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Kumari M, Yagnik KN, Gupta V, Singh IK, Gupta R, Verma PK, Singh A. Metabolomics-driven investigation of plant defense response against pest and pathogen attack. PHYSIOLOGIA PLANTARUM 2024; 176:e14270. [PMID: 38566280 DOI: 10.1111/ppl.14270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
The advancement of metabolomics has assisted in the identification of various bewildering characteristics of the biological system. Metabolomics is a standard approach, facilitating crucial aspects of system biology with absolute quantification of metabolites using minimum samples, based on liquid/gas chromatography, mass spectrometry and nuclear magnetic resonance. The metabolome profiling has narrowed the wide gaps of missing information and has enhanced the understanding of a wide spectrum of plant-environment interactions by highlighting the complex pathways regulating biochemical reactions and cellular physiology under a particular set of conditions. This high throughput technique also plays a prominent role in combined analyses of plant metabolomics and other omics datasets. Plant metabolomics has opened a wide paradigm of opportunities for developing stress-tolerant plants, ensuring better food quality and quantity. However, despite advantageous methods and databases, the technique has a few limitations, such as ineffective 3D capturing of metabolites, low comprehensiveness, and lack of cell-based sampling. In the future, an expansion of plant-pathogen and plant-pest response towards the metabolite architecture is necessary to understand the intricacies of plant defence against invaders, elucidation of metabolic pathway operational during defence and developing a direct correlation between metabolites and biotic stresses. Our aim is to provide an overview of metabolomics and its utilities for the identification of biomarkers or key metabolites associated with biotic stress, devising improved diagnostic methods to efficiently assess pest and pathogen attack and generating improved crop varieties with the help of combined application of analytical and molecular tools.
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Affiliation(s)
- Megha Kumari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Kalpesh Nath Yagnik
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul, Republic of Korea
| | - Praveen K Verma
- Plant-Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, India
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Feng L, Li Q, Zhou D, Jia M, Liu Z, Hou Z, Ren Q, Ji S, Sang S, Lu S, Yu J. B. subtilis CNBG-PGPR-1 induces methionine to regulate ethylene pathway and ROS scavenging for improving salt tolerance of tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:193-211. [PMID: 37812678 DOI: 10.1111/tpj.16489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/10/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
Soil salinity severely threatens plant growth and crop yields. The utilization of PGPR is an effective strategy for enhancing plant salt tolerance, but the mechanisms involved in this process have rarely been reported. In this study, we investigated the effects of Bacillus subtilis CNBG-PGPR-1 on improving plant salt tolerance and elucidated the molecular pathways involved. The results showed that CNBG-PGPR-1 significantly improved the cellular homeostasis and photosynthetic efficiency of leaves and reduced ion toxicity and osmotic stress caused by salt in tomato. Transcriptome analysis uncovered that CNBG-PGPR-1 enhanced plant salt tolerance through the activation of complex molecular pathways, with plant hormone signal transduction playing an important role. Comparative analysis and pharmacological experiments confirmed that the ethylene pathway was closely related to the beneficial effect of CNBG-PGPR-1 on improving plant salt tolerance. Furthermore, we found that methionine, a precursor of ethylene synthesis, significantly accumulated in response to CNBG-PGPR-1 in tomato. Exogenous L-methionine largely mimicked the beneficial effects of CNBG-PGPR-1 and activated the expression of ethylene pathway-related genes, indicating CNBG-PGPR-1 induces methionine accumulation to regulate the ethylene pathway in tomato. Finally, CNBG-PGPR-1 reduced salt-induced ROS by activating ROS scavenger-encoding genes, mainly involved in GSH metabolism and POD-related genes, which were also closely linked to methionine metabolism. Overall, our studies demonstrate that CNBG-PGPR-1-induced methionine is a key regulator in enhancing plant salt tolerance through the ethylene pathway and ROS scavenging, providing a novel understanding of the mechanism by which beneficial microbes improve plant salt tolerance.
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Affiliation(s)
- Liuchun Feng
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Qi Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Dongqin Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Mingyun Jia
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Zhuangzhuang Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Zhaoqi Hou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Quanjin Ren
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Shengdong Ji
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shifei Sang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shipeng Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Jinping Yu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
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Sondo M, Wonni I, Koïta K, Rimbault I, Barro M, Tollenaere C, Moulin L, Klonowska A. Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data. PLoS One 2023; 18:e0287084. [PMID: 38032916 PMCID: PMC10688718 DOI: 10.1371/journal.pone.0287084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.
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Affiliation(s)
- Moussa Sondo
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Kadidia Koïta
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Isabelle Rimbault
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Mariam Barro
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Charlotte Tollenaere
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Lionel Moulin
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Agnieszka Klonowska
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
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Sanchez-Gonzalez ME, Mora-Herrera ME, Wong-Villarreal A, De La Portilla-López N, Sanchez-Paz L, Lugo J, Vaca-Paulín R, Del Aguila P, Yañez-Ocampo G. Effect of pH and Carbon Source on Phosphate Solubilization by Bacterial Strains in Pikovskaya Medium. Microorganisms 2022; 11:microorganisms11010049. [PMID: 36677341 PMCID: PMC9866999 DOI: 10.3390/microorganisms11010049] [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: 11/01/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Phosphate-solubilizing bacteria (PSB) transform precipitated inorganic phosphorus into soluble orthophosphates. This study evaluated the efficiency of tricalcium and iron phosphate solubilization in Pikovskaya medium using five bacterial strains (A1, A2, A3, A5, and A6) cultured in acidic and alkaline pH levels. The bacterial strain that proved to be more efficient for P solubilization and was tolerant to pH variations was selected for assessing bacterial growth and P solubilization with glucose and sucrose in the culture medium. The bacterial strains were identified through 16S rRNA gene sequencing as Pseudomonas libanensis A1, Pseudomonas libanensis (A2), Bacillus pumilus (A3), Pseudomonas libanensis (A5), and Bacillus siamensis (A6). These five bacterial strains grew, tolerated pH changes, and solubilized inorganic phosphorus. The bacterial strain A3 solubilized FePO4 (4 mg L-1) and Ca3(PO4)2 (50 mg L-1). P solubilization was assayed with glucose and sucrose as carbon sources for A3 (Bacillus pumilus MN100586). After four culture days, Ca3(PO4)2 was solubilized, reaching 246 mg L-1 with sucrose in culture media. Using glucose as a carbon source, FePO4 was solubilized and reached 282 mg L-1 in six culture days. Our findings were: Pseudomonas libanensis, and Bacillus siamensis, as new bacteria, can be reported as P solubilizers with tolerance to acidic or alkaline pH levels. The bacterial strain B. pumilus grew using two sources of inorganic phosphorus and carbon, and it tolerated pH changes. For that reason, it is an ideal candidate for inorganic phosphorus solubilization and future production as a biofertilizer.
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Affiliation(s)
- Ma. Esther Sanchez-Gonzalez
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Martha E. Mora-Herrera
- Tenancingo Universitary Center, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | | | - Nadia De La Portilla-López
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Laura Sanchez-Paz
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Jorge Lugo
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Rocio Vaca-Paulín
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Pedro Del Aguila
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Gustavo Yañez-Ocampo
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
- Correspondence: ; Tel.: +52-722-2262-300
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Jiao H, Xu W, Hu Y, Tian R, Wang Z. Citric Acid in Rice Root Exudates Enhanced the Colonization and Plant Growth-Promoting Ability of Bacillus altitudinis LZP02. Microbiol Spectr 2022; 10:e0100222. [PMID: 36264248 PMCID: PMC9769925 DOI: 10.1128/spectrum.01002-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/24/2022] [Indexed: 01/05/2023] Open
Abstract
Exploration of the underlying mechanisms of plant-microbe interactions is very important. In the present study, citric acid in the root exudates of rice significantly enhanced the colonization of Bacillus altitudinis LZP02 in the rhizosphere. According to the results of transcriptome and reverse transcription-quantitative PCR or analyses, citric acid increased the expression of several genes involved in bacterial chemotaxis and biofilm formation in B. altitudinis LZP02. In addition, citric acid also increased the expression of several genes associated with S-adenosylmethionine biosynthesis and metabolism. Interestingly, the secretion of citric acid by rice roots could be increased by inoculation with B. altitudinis LZP02. The result indicated that citric acid might be a vital signal in the interaction between rice and B. altitudinis LZP02. Further verification showed that citric acid enhanced the plant growth-promoting ability of B. altitudinis LZP02. IMPORTANCE In a previous study, the mechanism by which citric acid in rice root exudates enhanced the colonization of Bacillus altitudinis LZP02 was discovered. The present study verified that citric acid increased the recruitment and rice growth-promoting ability of B. altitudinis LZP02. These findings serve as an interesting case for explaining the underlying mechanisms of plant-microbe interactions. Henceforth, citric acid and B. altitudinis LZP02 could be exploited for the development of sustainable agronomy.
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Affiliation(s)
- Huiwen Jiao
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, China
| | - Weihui Xu
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, China
| | - Yunlong Hu
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, China
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Zhigang Wang
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, China
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Dobrzyński J, Jakubowska Z, Dybek B. Potential of Bacillus pumilus to directly promote plant growth. Front Microbiol 2022; 13:1069053. [PMID: 36620067 PMCID: PMC9810630 DOI: 10.3389/fmicb.2022.1069053] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Plant Growth-Promoting Bacteria (PGPB) are a promising alternative to conventional fertilization. One of the most interesting PGPB strains, among the spore-forming bacteria of the phylum Firmicutes, is Bacillus pumilus. It is a bacterial species that inhabits a wide range of environments and shows resistance to abiotic stresses. So far, several PGPB strains of B. pumilus have been described, including B. pumilus LZP02, B. pumilus JPVS11, B. pumilus TUAT-1, B. pumilus TRS-3, and B. pumilus EU927414. These strains have been shown to produce a wide range of phytohormones and other plant growth-promoting substances. Therefore, they can affect various plant properties, including biometric traits, substance content (amino acids, proteins, fatty acids), and oxidative enzymes. Importantly, based on a study with B. pumilus WP8, it can be concluded that this bacterial species stimulates plant growth when the native microbiota of the inoculated soil is altered. However, there is still a lack of research with deeper insights into the structure of the native microbial community (after B. pumilus application), which would provide a better understanding of the functioning of this bacterial species in the soil and thus increase its effectiveness in promoting plant growth.
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Liu J, Zhi L, Zhang N, Zhang W, Meng D, Batool A, Ren X, Ji J, Niu Y, Li R, Li J, Song L. Transcriptomic analysis reveals the contribution of QMrl-7B to wheat root growth and development. FRONTIERS IN PLANT SCIENCE 2022; 13:1062575. [PMID: 36457528 PMCID: PMC9706392 DOI: 10.3389/fpls.2022.1062575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Roots are the major organs for water and nutrient acquisition and substantially affect plant growth, development and reproduction. Improvements to root system architecture are highly important for the increased yield potential of bread wheat. QMrl-7B, a major stable quantitative trait locus (QTL) that controls maximum root length (MRL), essentially contributes to an improved root system in wheat. To further analyze the biological functions of QMrl-7B in root development, two sets of Triticum aestivum near-isogenic lines (NILs), one with superior QMrl-7B alleles from cultivar Kenong 9204 (KN9204) named NILKN9204 and another with inferior QMrl-7B alleles from cultivar Jing 411 (J411) named NILJ411, were subjected to transcriptomic analysis. Among all the mapped genes analyzed, 4871 genes were identified as being differentially expressed between the pairwise NILs under different nitrogen (N) conditions, with 3543 genes expressed under normal-nitrogen (NN) condition and 2689 genes expressed under low-nitrogen (LN) condition. These genes encode proteins that mainly include N O 3 - transporters, phytohormone signaling components and transcription factors (TFs), indicating the presence of a complex regulatory network involved in root determination. In addition, among the 13524 LN-induced differentially expressed genes (DEGs) detected in this study, 4308 and 2463 were specifically expressed in the NILKN9204 and NILJ411, respectively. These DEGs reflect different responses of the two sets of NILs to varying N supplies, which likely involve LN-induced root growth. These results explain the better-developed root system and increased root vitality conferred by the superior alleles of QMrl-7B and provide a deeper understanding of the genetic underpinnings of root traits, pointing to a valuable locus suitable for future breeding efforts for sustainable agriculture.
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Affiliation(s)
- Jiajia Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Liya Zhi
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Deyuan Meng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Aamana Batool
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Ren
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ruiqi Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Liqiang Song
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
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Zhang Y, Huang K, Chen X, Wei M, Yu X, Su H, Gan P, Yu K. Inactivation of Ciliate Uronema Marinum under UV/Peroxydisulfate Advanced Disinfection System in Marine Water. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.122563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Transcriptome Analysis of the Responses of Rice Leaves to Chilling and Subsequent Recovery. Int J Mol Sci 2022; 23:ijms231810739. [PMID: 36142652 PMCID: PMC9502032 DOI: 10.3390/ijms231810739] [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: 08/24/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Improving chilling tolerance at the seedling stage in rice is essential for agricultural research. We combined a physiological analysis with transcriptomics in a variety Dular subjected to chilling followed by recovery at normal temperature to better understand the chilling tolerance mechanisms of rice. Chilling inhibited the synthesis of chlorophyll and non-structural carbohydrate (NSC) and disrupted the ion balance of the plant, resulting in the impaired function of rice leaves. The recovery treatment can effectively reverse the chilling-related injury. Transcriptome results displayed that 21,970 genes were identified at three different temperatures, and 11,732 genes were differentially expressed. According to KEGG analysis, functional categories for differentially expressed genes (DEGs) mainly included ribosome (8.72%), photosynthesis–antenna proteins (7.38%), phenylpropanoid biosynthesis (11.41%), and linoleic acid metabolism (10.07%). The subcellular localization demonstrated that most proteins were located in the chloroplasts (29.30%), cytosol (10.19%), and nucleus (10.19%). We proposed that some genes involved in photosynthesis, ribosome, phenylpropanoid biosynthesis, and linoleic acid metabolism may play key roles in enhancing rice adaptation to chilling stress and their recovery capacity. These findings provide a foundation for future research into rice chilling tolerance mechanisms.
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Soltanpour S, Tarinejad A, Hasanpur K, Majidi M. A meta-analysis of microarray data revealed hub genes and transcription factors involved in drought stress response in rice ( Oryza sativa L.). FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:898-916. [PMID: 35798354 DOI: 10.1071/fp22028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Although there are various studies attempted to clarify the genetic mechanism of plant response to drought stress that reduces crop yield, a meta-analysis can integrate the results of them to provide a better picture of the issue. Therefore, in this study, several microarray datasets of rice were meta-analysed under drought stress and normal condition using the R packages. Accordingly, differentially expressed genes (meta-DEGs) were identified. The results showed 643 and 677 upregulated and downregulated genes, respectively. The significant common Gene Ontology (GO) terms between the up- and downregulated genes were responses to abiotic stimulus , water deprivation , oxygen-containing compound and abscisic acid . The transcription factors (TF) survey showed that bHLH under drought stress activates up genes 42% more than down genes while bzip Homeodomain activates down genes 54% more than up genes. The hub downregulated genes obtained from this study were mainly related to photosynthesis and the hub upregulated genes were mainly related to stress tolerance which include heat shock proteins (HSPs), late embryogenesis abundant (LEAs), calmodulin-like protein (CML), phosphatase 2C (PP2Cs) and IAA genes. Moreover, this meta-analysis data were compared with other experimental data and the results confirmed the up and down expression of them. Our findings can provide novel insights into the molecular mechanism of rice (Oryza sativa L.) response to drought stress.
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Affiliation(s)
- Sedigheh Soltanpour
- Department of Agricultural Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - AliReza Tarinejad
- Department of Agricultural Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mohammad Majidi
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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Jiao H, Xu W, Chen W, Hu Y, Tian R, Wang Z. Complete Genome Sequence Data of Bacillus altitudinis LZP02, a Bacterium from the Rice Rhizosphere, for Studying the Promotion of Plant Growth. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:428-431. [PMID: 35417184 DOI: 10.1094/mpmi-01-22-0012-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Huiwen Jiao
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
| | - Weihui Xu
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
| | - Wenjing Chen
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
| | - Yunlong Hu
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL 60501, U.S.A
| | - Zhigang Wang
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
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12
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Tian Y, Fu X, Zhang G, Zhang R, Kang Z, Gao K, Mendgen K. Mechanisms in Growth-Promoting of Cucumber by the Endophytic Fungus Chaetomium globosum Strain ND35. J Fungi (Basel) 2022; 8:jof8020180. [PMID: 35205933 PMCID: PMC8878499 DOI: 10.3390/jof8020180] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 02/01/2023] Open
Abstract
Endophytic fungi are effective in plant growth and development by secreting various kinds of plant hormones and nutrients. However, the cellular and molecular interactions between the endophytic fungi and plant growth-promoting have remained less explored. The present study was designed to explore the effects of the infection and colonization events of Chaetomium globosum strain ND35 on cucumber growth and the expression pattern of some metabolically important genes in development of the cucumber radicle. The results demonstrated that strain ND35 can infect and colonize the outer layers (cortical cells) of cucumber root and form a symbiotic structure with the host cell, similar to a periarbuscular membrane and establish chemical communication with the plant. Through transcriptome analysis, we found the differentially expressed genes (DEGs) caused by strain ND35 were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, plant-pathogen interaction and photosynthesis. Correspondingly, the contents of reactive oxygen species (ROS), hydrogen peroxide (H2O2), indole-3-acetic acid (IAA), gibberellin (GA), zeatin (ZT), salicylic acid (SA), jasmonic acid (JA) and the activity of phenylalanine ammonia lyase (PAL), 4-coumarate-CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD) in ND35-colonized seedlings were generally higher than those of non-inoculated seedlings. Overall, the infection and colonization events of C. globosum strain ND35 increased cucumber growth through complex regulation of plant hormones biosynthesis and metabolism. Furthermore, although the endophytic fungus strain ND35 produced IAA, GA, ZT, and ergosterol in the fermentation broth, and there are enabled to promote growth of cucumber, it is uncertain whether there are ND35-derived microbial hormones in plants. This study of the interaction between cucumber and strain ND35 contributes to a better understanding of the plant-endophytic fungi interactions, and may help to develop new strategies for crop production.
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Affiliation(s)
- Yehan Tian
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China; (Y.T.); (X.F.); (R.Z.)
| | - Xuesong Fu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China; (Y.T.); (X.F.); (R.Z.)
| | - Gongchen Zhang
- Qingdao Academy of Agricultural Science, Qingdao 266100, China;
| | - Rui Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China; (Y.T.); (X.F.); (R.Z.)
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China;
| | - Kexiang Gao
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China; (Y.T.); (X.F.); (R.Z.)
- Correspondence:
| | - Kurt Mendgen
- Department of Biology, University of Constance, 78457 Constance, Germany;
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13
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Li S, Zhao S, Hu C, Mao C, Guo L, Yu H, Yu H. Whole Genome Sequence of an Edible Mushroom Stropharia rugosoannulata (Daqiugaigu). J Fungi (Basel) 2022; 8:jof8020099. [PMID: 35205854 PMCID: PMC8880121 DOI: 10.3390/jof8020099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Stropharia rugosoannulata, also known as Daqiugaigu in China, is a well-known edible mushroom that has been widely cultivated in China in recent years. Many studies have focused on its nutrients, bioactive compounds, and lignin degradation capacity, although there are few molecular and genetic breeding studies due to the lack of genomic information. Here, we present the 47.9 Mb genome sequence of an S. rugosoannulata monokaryotic strain (A15), which has 20 contigs and an N50 of 3.64 Mb, which was obtained by a combination of Illumina and Nanopore sequencing platforms. Further analysis predicted 12,752 protein-coding genes, including 486 CAZyme-encoding genes. Phylogenetic analysis revealed a close evolutionary relationship between S. rugosoannulata and Hypholoma sublateritium, Psilocybe cyanescens, and Galerina marginata based on single-copy orthologous genes. Proteomic analysis revealed different protein expression profiles between the cap and the stipe of the S. rugosoannulata fruiting body. The proteins of the stipe associated with carbon metabolism, energy production, and stress-response-related biological processes had higher abundance, whereas proteins involved in fatty acid synthesis and mRNA splicing showed higher expression in the cap than in the stipe. The genome of S. rugosoannulata will provide valuable genetic resources not only for comparative genomic analyses and evolutionary studies among Basidiomycetes but also for alleviating the bottlenecks that restrict the molecular breeding of this edible mushroom.
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Affiliation(s)
- Shuwen Li
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Shuxue Zhao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Chunhui Hu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Chengzhi Mao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
- Correspondence: (H.Y.); (H.Y.); Tel.: +86-532-58957640 (Hao Yu)
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
- Correspondence: (H.Y.); (H.Y.); Tel.: +86-532-58957640 (Hao Yu)
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Zhu X, Liu H, Wang Z, Tian R, Li S. Dimethyl phthalate damages Staphylococcus aureus by changing the cell structure, inducing oxidative stress and inhibiting energy metabolism. J Environ Sci (China) 2021; 107:171-183. [PMID: 34412780 DOI: 10.1016/j.jes.2021.01.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 06/13/2023]
Abstract
Dimethyl phthalate (DMP), used as a plasticizer in industrial products, exists widely in air, water and soil. Staphylococcus aureus is a typical model organism representing Gram-positive bacteria. The molecular mechanisms of DMP toxicology in S. aureus were researched by proteomic and transcriptomic analyses. The results showed that the cell wall, membrane and cell surface characteristics were damaged and the growth was inhibited in S. aureus by DMP. Oxidative stress was induced by DMP in S. aureus. The activities of succinic dehydrogenase (SDH) and ATPase were changed by DMP, which could impact energy metabolism. Based on proteomic and transcriptomic analyses, the oxidative phosphorylation pathway was enhanced and the glycolysis/gluconeogenesis and pentose phosphate pathways were inhibited in S. aureus exposed to DMP. The results of real-time reverse transcription quantitative PCR (RT-qPCR) further confirmed the results of the proteomic and transcriptomic analyses. Lactic acid, pyruvic acid and glucose were reduced by DMP in S. aureus, which suggested that DMP could inhibit energy metabolism. The results indicated that DMP damaged the cell wall and membrane, induced oxidative stress, and inhibited energy metabolism and activation in S. aureus.
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Affiliation(s)
- Xiaohui Zhu
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China; Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
| | - Hong Liu
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China; Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
| | - Zhigang Wang
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China; Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China.
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL 60501, USA
| | - Shenglin Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
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15
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Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus. Int J Mol Sci 2021; 22:ijms22179246. [PMID: 34502153 PMCID: PMC8431428 DOI: 10.3390/ijms22179246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/12/2023] Open
Abstract
Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of root growth and the development in the FO hybrid. Moreover, transcription factors such as MYB, ERF, bHLH, NAC, bZIP, and WRKY are thought to control downstream genes involved in root growth. Overall, this is the first study to provide a better understanding related to the regulation of the molecular mechanism of heterosis, which assists in rapeseed growth and yield improvement.
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Soni R, Keharia H. Phytostimulation and biocontrol potential of Gram-positive endospore-forming Bacilli. PLANTA 2021; 254:49. [PMID: 34383174 DOI: 10.1007/s00425-021-03695-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The spore-forming Bacillus and Paenibacillus species represent the phyla of beneficial bacteria for application as agricultural inputs in form of effective phytostimulators, biofertilizers, and biocontrol agents. The members of the genera Bacillus and Paenibacillus isolated from several ecological habitats are been thoroughly dissected for their effective application in the development of sustainable and eco-friendly agriculture. Numerous Bacillus and Paenibacillus species are reported as plant growth-promoting bacteria influencing the health and productivity of the food crops. This review narrates the mechanisms utilized by these species to enhance bioavailability and/or facilitate the acquisition of nutrients by the host plant, modulate plant hormones, stimulate host defense and stress resistance mechanisms, exert antagonistic action against soil and airborne pathogens, and alleviate the plant health. The mechanisms employed by Bacillus and Paenibacillus are seldom mutually exclusive. The comprehensive and systematic exploration of the aforementioned mechanisms in conjunction with the field investigations may assist in the exploration and selection of an effective biofertilizer and a biocontrol agent. This review aims to gather and discuss the literature citing the applications of Bacillus and Paenibacillus in the management of sustainable agriculture.
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Affiliation(s)
- Riteshri Soni
- Department of Biosciences, UGC Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India
| | - Hareshkumar Keharia
- Department of Biosciences, UGC Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India.
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17
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Vo KTX, Rahman MM, Rahman MM, Trinh KTT, Kim ST, Jeon JS. Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update. RICE (NEW YORK, N.Y.) 2021; 14:30. [PMID: 33721115 PMCID: PMC7960847 DOI: 10.1186/s12284-021-00461-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/28/2021] [Indexed: 05/19/2023]
Abstract
Biotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.
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Affiliation(s)
- Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Md Mizanor Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Md Mustafizur Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Kieu Thi Thuy Trinh
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463 South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
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18
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Amer B, Baidoo EEK. Omics-Driven Biotechnology for Industrial Applications. Front Bioeng Biotechnol 2021; 9:613307. [PMID: 33708762 PMCID: PMC7940536 DOI: 10.3389/fbioe.2021.613307] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.
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Affiliation(s)
- Bashar Amer
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Edward E. K. Baidoo
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- U.S. Department of Energy, Agile BioFoundry, Emeryville, CA, United States
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YAÑEZ-OCAMPO GUSTAVO, MORA-HERRERA MARTHAE, WONG-VILLARREAL ARNOLDO, DE LA PAZ-OSORIO DENISSEM, DE LA PORTILLA-LÓPEZ NADIA, LUGO JORGE, VACA-PAULÍN ROCIO, DEL ÁGUILA PEDRO. Isolated Phosphate-Solubilizing Soil Bacteria Promotes In vitro Growth of Solanum tuberosum L. Pol J Microbiol 2020; 69:357-365. [PMID: 33574865 PMCID: PMC7810110 DOI: 10.33073/pjm-2020-039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 11/29/2022] Open
Abstract
The capacity of four bacterial strains isolated from productive soil potato fields to solubilize tricalcium phosphate on Pikovskaya agar or in a liquid medium was evaluated. A bacterial strain was selected to evaluate in vitro capacity of plant-growth promotion on Solanum tuberosum L. culture. Bacterial strain A3 showed the highest value of phosphate solubilization, reaching a 20 mm-diameter halo and a concentration of 350 mg/l on agar and in a liquid medium, respectively. Bacterial strain A3 was identified by 16S rDNA analysis as Bacillus pumilus with 98% identity; therefore, it is the first report for Bacillus pumilus as phosphate solubilizer. Plant-growth promotion assayed by in vitro culture of potato microplants showed that the addition of bacterial strain A3 increased root and stems length after 28 days. It significantly increased stem length by 79.3%, and duplicated the fresh weight of control microplants. In this paper, results reported regarding phosphorus solubilization and growth promotion under in vitro conditions represent a step forward in the use of innocuous bacterial strain biofertilizer on potato field cultures.
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Affiliation(s)
- GUSTAVO YAÑEZ-OCAMPO
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - MARTHA E. MORA-HERRERA
- Tenancingo Universitary Center, Autonomous University of the State of Mexico, Toluca, Mexico
| | | | - DENISSE M. DE LA PAZ-OSORIO
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - NADIA DE LA PORTILLA-LÓPEZ
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - JORGE LUGO
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - ROCIO VACA-PAULÍN
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - PEDRO DEL ÁGUILA
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
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