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Hilário S, Gonçalves MFM, Matos I, Rangel LF, Sousa JA, Santos MJ, Ayra-Pardo C. Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter. Appl Microbiol Biotechnol 2024; 108:370. [PMID: 38861018 PMCID: PMC11166776 DOI: 10.1007/s00253-024-13210-6] [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: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.
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Affiliation(s)
- Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- GreenUPorto, Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences, University of Porto, Campus de Vairão, 747, 4485-646, Vila do Conde, Portugal.
| | - Micael F M Gonçalves
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Inês Matos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Luis F Rangel
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - José A Sousa
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Maria J Santos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Camilo Ayra-Pardo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
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Yeo YJ, Park AR, Vuong BS, Kim JC. Biocontrol of Fusarium head blight in rice using Bacillus velezensis JCK-7158. Front Microbiol 2024; 15:1358689. [PMID: 38915299 PMCID: PMC11194345 DOI: 10.3389/fmicb.2024.1358689] [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: 12/20/2023] [Accepted: 05/20/2024] [Indexed: 06/26/2024] Open
Abstract
Fusarium head blight (FHB) is a destructive disease caused by several species of Fusarium, such as Fusarium graminearum and F. asiaticum. FHB affects cereal crops, including wheat, barley, and rice, worldwide. Fusarium-infected kernels not only cause reduced yields but also cause quality loss by producing mycotoxins, such as trichothecenes and zearalenone, which are toxic to animals and humans. For decades, chemical fungicides have been used to control FHB because of their convenience and high control efficacy. However, the prolonged use of chemical fungicides has caused adverse effects, including the emergence of drug resistance to pathogens and environmental pollution. Biological control is considered one of the most promising alternatives to chemicals and can be used for integrated management of FHB due to the rare possibility of environment pollution and reduced health risks. In this study, Bacillus velezensis JCK-7158 isolated from rice was selected as an ecofriendly alternative to chemical fungicides for the management of FHB. JCK-7158 produced the extracellular enzymes protease, chitinase, gelatinase, and cellulase; the plant growth hormone indole-3-acetic acid; and the 2,3-butanediol precursor acetoin. Moreover, JCK-7158 exhibited broad antagonistic activity against various phytopathogenic fungi and produced iturin A, surfactin, and volatile substances as active antifungal compounds. It also enhanced the expression of PR1, a known induced resistance marker gene, in transgenic Arabidopsis plants expressing β-glucuronidase (GUS) fused with the PR1 promoter. Under greenhouse conditions, treatments with the culture broth and suspension concentrate formulation of JCK-7158 at a 1,000-fold dilution inhibited the development of FHB by 50 and 66%, respectively. In a field experiment, treatment with the suspension concentrate formulation of JCK-7158 at a 1,000-fold dilution effectively controlled the development of FHB with a control value of 55% and reduced the production of the mycotoxin nivalenol by 40%. Interestingly, treatment with JCK-7158 enhanced the expression of plant defense-related genes in salicylic acid, jasmonic acid, ethylene, and reactive oxygen species (ROS) signaling pathways before and after FHB pathogen inoculation. Taken together, our findings support that JCK-7158 has the potential to serve as a new biocontrol agent for the management of FHB.
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Affiliation(s)
- Yu Jeong Yeo
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju, Republic of Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju, Republic of Korea
- Plant Healthcare Research Institute, JAN153 Biotech Incorporated, Gwangju, Republic of Korea
| | - Bien Sy Vuong
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju, Republic of Korea
- Plant Healthcare Research Institute, JAN153 Biotech Incorporated, Gwangju, Republic of Korea
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Sun L, Wang D, Liu X, Zhou Y, Huang W, Guan X, Zhang X, Xie Z. The volatile organic compound acetoin enhances the colonization of Azorhizobium caulinodans ORS571 on Sesbania rostrata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169006. [PMID: 38040356 DOI: 10.1016/j.scitotenv.2023.169006] [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: 10/04/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023]
Abstract
Chemoreceptors play a crucial role in assisting bacterial sensing and response to environmental stimuli. Genome analysis of Azorhizobium caulinodans ORS571 revealed the presence of 43 putative chemoreceptors, but their biological functions remain largely unknown. In this study, we identified the chemoreceptor AmaP (methyl-accepting protein of A. caulinodans), characterized by the presence of the CHASE3 domain and exhibited a notable response to acetoin. Thus, we investigated the effect of acetoin sensing on its symbiotic association with the host. Our findings uncovered a compelling role for acetoin as a key player in enhancing various facets of A. caulinodans ORS571's performance including biofilm formation, colonization, and nodulation abilities. Notably, acetoin bolstered A. caulinodans ORS571's efficacy in promoting the growth of S. rostrata, even under moderate salt stress conditions. This study not only broadens our understanding of the AmaP protein with its distinctive CHASE3 domain but also highlights the promising potential of acetoin in fortifying the symbiotic relationship between A. caulinodans and Sesbania rostrata.
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Affiliation(s)
- Li Sun
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Dandan Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Xiaolin Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yanan Zhou
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Weiwei Huang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Xin Guan
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Xuexian Zhang
- School of Natural Sciences, Massey University at Albany, Auckland 0745, New Zealand
| | - Zhihong Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China.
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Nihorimbere G, Korangi Alleluya V, Nimbeshaho F, Nihorimbere V, Legrève A, Ongena M. Bacillus-based biocontrol beyond chemical control in central Africa: the challenge of turning myth into reality. FRONTIERS IN PLANT SCIENCE 2024; 15:1349357. [PMID: 38379944 PMCID: PMC10877027 DOI: 10.3389/fpls.2024.1349357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
Agricultural productivity in the Great Lakes Countries of Central Africa, including Burundi, Rwanda, and the Democratic Republic of Congo, is affected by a wide range of diseases and pests which are mainly controlled by chemical pesticides. However, more than 30% of the pesticides used in the region are banned in European Union due to their high toxicity. Globally available safe and eco-friendly biological alternatives to chemicals are virtually non-existent in the region. Bacillus PGPR-based biocontrol products are the most dominant in the market and have proven their efficacy in controlling major plant diseases reported in the region. With this review, we present the current situation of disease and pest management and urge the need to utilize Bacillus-based control as a possible sustainable alternative to chemical pesticides. A repertoire of strains from the Bacillus subtilis group that have shown great potential to antagonize local pathogens is provided, and efforts to promote their use, as well as the search for indigenous and more adapted Bacillus strains to local agro-ecological conditions, should be undertaken to make sustainable agriculture a reality in the region.
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Affiliation(s)
- Gaspard Nihorimbere
- Phytopathology- Applied Microbiology, Earth, and Life Institute, UCLouvain, Louvain-la-neuve, Belgium
- Unité de défense des végétaux, Institut des Sciences Agronomiques du Burundi, Bujumbura, Burundi
| | - Virginie Korangi Alleluya
- Microbial Processes and Interactions, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Chemical and Agricultural Industries, Faculty of Agricultural Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - François Nimbeshaho
- Microbial Processes and Interactions, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Laboratoire de Nutrition-Phytochimie, d’Ecologie et d’Environnement Appliquée, Centre Universitaire de Recherche et de Pédagogie Appliquées aux Sciences, Institut de Pédagogie Appliquée, Université du Burundi, Bujumbura, Burundi
| | - Venant Nihorimbere
- Département des Sciences et Technologie des Aliments, Faculté de Bio-Ingénierie, Université du Burundi, Bujumbura, Burundi
| | - Anne Legrève
- Phytopathology- Applied Microbiology, Earth, and Life Institute, UCLouvain, Louvain-la-neuve, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Rashad YM, Al Tami MS, Abdalla SA. Eliciting transcriptomic and antioxidant defensive responses against Rhizoctonia root rot of sorghum using the endophyte Aspergillus oryzae YRA3. Sci Rep 2023; 13:19823. [PMID: 37963959 PMCID: PMC10646029 DOI: 10.1038/s41598-023-46696-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023] Open
Abstract
Environmental pollution due to the improper use of the chemical fungicides represents a vital ecological problem, which affects human and animal health, as well as the microbial biodiversity and abundance in the soil. In this study, an endophytic fungus Aspergillus oryzae YRA3, isolated from the wild plant Atractylis carduus (Forssk.) C.Chr, was tested for its biocontrol activity against Rhizoctonia root rot of sorghum. The antagonistic potential of A. oryzae YRA3 was tested against Rhizoctonia solani in vitro. A full inhibition in the growth of R. solani was recorded indicating a strong antagonistic potential for this endophyte. To investigate the chemical composition of its metabolites, GC/MS analysis was used and thirty-two compounds in its culture filtrate were identified. Among these metabolites, some compounds with an antifungal background were detected including palmitic acid, 2-heptanone, and 2,3-butanediol. To these antifungal metabolites the antagonistic activity of A. oryzae YRA3 can be attributed. In the greenhouse experiment, treating of the infected sorghum plants with A. oryzae YRA3 significantly reduced severity of the Rhizoctonia root rot by 73.4%. An upregulation of the defensive genes (JERF3), (POD) and (CHI II) was recorded in sorghum roots when were inoculated with A. oryzae YRA3. In addition, an increment in the activity of peroxidase and polyphenol oxidase, as well as the total phenolic content in the sorghum roots was also recorded. Furthermore, the results obtained from the greenhouse experiment revealed a growth-promoting effect for inoculating the sorghum plants with A. oryzae YRA3. It can be concluded that A. oryzae YRA3 can be a probable biological agent to control this disease in sorghum. However, its evaluation under field conditions is highly needed in the future studies.
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Affiliation(s)
- Younes M Rashad
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, Alexandria, 21934, Egypt.
| | - Mona S Al Tami
- Department of Biology, College of Science, Qassim University, 51452, Qassim, Saudi Arabia
| | - Sara A Abdalla
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, Alexandria, 21934, Egypt
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Truong TTT, Chiu CC, Chen JY, Su PY, Nguyen TP, Trinh NN, Mimura T, Lee RH, Chang CH, Huang HJ. Uncovering molecular mechanisms involved in microbial volatile compounds-induced stomatal closure in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2023; 113:143-155. [PMID: 37985583 DOI: 10.1007/s11103-023-01379-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/18/2023] [Indexed: 11/22/2023]
Abstract
Microbial volatile compounds (mVCs) may cause stomatal closure to limit pathogen invasion as part of plant innate immune response. However, the mechanisms of mVC-induced stomatal closure remain unclear. In this study, we co-cultured Enterobacter aerogenes with Arabidopsis (Arabidopsis thaliana) seedlings without direct contact to initiate stomatal closure. Experiments using the reactive oxygen species (ROS)-sensitive fluorescent dye, H2DCF-DA, showed that mVCs from E. aerogenes enhanced ROS production in guard cells of wild-type plants. The involvement of ROS in stomatal closure was then demonstrated in an ROS production mutant (rbohD). In addition, we identified two stages of signal transduction during E. aerogenes VC-induced stomatal closure by comparing the response of wild-type Arabidopsis with a panel of mutants. In the early stage (3 h exposure), E. aerogenes VCs induced stomatal closure in wild-type and receptor-like kinase THESEUS1 mutant (the1-1) but not in rbohD, plant hormone-related mutants (nced3, erf4, jar1-1), or MAPK kinase mutants (mkk1 and mkk3). However, in the late stage (24 h exposure), E. aerogenes VCs induced stomatal closure in wild-type and rbohD but not in nced3, erf4, jar1-1, the1-1, mkk1 or mkk3. Taken together, our results suggest that E. aerogenes mVC-induced plant immune responses modulate stomatal closure in Arabidopsis by a multi-phase mechanism.
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Affiliation(s)
- Tu-Trinh Thi Truong
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
- Faculty of Technology, The University of Danang-Campus in Kontum, The University of Danang, Kon Tum City, 580000, Vietnam
| | - Chi-Chou Chiu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Jing-Yu Chen
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Pei-Yu Su
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Tri-Phuong Nguyen
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Ngoc-Nam Trinh
- Industrial University of Ho Chi Minh City, No. 12, Nguyen Van Bao, Ho Chi Minh City, Vietnam
| | - Tetsuro Mimura
- Kyoto University of Advanced Science, Kameoka, Kyoto, 621-8555, Japan
| | - Ruey-Hua Lee
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Ching-Han Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, No. 1, University Road, Tainan, 701, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan.
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, No. 1, University Road, Tainan, 701, Taiwan.
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan.
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Santos JBD, Cruz JDO, Geraldo LC, Dias EG, Queiroz PRM, Monnerat RG, Borges M, Blassioli-Moraes MC, Blum LEB. Detection and evaluation of volatile and non-volatile antifungal compounds produced by Bacillus spp. strains. Microbiol Res 2023; 275:127465. [PMID: 37543004 DOI: 10.1016/j.micres.2023.127465] [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: 05/22/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
The identification of antifungal compounds produced by microorganisms is crucial in the context of sustainable agriculture. Bacteria of the genus Bacillus have a broad spectrum of action that can influence plant growth and control pests, vectors of public health relevance and phytopathogens. Lipopeptides are the main compounds related to the biological control of several pathogen species. Strains with biotechnological potential are identified by means of in vitro bioassays and molecular tests. In this study, strains from the Bacillus Bank of Brazilian Agricultural Research Corporation (EMBRAPA/DF/Brazil) were selected to control the fungal pathogens Sclerotinia sclerotiorum and Fusarium oxysporum by pairing assays. The detection of genes for biosynthesis of antifungal compounds from strains with high pathogen-inhibition capacity was correlated with peptide synthesis, such as bacillomycin D, fengycin d, bacilysin and surfactin. Their gene expression in contact with the pathogen was analyzed by Real-Time PCR. The volatile organic compounds produced by selected Bacillus strains were identified and quantified. In co-culture assays, the inhibition zone between Bacillus strains and Sclerotinia sclerotiorum was evaluated by scanning electron microscopy. Thirteen potentially anti-pathogenic strains were selected. Genes related to the synthesis of antifungal peptides were detected in 11 of them. In five strains, all tested genes were detected. Bacillomycin was the most frequently found lipopeptide gene. The fungus-bacteria interaction potentiated the production of volatiles. Several ketones and other volatile compounds with antifungal activity were identified. Relevant morphological changes in the fungus were observed when paired with bacteria. The study demonstrated the efficacy of the selected strains with regard to the biological control of phytopathogens and their biotechnological potential.
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Affiliation(s)
- Jônatas Barros Dos Santos
- University of Brasília (UnB), Postgraduate Program in Agronomy, Faculty of Agronomy and Veterinary Medicine, Brasília 70910-900, Brazil.
| | - José de Oliveira Cruz
- University of Brasília (UnB), Postgraduate Program in Agronomy, Faculty of Agronomy and Veterinary Medicine, Brasília 70910-900, Brazil
| | - Leticia Costa Geraldo
- University of Brasília (UnB), Postgraduate Program in Agronomy, Faculty of Agronomy and Veterinary Medicine, Brasília 70910-900, Brazil
| | - Emanuel Guimarães Dias
- University of Brasília (UnB), Postgraduate Program in Agronomy, Faculty of Agronomy and Veterinary Medicine, Brasília 70910-900, Brazil
| | | | - Rose Gomes Monnerat
- Empresa Brasileira de Pesquisa Agropecuária (Brazilian Agricultural Research Corporation) Genetic Resources and Biotechnology (CENARGEN), Brasília 70770-917, Brazil
| | - Miguel Borges
- Empresa Brasileira de Pesquisa Agropecuária (Brazilian Agricultural Research Corporation) Genetic Resources and Biotechnology (CENARGEN), Brasília 70770-917, Brazil
| | - Maria Carolina Blassioli-Moraes
- Empresa Brasileira de Pesquisa Agropecuária (Brazilian Agricultural Research Corporation) Genetic Resources and Biotechnology (CENARGEN), Brasília 70770-917, Brazil
| | - Luiz Eduardo Bassay Blum
- University of Brasília (UnB), Postgraduate Program in Agronomy, Faculty of Agronomy and Veterinary Medicine, Brasília 70910-900, Brazil
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Arora S, Babele PK, Jha PN. Biochemical and metabolic signatures are fundamental to drought adaptation in PGPR Enterobacter bugandensis WRS7. Mol Omics 2023; 19:640-652. [PMID: 37338418 DOI: 10.1039/d3mo00051f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Drought alone causes more annual loss in crop yield than the sum of all other environmental stresses. There is growing interest in harnessing the potential of stress-resilient PGPR in conferring plant resistance and enhancing crop productivity in drought-affected agroecosystems. A detailed understanding of the complex physiological and biochemical responses will open up the avenues to stress adaptation mechanisms of PGPR communities under drought. It will pave the way for rhizosphere engineering through metabolically engineered PGPR. Therefore, to reveal the physiological and metabolic networks in response to drought-mediated osmotic stress, we performed biochemical analyses and applied untargeted metabolomics to investigate the stress adaptation mechanisms of a PGPR Enterobacter bugendensis WRS7 (Eb WRS7). Drought caused oxidative stress and resulted in slower growth rates in Eb WRS7. However, Eb WRS7 could tolerate drought stress and did not show changes in cell morphology under stress conditions. Overproduction of ROS caused lipid peroxidation (increment in MDA) and eventually activated antioxidant systems and cell signalling cascades, which led to the accumulation of ions (Na+, K+, and Ca2+), osmolytes (proline, exopolysaccharides, betaine, and trehalose), and modulated lipid dynamics of the plasma membranes for osmosensing and osmoregulation, suggesting an osmotic stress adaption mechanism in PGPR Eb WRS7. Finally, GC-MS-based metabolite profiling and deregulated metabolic responses highlighted the role of osmolytes, ions, and intracellular metabolites in regulating Eb WRS7 metabolism. Our results suggest that understanding the role of metabolites and metabolic pathways can be exploited for future metabolic engineering of PGPR and developing bio inoculants for plant growth promotion under drought-affected agroecosystems.
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Affiliation(s)
- Saumya Arora
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Piyoosh K Babele
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Prabhat Nath Jha
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
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Tsai SH, Hsiao YC, Chang PE, Kuo CE, Lai MC, Chuang HW. Exploring the Biologically Active Metabolites Produced by Bacillus cereus for Plant Growth Promotion, Heat Stress Tolerance, and Resistance to Bacterial Soft Rot in Arabidopsis. Metabolites 2023; 13:metabo13050676. [PMID: 37233717 DOI: 10.3390/metabo13050676] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023] Open
Abstract
Eight gene clusters responsible for synthesizing bioactive metabolites associated with plant growth promotion were identified in the Bacillus cereus strain D1 (BcD1) genome using the de novo whole-genome assembly method. The two largest gene clusters were responsible for synthesizing volatile organic compounds (VOCs) and encoding extracellular serine proteases. The treatment with BcD1 resulted in an increase in leaf chlorophyll content, plant size, and fresh weight in Arabidopsis seedlings. The BcD1-treated seedlings also accumulated higher levels of lignin and secondary metabolites including glucosinolates, triterpenoids, flavonoids, and phenolic compounds. Antioxidant enzyme activity and DPPH radical scavenging activity were also found to be higher in the treated seedlings as compared with the control. Seedlings pretreated with BcD1 exhibited increased tolerance to heat stress and reduced disease incidence of bacterial soft rot. RNA-seq analysis showed that BcD1 treatment activated Arabidopsis genes for diverse metabolite synthesis, including lignin and glucosinolates, and pathogenesis-related proteins such as serine protease inhibitors and defensin/PDF family proteins. The genes responsible for synthesizing indole acetic acid (IAA), abscisic acid (ABA), and jasmonic acid (JA) were expressed at higher levels, along with WRKY transcription factors involved in stress regulation and MYB54 for secondary cell wall synthesis. This study found that BcD1, a rhizobacterium producing VOCs and serine proteases, is capable of triggering the synthesis of diverse secondary metabolites and antioxidant enzymes in plants as a defense strategy against heat stress and pathogen attack.
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Affiliation(s)
- Sih-Huei Tsai
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi 600355, Taiwan
| | - Yi-Chun Hsiao
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi 600355, Taiwan
| | - Peter E Chang
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi 600355, Taiwan
| | - Chen-En Kuo
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi 600355, Taiwan
| | - Mei-Chun Lai
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi 600355, Taiwan
| | - Huey-Wen Chuang
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi 600355, Taiwan
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Rani A, Rana A, Dhaka RK, Singh AP, Chahar M, Singh S, Nain L, Singh KP, Minz D. Bacterial volatile organic compounds as biopesticides, growth promoters and plant-defense elicitors: Current understanding and future scope. Biotechnol Adv 2023; 63:108078. [PMID: 36513315 DOI: 10.1016/j.biotechadv.2022.108078] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Bacteria emit a large number of volatile organic compounds (VOCs) into the environment. VOCs are species-specific and their emission depends on environmental conditions, such as growth medium, pH, temperature, incubation time and interaction with other microorganisms. These VOCs can enhance plant growth, suppress pathogens and act as signaling molecules during plant-microorganism interactions. Some bacterial VOCs have been reported to show strong antimicrobial, nematicidal, pesticidal, plant defense, induced tolerance and plant-growth-promoting activities under controlled conditions. Commonly produced antifungal VOCs include dimethyl trisulfide, dimethyl disulfide, benzothiazole, nonane, decanone and 1-butanol. Species of Bacillus, Pseudomonas, Arthrobacter, Enterobacter and Burkholderia produce plant growth promoting VOCs, such as acetoin and 2,3-butenediol. These VOCs affect expression of genes involved in defense and development in plant species (i.e., Arabidopsis, tobacco, tomato, potato, millet and maize). VOCs are also implicated in altering pathogenesis-related genes, inducing systemic resistance, modulating plant metabolic pathways and acquiring nutrients. However, detailed mechanisms of action of VOCs need to be further explored. This review summarizes the bioactive VOCs produced by diverse bacterial species as an alternative to agrochemicals, their mechanism of action and challenges for employment of bacterial VOCs for sustainable agricultural practices. Future studies on technological improvements for bacterial VOCs application under greenhouse and open field conditions are warranted.
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Affiliation(s)
- Annu Rani
- Department of Microbiology, College of Basic Science & Humanities, Chaudhary Charan Singh Haryana Agricultural University (CCS HAU), Hisar, India
| | - Anuj Rana
- Department of Microbiology, College of Basic Science & Humanities, Chaudhary Charan Singh Haryana Agricultural University (CCS HAU), Hisar, India; Centre for Bio-Nanotechnology, CCS HAU, Hisar, India.
| | - Rahul Kumar Dhaka
- Centre for Bio-Nanotechnology, CCS HAU, Hisar, India; Department of Chemistry, College of Basic Science & Humanities, CCS HAU, Hisar, India
| | - Arvind Pratap Singh
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Madhvi Chahar
- Department of Bio & Nano Technology, Guru Jambheshwar University of Science & Technology, Hisar, India
| | - Surender Singh
- Department of Microbiology, Central University of Haryana, Mahendargarh, India
| | - Lata Nain
- Division of Microbiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture & Technology, Pantnagar, India; Vice Chancellor's Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, UP, India
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel.
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Yang Q, Zhang H, You J, Yang J, Zhang Q, Zhao J, Aimaier R, Zhang J, Han S, Zhao H, Zhao H. Transcriptome and metabolome analyses reveal that Bacillus subtilis BS-Z15 lipopeptides mycosubtilin homologue mediates plant defense responses. FRONTIERS IN PLANT SCIENCE 2023; 13:1088220. [PMID: 36815011 PMCID: PMC9940755 DOI: 10.3389/fpls.2022.1088220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/30/2022] [Indexed: 05/30/2023]
Abstract
Microbial-plant interactions protect plants from external stimuli, releasing various elicitor that activate the plants defense response and regulate its growth. Bacillus subtilis BS-Z15 was screened from cotton inter-rhizosphere soil, antagonized various plant pathogens, and protected cotton against Verticillium dahliae. This study showed that the BS-Z15 lipopeptide mycosubtilin homologue could act as an elicitor to induce systemic resistance (ISR) in plants. Mycosubtilin homologue induced ROS burst and deposition, callose deposition, MAPK cascade phosphorylation, and up-regulated PR1 and PDF1.2 gene expression in Arabidopsis seedlings, moreover enhanced resistance of Arabidopsis to Pseudomonas syringae pv. Tomato DC3000 (Pst DC3000) and V. dahliae. Transcriptome analysis was then used to evaluate the impact of mycosubtilin homologue on plant gene expression control. Mycosubtilin homologues activated Arabidopsis ISR on genes in metabolic pathways such as Arabidopsis plant-pathogen interactions, phenylpropanoid biosynthesis, MAPK signaling pathway, and phytohormone signaling. These analyses revealed that mycosubtilin homologues mediate the regulation of plant systemic resistance and growth and development by affecting related metabolites in glycolysis and gluconeogenesis, pentose phosphate pathway, tricarboxylic acid cycle, and amino acid metabolism in Arabidopsis. These findings confirmed that a mycosubtilin homologue could trigger the initiation of the Arabidopsis ISR by interacting with a variety of PTI components and transcriptional metabolic signaling pathways.
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Affiliation(s)
- Qilin Yang
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Hui Zhang
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Jia You
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Jun Yang
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Qi Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jinjin Zhao
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Reyihanguli Aimaier
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Jingbo Zhang
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Heping Zhao
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Huixin Zhao
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
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12
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Yang P, Zhao Z, Fan J, Liang Y, Bernier MC, Gao Y, Zhao L, Opiyo SO, Xia Y. Bacillus proteolyticus OSUB18 triggers induced systemic resistance against bacterial and fungal pathogens in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1078100. [PMID: 36755698 PMCID: PMC9900001 DOI: 10.3389/fpls.2023.1078100] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/04/2023] [Indexed: 05/27/2023]
Abstract
Pseudomonas syringae and Botrytis cinerea cause destructive bacterial speck and grey mold diseases in many plant species, leading to substantial economic losses in agricultural production. Our study discovered that the application of Bacillus proteolyticus strain OSUB18 as a root-drench enhanced the resistance of Arabidopsis plants against P. syringae and B. cinerea through activating Induced Systemic Resistance (ISR). The underlying mechanisms by which OSUB18 activates ISR were studied. Our results revealed that the Arabidopsis plants with OSUB18 root-drench showed the enhanced callose deposition and ROS production when inoculated with Pseudomonas syringae and Botrytis cinerea pathogens, respectively. Also, the increased salicylic acid (SA) levels were detected in the OSUB18 root-drenched plants compared with the water root-drenched plants after the P. syringae infection. In contrast, the OSUB18 root-drenched plants produced significantly higher levels of jasmonyl isoleucine (JA-Ile) than the water root-drenched control after the B. cinerea infection. The qRT-PCR analyses indicated that the ISR-responsive gene MYC2 and the ROS-responsive gene RBOHD were significantly upregulated in OSUB18 root-drenched plants upon both pathogen infections compared with the controls. Also, twenty-four hours after the bacterial or fungal inoculation, the OSUB18 root-drenched plants showed the upregulated expression levels of SA-related genes (PR1, PR2, PR5, EDS5, and SID2) or JA-related genes (PDF1.2, LOX3, JAR1 and COI1), respectively, which were consistent with the related hormone levels upon these two different pathogen infections. Moreover, OSUB18 can trigger ISR in jar1 or sid2 mutants but not in myc2 or npr1 mutants, depending on the pathogen's lifestyles. In addition, OSUB18 prompted the production of acetoin, which was reported as a novel rhizobacterial ISR elicitor. In summary, our studies discover that OSUB18 is a novel ISR inducer that primes plants' resistance against bacterial and fungal pathogens by enhancing the callose deposition and ROS accumulation, increasing the production of specific phytohormones and other metabolites involved in plant defense, and elevating the expression levels of multiple defense genes.
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Affiliation(s)
- Piao Yang
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH, United States
| | - Zhenzhen Zhao
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH, United States
| | - Jiangbo Fan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yinping Liang
- College of Grassland Science, Shanxi Agriculture University, Taigu, China
| | - Matthew C. Bernier
- Campus Chemical Instrument Center, Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH, United States
| | - Yu Gao
- Ohio State University (OSU) South Centers, Piketon, OH, United States
- Department of Extension, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States
| | - Lijing Zhao
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH, United States
| | - Stephen Obol Opiyo
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH, United States
| | - Ye Xia
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH, United States
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Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2 T. AMB Express 2023; 13:9. [PMID: 36680648 PMCID: PMC9867790 DOI: 10.1186/s13568-023-01514-1] [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: 07/21/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting (PGP) effect of strain ATSA2T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass, and chlorophyll contents following strain ATSA2T treatment. Strain ATSA2T displayed PGP traits such as indole acetic acid (IAA, 62.9 μg/mL) and siderophore production, and phosphate solubilization activity. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2T in agricultural biotechnology.
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14
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Pazarlar S, Madriz-Ordeñana K, Thordal-Christensen H. Bacillus cereus EC9 protects tomato against Fusarium wilt through JA/ET-activated immunity. FRONTIERS IN PLANT SCIENCE 2022; 13:1090947. [PMID: 36589090 PMCID: PMC9798288 DOI: 10.3389/fpls.2022.1090947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The mechanisms of action and the limitations of effectiveness of natural biocontrol agents should be determined in order to convert them into end products that can be used in practice. Rhizosphere Bacillus spp. protect plants from various pathogens by displaying several modes of action. However, the ability of Bacillus spp. to control plant diseases depends on the interaction between the bacteria, host, and pathogen, and the environmental conditions. We found that soil drenching of tomato plants with the non-antifungal Bacillus cereus strain EC9 (EC9) enhances plant defense against Fusarium oxysporum f. sp. lycopersici (Fol). To study the involvement of plant defense-related phytohormones in the regulation of EC9-activated protection against Fol, we conducted plant bioassays in tomato genotypes impaired in salicylic acid (SA) accumulation, jasmonic acid (JA) biosynthesis, and ethylene (ET) production, and analyzed the transcript levels of pathways-related marker genes. Our results indicate that JA/ET-dependent signaling is required for EC9-mediated protection against Fol in tomato. We provide evidence that EC9 primes tomato plants for enhanced expression of proteinase inhibitor I (PI-I) and ethylene receptor4 (ETR4). Moreover, we demonstrated that EC9 induces callose deposition in tomato roots. Understanding the involvement of defense-related phytohormones in EC9-mediated defense against Fusarium wilt has increased our knowledge of interactions between non-antifungal plant defense-inducing rhizobacteria and plants.
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Affiliation(s)
- Sercan Pazarlar
- Department of Plant Protection, Faculty of Agriculture, Ege University, Izmir, Turkey
- Department of Plant and Environmental Sciences, Section for Plant and Soil Science, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth Madriz-Ordeñana
- Department of Plant and Environmental Sciences, Section for Plant and Soil Science, University of Copenhagen, Copenhagen, Denmark
| | - Hans Thordal-Christensen
- Department of Plant and Environmental Sciences, Section for Plant and Soil Science, University of Copenhagen, Copenhagen, Denmark
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15
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Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens. Int J Mol Sci 2022; 23:ijms232415561. [PMID: 36555201 PMCID: PMC9779691 DOI: 10.3390/ijms232415561] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Fungal phytopathogens are challenging to control due to their penetration into plant tissues. Therefore, plant-colonizing bacteria could serve as an excellent weapon in fighting fungal infections. In this study, we aim to determine the biocontrol potential of the new endophytic strain Serratia quinivorans KP32, isolated from the roots of Petroselinum crispum L.; identify the related mechanisms; and understand the basis of its antagonistic interaction with taxonomically diverse fungi at the molecular level. The KP32 strain presented biological activity against Rhizoctonia solani, Colletotrichum dematium, Fusarium avenaceum, and Sclerotinia sclerotiorum, and its ability to inhibit the growth of the phytopathogens was found to be mediated by a broad spectrum of biocontrol features, such as the production of a number of lytic enzymes (amylases, chitinases, and proteases), siderophores, volatile organic and inorganic compounds, salicylic acid, and N-acyl-homoserine lactones. The higher expression of chitinase (chiA) and genes involved in the biosynthesis of hydrogen cyanide (hcnC), enterobactin (entB), and acetoin (budA) in bacteria exposed to fungal filtrates confirmed that these factors could act in combination, leading to a synergistic inhibitory effect of the strain against phytopathogens. We also confirm the active movement, self-aggregation, exopolysaccharide production, and biofilm formation abilities of the KP32 strain, which are essential for effective plant colonization. Its biological activity and colonization potential indicate that KP32 holds tremendous potential for use as an active biopesticide and plant growth promoter.
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16
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Suriani NL, Suprapta DN, Suarsana IN, Reddy MS, Gunawan S, Herlambang S, Resiani NMD, Pratiwi E, Sabullah MK, Alfarraj S, Ansari MJ. Piper caninum extract and Brevibacillus agri mixture suppresses rice leaf spot pathogen; Nigrospora oryzae and improves the production of red rice (Oryza sativa L). FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1080481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Under the guise of enhancing productivity, using pesticides and artificial fertilizers in agriculture affects both the environment and living things. High chemical residues in food and the environment disrupt the health of consumers. One of the solutions that can bring about a reduction in the use of pesticides and chemicals is switching to organic fertilizers. The application of biopesticides originating from biological sources such as plant extracts and the use of microbes is gaining global acceptance. Therefore, this study aimed to obtain the best biopesticides and biostimulants that could suppress the leaf spot pathogen, Nigrospora oryzae, and increase the growth and yield of Bali red rice. The study contained four treatments, namely untreated control (F0), Piper caninum leaf extract (F1), Brevibacillus agri (F2), and fermented P. caninum leaf extract plus B. agri (F3). The treatments were arranged in a randomized complete block design, and each treatment was replicated three times. The parameters measured were the number of tillers per plant, number of leafs per plant, chlorophyll content, number of grains per panicle, grain weight, and grain yield. Furthermore, antimicrobial and antioxidants were assayed using SEM. GC-MS. At the end of the experiment, the disease index of the leaf spot was measured. The results showed that F3 significantly suppressed leaf spots caused by N. oryzae compared to other treatments, including untreated control in red rice. Additionally, the F3 significantly increased the number of productive tillers, number of grains per panicle, and grain yield compared to all other treatments. The F3 enhanced the crop yield at 6.19 tons/ha, an increase of 50% compared to the untreated control. The SEM.GC-MS results showed the presence of 2.3 butanediol, tetra-decanoic acid, butanoic acid, ethyl ester, benzene propanal, 3-(1,1-dimethylethyl)-a-methyl, a-N-Normethadol in treated plants with P. canicum plus B. agri.
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17
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Khan AR, Mustafa A, Hyder S, Valipour M, Rizvi ZF, Gondal AS, Yousuf Z, Iqbal R, Daraz U. Bacillus spp. as Bioagents: Uses and Application for Sustainable Agriculture. BIOLOGY 2022; 11:biology11121763. [PMID: 36552272 PMCID: PMC9775066 DOI: 10.3390/biology11121763] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Food security will be a substantial issue in the near future due to the expeditiously growing global population. The current trend in the agriculture industry entails the extravagant use of synthesized pesticides and fertilizers, making sustainability a difficult challenge. Land degradation, lower production, and vulnerability to both abiotic and biotic stresses are problems caused by the usage of these pesticides and fertilizers. The major goal of sustainable agriculture is to ameliorate productivity and reduce pests and disease prevalence to such a degree that prevents large-scale damage to crops. Agriculture is a composite interrelation among plants, microbes, and soil. Plant microbes play a major role in growth promotion and improve soil fertility as well. Bacillus spp. produces an extensive range of bio-chemicals that assist in plant disease control, promote plant development, and make them suitable for agricultural uses. Bacillus spp. support plant growth by N fixation, P and K solubilization, and phytohormone synthesis, in addition to being the most propitious biocontrol agent. Moreover, Bacilli excrete extracellular metabolites, including antibiotics, lytic enzymes, and siderophores, and demonstrate antagonistic activity against phytopathogens. Bacillus spp. boosts plant resistance toward pathogens by inducing systemic resistance (ISR). The most effective microbial insecticide against insects and pests in agriculture is Bacillus thuringiensis (Bt). Additionally, the incorporation of toxin genes in genetically modified crops increases resistance to insects and pests. There is a constant increase in the identified Bacillus species as potential biocontrol agents. Moreover, they have been involved in the biosynthesis of metallic nanoparticles. The main objective of this review article is to display the uses and application of Bacillus specie as a promising biopesticide in sustainable agriculture. Bacillus spp. strains that are antagonistic and promote plant yield attributes could be valuable in developing novel formulations to lead the way toward sustainable agriculture.
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Affiliation(s)
- Aimen Razzaq Khan
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
| | - Adeena Mustafa
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
| | - Sajjad Hyder
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
- Correspondence: (S.H.); (M.V.)
| | - Mohammad Valipour
- Department of Engineering and Engineering Technology, Metropolitan State University of Denver, Denver, CO 80217, USA
- Correspondence: (S.H.); (M.V.)
| | - Zarrin Fatima Rizvi
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
| | - Amjad Shahzad Gondal
- Department of Plant Pathology, Bahauddin Zakariya University Multan, Multan 60000, Pakistan
| | - Zubaida Yousuf
- Department of Botany, Lahore College for Women University, Lahore 54000, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Umar Daraz
- State Key Laboratory of Grassland Agroecosystem, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
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Boby N, Abbas MA, Lee EB, Im ZE, Lee SJ, Park SC. Microbiota modulation and anti-obesity effects of fermented Pyrus ussuriensis Maxim extract against high-fat diet-induced obesity in rats. Biomed Pharmacother 2022; 154:113629. [PMID: 36058150 DOI: 10.1016/j.biopha.2022.113629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022] Open
Abstract
Pyrus ussuriensis Maxim (Korean pear) has been used for hundreds of years as a traditional herbal medicine due to its strong phytochemical profile and pharmacological efficacy. In this study, we evaluated the anti-obesity potential of Pyrus ussuriensis Maxim extracts (PUE) and investigated the underlying mechanisms using a combination of in vitro, in vivo, and microbiota regulation approaches. In an adipogenesis assay, the fermented (F)PUE and non-fermented (NF)PUE significantly reduced the differentiation of 3T3-L1 preadipocyte in a dose-dependent manner with an IC50 of 85.33 and 96.67 µg/mL, respectively. In a high-fat diet (HFD)-induced obese rat model (n = 8 animals/group), oral administration of FPUE additionally reduced the total body weight gain significantly. No difference in food intake was observed, however, between the control-chow diet, FPUE, and NFPUE-treated HFD rats. Adipose tissue mass and systemic insulin resistance were markedly reduced in FPUE-treated HFD rats, in a dose-dependent manner. Treatment with FPUE also greatly improved obesity-related biomarkers, including total cholesterol, leptin, active ghrelin, Total GIP, adiponectin, and proinflammatory cytokines. Moreover, FPUE significantly suppressed HFD-induced adipogenic genes expression, while increasing fatty acid oxidation-related genes expression. Additionally, FPUE treatment attenuated the HFD-induced Firmicutes proportion within the intestinal microbiota by regulating key metabolic pathways, thus enhancing microbial population diversity (e.g., increasing Bacteroides, Bifidobacterium, Prevotella, Eubacterium, and Clostridium). Together, these results reveal a strong anti-obesity potential of FPUE through adipogenesis, lipid metabolism, weight reduction, and microbiota regulation, raising the possibility of developing FPUE as a novel therapeutic agent to control obesity and obesity-associated metabolic disorders.
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Affiliation(s)
- Naila Boby
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, the Republic of Korea; Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, the Republic of Korea; Cardiovascular Research Institute, Kyungpook National University School of Medicine, Gukchabosang-ro 680, Jung-Gu, Daegu 41944, the Republic of Korea.
| | - Muhammad Aleem Abbas
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, the Republic of Korea.
| | - Eon-Bee Lee
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, the Republic of Korea.
| | - Zi-Eum Im
- Institute of Forest Resources Development, Andong-si, Gyeongsangbuk-do 36605, the Republic of Korea.
| | - Seung-Jin Lee
- Developmental and Reproductive Toxicology Research Group, Korea Institute of Toxicology, Daejeon 34114, the Republic of Korea.
| | - Seung-Chun Park
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, the Republic of Korea; Cardiovascular Research Institute, Kyungpook National University School of Medicine, Gukchabosang-ro 680, Jung-Gu, Daegu 41944, the Republic of Korea.
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Fermented Milk Product Enriched with γ-PGA, Peptides and GABA by Novel Co-Fermentation with Bacillus subtilis and Lactiplantibacillus plantarum. FERMENTATION 2022. [DOI: 10.3390/fermentation8080404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Milk was co-fermented with Bacillus subtilis HA and Lactiplantibacillus plantarum EJ2014 to produce a dairy ingredient enriched with poly-γ-glutamic acid (γ-PGA) and γ-aminobutyric acid (GABA). The first fermentation of milk with B. subtilis HA resulted in a viscous broth with pH 6.56, 0.26% acidity, 1.40 mg/g tyrosine equivalent, and 17.21 U/g protease activity. The viable cell counts of B. subtilis indicated 8.74 log CFU/mL, and the consistency index of the alkaline fermented milk was 1.82 Pa·sn. In addition, 4.65% mucilage was produced with 35.93% γ-PGA content. The milk co-fermented by L. plantarum indicated 1.34% acidity and pH 4.91. The viable bacterial counts of B. subtilis decreased to 4.44 log CFU/mL, whereas those of L. plantarum increased to 9.42 log CFU/mL. Monosodium glutamate (MSG) as a precursor was effectively converted into γ-PGA by B. subtilis, and then residual MSG was completely converted into GABA by L. plantarum with a yield of 26.15 mg/g. Furthermore, the co-fermented milk produced volatiles, including hexanoic acid, 2,3-butanediol, and acetoin, which may be responsible for its aged cheese-like aroma.
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20
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Riu M, Kim MS, Choi SK, Oh SK, Ryu CM. Elicitation of Innate Immunity by a Bacterial Volatile 2-Nonanone at Levels below Detection Limit in Tomato Rhizosphere. Mol Cells 2022; 45:502-511. [PMID: 35791736 PMCID: PMC9260139 DOI: 10.14348/molcells.2022.2009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/27/2022] Open
Abstract
Bacterial volatile compounds (BVCs) exert beneficial effects on plant protection both directly and indirectly. Although BVCs have been detected in vitro, their detection in situ remains challenging. The purpose of this study was to investigate the possibility of BVCs detection under in situ condition and estimate the potentials of in situ BVC to plants at below detection limit. We developed a method for detecting BVCs released by the soil bacteria Bacillus velezensis strain GB03 and Streptomyces griseus strain S4-7 in situ using solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME-GC-MS). Additionally, we evaluated the BVC detection limit in the rhizosphere and induction of systemic immune response in tomato plants grown in the greenhouse. Two signature BVCs, 2-nonanone and caryolan-1-ol, of GB03 and S4-7 respectively were successfully detected using the soil-vial system. However, these BVCs could not be detected in the rhizosphere pretreated with strains GB03 and S4-7. The detection limit of 2-nonanone in the tomato rhizosphere was 1 µM. Unexpectedly, drench application of 2-nonanone at 10 nM concentration, which is below its detection limit, protected tomato seedlings against Pseudomonas syringae pv. tomato. Our finding highlights that BVCs, including 2-nonanone, released by a soil bacterium are functional even when present at a concentration below the detection limit of SPME-GC-MS.
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Affiliation(s)
- Myoungjoo Riu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Sang-Keun Oh
- Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Choong-Min Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
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21
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Kim B, Park AR, Song CW, Song H, Kim JC. Biological Control Efficacy and Action Mechanism of Klebsiella pneumoniae JCK-2201 Producing Meso-2,3-Butanediol Against Tomato Bacterial Wilt. Front Microbiol 2022; 13:914589. [PMID: 35910601 PMCID: PMC9333516 DOI: 10.3389/fmicb.2022.914589] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a fatal disease that affects the production of tomatoes and many other crops worldwide. As an effective strategy to manage bacterial wilt, biological control agents using plant growth-promoting rhizobacteria (PGPR) are being developed. In this study, we screened 2,3-butanediol (BDO)-producing PGPR to control tomato bacterial wilt and investigated the action mechanism of the disease control agent. Of the 943 strains isolated from soil, Klebsiella pneumoniae strain JCK-2201 produced the highest concentration of 2,3-BDO. The culture broth of K. pneumoniae JCK-2201 did not show any direct activity on R. solanacearum in vitro, but a 100-fold dilution effectively controlled tomato bacterial wilt with a control value of 77% in vivo. Fermentation utilizing K. pneumoniae JCK-2201 was optimized to produce 48 g/L of meso-2,3-BDO, which is 50% of the sucrose conversion efficiency. In addition, the control efficacy and mechanism of meso-2,3-BDO produced by JCK-2201 in tomato bacterial wilt were determined by comparative analysis with Bacillus licheniformis DSM13 producing meso-2,3-BDO and B. licheniformis DSM13 ΔalsS that did not produce 2,3-BDO, as the step of converting pyruvate to α-acetolactate was omitted. Tomato seedlings treated with the K. pneumoniae JCK-2201 (500-fold dilution) and B. licheniformis DSM13 (100-fold dilution) culture broth produced meso-2,3-BDO that significantly reduced R. solanacearum-induced disease severity with control values of 55% and 63%, respectively. The formulated meso-2,3-BDO 9% soluble concentrate (SL; 1,000-fold dilution) showed 87% control against tomato bacterial wilt in the field condition. Klebsiella pneumoniae JCK-2201 and B. licheniformis DSM13 treatment induced the expression of plant defense marker genes, such as LePR1, LePR2, LePR5, LePR3, and PI-II, in the salicylic acid and jasmonic acid signaling pathways at 4 days after inoculation. These results show that 2,3-BDO-producing bacteria and 2,3-BDO are potential biological control agents that act through induction of resistance for controlling tomato bacterial wilt.
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Affiliation(s)
- Bora Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju, South Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju, South Korea
| | - Chan Woo Song
- Research and Department Center, GS Caltex Corporation, Daejeon, South Korea
| | - Hyohak Song
- Research and Department Center, GS Caltex Corporation, Daejeon, South Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju, South Korea
- *Correspondence: Jin-Cheol Kim,
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22
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Boss BL, Wanees AE, Zaslow SJ, Normile TG, Izquierdo JA. Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata. BMC Genomics 2022; 23:508. [PMID: 35831788 PMCID: PMC9281055 DOI: 10.1186/s12864-022-08738-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Background The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biodegradation and bioremediation in sediments and sandy soils. A Sphingobium sp. isolate was obtained from the rhizosphere of the beachgrass Ammophila breviligulata with a variety of plant growth-promoting properties and designated as Sphingobium sp. strain AEW4. Results Analysis of the 16S rRNA gene as well as full genome nucleotide and amino acid identities revealed that this isolate is most similar to Sphingobium xenophagum and Sphingobium hydrophobicum. Comparative genomics analyses indicate that the genome of strain AEW4 contains unique features that explain its relationship with a plant host as a PGPR, including pathways involved in monosaccharide utilization, fermentation pathways, iron sequestration, and resistance to osmotic stress. Many of these unique features are not broadly distributed across the genus. In addition, pathways involved in the metabolism of salicylate and catechol, phenyl acetate degradation, and DNA repair were also identified in this organism but not in most closely related organisms. Conclusion The genome of Sphingobium sp. strain AEW4 contains a number of distinctive features that are crucial to explain its role as a plant-growth promoting rhizobacterium, and comparative genomics analyses support its classification as a relevant Sphingobium strain involved in plant growth promotion of beachgrass and other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08738-8.
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Affiliation(s)
- Brianna L Boss
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Abanoub E Wanees
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Shari J Zaslow
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Tyler G Normile
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
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23
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Synergism between Streptomyces viridosporus HH1 and Rhizophagus irregularis Effectively Induces Defense Responses to Fusarium Wilt of Pea and Improves Plant Growth and Yield. J Fungi (Basel) 2022; 8:jof8070683. [PMID: 35887440 PMCID: PMC9318455 DOI: 10.3390/jof8070683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
Fusarium wilt is a detrimental disease of pea crop, resulting in severe damage and a reduction in its yield. Developing synergistically enhanced bioagents for disease management and growth promotion is pivotal for food safety, security, and sustainability. In this study, biocontrol potential of treating pea plants with Streptomycesviridosporus HH1 and/or their colonization with Rhizophagusirregularis against infection with Fusarium wilt was investigated. Impacts on the expression profiles of defense-related genes, biochemical, and ultrastructural levels, as well as the growth and yield of pea plants in response to these treatments, were also investigated. Data obtained indicated the antifungal activity of S. viridosporus HH1 against F. oxysporum f.sp. pisi in vitro. Furthermore, the GC-MS analysis revealed production of different bioactive compounds by S. viridosporus HH1, including 2,3-butanediol, thioglycolic acid, and phthalic acid. The results from the greenhouse experiment exhibited a synergistic biocontrol activity, resulting in a 77% reduction in disease severity in pea plants treated with S. viridosporus HH1 and colonized with R. irregularis. In this regard, this dual treatment overexpressed the responsive factor JERF3 (5.6-fold) and the defense-related genes β-1,3-glucanase (8.2-fold) and the pathogenesis-related protein 1 (14.5-fold), enhanced the total phenolic content (99.5%), induced the antioxidant activity of peroxidase (64.3%) and polyphenol oxidase (31.6%) enzymes in pea plants, reduced the antioxidant stress, and improved their hypersensitivity at the ultrastructural level in response to the Fusarium wilt pathogen. Moreover, a synergistic growth-promoting effect was also recorded in pea plants in response to this dual treatment. In this regard, due to this dual treatment, elevated levels of photosynthetic pigments and improved growth parameters were observed in pea leaves, leading to an increment in the yield (113%). In addition, application of S. viridosporus enhanced the colonization levels with R. irregularis in pea roots. Based on the obtained data, we can conclude that treating pea plants with S. viridosporus HH1 and colonization with R. irregularis have synergistic biocontrol activity and growth-promoting effects on pea plants against Fusarium wilt. Despite its eco-safety and effectiveness, a field evaluation of this treatment before a use recommendation is quite necessary.
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24
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Medina-Paz F, Herrera-Estrella L, Heil M. All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean ( Phaseolus vulgaris) in Its Centre of Domestication. PLANTS (BASEL, SWITZERLAND) 2022; 11:1631. [PMID: 35807585 PMCID: PMC9269403 DOI: 10.3390/plants11131631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.
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Affiliation(s)
- Francisco Medina-Paz
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad de Genómica Avanzada, Irapuato 36824, GTO, Mexico; or
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79424, USA
| | - Martin Heil
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
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25
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Duraisamy K, Ha A, Kim J, Park AR, Kim B, Song CW, Song H, Kim JC. Enhancement of Disease Control Efficacy of Chemical Fungicides Combined with Plant Resistance Inducer 2,3-Butanediol against Turfgrass Fungal Diseases. THE PLANT PATHOLOGY JOURNAL 2022; 38:182-193. [PMID: 35678051 PMCID: PMC9343906 DOI: 10.5423/ppj.oa.02.2022.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/15/2023]
Abstract
Turfgrass, the most widely grown ornamental crop, is severely affected by fungal pathogens including Sclerotinia homoeocarpa, Rhizoctonia solani, and Magnaporthe poae. At present, turfgrass fungal disease management predominantly relies on synthetic fungicide treatments. However, the extensive application of fungicides to the soil increases residual detection frequency, raising concerns for the environment and human health. The bacterial volatile compound, 2,3-butanediol (BDO), was found to induce plant resistance. In this study, we evaluated the disease control efficacy of a combination of stereoisomers of 2,3-BDO and commercial fungicides against turfgrass fungal diseases in both growth room and fields. In the growth room experiment, the combination of 0.9% 2R,3R-BDO (levo) soluble liquid (SL) formulation and 9% 2R,3S-BDO (meso) SL with half concentration of fungicides significantly increased the disease control efficacy against dollar spot and summer patch disease when compared to the half concentration of fungicide alone. In field experiments, the disease control efficiency of levo 0.9% and meso 9% SL, in combination with a fungicide, was confirmed against dollar spot and large patch disease. Additionally, the induction of defense-related genes involved in the salicylic acid and jasmonic acid/ethylene signaling pathways and reactive oxygen species detoxification-related genes under Clarireedia sp. infection was confirmed with levo 0.9% and meso 9% SL treatment in creeping bentgrass. Our findings suggest that 2,3-BDO isomer formulations can be combined with chemical fungicides as a new integrated tool to control Clarireedia sp. infection in turfgrass, thereby reducing the use of chemical fungicides.
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Affiliation(s)
- Kalaiselvi Duraisamy
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186,
Korea
- Plant Healthcare Research Institute, JAN153 Biotech Incorporated, Gwangju 61186,
Korea
| | - Areum Ha
- Plant Healthcare Research Institute, JAN153 Biotech Incorporated, Gwangju 61186,
Korea
| | - Jongmun Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186,
Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186,
Korea
| | - Bora Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186,
Korea
| | - Chan Woo Song
- Research and Development Center, GS Caltex Corporation, Daejeon 34122,
Korea
| | - Hyohak Song
- Research and Development Center, GS Caltex Corporation, Daejeon 34122,
Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186,
Korea
- Plant Healthcare Research Institute, JAN153 Biotech Incorporated, Gwangju 61186,
Korea
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26
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Du J, Gao Q, Ji C, Song X, Liu Y, Li H, Li C, Zhang P, Li J, Liu X. Bacillus licheniformis JF-22 to Control Meloidogyne incognita and Its Effect on Tomato Rhizosphere Microbial Community. Front Microbiol 2022; 13:863341. [PMID: 35464941 PMCID: PMC9022077 DOI: 10.3389/fmicb.2022.863341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Meloidogyne incognita is one of the most destructive soil pests, causing serious economic losses in tomato production. Here, in vitro experiments demonstrated that the Bacillus licheniformis strain JF-22 has the potential to prevent M. incognita infection. A pot experiment confirmed that B. licheniformis strain JF-22 isolated from the tomato rhizosphere soil and planted in the tomato root-knot nematode disease area effectively prevented and controlled M. incognita, reducing its negative effect on tomato growth. Additionally, the composition of volatile substances secreted by B. licheniformis strain JF-22 was analyzed using solid-phase microextraction and gas chromatography–mass spectrometry. We detected acetoin, 2,3-Butanediol, [R-(R*,R*) ]-, and hexamethyl cyclotrisiloxane as the main components among these volatiles. Using MiSeq sequencing technology and bioinformatics, we analyzed the influence of B. licheniformis strain JF-22 on the microbial community of the tomato rhizosphere. B. licheniformis strain JF-22 changed the composition of the microbial community; particularly, it significantly reduced the diversity of the fungal community. Furthermore, using the FUNGuild and PICRUSt databases, we predicted the effect of JF-22 on microbial community function. In conclusion, B. licheniformis strain JF-22 may be considered as a potential biocontrol agent against M. incognita.
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Affiliation(s)
- Jianfeng Du
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China.,College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Qixiong Gao
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Chao Ji
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China.,College of Biological and Agricultural Engineering, Weifang University, Weifang, China
| | - Xin Song
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Yue Liu
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Huying Li
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Chaohui Li
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Pengcheng Zhang
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Jintai Li
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Xunli Liu
- College of Forestry, Shandong Agriculture University, Taian, China.,Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
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27
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Mirzaee H, Ariens E, Blaskovich MAT, Clark RJ, Schenk PM. Biostimulation of Bacteria in Liquid Culture for Identification of New Antimicrobial Compounds. Pharmaceuticals (Basel) 2021; 14:1232. [PMID: 34959632 PMCID: PMC8706287 DOI: 10.3390/ph14121232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/05/2022] Open
Abstract
We hypothesized that environmental microbiomes contain a wide range of bacteria that produce yet uncharacterized antimicrobial compounds (AMCs) that can potentially be used to control pathogens. Over 600 bacterial strains were isolated from soil and food compost samples, and 68 biocontrol bacteria with antimicrobial activity were chosen for further studies based on inhibition assays against a wide range of food and plant pathogens. For further characterization of the bioactive compounds, a new method was established that used living pathogens in a liquid culture to stimulate bacteria to produce high amounts of AMCs in bacterial supernatants. A peptide gel electrophoresis microbial inhibition assay was used to concurrently achieve size separation of the antimicrobial peptides. Fifteen potential bioactive peptides were then further characterized by tandem MS, revealing cold-shock proteins and 50S ribosomal proteins. To identify non-peptidic AMCs, bacterial supernatants were analyzed by HPLC followed by GC/MS. Among the 14 identified bioactive compounds, 3-isobutylhexahydropyrrolo[1,2-a]pyrazine-1,4-dione and 2-acetyl-3-methyl-octahydropyrrolo[1,2-a]piperazine-1,4-dione were identified as new AMCs. Our work suggests that antimicrobial compound production in microbes is enhanced when faced with a threat from other microorganisms, and that this approach can rapidly lead to the development of new antimicrobials with the potential for upscaling.
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Affiliation(s)
- Hooman Mirzaee
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Emily Ariens
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Mark A. T. Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Richard J. Clark
- Peptide Chemical Biology Laboratory, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Peer M. Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
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28
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Comeau D, Balthazar C, Novinscak A, Bouhamdani N, Joly DL, Filion M. Interactions Between Bacillus Spp., Pseudomonas Spp. and Cannabis sativa Promote Plant Growth. Front Microbiol 2021; 12:715758. [PMID: 34616381 PMCID: PMC8488376 DOI: 10.3389/fmicb.2021.715758] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) deploy several mechanisms to improve plant health, growth and yield. The aim of this study was to evaluate the efficacy of two Pseudomonas spp. strains and three Bacillus spp. strains used as single treatments and in consortia to improve the yield of Cannabis sativa and characterize the impact of these treatments on the diversity, structure and functions of the rhizosphere microbiome. Herein, we demonstrate a significant C. sativa yield increase up to 70% when inoculated with three different Pseudomonas spp./Bacillus spp. consortia but not with single inoculation treatments. This growth-promoting effect was observed in two different commercial soil substrates commonly used to grow cannabis: Promix and Canna coco. Marker-based genomic analysis highlighted Bacillus spp. as the main modulator of the rhizosphere microbiome diversity and Pseudomonas spp. as being strongly associated with plant growth promotion. We describe an increase abundance of predicted PGPR metabolic pathways linked with growth-promoting interactions in C. sativa.
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Affiliation(s)
- Dominique Comeau
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Carole Balthazar
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Amy Novinscak
- Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC, Canada
| | - Nadia Bouhamdani
- Department of Chemistry and Biochemistry, University of Moncton, Moncton, NB, Canada
| | - David L Joly
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Martin Filion
- Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
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29
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Liu Y, Wang X, Ma L, Lü M, Zhang W, Lü C, Gao C, Xu P, Ma C. Dehydrogenation Mechanism of Three Stereoisomers of Butane-2,3-Diol in Pseudomonas putida KT2440. Front Bioeng Biotechnol 2021; 9:728767. [PMID: 34513815 PMCID: PMC8427195 DOI: 10.3389/fbioe.2021.728767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas putida KT2440 is a promising chassis of industrial biotechnology due to its metabolic versatility. Butane-2,3-diol (2,3-BDO) is a precursor of numerous value-added chemicals. It is also a microbial metabolite which widely exists in various habiting environments of P. putida KT2440. It was reported that P. putida KT2440 is able to use 2,3-BDO as a sole carbon source for growth. There are three stereoisomeric forms of 2,3-BDO: (2R,3R)-2,3-BDO, meso-2,3-BDO and (2S,3S)-2,3-BDO. However, whether P. putida KT2440 can utilize three stereoisomeric forms of 2,3-BDO has not been elucidated. Here, we revealed the genomic and enzymic basis of P. putida KT2440 for dehydrogenation of different stereoisomers of 2,3-BDO into acetoin, which will be channeled to central mechanism via acetoin dehydrogenase enzyme system. (2R,3R)-2,3-BDO dehydrogenase (PP0552) was detailedly characterized and identified to participate in (2R,3R)-2,3-BDO and meso-2,3-BDO dehydrogenation. Two quinoprotein alcohol dehydrogenases, PedE (PP2674) and PedH (PP2679), were confirmed to be responsible for (2S,3S)-2,3-BDO dehydrogenation. The function redundancy and inverse regulation of PedH and PedE by lanthanide availability provides a mechanism for the adaption of P. putida KT2440 to variable environmental conditions. Elucidation of the mechanism of 2,3-BDO catabolism in P. putida KT2440 would provide new insights for bioproduction of 2,3-BDO-derived chemicals based on this robust chassis.
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Affiliation(s)
- Yidong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiuqing Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Liting Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wen Zhang
- Center for Gene and Immunotherapy, The Second Hospital of Shandong University, Jinan, China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Asghar A, Tan YC, Zahoor M, Zainal Abidin SA, Yow YY, Khan E, Lahiri C. A scaffolded approach to unearth potential antibacterial components from epicarp of Malaysian Nephelium lappaceum L. Sci Rep 2021; 11:13859. [PMID: 34226594 PMCID: PMC8257635 DOI: 10.1038/s41598-021-92622-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/10/2021] [Indexed: 11/09/2022] Open
Abstract
The emergence and spread of antimicrobial resistance have been of serious concern to human health and the management of bacterial infectious diseases. Effective treatment of these diseases requires the development of novel therapeutics, preferably free of side effects. In this regard, natural products are frequently conceived to be potential alternative sources for novel antibacterial compounds. Herein, we have evaluated the antibacterial activity of the epicarp extracts of the Malaysian cultivar of yellow rambutan fruit (Nephelium lappaceum L.) against six pathogens namely, Bacillus subtilis, methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes, Pseudomonas aeruginosa, Klebsiella pneumoniae and Salmonella enterica. Among a series of solvent extracts, fractions of ethyl acetate and acetone have revealed significant activity towards all tested strains. Chemical profiling of these fractions, via HPLC, LC-MS and GC-MS, has generated a library of potentially bioactive compounds. Downstream virtual screening, pharmacological prediction, and receptor-ligand molecular dynamics simulation have eventually unveiled novel potential antibacterial compounds, which can be extracted for medicinal use. We report compounds like catechin, eplerenone and oritin-4-beta-ol to be computationally inhibiting the ATP-binding domain of the chaperone, DnaK of P. aeruginosa and MRSA. Thus, our work follows the objective to propose new antimicrobials capable of perforating the barrier of resistance posed by both the gram positives and the negatives.
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Affiliation(s)
- Ali Asghar
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Yong Chiang Tan
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Mohammad Zahoor
- Department of Biochemistry, University of Malakand, Chakdara, Pakistan
| | | | - Yoon-Yen Yow
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Ezzat Khan
- Department of Chemistry, University of Bahrain, Sakhir, Bahrain
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia.
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Paenibacillus polymyxa (LM31) as a new feed additive: Antioxidant and antimicrobial activity and its effects on growth, blood biochemistry, and intestinal bacterial populations of growing Japanese quail. Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2021.114920] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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32
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C4 Bacterial Volatiles Improve Plant Health. Pathogens 2021; 10:pathogens10060682. [PMID: 34072921 PMCID: PMC8227687 DOI: 10.3390/pathogens10060682] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/24/2021] [Indexed: 02/04/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) associated with plant roots can trigger plant growth promotion and induced systemic resistance. Several bacterial determinants including cell-wall components and secreted compounds have been identified to date. Here, we review a group of low-molecular-weight volatile compounds released by PGPR, which improve plant health, mostly by protecting plants against pathogen attack under greenhouse and field conditions. We particularly focus on C4 bacterial volatile compounds (BVCs), such as 2,3-butanediol and acetoin, which have been shown to activate the plant immune response and to promote plant growth at the molecular level as well as in large-scale field applications. We also disc/ uss the potential applications, metabolic engineering, and large-scale fermentation of C4 BVCs. The C4 bacterial volatiles act as airborne signals and therefore represent a new type of biocontrol agent. Further advances in the encapsulation procedure, together with the development of standards and guidelines, will promote the application of C4 volatiles in the field.
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Santoyo G, Urtis-Flores CA, Loeza-Lara PD, Orozco-Mosqueda MDC, Glick BR. Rhizosphere Colonization Determinants by Plant Growth-Promoting Rhizobacteria (PGPR). BIOLOGY 2021; 10:biology10060475. [PMID: 34072072 PMCID: PMC8229920 DOI: 10.3390/biology10060475] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Plant growth-promoting rhizobacteria (PGPR) are an eco-friendly alternative to the use of chemicals in agricultural production and crop protection. However, the efficacy of PGPR as bioinoculants can be diminished by a low capacity to colonize spaces in the rhizosphere. In this work, we review pioneering and recent developments on several important functions that rhizobacteria exhibit in order to compete, colonize, and establish themselves in the plant rhizosphere. Therefore, the use of highly competitive strains in open field trials should be a priority, in order to have consistent and better results in agricultural production activities. Abstract The application of plant growth-promoting rhizobacteria (PGPR) in the field has been hampered by a number of gaps in the knowledge of the mechanisms that improve plant growth, health, and production. These gaps include (i) the ability of PGPR to colonize the rhizosphere of plants and (ii) the ability of bacterial strains to thrive under different environmental conditions. In this review, different strategies of PGPR to colonize the rhizosphere of host plants are summarized and the advantages of having highly competitive strains are discussed. Some mechanisms exhibited by PGPR to colonize the rhizosphere include recognition of chemical signals and nutrients from root exudates, antioxidant activities, biofilm production, bacterial motility, as well as efficient evasion and suppression of the plant immune system. Moreover, many PGPR contain secretion systems and produce antimicrobial compounds, such as antibiotics, volatile organic compounds, and lytic enzymes that enable them to restrict the growth of potentially phytopathogenic microorganisms. Finally, the ability of PGPR to compete and successfully colonize the rhizosphere should be considered in the development and application of bioinoculants.
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Affiliation(s)
- Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico;
- Correspondence:
| | - Carlos Alberto Urtis-Flores
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico;
| | - Pedro Damián Loeza-Lara
- Licenciatura en Genómica Alimentaria, Universidad de La Ciénega del Estado de Michoacán de Ocampo, Sahuayo 59103, Mexico;
| | - Ma. del Carmen Orozco-Mosqueda
- Facultad de Agrobiología “Presidente Juárez”, Universidad Michoacana de San Nicolás de Hidalgo, Melchor Ocampo, Uruapan 60170, Mexico;
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
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Magotra S, Bhagat N, Ambardar S, Ali T, Hurek BR, Hurek T, Verma PK, Vakhlu J. Field evaluation of PGP Bacillus sp. strain D5 native to Crocus sativus, in traditional and non traditional areas, and mining of PGP genes from its genome. Sci Rep 2021; 11:5454. [PMID: 33750799 PMCID: PMC7943801 DOI: 10.1038/s41598-021-84585-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/11/2020] [Indexed: 01/31/2023] Open
Abstract
Native Bacillus sp. strain D5 coded as (Bar D5) has been isolated from the saffron corm that showed plant growth promotion (PGP) properties and also inhibits the growth of corm rot causing Fusarium oxysporum R1 (Fox R1) in-vitro. Bar D5 was more efficient PGP bacterium in comparison to earlier reported native bio-formulations by our group. Pot assays and field evaluation of Bar D5 confirmed its in-vivo efficacy for PGP traits and biocontrol activity as well. Pot trials were followed by field trials at traditional (Kishtwar) and non-traditional (R.S Pura) saffron cultivation areas in Jammu and Kashmir. At both places, Bar D5 bio-formulation treatment led to the increase in root number & length, shoot number & length, flower number and number & weight of daughter corms. Additionally, it also decreased the corm rot disease incidence significantly. Priming of corms with bio-formulation resulted in the reduction of pathogenic fungal load by three fold at the depth of corm sowing from ground level. The shelf life/viability of Bar D5 based bio-formulation was found to be 52% (viable spores) for one year at room temperature. Draft genome sequence of Bar D5 revealed the presence of genes necessary for PGP and biocontrol activity. Further, confirmation of gene sequences and annotation was done by amplification, re-sequencing and mapping of PGP and biocontrol genes on draft genome. Bar D5 based bio-formulation can be provided to companies/researchers interested in saffron cultivation or bio-formulation production for commercial exploitation, since saffron is grown as revenue crop across continents. The present study bridges the gap between genomics and its field application.
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Affiliation(s)
- Shanu Magotra
- grid.412986.00000 0001 0705 4560Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006 India ,grid.448792.40000 0004 4678 9721University Institute of Biotechnology, Chandigarh University, Punjab, 140413 India
| | - Nancy Bhagat
- grid.412986.00000 0001 0705 4560Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006 India
| | - Sheetal Ambardar
- grid.22401.350000 0004 0502 9283National Center for Biological Sciences, Bellary Road, Bangalore, 560065 India
| | - Tahir Ali
- grid.412986.00000 0001 0705 4560Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006 India
| | - Barbara Reinhold Hurek
- grid.7704.40000 0001 2297 4381Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, P.O. Box 33 04 40, Bremen, Germany
| | - Thomas Hurek
- grid.7704.40000 0001 2297 4381Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, P.O. Box 33 04 40, Bremen, Germany
| | - Praveen Kumar Verma
- grid.419632.b0000 0001 2217 5846Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Jyoti Vakhlu
- grid.412986.00000 0001 0705 4560Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006 India
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Vivek N, Hazeena SH, Alphy MP, Kumar V, Magdouli S, Sindhu R, Pandey A, Binod P. Recent advances in microbial biosynthesis of C3 - C5 diols: Genetics and process engineering approaches. BIORESOURCE TECHNOLOGY 2021; 322:124527. [PMID: 33340948 DOI: 10.1016/j.biortech.2020.124527] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 05/22/2023]
Abstract
Diols derived from renewable feedstocks have significant commercial interest in polymer, pharmaceutical, cosmetics, flavors and fragrances, food and feed industries. In C3-C5 diols biological processes of 1,3-propanediol, 1,2-propanediol and 2,3-butanediol have been commercialized as other isomers are non-natural metabolites and lack natural biosynthetic pathways. However, the developments in the field of systems and synthetic biology paved a new path to learn, build, construct, and test for efficient chassis strains. The current review addresses the recent advancements in metabolic engineering, construction of novel pathways, process developments aimed at enhancing in production of C3-C5 diols. The requisites on developing an efficient and sustainable commercial bioprocess for C3-C5 diols were also discussed.
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Affiliation(s)
- Narisetty Vivek
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Sulfath Hakkim Hazeena
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Maria Paul Alphy
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Sara Magdouli
- Centre technologique des résidus industriels, University of Quebec in Abitibi Témiscamingue, Quebec, Canada
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research (CSIR-IITR), 31MG Marg, Lucknow 226 001, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.
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Snak A, Vendruscolo ECG, dos Santos MF, Fiorini A, Mesa D. Genome sequencing and analysis of plant growth-promoting attributes from Leclercia adecarboxylata. Genet Mol Biol 2021; 44:e20200130. [PMID: 33503198 PMCID: PMC7839631 DOI: 10.1590/1678-4685-gmb-2020-0130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/11/2020] [Indexed: 11/22/2022] Open
Abstract
Plant growth-promoting bacteria are ecological alternatives for fertilization, mainly for gramineous. Since plant x bacteria interaction is genotype and strain dependent, searching for new strains may contribute to the development of new biofertilizers. We aim to characterize plant growth-promoting capacity of Leclercia adecarboxylata strain Palotina, formerly isolated by our group in corn. A single isolated colony was taken and its genome was sequenced using Illumina technology. The whole genome was compared to other Leclercia adecarboxylata strains, and their biological and growth-promoting traits, such as P solubilization and auxin production, were tested. Following that, a 4.8 Mb genome of L. adecarboxylata strain Palotina was assembled and the functional annotation was carried out. This paper is the first to report the genes associated with plant growth promotion demonstrating in vitro indole acid production by this strain. These results project the endophyte as a potential biofertilizer for further commercial exploitation.
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Affiliation(s)
- Aline Snak
- Universidade Federal do Paraná, Labiogen-Laboratório de Bioquímica e
Genética, Palotina, PR, Brazil
| | | | | | - Adriana Fiorini
- Universidade Federal do Paraná, Labiogen-Laboratório de Bioquímica e
Genética, Palotina, PR, Brazil
- Universidade Federal do Paraná, Departamento de Biociências,
Palotina, PR, Brazil
| | - Dany Mesa
- Universidade Federal do Paraná, Departamento de Bioquímica, Centro
Politécnico, Jardim das Américas, Curitiba, PR, Brazil
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Lee SM, Kong HG, Song GC, Ryu CM. Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. THE ISME JOURNAL 2021; 15:330-347. [PMID: 33028974 PMCID: PMC7852523 DOI: 10.1038/s41396-020-00785-x] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/27/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease suppression is largely unknown. Here, we analyzed the rhizosphere microbial community of a healthy and diseased tomato plant grown <30-cm apart in a greenhouse at three different locations in South Korea. The abundance of Gram-positive Actinobacteria and Firmicutes phyla was lower in diseased rhizosphere soil (DRS) than in healthy rhizosphere soil (HRS) without changes in the causative Ralstonia solanacearum population. Artificial disruption of Gram-positive bacteria in HRS using 500-μg/mL vancomycin increased bacterial wilt occurrence in tomato. To identify HRS-specific and plant-protective Gram-positive bacteria species, Brevibacterium frigoritolerans HRS1, Bacillus niacini HRS2, Solibacillus silvestris HRS3, and Bacillus luciferensis HRS4 were selected from among 326 heat-stable culturable bacteria isolates. These four strains did not directly antagonize R. solanacearum but activated plant immunity. A synthetic community comprising these four strains displayed greater immune activation against R. solanacearum and extended plant protection by 4 more days in comparison with each individual strain. Overall, our results demonstrate for the first time that dysbiosis of the protective Gram-positive bacterial community in DRS promotes the incidence of disease.
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Affiliation(s)
- Sang-Moo Lee
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Hyun Gi Kong
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, 54875, South Korea
| | - Geun Cheol Song
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea.
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Liu L, Zhao X, Huang Y, Ke L, Wang R, Qi G. Protecting tobacco plants from O 3 injury by Bacillus velezensis with production of acetoin. PHYSIOLOGIA PLANTARUM 2020; 170:158-171. [PMID: 32386333 DOI: 10.1111/ppl.13120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPRs) confer benefits to crops by producing volatile organic compounds (VOCs) to trigger induced systemic tolerance (IST). Here we show that Bacillus velezensis GJ11, a kind of PGPRs, produce VOCs such as 2,3-butanediol and acetoin to trigger IST and cause stomatal closure against O3 injury in tobacco plants. Compared to 2,3-butanediol, acetoin was more effective on triggering IST against O3 injury. The bdh-knockout strain GJ11Δbdh with a blocked metabolic pathway from acetoin to 2,3-butanediol produced more acetoin triggering stronger IST against O3 injury than GJ11. Both acetoin and GJ11Δbdh effectively enhance the antioxidant enzymes activity (e.g. superoxide dismutase and catalases) that is favorable for scavenging the reactive oxygen species like H2 O2 in leaves after exposure to O3 . Consequently, less H2 O2 accumulation was observed, and reasonably less chlorophylls and proteins were damaged by H2 O2 in the tobacco leaves treated with acetoin or GJ11Δbdh. The field experiment also showed that both acetoin and GJ11Δbdh could protect tobacco plants from O3 injury after application by root-drench. This study provides new insights into the role of rhizobacterial B. velezensis and its volatile component of acetoin in triggering defense responses against stresses such as O3 in plants.
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Affiliation(s)
- Lidong Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yong Huang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Technology Center, Enshi State Tobacco Cooperation, Hubei Province Tobacco CO., Ltd., Enshi, China
| | - Luxin Ke
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Rui Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Technology Center, Enshi State Tobacco Cooperation, Hubei Province Tobacco CO., Ltd., Enshi, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Wang CJ, Wang YZ, Chu ZH, Wang PS, Liu BY, Li BY, Yu XL, Luan BH. Endophytic Bacillus amyloliquefaciens YTB1407 elicits resistance against two fungal pathogens in sweet potato (Ipomoea batatas (L.) Lam.). JOURNAL OF PLANT PHYSIOLOGY 2020; 253:153260. [PMID: 32846310 DOI: 10.1016/j.jplph.2020.153260] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The endophytic Bacillus amyloliquefaciens YTB1407 was previously reported to promote the growth of sweet potato (Ipomoea batatas cv. Yanshu 25). Here, we demonstrate in both in vitro and pot trial assays that pre-treatment with YTB1407 suspension could enhance resistance against root rot disease and black rot disease, caused by Fusarium solani Mart. Sacc. f. sp. batatas McClure and Ceratocystis fimbriata Ell. & Halst on sweet potato, respectively. When seedlings were infected with fungal pathogens at 10 days post irrigation, pre-treatment with YTB1407 suspension decreased these pathogens and YTB1407 bacterial biomass in sweet potato roots. The pre-treatment activated the expression of salicylic acid (SA)-responsive PR-1 gene, raised SA content, and reduced hydrogen peroxide (H2O2) in the host to resist F. solani, while it enhanced the expression levels of SA-responsive NPR1 and PR1 genes and increased SA content to resist C. fimbriata. The disease resistance control effect initiated by pre-treatment with YTB1407 for root rot pathogen (F. solani) was better than for black rot pathogen (C. fimbriata). The results indicated that Bacillus amyloliquefaciens YTB1407 played a pivotal role in enhancing resistance to two fungi pathogens in sweet potato, through production of some antifungal metabolites to decrease infection in the early stage as well as induction of SA-dependent systemic resistance.
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Affiliation(s)
- Cui-Juan Wang
- Institute of Plant Protection, Yantai Academy of Agricultural Sciences, Yantai, 265500, PR China
| | - Ying-Zi Wang
- Institute of Plant Protection, Yantai Academy of Agricultural Sciences, Yantai, 265500, PR China.
| | - Zhao-Hui Chu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China.
| | - Pei-Song Wang
- Institute of Plant Protection, Yantai Academy of Agricultural Sciences, Yantai, 265500, PR China
| | - Bao-You Liu
- Institute of Plant Protection, Yantai Academy of Agricultural Sciences, Yantai, 265500, PR China
| | - Bao-Yan Li
- Institute of Plant Protection, Yantai Academy of Agricultural Sciences, Yantai, 265500, PR China
| | - Xiao-Li Yu
- Institute of Plant Protection, Yantai Academy of Agricultural Sciences, Yantai, 265500, PR China
| | - Bing-Hui Luan
- Institute of Plant Protection, Yantai Academy of Agricultural Sciences, Yantai, 265500, PR China
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40
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Whole-Genome Sequence of a Plant Growth-Promoting Strain, Serratia marcescens BTL07, Isolated from the Rhizoplane of Capsicum annuum L. Microbiol Resour Announc 2020; 9:9/18/e01484-19. [PMID: 32354984 PMCID: PMC7193939 DOI: 10.1128/mra.01484-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serratia marcescens strain BTL07, which has the ability to promote growth and suppress plant diseases, was isolated from the rhizoplane of a chili plant. The draft genome sequence data of the strain will contribute to advancing our understanding of the molecular mechanisms underlying plant growth promotion and tolerance to different stresses. Serratia marcescens strain BTL07, which has the ability to promote growth and suppress plant diseases, was isolated from the rhizoplane of a chili plant. The draft genome sequence data of the strain will contribute to advancing our understanding of the molecular mechanisms underlying plant growth promotion and tolerance to different stresses.
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Vereecke D, Zhang Y, Francis IM, Lambert PQ, Venneman J, Stamler RA, Kilcrease J, Randall JJ. Functional Genomics Insights Into the Pathogenicity, Habitat Fitness, and Mechanisms Modifying Plant Development of Rhodococcus sp. PBTS1 and PBTS2. Front Microbiol 2020; 11:14. [PMID: 32082278 PMCID: PMC7002392 DOI: 10.3389/fmicb.2020.00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/06/2020] [Indexed: 01/05/2023] Open
Abstract
Pistachio Bushy Top Syndrome (PBTS) is a recently emerged disease that has strongly impacted the pistachio industry in California, Arizona, and New Mexico. The disease is caused by two bacteria, designated PBTS1 that is related to Rhodococcus corynebacterioides and PBTS2 that belongs to the species R. fascians. Here, we assessed the pathogenic character of the causative agents and examined their chromosomal sequences to predict the presence of particular functions that might contribute to the observed co-occurrence and their effect on plant hosts. In diverse assays, we confirmed the pathogenicity of the strains on "UCB-1" pistachio rootstock and showed that they can also impact the development of tobacco species, but concurrently inconsistencies in the ability to induce symptoms were revealed. We additionally evidence that fas genes are present only in a subpopulation of pure PBTS1 and PBTS2 cultures after growth on synthetic media, that these genes are easily lost upon cultivation in rich media, and that they are enriched for in an in planta environment. Analysis of the chromosomal sequences indicated that PBTS1 and PBTS2 might have complementary activities that would support niche partitioning. Growth experiments showed that the nutrient utilization pattern of both PBTS bacteria was not identical, thus avoiding co-inhabitant competition. PBTS2 appeared to have the potential to positively affect the habitat fitness of PBTS1 by improving its resistance against increased concentrations of copper and penicillins. Finally, mining the chromosomes of PBTS1 and PBTS2 suggested that the bacteria could produce cytokinins, auxins, and plant growth-stimulating volatiles and that PBTS2 might interfere with ethylene levels, in support of their impact on plant development. Subsequent experimentation supported these in silico predictions. Altogether, our data provide an explanation for the observed pathogenic behavior and unveil part of the strategies used by PBTS1 and PBTS2 to interact with plants.
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Affiliation(s)
- Danny Vereecke
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Yucheng Zhang
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Isolde M Francis
- Department of Biology, California State University, Bakersfield, CA, United States
| | - Paul Q Lambert
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Jolien Venneman
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Rio A Stamler
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - James Kilcrease
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Jennifer J Randall
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
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Pršić J, Ongena M. Elicitors of Plant Immunity Triggered by Beneficial Bacteria. FRONTIERS IN PLANT SCIENCE 2020; 11:594530. [PMID: 33304371 PMCID: PMC7693457 DOI: 10.3389/fpls.2020.594530] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/07/2020] [Indexed: 05/19/2023]
Abstract
The molecular basis of plant immunity triggered by microbial pathogens is being well-characterized as a complex sequential process leading to the activation of defense responses at the infection site, but which may also be systemically expressed in all organs, a phenomenon also known as systemic acquired resistance (SAR). Some plant-associated and beneficial bacteria are also able to stimulate their host to mount defenses against pathogen ingress via the phenotypically similar, induced systemic resistance phenomenon. Induced systemic resistance resembles SAR considering its mechanistic principle as it successively involves recognition at the plant cell surface, stimulation of early cellular immune-related events, systemic signaling via a fine-tuned hormonal cross-talk and activation of defense mechanisms. It thus represents an indirect but efficient mechanism by which beneficial bacteria with biocontrol potential improve the capacity of plants to restrict pathogen invasion. However, according to our current vision, induced systemic resistance is specific considering some molecular aspects underpinning these different steps. Here we overview the chemical diversity of compounds that have been identified as induced systemic resistance elicitors and thereby illustrating the diversity of plants species that are responsive as well as the range of pathogens that can be controlled via this phenomenon. We also point out the need for further investigations allowing better understanding how these elicitors are sensed by the host and the diversity and nature of the stimulated defense mechanisms.
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Subrahmanyam G, Kumar A, Sandilya SP, Chutia M, Yadav AN. Diversity, Plant Growth Promoting Attributes, and Agricultural Applications of Rhizospheric Microbes. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2020. [DOI: 10.1007/978-3-030-38453-1_1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Eckshtain-Levi N, Harris SL, Roscios RQ, Shank EA. Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana. PHYTOBIOMES JOURNAL 2020; 4:303-313. [PMID: 34661038 PMCID: PMC8519414 DOI: 10.1094/pbiomes-02-20-0019-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Plant-growth-promoting bacteria (PGPB) are used to improve plant health and promote crop production. However, because some PGPB (including Bacillus subtilis) do not maintain substantial colonization on plant roots over time, it is unclear how effective PGPB are throughout the plant growing cycle. A better understanding of the dynamics of plant root community assembly is needed to develop and harness the potential of PGPB. Although B. subtilis is often a member of the root microbiome, it does not efficiently monoassociate with plant roots. We hypothesized that B. subtilis may require other primary colonizers to efficiently associate with plant roots. We utilized a previously designed hydroponic system to add bacteria to Arabidopsis thaliana roots and monitor their attachment over time. We inoculated seedlings with B. subtilis and individual bacterial isolates from the native A. thaliana root microbiome either alone or together. We then measured how the coinoculum affected the ability of B. subtilis to colonize and maintain on A. thaliana roots. We screened 96 fully genome-sequenced strains and identified five bacterial strains that were able to significantly improve the maintenance of B. subtilis. Three of these rhizobacteria also increased the maintenance of two strains of B. amyloliquefaciens commonly used in commercially available bioadditives. These results not only illustrate the utility of this model system to address questions about plant-microbe interactions and how other bacteria affect the ability of PGPB to maintain their relationships with plant roots but also may help inform future agricultural interventions to increase crop yields.
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Affiliation(s)
- Noam Eckshtain-Levi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Susanna Leigh Harris
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Reizo Quilat Roscios
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Elizabeth Anne Shank
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
- Corresponding author: E. A. Shank;
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Wu Z, Huang Y, Li Y, Dong J, Liu X, Li C. Biocontrol of Rhizoctonia solani via Induction of the Defense Mechanism and Antimicrobial Compounds Produced by Bacillus subtilis SL-44 on Pepper ( Capsicum annuum L.). Front Microbiol 2019; 10:2676. [PMID: 31849858 PMCID: PMC6892779 DOI: 10.3389/fmicb.2019.02676] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022] Open
Abstract
Pepper seedling wilt disease is the main cause of crop yield reduction. Biocontrol agents are widely used to control plant diseases caused by pathogenic fungi and activate plant defense systems. Our preliminary work showed that Bacillus subtilis SL-44 played a significant role in the reduction of wilt disease severity on pepper plants. To evaluate biological control mechanism of B. subtilis SL-44 on wilt disease caused by Rhizoctonia solani, the activities of the related enzymes were detected in the pepper seedling with different treatment in this study. Fluorescence microscopy combined with different dyes showed that B. subtilis SL-44 induced a large amount of active oxygen and callose accumulation in pepper leaves. The defense-related enzyme activities in pepper were improved significantly when treated with B. subtilis SL-44, including peroxidase, catalase, superoxide dismutase, polyphenol oxidase, and phenylalanine ammonia lyase. The activity of chitinase and β-1,3-glucanase in B. subtilis SL-44-treated pepper was also enhanced. Furthermore, the expression level of pepper-resistance gene CaPIN II was significantly increased in B. subtilis SL-44 treatment. Besides, B. subtilis SL-44 filtrate led to the death of the pathogenic fungus by fracturing the mycelia and leaking of the cell contents. Surfactin, iturin, and fengycin were found in B. subtilis SL-44 crude extracts, which could be effective antifungal compounds against R. solani. The results suggest that B. subtilis SL-44 could not only activate induced systemic resistance of pepper seedling against wilt disease caused by R. solani by jasmonic acid-dependent signaling pathway but also produce antifungal compounds to inhibit or even damage the mycelium growth of R. solani. The findings of this study provide novel guidance in plant protection development.
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Affiliation(s)
- Zhansheng Wu
- Department of Bioengineering, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, China.,Department of Environmental and Biological Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, China
| | - Yuanyuan Huang
- Department of Environmental and Biological Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, China
| | - Yan Li
- Department of Environmental and Biological Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, China
| | - Jiawei Dong
- Department of Environmental and Biological Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, China
| | - Xiaochen Liu
- Department of Bioengineering, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, China
| | - Chun Li
- Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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Engineering Bacillus velezensis with high production of acetoin primes strong induced systemic resistance in Arabidopsis thaliana. Microbiol Res 2019; 227:126297. [DOI: 10.1016/j.micres.2019.126297] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/02/2019] [Accepted: 07/12/2019] [Indexed: 11/18/2022]
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Nelkner J, Tejerizo GT, Hassa J, Lin TW, Witte J, Verwaaijen B, Winkler A, Bunk B, Spröer C, Overmann J, Grosch R, Pühler A, Schlüter AA. Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics. Genes (Basel) 2019; 10:E601. [PMID: 31405015 PMCID: PMC6722718 DOI: 10.3390/genes10080601] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 01/17/2023] Open
Abstract
The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.
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Affiliation(s)
- Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Gonzalo Torres Tejerizo
- Facultad de Ciencias Exactas, Departamento de Ciencias Biologicas, IBBM, Universidad Nacional de La Plata, Calle 115 y 47, 1900 La Plata, Argentina
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Timo Wentong Lin
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Julian Witte
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Bart Verwaaijen
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - And Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
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Kong HG, Song GC, Ryu CM. Inheritance of seed and rhizosphere microbial communities through plant-soil feedback and soil memory. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:479-486. [PMID: 31054200 DOI: 10.1111/1758-2229.12760] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/23/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Since the discovery of the role of microbes in the phytobiome, microbial communities (microbiota) have been identified and characterized based on host species, development, distribution, and condition. The microbiota in the plant rhizosphere is believed to have been established prior to seed germination and innate immune development. However, the microbiota in seeds has received little attention. Although our knowledge of the distribution of microbiota in plant seeds and rhizosphere is currently limited, the impact of these microbiota is likely to be greater than expected. This minireview suggests a new function of microbial inheritance from the seed to root and from the first generation of plants to the next. Surprisingly, recruitment and accumulation of microbiota by biotic and abiotic stresses affect plant immunity in the next generation through plant-soil feedback and soil memory. To illustrate this process, we propose a new term called 'microbiota-induced soil inheritance (MISI).' A comprehensive understanding of MISI will provide novel insights into plant-microbe interactions and plant immunity inheritance.
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Affiliation(s)
- Hyun Gi Kong
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon, 34141, South Korea
| | - Geun Cheol Song
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon, 34141, South Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon, 34141, South Korea
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Lee SA, Kim Y, Kim JM, Chu B, Joa JH, Sang MK, Song J, Weon HY. A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments. Sci Rep 2019; 9:9300. [PMID: 31243310 PMCID: PMC6594962 DOI: 10.1038/s41598-019-45660-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/10/2019] [Indexed: 01/21/2023] Open
Abstract
Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax, Enterobacter, Pseudomonas, Rhizobium, Streptomyces, and Variovorax, members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.
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Affiliation(s)
- Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jeong Myeong Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Bora Chu
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jae-Ho Joa
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural & Herbal Science, RDA, Jeju, 63240, South Korea
| | - Mee Kyung Sang
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea.
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Defining the Genetic Basis of Plant⁻Endophytic Bacteria Interactions. Int J Mol Sci 2019; 20:ijms20081947. [PMID: 31010043 PMCID: PMC6515357 DOI: 10.3390/ijms20081947] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 01/17/2023] Open
Abstract
Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined.
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