposed an innovative experimental setup to select mycohyphospheric bacteria associated to arbuscular mycorrhizal fungal hyphae, indigenous of soils where agronomic plant have been grown and trapped in membrane bag filled with RP. A subset of 25 bacterial isolates from 44 mycohyphospheric morphotypes was tested for P solubilizing activities. These two bacterial subsets were then screened for additional plant growth-promoting (PGP) traits, and 16S rDNA sequencing was performed for their identification. Overall, the two isolation experiments resulted in diverse phylogenetic affiliations of the PSB collection, showing only 4 genera (24%) and 5 species (17%) shared between the two communities, thus underlining the value of the two protocols, including the innovative mycohyphospheric isolate selection method, for selecting a greater biodiversity of cultivable PSB. All the rhizoplane and mycohyphospheric PSB were positive for ammonia production. Indol-3-acetic acid (IAA) production was observed for 13 and 20 isolates, respectively among rhizoplane and mycohyphospheric PSB, ranging, respectively, from 32.52 to 330.27 μg mL-1 and from 41.4 to 963.9 μg mL-1. Only five rhizoplane and 12 mycohyphospheric isolates were positively screened for N2 fixation. Four rhizoplane PSB were identified as siderophore producers, while none of the mycohyphospheric isolates were. The phenotype of one PSB rhizoplane isolate, assigned to Pseudomonas, showed four additive PGP activities. Some bacterial strains belonging to the dominant genera Bacillus and Pseudomonas could be considered potential candidates for further formulation of biofertilizer in order to develop bioinoculant consortia that promote plant P nutrition and growth in RP-enriched soils.
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Affiliation(s)
- Amandine Ducousso-Détrez
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, QC, Canada
- Université du Littoral Côte d’Opale, UR, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), SFR Condorcet FR CNRS, Calais, France
| | - Zakaria Lahrach
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, QC, Canada
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir, Morocco
| | - Joël Fontaine
- Université du Littoral Côte d’Opale, UR, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), SFR Condorcet FR CNRS, Calais, France
| | - Anissa Lounès-Hadj Sahraoui
- Université du Littoral Côte d’Opale, UR, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), SFR Condorcet FR CNRS, Calais, France
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, QC, Canada
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir, Morocco
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27
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Zhang C, de Pasquale S, Hartman K, Stanley CE, Berendsen RL, van der Heijden MGA. The microbial contribution to litter decomposition and plant growth. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13205. [PMID: 38018445 PMCID: PMC10866077 DOI: 10.1111/1758-2229.13205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/06/2023] [Indexed: 11/30/2023]
Abstract
Soil and plant roots are colonized by highly complex and diverse communities of microbes. It has been proposed that bacteria and fungi have synergistic effects on litter decomposition, but experimental evidence supporting this claim is weak. In this study, we manipulated the composition of two microbial kingdoms (Bacteria and Fungi) in experimental microcosms. In microcosms that were inoculated with fungi, litter loss was 47% higher than in microcosms that were not inoculated or only inoculated with bacteria. Combined inoculation with both bacteria and fungi did not significantly enhance decomposition compared with the fungi-only treatments, and, as such, we found no evidence for complementary effects using our experimental setup. Inoculation with fungi also had a positive impact on plant growth after 4 and 8 weeks (480% and 710% growth stimulation, respectively). After 16 weeks, plant biomass was highest in microcosms where both bacteria and fungi were present pointing to fungal-bacterial complementarity in stimulating plant growth. Overall, this study suggests that fungi are the main decomposers of plant litter and that the inoculated fungi contribute to plant growth in our experimental system.
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Affiliation(s)
- Changfeng Zhang
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Simone de Pasquale
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Kyle Hartman
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Claire E. Stanley
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Roeland L. Berendsen
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
| | - Marcel G. A. van der Heijden
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
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28
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Tang H, Zhong Z, Hou J, You L, Zhao Z, Kwok LY, Bilige M. Metagenomic analysis revealed the potential of lactic acid bacteria in improving natural saline-alkali land. Int Microbiol 2024; 27:311-324. [PMID: 37386210 DOI: 10.1007/s10123-023-00388-4] [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: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 07/01/2023]
Abstract
Management and improving saline-alkali land is necessary for sustainable agricultural development. We conducted a field experiment to investigate the effects of spraying lactic acid bacteria (LAB) on the cucumber and tomato plant soils. Three treatments were designed, including spraying of water, viable or sterilized LAB preparations to the soils of cucumber and tomato plants every 20 days. Spraying sterilized or viable LAB could reduce the soil pH, with a more obvious effect by using viable LAB, particularly after multiple applications. Metagenomic sequencing revealed that the soil microbiota in LAB-treated groups had higher alpha-diversity and more nitrogen-fixing bacteria compared with the water-treated groups. Both viable and sterilized LAB, but not water application, increased the complexity of the soil microbiota interactive network. The LAB-treated subgroups were enriched in some KEGG pathways compared with water or sterilized LAB subgroups, such as environmental information processing-related pathways in cucumber plant; and metabolism-related pathways in tomato plant, respectively. Redundancy analysis revealed association between some soil physico-chemical parameters (namely soil pH and total nitrogen) and bacterial biomarkers (namely Rhodocyclaceae, Pseudomonadaceae, Gemmatimonadaceae, and Nitrosomonadales). Our study demonstrated that LAB is a suitable strategy for decreasing soil pH and improving the microbial communities in saline-alkali land.
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Affiliation(s)
- Hai Tang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhi Zhong
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Jingqing Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Lijun You
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhixin Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Menghe Bilige
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
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Praise S, Miyazawa M, Phung LD, Nishiyama M, Kumar A, Watanabe T. Impact of nCuO containing treated wastewater on soil microbes and dissolved organic matter in paddy field leachate. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122923. [PMID: 37977365 DOI: 10.1016/j.envpol.2023.122923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
Using treated wastewater (TWW) resources in agriculture is a major pathway for disseminating nanoparticles. Copper-oxide nanoparticles (nCuO) offer potential benefits, but their presence in the environment poses risks to agricultural and environmental sustainability. This study examined soil microbial transformations and the composition of leachate dissolved organic matter (DOM) of paddy soils irrigated with nCuO-contaminated TWW at different concentrations (T2: 0.02 mgL-1, T3: 0.2 mgL-1, T4: 2.0 mgL-1) and examined the differences in Cu source (T5: 0.2 mgL-1 CuSO4). Results showed negative impacts on the absolute microbial abundance with up to 46 % reduction relative to the control treatment (T1). Changes in relative abundance of specific microbes at the genus level deviated from the corresponding phyla. Acidobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia phyla increased in the surface (0-3 cm) and subsurface (3-15 cm) layers responding differently to nCuO. In the 0-3 cm layer, Nitrospirae, Euryarchaeota, and Crenarchaeota increased, but only Dechloromonas genus from Proteobacteria increased with increasing nCuO. No significant variations were observed in the DOM composition, except in T4, which had a significantly low content of dissolved organic carbon (DOC), total dissolved nitrogen, and terrestrial humic-like and protein-like components. Ninety-eight distinct genera were identified, of which 44%, including 15 bacteria and two archaea, varied between the surface and subsurface, among treatments, and significantly correlated with more DOM parameters in the subsurface. T4 had the highest microbial diversity in the 0-3 layer, and Cu treatments slightly increased the diversity index in the subsurface. Moreover, the effects differed by Cu source, with T3 showing 10 % more reduction in the subsurface and 17 % less reduction in the surface than T5. The variable microbial responses to nCuO and their strong correlations with DOM highlight the need to consider the potential consequences of low nCuO concentrations on biogeochemical cycles.
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Affiliation(s)
- Susan Praise
- Faculty of Agriculture, Yamagata University, Yamagata, Wakaba Machi 1-23, Tsuruoka Shi, Yamagata, 997-8555, Japan.
| | - Masaaki Miyazawa
- Faculty of Agriculture, Yamagata University, Yamagata, Wakaba Machi 1-23, Tsuruoka Shi, Yamagata, 997-8555, Japan.
| | - Luc Duc Phung
- Faculty of Agriculture, Yamagata University, Yamagata, Wakaba Machi 1-23, Tsuruoka Shi, Yamagata, 997-8555, Japan.
| | - Masateru Nishiyama
- Faculty of Agriculture, Yamagata University, Yamagata, Wakaba Machi 1-23, Tsuruoka Shi, Yamagata, 997-8555, Japan.
| | - Arun Kumar
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India.
| | - Toru Watanabe
- Faculty of Agriculture, Yamagata University, Yamagata, Wakaba Machi 1-23, Tsuruoka Shi, Yamagata, 997-8555, Japan.
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Lee SM, Thapa Magar R, Jung MK, Kong HG, Song JY, Kwon JH, Choi M, Lee HJ, Lee SY, Khan R, Kim JF, Lee SW. Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health. THE ISME JOURNAL 2024; 18:wrae120. [PMID: 38952008 PMCID: PMC11253211 DOI: 10.1093/ismejo/wrae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.
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Affiliation(s)
- Sang-Moo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Roniya Thapa Magar
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Min Kyeong Jung
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyun Gi Kong
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Joo Hwan Kwon
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Minseo Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyoung Ju Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Jihyun F Kim
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Microbiome Initiative, Yonsei University, Seoul 03722, Republic of Korea
| | - Seon-Woo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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Pazos-Rojas LA, Cuellar-Sánchez A, Romero-Cerón AL, Rivera-Urbalejo A, Van Dillewijn P, Luna-Vital DA, Muñoz-Rojas J, Morales-García YE, Bustillos-Cristales MDR. The Viable but Non-Culturable (VBNC) State, a Poorly Explored Aspect of Beneficial Bacteria. Microorganisms 2023; 12:39. [PMID: 38257865 PMCID: PMC10818521 DOI: 10.3390/microorganisms12010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Many bacteria have the ability to survive in challenging environments; however, they cannot all grow on standard culture media, a phenomenon known as the viable but non-culturable (VBNC) state. Bacteria commonly enter the VBNC state under nutrient-poor environments or under stressful conditions. This review explores the concept of the VBNC state, providing insights into the beneficial bacteria known to employ this strategy. The investigation covers different chemical and physical factors that can induce the latency state, cell features, and gene expression observed in cells in the VBNC state. The review also covers the significance and applications of beneficial bacteria, methods of evaluating bacterial viability, the ability of bacteria to persist in environments associated with higher organisms, and the factors that facilitate the return to the culturable state. Knowledge about beneficial bacteria capable of entering the VBNC state remains limited; however, beneficial bacteria in this state could face adverse environmental conditions and return to a culturable state when the conditions become suitable and continue to exert their beneficial effects. Likewise, this unique feature positions them as potential candidates for healthcare applications, such as the use of probiotic bacteria to enhance human health, applications in industrial microbiology for the production of prebiotics and functional foods, and in the beer and wine industry. Moreover, their use in formulations to increase crop yields and for bacterial bioremediation offers an alternative pathway to harness their beneficial attributes.
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Affiliation(s)
- Laura Abisaí Pazos-Rojas
- Faculty of Stomatology, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico; (L.A.P.-R.); (A.R.-U.)
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Alma Cuellar-Sánchez
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Ana Laura Romero-Cerón
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - América Rivera-Urbalejo
- Faculty of Stomatology, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico; (L.A.P.-R.); (A.R.-U.)
| | - Pieter Van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Diego Armando Luna-Vital
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Jesús Muñoz-Rojas
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
| | - Yolanda Elizabeth Morales-García
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
- Faculty of Biological Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico
| | - María del Rocío Bustillos-Cristales
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
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Kar S, Mishra SK, Misra S, Agarwal R, Kumar S, Chauhan PS. Endophytic Alkalotolerant Plant Growth-Promoting Bacteria Render Maize (Zea mays L.) Growth Under Alkaline Stress. Curr Microbiol 2023; 81:43. [PMID: 38117393 DOI: 10.1007/s00284-023-03557-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023]
Abstract
This study investigates the role of bacterial endophytes from extreme alkaline environments in alleviating alkaline stress and plant development. Stressful environmental factors, such as soil acidity and alkalinity/sodicity, frequently affect plant development. In the present study, alkaline-tolerant endophytic strains were isolated from three plant species Saccharum munja, Calotropis procera, and Chenopodium album, and 15 out of the total of 48 isolates were selected for further examination of their abiotic stress tolerance. Molecular analysis based on 16S rRNA gene sequencing revealed strains from Enterobacter, Acinetobacter, Stenotrophomonas, Bacillus, Lysinibacillus, and Mammaliicoccus genera. Out of 15 isolates based on their quantitative PGP traits and abiotic stress tolerance, 6 were finally selected for greenhouse experiments. Under alkaline conditions, results demonstrated that the strains from the genera Enterobacter, Bacillus, Stenotrophomonas, and Lysinibacillus had beneficial effects on maize growth. These findings suggest that using a combination of bacteria with multiple plant growth-promoting attributes could be a sustainable approach to enhance agricultural yield, even in a challenging alkaline environment. The study concludes that the application of bacterial endophytes from plants growing in extremely alkaline environments might provide other plants with similar stress-tolerance abilities. The outcome of the study provides a basis for future exploration of the mechanisms underlying endophyte-induced stress tolerance.
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Affiliation(s)
- Srishti Kar
- Microbial Technologies Division, Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Shashank Kumar Mishra
- Microbial Technologies Division, Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Sankalp Misra
- Microbial Technologies Division, Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, Uttar Pradesh, 225003, India
| | - Renuka Agarwal
- Microbial Technologies Division, Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Susheel Kumar
- Microbial Technologies Division, Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Puneet Singh Chauhan
- Microbial Technologies Division, Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
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Williamson J, Matthews AC, Raymond B. Competition and co-association, but not phosphorous availability, shape the benefits of phosphate-solubilizing root bacteria for maize ( Zea mays). Access Microbiol 2023; 5:000543.v3. [PMID: 38188242 PMCID: PMC10765048 DOI: 10.1099/acmi.0.000543.v3] [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: 12/09/2022] [Accepted: 11/16/2023] [Indexed: 01/09/2024] Open
Abstract
Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilizing rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. We used maize-associated rhizobacteria with varying phosphate solubilization ability in experiments in soil, sterilized soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated the intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: the beneficial effects of one Serratia isolate were only detectable when plants were inoculated with a single strain and the beneficial effects of a competition-sensitive Rhizobium was only detectable in sterilized soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilization may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.
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Affiliation(s)
- Joseph Williamson
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
- Centre for Biodiversity and Environment Research, Department of Genetics, University College London, Gower St, London, WC1E 6BT, UK
| | - Andrew Charles Matthews
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
- College of Life and Environmental Sciences, Penryn campus, University of Exeter, Penryn, TR10 9FE, UK
| | - Ben Raymond
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
- College of Life and Environmental Sciences, Penryn campus, University of Exeter, Penryn, TR10 9FE, UK
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Kim J, de Lorenzo V, Goñi‐Moreno Á. Pressure-dependent growth controls 3D architecture of Pseudomonas putida microcolonies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:708-715. [PMID: 37231623 PMCID: PMC10667634 DOI: 10.1111/1758-2229.13182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
Colony formation is key to many ecological and biotechnological processes. In its early stages, colony formation involves the concourse of a number of physical and biological parameters for generation of a distinct 3D structure-the specific influence of which remains unclear. We focused on a thus far neglected aspect of the process, specifically the consequences of the differential pressure experienced by cells in the middle of a colony versus that endured by bacteria located in the growing periphery. This feature was characterized experimentally in the soil bacterium Pseudomonas putida. Using an agent-based model we recreated the growth of microcolonies in a scenario in which pressure was the only parameter affecting proliferation of cells. Simulations exposed that, due to constant collisions with other growing bacteria, cells have virtually no free space to move sideways, thereby delaying growth and boosting chances of overlapping on top of each other. This scenario was tested experimentally on agar surfaces. Comparison between experiments and simulations suggested that the inside/outside differential pressure determines growth, both timewise and in terms of spatial directions, eventually moulding colony shape. We thus argue that-at least in the case studied-mere physical pressure of growing cells suffices to explain key dynamics of colony formation.
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Affiliation(s)
- Juhyun Kim
- School of Life ScienceBK21 FOUR KNU Creative BioResearch Group Kyungpook National UniversityDaeguRepublic of Korea
| | - Víctor de Lorenzo
- Systems Biology DepartmentCentro Nacional de Biotecnología (CNB‐CSIC)Cantoblanco‐MadridSpain
| | - Ángel Goñi‐Moreno
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)‐Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC)MadridSpain
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Goswami SK, Kashyap AS, Kumar R, Gujjar RS, Singh A, Manzar N. Harnessing Rhizospheric Microbes for Eco-friendly and Sustainable Crop Production in Saline Environments. Curr Microbiol 2023; 81:14. [PMID: 38006515 DOI: 10.1007/s00284-023-03538-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/24/2023] [Indexed: 11/27/2023]
Abstract
Soil salinization is a global issue that negatively impacts crop yield and has become a prime concern for researchers worldwide. Many important crop plants are susceptible to salinity-induced stresses, including ionic and osmotic stress. Approximately, 20% of the world's cultivated and 33% of irrigated land is affected by salt. While various agricultural practices have been successful in alleviating salinity stress, they can be costly and not environment-friendly. Therefore, there is a need for cost-effective and eco-friendly practices to improve soil health. One promising approach involves utilizing microbes found in the vicinity of plant roots to mitigate the effects of salinity stress and enhance plant growth as well as crop yield. By exploiting the salinity tolerance of plants and their associated rhizospheric microorganisms, which have plant growth-promoting properties, it is possible to reduce the adverse effects of salt stress on crop plants. The soil salinization is a common problem in the world, due to which we are unable to use the saline land. To make proper use of this land for different crops, microorganisms can play an important role. Looking at the increasing population of the world, this will be an appreciated effort to make the best use of the wasted land for food security. The updated information on this issue is needed. In this context, this article provides a concise review of the latest research on the use of salt-tolerant rhizospheric microorganisms to mitigate salinity stress in crop plants.
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Affiliation(s)
- Sanjay K Goswami
- ICAR-Indian Institute of Sugarcane Research, Rai Bareli Road, Dilkusha, Lucknow, Uttar Pradesh, 220026, India
| | - Abhijeet S Kashyap
- ICAR-National Bureau of Agriculturally Important Microorganism, Mau, 275103, India
| | - Rajeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Rai Bareli Road, Dilkusha, Lucknow, Uttar Pradesh, 220026, India
| | - Ranjit Singh Gujjar
- ICAR-Indian Institute of Sugarcane Research, Rai Bareli Road, Dilkusha, Lucknow, Uttar Pradesh, 220026, India.
| | - Arjun Singh
- ICAR-CSSRI Regional Research Station, Rai Bareli Road, Dilkusha, Lucknow, Uttar Pradesh, 220026, India
| | - Nazia Manzar
- ICAR-National Bureau of Agriculturally Important Microorganism, Mau, 275103, India
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Wójcik M, Koper P, Żebracki K, Marczak M, Mazur A. Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil. Int J Mol Sci 2023; 24:16679. [PMID: 38069003 PMCID: PMC10706249 DOI: 10.3390/ijms242316679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.
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Affiliation(s)
| | | | | | | | - Andrzej Mazur
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (P.K.); (K.Ż.); (M.M.)
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Lee DH, Kim YK, Son Y, Park GH, Kwon HY, Park Y, Park EJ, Lee SY, Kim HJ. Multivariate Analysis among Marker Compounds, Environmental Factors, and Fruit Quality of Schisandra chinensis at Different Locations in South Korea. PLANTS (BASEL, SWITZERLAND) 2023; 12:3877. [PMID: 38005775 PMCID: PMC10675420 DOI: 10.3390/plants12223877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
This study aimed to investigate the correlation among the contents of marker compounds, growth characteristics, and environmental factors of Schisandra chinensis fruits across South Korea. The fruits were collected from 36 cultivation sites in 28 regions across the country. We investigated nine growth characteristics, twelve soil physicochemical properties, eight meteorological data, and three marker compounds in this study. We optimized and validated an optimized method for quantifying marker compounds using UPLC and performed correlation analysis among the contents of marker compounds, growth characteristics, and environmental factors. The UPLC-UV method for analyzing marker compounds was validated by measuring linearity, LOD, LOQ, precision, and accuracy. The marker compounds were negatively correlated with the fruit size and sugar contents, and growth characteristics were negatively correlated with some physicochemical properties of the soil. The results of this study can be used as basic data for the standard cultural practices and quality control of S. chinensis fruits.
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Affiliation(s)
- Dong Hwan Lee
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju-si 36040, Republic of Korea; (D.H.L.); (Y.-K.K.); (Y.S.); (G.H.P.); (H.-Y.K.); (S.-Y.L.)
| | - Young-Ki Kim
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju-si 36040, Republic of Korea; (D.H.L.); (Y.-K.K.); (Y.S.); (G.H.P.); (H.-Y.K.); (S.-Y.L.)
| | - Yonghwan Son
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju-si 36040, Republic of Korea; (D.H.L.); (Y.-K.K.); (Y.S.); (G.H.P.); (H.-Y.K.); (S.-Y.L.)
| | - Gwang Hun Park
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju-si 36040, Republic of Korea; (D.H.L.); (Y.-K.K.); (Y.S.); (G.H.P.); (H.-Y.K.); (S.-Y.L.)
| | - Hae-Yun Kwon
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju-si 36040, Republic of Korea; (D.H.L.); (Y.-K.K.); (Y.S.); (G.H.P.); (H.-Y.K.); (S.-Y.L.)
| | - Youngki Park
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (Y.P.); (E.-J.P.)
| | - Eung-Jun Park
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (Y.P.); (E.-J.P.)
| | - Sun-Young Lee
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju-si 36040, Republic of Korea; (D.H.L.); (Y.-K.K.); (Y.S.); (G.H.P.); (H.-Y.K.); (S.-Y.L.)
| | - Hyun-Jun Kim
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju-si 36040, Republic of Korea; (D.H.L.); (Y.-K.K.); (Y.S.); (G.H.P.); (H.-Y.K.); (S.-Y.L.)
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Ujvári G, Capo L, Grassi A, Cristani C, Pagliarani I, Turrini A, Blandino M, Giovannetti M, Agnolucci M. Agronomic strategies to enhance the early vigor and yield of maize. Part I: the role of seed applied biostimulant, hybrid and starter fertilization on rhizosphere bacteria profile and diversity. FRONTIERS IN PLANT SCIENCE 2023; 14:1240310. [PMID: 38023909 PMCID: PMC10651756 DOI: 10.3389/fpls.2023.1240310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
The sustainable intensification of maize-based systems may reduce greenhouse-gas emissions and the excessive use of non-renewable inputs. Considering the key role that the microbiological fertility has on crop growth and resilience, it is worth of interest studying the role of cropping system on the rhizosphere bacterial communities, that affect soil health and biological soil fertility. In this work we monitored and characterized the diversity and composition of native rhizosphere bacterial communities during the early growth phases of two maize genotypes of different early vigor, using a nitrogen (N)-phosphorus (P) starter fertilization and a biostimulant seed treatment, in a growth chamber experiment, by polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA gene and amplicon sequencing. Cluster analyses showed that the biostimulant treatment affected the rhizosphere bacterial microbiota of the ordinary hybrid more than that of the early vigor, both at plant emergence and at the 5-leaf stage. Moreover, the diversity indices calculated from the community profiles, revealed significant effects of NP fertilization on richness and the estimated effective number of species (H2) in both maize genotypes, while the biostimulant had a positive effect on plant growth promoting community of the ordinary hybrid, both at the plant emergence and at the fifth leaf stage. Our data showed that maize genotype was the major factor shaping rhizosphere bacterial community composition suggesting that the root system of the two maize hybrids recruited a different microbiota. Moreover, for the first time, we identified at the species and genus level the predominant native bacteria associated with two maize hybrids differing for vigor. These results pave the way for further studies to be performed on the effects of cropping system and specific crop practices, considering also the application of biostimulants, on beneficial rhizosphere microorganisms.
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Affiliation(s)
- Gergely Ujvári
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Luca Capo
- Department of Agriculture, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Arianna Grassi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Caterina Cristani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Irene Pagliarani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Massimo Blandino
- Department of Agriculture, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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Wang H, Du X, Zhang Z, Feng F, Zhang J. Rhizosphere interface microbiome reassembly by arbuscular mycorrhizal fungi weakens cadmium migration dynamics. IMETA 2023; 2:e133. [PMID: 38868220 PMCID: PMC10989832 DOI: 10.1002/imt2.133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 06/14/2024]
Abstract
The prevalence of cadmium (Cd)-polluted agricultural soils is increasing globally, and arbuscular mycorrhizal fungi (AMF) can reduce the absorption of heavy metals by plants and improve mineral nutrition. However, the immobilization of the rhizosphere on cadmium is often overlooked. In this study, Glomus mosseae and Medicago sativa were established as symbiotes, and Cd migration and environmental properties in the rhizosphere were analyzed. AMF reduced Cd migration, and Cd2+ changed to an organic-bound state. AMF symbiosis treatment and Cd exposure resulted in microbial community variation, exhibiting a distinct deterministic process (|βNTI| > 2), which ultimately resulted in a core microbiome function of heavy metal resistance and nutrient cycling. AMF increased available N and P, extracellular enzyme activity (LaC, LiP, and CAT), organic matter content (TOC, EOC, and GRSP), and Eh of the rhizosphere soil, significantly correlating with decreased Cd migration (p < 0.05). Furthermore, AMF significantly affected root metabolism by upregulating 739 metabolites, with flavonoids being the main factor causing microbiome variation. The structural equation model and variance partial analysis revealed that the superposition of the root metabolites, microbial, and soil exhibited the maximum explanation rate for Cd migration reduction (42.4%), and the microbial model had the highest single explanation rate (15.5%). Thus, the AMF in the rhizosphere microenvironment can regulate metabolite-soil-microbial interactions, reducing Cd migration. In summary, the study provides a new scientific explanation for how AMF improves plant Cd tolerance and offers a sustainable solution that could benefit both the environment and human health.
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Affiliation(s)
- Hong‐Rui Wang
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Xin‐Ran Du
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Zhuo‐Yun Zhang
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Fu‐Juan Feng
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Jia‐Ming Zhang
- College of Life ScienceNortheast Forestry UniversityHarbinChina
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Li J, Wang J, Liu H, Macdonald CA, Singh BK. Microbial inoculants with higher capacity to colonize soils improved wheat drought tolerance. Microb Biotechnol 2023; 16:2131-2144. [PMID: 37815273 PMCID: PMC10616649 DOI: 10.1111/1751-7915.14350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023] Open
Abstract
Microbial inoculants have gained increasing attention worldwide as an eco-friendly solution for improving agriculture productivity. Several studies have demonstrated their potential benefits, such as enhanced resistance to drought, salinity, and pathogens. However, the beneficial impacts of inoculants remain inconsistent. This variability is attributed to limited knowledge of the mechanisms by which microbial inoculants affect crop growth and a lack of ecological characteristics of these inoculants that limit our ability to predict their beneficial effects. The first important step is believed to be the evaluation of the inoculant's ability to colonize new habitats (soils and plant roots), which could provide crops with beneficial functions and improve the consistency and efficiency of the inoculants. In this study, we aimed to investigate the impact of three microbial inoculants (two bacterial: P1 and P2, and one fungal: P3) on the growth and stress responses of three wheat varieties in two different soil types under drought conditions. Furthermore, we investigated the impact of microbial inoculants on soil microbial communities. Plant biomass and traits were measured, and high-throughput sequencing was used to characterize bulk and rhizosphere soil microbiomes after exposure to drought stress. Under drought conditions, plant shoot weight significantly increased (11.37%) under P1 treatments compared to uninoculated controls. In addition, total nitrogen enzyme activity increased significantly under P1 in sandy soil but not in clay soil. Importantly, network analyses revealed that P1, consisting of Bacillus paralicheniformis and Bacillus subtilis, emerged as the keystone taxa in sandy soil. Conversely, P2 and P3 failed to establish as keystone taxa, which may explain their insignificant impact on wheat performance under drought conditions. In conclusion, our study emphasizes the importance of effective colonization by microbial inoculants in promoting crop growth under drought conditions. Our findings support the development of microbial inoculants that robustly colonize plant roots for improved agricultural productivity.
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Affiliation(s)
- Jiayu Li
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, New South Wales, Penrith, Australia
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
| | - Catriona A Macdonald
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, New South Wales, Penrith, Australia
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Boondaeng A, Vaithanomsat P, Apiwatanapiwat W, Trakunjae C, Janchai P, Suriyachai N, Kreetachat T, Wongcharee S, Imman S. Biological Conversion of Agricultural Wastes into Indole-3-acetic Acid by Streptomyces lavenduligriseus BS50-1 Using a Response Surface Methodology (RSM). ACS OMEGA 2023; 8:40433-40441. [PMID: 37929142 PMCID: PMC10620907 DOI: 10.1021/acsomega.3c05004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Agricultural waste is an alternative source for plant growth regulator biosynthesis by microorganisms. Actinobacteria are important soil microbes that significantly impact the soil as plant growth-promoting rhizobacteria and biofertilizers. This study focused on developing low-cost medium based on bagasse to improve indole-3-acetic acid (IAA) production by Streptomyces lavenduligriseus BS50-1 using a response surface methodology (RSM). Among 34 actinobacterial strains, S. lavenduligriseus BS50-1 produced the highest IAA level within the selected medium. An RSM based on a central composite design optimized the appropriate nutrients for IAA production. Thus, glucose hydrolysate and l-tryptophan at concentrations of 3.55 and 5.0 g/L, respectively, were the optimal factors that improved IAA production from 37.50 to 159.47 μg/mL within 168 h. This study reported a potential application of leftover bagasse as the raw material for cultivating actinobacteria, which efficiently produce IAA to promote plant growth.
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Affiliation(s)
- Antika Boondaeng
- Kasetsart Agricultural
and Agro-Industrial Product Improvement Institute, Kasetsart University, Bangkok 10900, Thailand
| | - Pilanee Vaithanomsat
- Kasetsart Agricultural
and Agro-Industrial Product Improvement Institute, Kasetsart University, Bangkok 10900, Thailand
| | - Waraporn Apiwatanapiwat
- Kasetsart Agricultural
and Agro-Industrial Product Improvement Institute, Kasetsart University, Bangkok 10900, Thailand
| | - Chanaporn Trakunjae
- Kasetsart Agricultural
and Agro-Industrial Product Improvement Institute, Kasetsart University, Bangkok 10900, Thailand
| | - Phornphimon Janchai
- Kasetsart Agricultural
and Agro-Industrial Product Improvement Institute, Kasetsart University, Bangkok 10900, Thailand
| | - Nopparat Suriyachai
- School of Energy and Environment, University
of Phayao, Tambon Maeka, Amphur Muang, Phayao 56000, Thailand
| | - Torpong Kreetachat
- School of Energy and Environment, University
of Phayao, Tambon Maeka, Amphur Muang, Phayao 56000, Thailand
| | - Surachai Wongcharee
- Field
of Environmental Engineering, Faculty of Engineering, Mahasarakham University, Khamriang, Kantarawichai, Mahasarakham 44150, Thailand
| | - Saksit Imman
- School of Energy and Environment, University
of Phayao, Tambon Maeka, Amphur Muang, Phayao 56000, Thailand
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Martínez-Calvo A, Trenado-Yuste C, Lee H, Gore J, Wingreen NS, Datta SS. Interfacial morphodynamics of proliferating microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563665. [PMID: 37961366 PMCID: PMC10634769 DOI: 10.1101/2023.10.23.563665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of the interface between such domains-which in turn influences the interactions between cells and overall community function? Here, we address this question by developing a continuum model of a 2D spatially-structured microbial community with two distinct cell types. We find that, depending on the balance of the different cell proliferation rates and substrate friction coefficients, the interface between domains is either stable and smooth, or unstable and develops finger-like protrusions. We establish quantitative principles describing when these different interfacial behaviors arise, and find good agreement both with the results of previous experimental reports as well as new experiments performed here. Our work thus helps to provide a biophysical basis for understanding the interfacial morphodynamics of proliferating microbial communities, as well as a broader range of proliferating active systems.
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Lei LY, Xiong ZX, Li JL, Yang DZ, Li L, Chen L, Zhong QF, Yin FY, Li RX, Cheng ZQ, Xiao SQ. Biological control of Magnaporthe oryzae using natively isolated Bacillus subtilis G5 from Oryza officinalis roots. Front Microbiol 2023; 14:1264000. [PMID: 37876784 PMCID: PMC10591090 DOI: 10.3389/fmicb.2023.1264000] [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: 07/20/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023] Open
Abstract
Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production causing significant crop losses and impacting grain quality. The annual loss of rice production due to this disease ranges from 10% to 30%. The use of biologically controlled strains, instead of chemical pesticides, to control plant diseases has become a research hotspot. In this study, an antagonistic endophytic bacterial strain was isolated from the roots of Oryza officinalis using the traditional isolation and culture methods. A phylogenetic tree based on 16S RNA and whole-genome sequencing identified isolate G5 as a strain of Bacillus subtilis. This isolate displayed strong antagonistic effects against different physiological strains of M. oryzae. After co-culture in LB medium for 7 days, the inhibition rates of the mycelial growth of four strains of M. oryzae, ZB15, WH97, Guy11, and T-39800E were 98.07 ± 0.0034%, 98.59 ± 0.0051%, 99.16 ± 0.0012%, and 98.69 ± 0.0065%, respectively. Isolate G5 significantly inhibited the formation of conidia of M. oryzae, with an inhibition rate of 97% at an OD600 of 2. Isolate G5 was able to provide 66.81% protection against rice blast under potted conditions. Whole-genome sequencing revealed that the genome size of isolate G5 was 4,065,878 bp, including 4,182 coding genes. Using the anti-SMASH software, 14 secondary metabolite synthesis gene clusters were predicted to encode antifungal substances, such as fengycin, surfactin, and bacilysin. The G5 isolate also contained genes related to plant growth promotion. These findings provide a theoretical basis for expounding the biocontrol mechanisms of this strain and suggest further development of biogenic agents that could effectively inhibit rice blast pathogen growth and reduce crop damage, while being environmentally friendly, conducive to ecological development, and a sustainable alternative to chemical pesticides. This study also enriches the relevant research on endophytes of wild rice, which proves that wild rice is a valuable microbial resource bank.
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Affiliation(s)
- Ling-Yun Lei
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Zi-Xuan Xiong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Jin-Lu Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - De-Zheng Yang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Liu Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ling Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiao-Fang Zhong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fu-You Yin
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Rong-Xin Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Zai-Quan Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Su-Qin Xiao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Aizaz M, Lubna, Ahmad W, Khan I, Asaf S, Bilal S, Jan R, Asif S, Waqas M, Khan AL, Kim KM, AL-Harrasi A. Exploring the potential of halotolerant bacteria from coastal regions to mitigate salinity stress in wheat: physiological, molecular, and biochemical insights. FRONTIERS IN PLANT SCIENCE 2023; 14:1224731. [PMID: 37810397 PMCID: PMC10556533 DOI: 10.3389/fpls.2023.1224731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Salinity stress, a significant global abiotic stress, is caused by various factors such as irrigation with saline water, fertilizer overuse, and drought conditions, resulting in reduced agricultural production and sustainability. In this study, we investigated the use of halotolerant bacteria from coastal regions characterized by high salinity as a solution to address the major environmental challenge of salinity stress. To identify effective microbial strains, we isolated and characterized 81 halophilic bacteria from various sources, such as plants, rhizosphere, algae, lichen, sea sediments, and sea water. We screened these bacterial strains for their plant growth-promoting activities, such as indole acetic acid (IAA), phosphate solubilization, and siderophore production. Similarly, the evaluation of bacterial isolates through bioassay revealed that approximately 22% of the endophytic isolates and 14% of rhizospheric isolates exhibited a favorable influence on seed germination and seedling growth. Among the tested isolates, GREB3, GRRB3, and SPSB2 displayed a significant improvement in all growth parameters compared to the control. As a result, these three isolates were utilized to evaluate their efficacy in alleviating the negative impacts of salt stress (150 mM, 300 mM, and seawater (SW)) on the growth of wheat plants. The result showed that shoot length significantly increased in plants inoculated with bacterial isolates up to 15% (GREB3), 16% (GRRB3), and 24% (SPSB2), respectively, compared to the control. The SPSB2 strain was particularly effective in promoting plant growth and alleviating salt stress. All the isolates exhibited a more promotory effect on root length than shoot length. Under salt stress conditions, the GRRB3 strain significantly impacted root length, leading to a boost of up to 6%, 5%, and 3.8% at 150 mM, 300 mM, and seawater stress levels, respectively. The bacterial isolates also positively impacted the plant's secondary metabolites and antioxidant enzymes. The study also identified the WDREB2 gene as highly upregulated under salt stress, whereas DREB6 was downregulated. These findings demonstrate the potential of beneficial microbes as a sustainable approach to mitigate salinity stress in agriculture.
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Affiliation(s)
- Muhammad Aizaz
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
| | - Lubna
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
| | - Waqar Ahmad
- Department of Engineering Technology, University of Houston, Sugar Land, TX, United States
| | - Ibrahim Khan
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
| | - Saqib Bilal
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Waqas
- Department of Agriculture Extension, Government of Khyber Pakhtunkhwa, Mardan, Pakistan
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, United States
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed AL-Harrasi
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
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Huang S, Zhang X, Song Z, Rahman MU, Fan B. Transcriptional Profiling and Transposon Mutagenesis Study of the Endophyte Pantoea eucalypti FBS135 Adapting to Nitrogen Starvation. Int J Mol Sci 2023; 24:14282. [PMID: 37762583 PMCID: PMC10532344 DOI: 10.3390/ijms241814282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The research on plant endophytes has been drawing a lot of attention in recent years. Pantoea belongs to a group of endophytes with plant growth-promoting activity and has been widely used in agricultural fields. In our earlier studies, Pantoea eucalypti FBS135 was isolated from healthy-growing Pinus massoniana and was able to promote pine growth. P. eucalypti FBS135 can grow under extremely low nitrogen conditions. To understand the mechanism of the low-nitrogen tolerance of this bacterium, the transcriptome of FBS135 in the absence of nitrogen was examined in this study. We found that FBS135 actively regulates its gene expression in response to nitrogen deficiency. Nearly half of the number (4475) of genes in FBS135 were differentially expressed under this condition, mostly downregulated, while it significantly upregulated many transportation-associated genes and some nitrogen metabolism-related genes. In the downregulated genes, the ribosome pathway-related ones were significantly enriched. Meanwhile, we constructed a Tn5 transposon library of FBS135, from which four genes involved in low-nitrogen tolerance were screened out, including the gene for the host-specific protein J, RNA polymerase σ factor RpoS, phosphoribosamine-glycine ligase, and serine acetyltransferase. Functional analysis of the genes revealed their potential roles in the adaptation to nitrogen limitation. The results obtained in this work shed light on the mechanism of endophytes represented by P. eucalypti FBS135, at the overall transcriptional level, to an environmentally limited nitrogen supply and provided a basis for further investigation on this topic.
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Affiliation(s)
- Shengquan Huang
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Xiuyu Zhang
- Department of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zongwen Song
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Mati Ur Rahman
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Ben Fan
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
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Wang W, Sheng Y. Enhanced nitrogen removal in low-carbon saline wastewater by adding functional bacteria into Sesuvium portulacastrum constructed wetlands. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115234. [PMID: 37418946 DOI: 10.1016/j.ecoenv.2023.115234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/07/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Functional bacterial communities (FBC) have members of different taxonomic biochemical groups, such as N2-fixation, nitrification and denitrification. This study explored the mechanism of the FBC from an upflow three-dimensional biofilm electrode reactor on enhancing the nitrogen removal efficiencies in a Sesuvium potulacastum (S. potulacastum) constructed wetland. There were high abundances of denitrifying bacteria detected in the FBC, and they had potential metabolic processes for nitrogen reduction. In the constructed wetland, cellular nitrogen compounds of S. potulacastum were enriched by overexpressed differentially expressed genes (DEGs), and the napA, narG, nirK, nirS, qnorB, and NosZ genes related to the denitrification process had more copies under FBC treatment. Nitrogen metabolism in root bacterial communities (RBCs) was activated in the FBC group compared with the control group without FBC. Finally, these FBCs improved the removal efficiencies of DTN (dissolved total nitrogen), NO3¯-N, NO2¯-N, and NH4+-N by 84.37 %, 87.42 %, 67.51 %, and 92.57 %, respectively, and their final concentrations met the emission standards of China. These findings indicate that adding FBC into S. potulacastum-constructed wetlands would result in high nitrogen removal efficiencies from wastewater and have large potential applications in further water treatment technology.
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Affiliation(s)
- Wenjing Wang
- Research Center for Coastal Environment Engineering Technology of Shandong Province, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| | - Yanqing Sheng
- Research Center for Coastal Environment Engineering Technology of Shandong Province, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China.
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Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
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Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
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Tauro TP, Nezomba H, Mtambanengwe F, Mapfumo P. Increasing phosphorus rate alters microbial dynamics and soil available P in a Lixisol of Zimbabwe. PLoS One 2023; 18:e0291226. [PMID: 37682930 PMCID: PMC10490935 DOI: 10.1371/journal.pone.0291226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Soil phosphorus (P) deficiency is a major challenge to food security in most parts of sub-Saharan Africa, including Zimbabwe, where farmers largely depend on local organic nutrient resources as fertilizer in the production of crops. Soil microorganisms can contribute to synchronous availability of soil P to plants through regulating immobilization and mineralization cycles of soil P pools but their activity may be influenced by antecedent soil P, P fertilizer application regimes and P uptake by plants. Using soils collected from plots where Crotalaria juncea (high quality), Calliandra calothyrsus (medium quality), cattle manure (variable quality), maize stover and Pinus patula sawdust (both low quality) were applied at the rate of 4 t C ha-1 with 16 kg P ha-1 at the start of every season over 16 seasons. A pot study was conducted to evaluate the influence of increasing inorganic P fertilizer rates (26 and 36 kg P ha-1) on soil microbial dynamics, soil P pools, and maize P uptake. Results indicated that nineteen (19) fungal and forty-two (42) bacterial colonies were identified over the study period. Fungi dominated bacteria on day one, with Aspergillus niger showing a 30-98% abundance that depends on organic resource quality. Overall, microbial diversity peaked activity characterized succession on day 29, which coincided with a significant (P<0.05) increase in P availability. Increasing P rate to 26 kg P ha-1 amplified the microbial diverse peak activity under medium-high quality resources while under the control the peak emerged earlier on day 15. Mucor and Bacillus had peak abundances on day 43 and 57, respectively, across treatments regardless of P rates. Treatment and P rate had a significant (P<0.01) effect on microbial P. Bacteria were more responsive to added P than fungi. Increasing P to 36 kg P ha-1 also stimulated an earlier microbial diverse peak activity under maize stover on day 15. Addition of P alone, without supplying complementary nutrients such as N, did not have a positive effect on maize P uptake. Farmers need to co-apply medium-high quality organic resources with high fertilizer P rates to increase microbial diversity, plant available P and maize growth on sandy soils (Lixisols). Our results suggest that there is a need to reconsider existing P fertilizer recommendations, currently pegged at between 26 and 30 kg P ha-1, for maize production on sandy soils as well as develop new fertilizer formulations to intensify crop production in Zimbabwe.
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Affiliation(s)
- Tonny P. Tauro
- Department of Soil Science & Environment, University of Zimbabwe, Harare, Zimbabwe
- Department of Natural Resources Management, Marondera University of Agricultural Sciences & Technology, Marondera, Zimbabwe
| | - Hatirarami Nezomba
- Department of Soil Science & Environment, University of Zimbabwe, Harare, Zimbabwe
| | | | - Paul Mapfumo
- Department of Soil Science & Environment, University of Zimbabwe, Harare, Zimbabwe
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49
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Ajeethan N, Yurgel SN, Abbey L. Role of Bacteria-Derived Flavins in Plant Growth Promotion and Phytochemical Accumulation in Leafy Vegetables. Int J Mol Sci 2023; 24:13311. [PMID: 37686117 PMCID: PMC10488295 DOI: 10.3390/ijms241713311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Sinorhizobium meliloti 1021 bacteria secretes a considerable amount of flavins (FLs) and can form a nitrogen-fixing symbiosis with legumes. This strain is also associated with non-legume plants. However, its role in plant growth promotion (PGP) of non-legumes is not well understood. The present study evaluated the growth and development of lettuce (Lactuca sativa) and kale (Brassica oleracea var. acephala) plants inoculated with S. meliloti 1021 (FL+) and its mutant 1021ΔribBA, with a limited ability to secrete FLs (FL-). The results from this study indicated that inoculation with 1021 significantly (p < 0.05) increased the lengths and surface areas of the roots and hypocotyls of the seedlings compared to 1021ΔribBA. The kale and lettuce seedlings recorded 19% and 14% increases in total root length, respectively, following inoculation with 1021 compared to 1021ΔribBA. A greenhouse study showed that plant growth, photosynthetic rate, and yield were improved by 1021 inoculation. Moreover, chlorophylls a and b, and total carotenoids were more significantly (p < 0.05) increased in kale plants associated with 1021 than non-inoculated plants. In kale, total phenolics and flavonoids were significantly (p < 0.05) increased by 6% and 23%, respectively, and in lettuce, the increments were 102% and 57%, respectively, following 1021 inoculation. Overall, bacterial-derived FLs enhanced kale and lettuce plant growth, physiological indices, and yield. Future investigation will use proteomic approaches combined with plant physiological responses to better understand host-plant responses to bacteria-derived FLs.
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Affiliation(s)
- Nivethika Ajeethan
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Halifax, NS B2N 5E3, Canada
| | - Svetlana N. Yurgel
- USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA;
| | - Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Halifax, NS B2N 5E3, Canada
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50
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Ruan M, Hu Z, Zhu Q, Li Y, Nie X. 16S rDNA Sequencing-Based Insights into the Bacterial Community Structure and Function in Co-Existing Soil and Coal Gangue. Microorganisms 2023; 11:2151. [PMID: 37763995 PMCID: PMC10536285 DOI: 10.3390/microorganisms11092151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Coal gangue is a solid waste emitted during coal production. Coal gangue is deployed adjacent to mining land and has characteristics similar to those of the soils of these areas. Coal gangue-soil ecosystems provide habitats for a rich and active bacterial community. However, co-existence networks and the functionality of soil and coal gangue bacterial communities have not been studied. Here, we performed Illumina MiSeq high-throughput sequencing, symbiotic network and statistical analyses, and microbial phenotype prediction to study the microbial community in coal gangue and soil samples from Shanxi Province, China. In general, the structural difference between the bacterial communities in coal gangue and soil was large, indicating that interactions between soil and coal gangue are limited but not absent. The bacterial community exhibited a significant symbiosis network in soil and coal gangue. The co-occurrence network was primarily formed by Proteobacteria, Firmicutes, and Actinobacteria. In addition, BugBase microbiome phenotype predictions and PICRUSt bacterial functional potential predictions showed that transcription regulators represented the highest functional category of symbiotic bacteria in soil and coal gangue. Proteobacteria played an important role in various processes such as mobile element pathogenicity, oxidative stress tolerance, and biofilm formation. In general, this work provides a theoretical basis and data support for the in situ remediation of acidified coal gangue hills based on microbiological methods.
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Affiliation(s)
- Mengying Ruan
- Institute of Land Reclamation and Ecological Restoration, China University of Mining and Technology-Beijing, Beijing 100083, China; (M.R.); (X.N.)
| | - Zhenqi Hu
- China University of Mining and Technology, Xuzhou 221116, China;
| | - Qi Zhu
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China;
| | - Yuanyuan Li
- China University of Mining and Technology, Xuzhou 221116, China;
| | - Xinran Nie
- Institute of Land Reclamation and Ecological Restoration, China University of Mining and Technology-Beijing, Beijing 100083, China; (M.R.); (X.N.)
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