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Tian Y, Liu Y, Yue L, Zhao X, Zhou Q, Uwaremwe C, Wang Y, Chen G, Sha Y, Zhang Y, Wang R. Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions. Microbiol Res 2024; 287:127855. [PMID: 39079269 DOI: 10.1016/j.micres.2024.127855] [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: 05/31/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 08/22/2024]
Abstract
Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.
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Affiliation(s)
- Yuan Tian
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Yue
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xia Zhao
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Zhou
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Constantine Uwaremwe
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Gaofeng Chen
- Gansu Shangnong Biotechnology Co. Ltd, Baiyin 730900, China
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yubao Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ruoyu Wang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Saikat TA, Sayem Khan MA, Islam MS, Tasnim Z, Ahmed S. Characterization and genome mining of Bacillus subtilis BDSA1 isolated from river water in Bangladesh: A promising bacterium with diverse biotechnological applications. Heliyon 2024; 10:e34369. [PMID: 39114027 PMCID: PMC11305188 DOI: 10.1016/j.heliyon.2024.e34369] [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: 02/19/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
The metabolic versatility of Bacillus subtilis makes it useful for a wide range of applications in biotechnology, from bioremediation to industrially important metabolite production. Understanding the molecular attributes of the biocontrol characteristics of B. subtilis is necessary for its tailored use in the environment and industry. Therefore, the present study aimed to conduct phenotypic characterization and whole genome analysis of the B. subtilis BDSA1 isolated from polluted river water from Dhaka, Bangladesh to explore its biotechnological potential. The chromium reduction capacity at 100 ppm Cr (VI) showed that B. subtilis BDSA1 reduced 40 % of Cr (VI) within 24hrs at 37 °C. Exposure of this bacterium to 200 ppm cadmium resulted in 43 % adsorption following one week of incubation at 37 °C. Molecular detection of chrA and czcC gene confirmed chromium and cadmium resistance characteristics of BDSA1. The size of the genome of the B. subtilis BDSA1 was 4.2 Mb with 43.4 % GC content. Genome annotation detected the presence of numerous genes involved in the degradation of xenobiotics, resistance to abiotic stress, production of lytic enzymes, siderophore formation, and plant growth promotion. The assembled genome also carried chromium, cadmium, copper, and arsenic resistance-related genes, notably cadA, czcD, czrA, arsB etc. Genome mining revealed six biosynthetic gene clusters for bacillaene, bacillibacin, bacilysin, subtilosin, fengycin and surfactin. Importantly, BDSA1 was predicted to be non-pathogenic to humans and had only two acquired antimicrobial resistance genes. The pan-genome analysis showed the openness of the B. subtilis pan-genome. Our findings suggested that B. subtilis BDSA1 might be a promising candidate for diverse biotechnological uses.
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Affiliation(s)
| | - Md Abu Sayem Khan
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md Saiful Islam
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Zarin Tasnim
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Sangita Ahmed
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
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Behrendt U, Burghard V, Wende S, Ulrich K, Wolf J, Neumann-Schaal M, Ulrich A. Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus. Syst Appl Microbiol 2024; 47:126516. [PMID: 38772267 DOI: 10.1016/j.syapm.2024.126516] [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: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038T (=LMG 33092 T = DSM 115926 T). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.
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Affiliation(s)
- Undine Behrendt
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Valentin Burghard
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Sonja Wende
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Kristina Ulrich
- Johann Heinrich Von Thünen Institute, Institute of Forest Genetics, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany.
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Andreas Ulrich
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
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Cheng C, Su S, Bo S, Zheng C, Liu C, Zhang L, Xu S, Wang X, Gao P, Fan K, He Y, Zhou D, Gong Y, Zhong G, Liu Z. A Bacillus velezensis strain isolated from oats with disease-preventing and growth-promoting properties. Sci Rep 2024; 14:12950. [PMID: 38839805 PMCID: PMC11153497 DOI: 10.1038/s41598-024-63756-8] [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: 01/04/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
Endophytes have been shown to promote plant growth and health. In the present study, a Bacillus velezensis CH1 (CH1) strain was isolated and identified from high-quality oats, which was capable of producing indole-3-acetic acid (IAA) and strong biofilms, and capabilities in the nitrogen-fixing and iron carriers. CH1 has a 3920 kb chromosome with 47.3% GC content and 3776 code genes. Compared genome analysis showed that the largest proportion of the COG database was metabolism-related (44.79%), and 1135 out of 1508 genes were associated with the function "biosynthesis, transport, and catabolism of secondary metabolites." Furthermore, thirteen gene clusters had been identified in CH1, which were responsible for the synthesis of fifteen secondary metabolites that exhibit antifungal and antibacterial properties. Additionally, the strain harbors genes involved in plant growth promotion, such as seven putative genes for IAA production, spermidine and polyamine synthase genes, along with multiple membrane-associated genes. The enrichment of these functions was strong evidence of the antimicrobial properties of strain CH1, which has the potential to be a biofertilizer for promoting oat growth and disease resistance.
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Affiliation(s)
- Chao Cheng
- School of Life Science and Technology, Jining Normal University, Ulanqab, 012000, China.
| | - Shaofeng Su
- Inner Mongolia Academy of Agriculture and Husbandry Science, Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Affairs, Hohhot, 010000, China
| | - Suling Bo
- College of Computer Information, Inner Mongolia Medical University, Hohhot, 010000, China
| | - Chengzhong Zheng
- Ulanqab Institute for Agricultural and Forestry Science, Ulanqab, 012000, China
| | - Chunfang Liu
- Ulanqab Center for Disease Control and Prevention, Ulanqab, 012000, China
| | - Linchong Zhang
- Jinyu Baoling Biological Drugs Co., LTD, Hohhot, 010000, China
| | - Songhe Xu
- School of Life Science and Technology, Jining Normal University, Ulanqab, 012000, China
| | - Xiaoyun Wang
- School of Life Science and Technology, Jining Normal University, Ulanqab, 012000, China
| | - Pengfei Gao
- Vocational and Technical College of Ulanqab, Ulanqab, 012000, China
| | - Kongxi Fan
- Inner Mongolia Agricultural University, Hohhot, 010000, China
| | - Yiwei He
- School of Life Science and Technology, Jining Normal University, Ulanqab, 012000, China
| | - Di Zhou
- The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010000, China
| | - Yanchun Gong
- Agriculture and Animal Husbandry Technology Promotion Center of Inner Mongolia, Hohhot, 010000, China
| | - Gang Zhong
- Agriculture and Animal Husbandry Technology Promotion Center of Inner Mongolia, Hohhot, 010000, China
| | - Zhiguo Liu
- Inner Mongolia Agricultural University, Hohhot, 010000, China.
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 100000, China.
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Zhao Y, Ding WJ, Xu L, Sun JQ. A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas. Front Microbiol 2024; 15:1395477. [PMID: 38817968 PMCID: PMC11138164 DOI: 10.3389/fmicb.2024.1395477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.
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Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wen-Jing Ding
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Jiao W, Wen J, Li N, Ou T, Qiu C, Ji Y, Lin K, Liu X, Xie J. The biocontrol potentials of rhizospheric bacterium Bacillus velezensis K0T24 against mulberry bacterial wilt disease. Arch Microbiol 2024; 206:213. [PMID: 38616201 DOI: 10.1007/s00203-024-03935-3] [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: 02/20/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Mulberry bacterial wilt disease, caused by Ralstonia pseudosolanacearum, is a devastating soil-borne disease in the silk-mulberry-related industry. In this study, through high-throughput sequencing, we compared the rhizosphere bacterial composition of the mulberry-resistant cultivar (K10) and susceptible cultivar (G12), confirming Bacillus as a genus-level biomarker for K10. Next, twelve Bacillus spp. isolates, derived from the rhizosphere of K10, were screened for their antagonistic activity against R. pseudosolanacearum. The isolate showing strong antagonism was identified as B. velezensis K0T24 and selected for further analysis. The fermentation supernatant of B. velezensis K0T24 significantly inhibited the growth of R. pseudosolanacearum (82.47%) and the expression of its pathogenic genes. Using B. velezensis K0T24 in mulberry seedlings also increased defense enzyme activities and achieved a control efficacy of up to 55.17% against mulberry bacterial wilt disease. Collectively, our findings demonstrate the potential of B. velezensis K0T24 in suppressing mulberry bacterial wilt disease.
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Affiliation(s)
- Wenlian Jiao
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Ju Wen
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Na Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Ting Ou
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Changyu Qiu
- Guangxi Key Laboratory of Sericultural Genetic Improvement and Efficient Breeding, Guangxi Zhuang Autonomous Region Sericultural Technology Promotion Station, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Yutong Ji
- Westa College, Southwest University, Chongqing, 400715, China
| | - Kai Lin
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Xiaojiao Liu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China.
| | - Jie Xie
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China.
- Westa College, Southwest University, Chongqing, 400715, China.
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Kang W, Duan Y, Lei P. Transcriptomic changes in soybean underlying growth promotion and defense against cyst nematode after Bacillus simplex Sneb545 treatment. Gene 2024; 898:148080. [PMID: 38101712 DOI: 10.1016/j.gene.2023.148080] [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: 08/24/2023] [Revised: 11/11/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Bacillus simplex Sneb45 is a plant-growth-promoting rhizobacterium that promotes soybean growth and systemic resistance to cyst nematode. To investigate transcriptional changes in soybean roots in response to B. simplex Sneb45 treatment, transcriptome analysis and quantitative real-time PCR were conducted to detect and validate the differentially expressed genes (DEGs). In total, 19,109 DEGs were obtained. After B. simplex Sneb545 treatment, 970 and 1265 genes were up- and down-regulated at 5 days post-inoculation (dpi), respectively, and 142 and 47 genes were up- and down-regulated at 10 dpi, respectively, compared with untreated soybean roots. Functional annotation of DEGs indicated that B. simplex Sneb545 regulated soybean growth and defense against cyst nematode possibly through genes related to auxin, gibberellin, and NB-LRR protein. In addition, GO and KEGG enrichment analyses indicated that the DEGs were enriched in metabolism, signal transduction, and plant-pathogen interaction pathways. Moreover, the auxin and gibberellin contents were lower in B. simplex Sneb545-treated soybean roots than in untreated roots at 5 dpi. B. simplex Sneb545 possibly altered the expression of wound-induced protein and NAC transcription factor to regulate soybean growth and defense against cyst nematode. Our study provided deep insights into the alterations in soybean transcriptome after exposure to B. simplex Sneb45 and a theoretical basis for further exploring molecular functions underlying the biological control activity of B. simplex Sneb545.
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Affiliation(s)
- Wenshu Kang
- College of Environment, Shenyang University, Shenyang 110044, PR China
| | - Yuxi Duan
- College of plant protection, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Piao Lei
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China.
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Dal’Rio I, Lopes EDS, Santaren KCF, Rosado AS, Seldin L. Co-inoculation of the endophytes Bacillus thuringiensis CAPE95 and Paenibacillus polymyxa CAPE238 promotes Tropaeolum majus L. growth and enhances its root bacterial diversity. Front Microbiol 2024; 15:1356891. [PMID: 38585693 PMCID: PMC10996857 DOI: 10.3389/fmicb.2024.1356891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/12/2024] [Indexed: 04/09/2024] Open
Abstract
Tropaeolum majus L. is a versatile edible plant that is widely explored due to its medicinal properties and as a key element in intercropping systems. Its growth could be improved by the use of biofertilizers that can enhance nutrient uptake by the plant or provide tolerance to different abiotic and biotic stresses. In a previous study, 101 endophytes isolated from T. majus roots showed more than three plant growth-promoting (PGP) features in vitro, such as phosphate mineralization/solubilization, production of siderophores, antimicrobial substances and indole-related compounds, and presence of the nifH gene. To provide sustainable alternatives for biofertilization, the genomes of two promising endophytes-CAPE95 and CAPE238-were sequenced to uncover metabolic pathways related to biofertilization. Greenhouse experiments were conducted with 216 seeds and 60 seedlings, half co-inoculated with the endophytes (treatment) and half inoculated with 1X PBS (control), and the impact of the co-inoculation on the plant's bacteriome was accessed through 16S rRNA gene metabarcoding. The strains CAPE95 and CAPE238 were taxonomically assigned as Bacillus thuringiensis and Paenibacillus polymyxa, respectively. Metabolic pathways related to the enhancement of nutrient availability (nitrogen fixation, sulfate-sulfur assimilation), biosynthesis of phytohormones (indole-3-acetic acid precursors) and antimicrobial substances (bacilysin, paenibacillin) were found in their genomes. The in vivo experiments showed that treated seeds exhibited faster germination, with a 20.3% higher germination index than the control on the eleventh day of the experiment. Additionally, treated seedlings showed significantly higher plant height and leaf diameters (p < 0.05). The bacterial community of the treated plants was significantly different from that of the control plants (p < 0.001) and showed a higher richness and diversity of species (Chao and Shannon indexes, p < 0.001). A higher relative abundance of potential synergistic PGP bacteria was also shown in the bacteriome of the treated plants, such as Lysinibacillus and Geobacter. For the first time, co-inoculation of B. thuringiensis and P. polymyxa was shown to have great potential for application as a biofertilizer to T. majus plants. The bacterial consortium used here could also be explored in other plant species in the future.
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Affiliation(s)
- Isabella Dal’Rio
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Bioscience, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Eliene dos Santos Lopes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Alexandre Soares Rosado
- Bioscience, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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Behr JH, Kuhl-Nagel T, Sommermann L, Moradtalab N, Chowdhury SP, Schloter M, Windisch S, Schellenberg I, Maccario L, Sørensen SJ, Rothballer M, Geistlinger J, Smalla K, Ludewig U, Neumann G, Grosch R, Babin D. Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere. FEMS Microbiol Ecol 2024; 100:fiae003. [PMID: 38224956 PMCID: PMC10847717 DOI: 10.1093/femsec/fiae003] [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: 11/09/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates and rhizosphere metabolites, physiological stress indicators, and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon, and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, and Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, and ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits, and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.
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Affiliation(s)
- Jan Helge Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Theresa Kuhl-Nagel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Narges Moradtalab
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis
(COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Saskia Windisch
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Lorrie Maccario
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Michael Rothballer
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Uwe Ludewig
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Doreen Babin
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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10
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Speckmann B, Ehring E, Hu J, Rodriguez Mateos A. Exploring substrate-microbe interactions: a metabiotic approach toward developing targeted synbiotic compositions. Gut Microbes 2024; 16:2305716. [PMID: 38300741 PMCID: PMC10841028 DOI: 10.1080/19490976.2024.2305716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Gut microbiota is an important modulator of human health and contributes to high inter-individual variation in response to food and pharmaceutical ingredients. The clinical outcomes of interventions with prebiotics, probiotics, and synbiotics have been mixed and often unpredictable, arguing for novel approaches for developing microbiome-targeted therapeutics. Here, we review how the gut microbiota determines the fate of and individual responses to dietary and xenobiotic compounds via its immense metabolic potential. We highlight that microbial metabolites play a crucial role as targetable mediators in the microbiota-host health relationship. With this in mind, we expand the concept of synbiotics beyond prebiotics' role in facilitating growth and engraftment of probiotics, by focusing on microbial metabolism as a vital mode of action thereof. Consequently, we discuss synbiotic compositions that enable the guided metabolism of dietary or co-formulated ingredients by specific microbes leading to target molecules with beneficial functions. A workflow to develop novel synbiotics is presented, including the selection of promising target metabolites (e.g. equol, urolithin A, spermidine, indole-3 derivatives), identification of suitable substrates and producer strains applying bioinformatic tools, gut models, and eventually human trials.In conclusion, we propose that discovering and enabling specific substrate-microbe interactions is a valuable strategy to rationally design synbiotics that could establish a new category of hybrid nutra-/pharmaceuticals.
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Affiliation(s)
| | | | - Jiaying Hu
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Ana Rodriguez Mateos
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
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11
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Jiang ZM, Mou T, Sun Y, Su J, Yu LY, Zhang YQ. Environmental distribution and genomic characteristics of Solirubrobacter, with proposal of two novel species. Front Microbiol 2023; 14:1267771. [PMID: 38107860 PMCID: PMC10722151 DOI: 10.3389/fmicb.2023.1267771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 12/19/2023] Open
Abstract
Solirubrobacter spp. were abundant in soil samples collected from deserts and other areas with high UV radiation. In addition, a novel Solirubrobacter species, with strain CPCC 204708T as the type, was isolated and identified from sandy soil sample collected from the Badain Jaran Desert of the Inner Mongolia autonomous region. Strain CPCC 204708T was Gram-stain positive, rod-shaped, non-motile, non-spore-forming, and grew optimally at 28-30°C, pH 7.0-8.0, and in the absence of NaCl. Analysis of the 16S rRNA gene sequence of strain CPCC 204708T showed its identity within the genus Solirubrobacter, with highest nucleotide similarities (97.4-98.2%) to other named Solirubrobacter species. Phylogenetic and genomic analyses indicated that the strain was most closely related to Solirubrobacter phytolaccae KCTC 29190T, while represented a distinct species, as confirmed from physiological properties and comparison. The name Solirubrobacter deserti sp. nov. was consequently proposed, with CPCC 204708T (= DSM 105495T = NBRC 112942T) as the type strain. Genomic analyses of the Solirubrobacter spp. also suggested that Solirubrobacter sp. URHD0082 represents a novel species, for which the name Candidatus "Solirubrobacter pratensis" sp. nov. was proposed. Genomic analysis of CPCC 204708T revealed the presence of genes related to its adaptation to the harsh environments of deserts and may also harbor genes functional in plant-microbe interactions. Pan-genomic analysis of available Solirubrobacter spp. confirmed the presence of many of the above genes as core components of Solirubrobacter genomes and suggests they may possess beneficial potential for their associate plant and may be important resources for bioactive compounds.
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Affiliation(s)
- Zhu-Ming Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Dao-di Herb, Beijing, China
| | - Tong Mou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Dao-di Herb, Beijing, China
| | - Ye Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Dao-di Herb, Beijing, China
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12
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Shi L, Zhu X, Qian T, Du J, Du Y, Ye J. Mechanism of Salt Tolerance and Plant Growth Promotion in Priestia megaterium ZS-3 Revealed by Cellular Metabolism and Whole-Genome Studies. Int J Mol Sci 2023; 24:15751. [PMID: 37958734 PMCID: PMC10647267 DOI: 10.3390/ijms242115751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Approximately one-third of agricultural land worldwide is affected by salinity, which limits the productivity and sustainability of crop ecosystems. Plant-growth-promoting rhizobacteria (PGPR) are a potential solution to this problem, as PGPR increases crop yield through improving soil fertility and stress resistance. Previous studies have shown that Priestia megaterium ZS-3(ZS-3) can effectively help plants tolerate salinity stress. However, how ZS-3 regulates its metabolic adaptations in saline environments remains unclear. In this study, we monitored the metabolic rearrangement of compatibilisers in ZS-3 and combined the findings with genomic data to reveal how ZS-3 survives in stressful environments, induces plant growth, and tolerates stress. The results showed that ZS-3 tolerated salinity levels up to 9%. In addition, glutamate and trehalose help ZS-3 adapt to osmotic stress under low NaCl stress, whereas proline, K+, and extracellular polysaccharides regulate the osmotic responses of ZS-3 exposed to high salt stress. Potting experiments showed that applying the ZS-3 strain in saline and neutral soils could effectively increase the activities of soil acid phosphatase, urease, and invertase in both soils, thus improving soil fertility and promoting plant growth. In addition, strain ZS-3-GFP colonised the rhizosphere and leaves of Cinnamomum camphora well, as confirmed by confocal microscopy and resistance plate count analysis. Genomic studies and in vitro experiments have shown that ZS-3 exhibits a variety of beneficial traits, including plant-promoting, antagonistic, and other related traits (such as resistance to saline and heavy metal stress/tolerance, amino acid synthesis and transport, volatile compound synthesis, micronutrient utilisation, and phytohormone biosynthesis/regulatory potential). The results support that ZS-3 can induce plant tolerance to abiotic stresses. These data provide important clues to further reveal the interactions between plants and microbiomes, as well as the mechanisms by which micro-organisms control plant health.
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Affiliation(s)
- Lina Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (L.S.); (X.Z.); (T.Q.); (J.D.); (Y.D.)
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoxia Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (L.S.); (X.Z.); (T.Q.); (J.D.); (Y.D.)
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing 210037, China
| | - Ting Qian
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (L.S.); (X.Z.); (T.Q.); (J.D.); (Y.D.)
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing 210037, China
| | - Jiazhou Du
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (L.S.); (X.Z.); (T.Q.); (J.D.); (Y.D.)
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanyuan Du
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (L.S.); (X.Z.); (T.Q.); (J.D.); (Y.D.)
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing 210037, China
| | - Jianren Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (L.S.); (X.Z.); (T.Q.); (J.D.); (Y.D.)
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing 210037, China
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13
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Lei LY, Xiong ZX, Li JL, Yang DZ, Li L, Chen L, Zhong QF, Yin FY, Li RX, Cheng ZQ, Xiao SQ. Biological control of Magnaporthe oryzae using natively isolated Bacillus subtilis G5 from Oryza officinalis roots. Front Microbiol 2023; 14:1264000. [PMID: 37876784 PMCID: PMC10591090 DOI: 10.3389/fmicb.2023.1264000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023] Open
Abstract
Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production causing significant crop losses and impacting grain quality. The annual loss of rice production due to this disease ranges from 10% to 30%. The use of biologically controlled strains, instead of chemical pesticides, to control plant diseases has become a research hotspot. In this study, an antagonistic endophytic bacterial strain was isolated from the roots of Oryza officinalis using the traditional isolation and culture methods. A phylogenetic tree based on 16S RNA and whole-genome sequencing identified isolate G5 as a strain of Bacillus subtilis. This isolate displayed strong antagonistic effects against different physiological strains of M. oryzae. After co-culture in LB medium for 7 days, the inhibition rates of the mycelial growth of four strains of M. oryzae, ZB15, WH97, Guy11, and T-39800E were 98.07 ± 0.0034%, 98.59 ± 0.0051%, 99.16 ± 0.0012%, and 98.69 ± 0.0065%, respectively. Isolate G5 significantly inhibited the formation of conidia of M. oryzae, with an inhibition rate of 97% at an OD600 of 2. Isolate G5 was able to provide 66.81% protection against rice blast under potted conditions. Whole-genome sequencing revealed that the genome size of isolate G5 was 4,065,878 bp, including 4,182 coding genes. Using the anti-SMASH software, 14 secondary metabolite synthesis gene clusters were predicted to encode antifungal substances, such as fengycin, surfactin, and bacilysin. The G5 isolate also contained genes related to plant growth promotion. These findings provide a theoretical basis for expounding the biocontrol mechanisms of this strain and suggest further development of biogenic agents that could effectively inhibit rice blast pathogen growth and reduce crop damage, while being environmentally friendly, conducive to ecological development, and a sustainable alternative to chemical pesticides. This study also enriches the relevant research on endophytes of wild rice, which proves that wild rice is a valuable microbial resource bank.
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Affiliation(s)
- Ling-Yun Lei
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Zi-Xuan Xiong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Jin-Lu Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - De-Zheng Yang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Liu Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ling Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiao-Fang Zhong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fu-You Yin
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Rong-Xin Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Zai-Quan Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Su-Qin Xiao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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14
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Zhao H, Sun N, Huang L, Qian R, Lin X, Sun C, Zhu Y. Azospirillum brasilense activates peroxidase-mediated cell wall modification to inhibit root cell elongation. iScience 2023; 26:107144. [PMID: 37534167 PMCID: PMC10391928 DOI: 10.1016/j.isci.2023.107144] [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: 10/14/2022] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 08/04/2023] Open
Abstract
The molecular mechanism of beneficial bacterium Azospirillum brasilense-mediated root developmental remain elusive. A. brasilense elicited extensively transcriptional changes but inhibited primary root elongation in Arabidopsis. By analyzing root cell type-specific developmental markers, we demonstrated that A. brasilense affected neither overall organization nor cell division of primary root meristem. The cessation of primary root resulted from reduction of cell elongation, which is probably because of bacterially activated peroxidase that will lead to cell wall cross-linking at consuming of H2O2. The activated peroxidase combined with downregulated cell wall loosening enzymes consequently led to cell wall thickness, whereas inhibiting peroxidase restored root growth under A. brasilense inoculation. We further showed that peroxidase activity was probably promoted by cadaverine secreted by A. brasilense. These results suggest that A. brasilense inhibits root elongation by activating peroxidase and inducing cell wall modification in Arabidopsis, in which cadaverine released by A. brasilense is a potential signal compound.
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Affiliation(s)
- Hongcheng Zhao
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Natural Resource & Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Nan Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Natural Resource & Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lin Huang
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Natural Resource & Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ruyi Qian
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Natural Resource & Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xianyong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Natural Resource & Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengliang Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Natural Resource & Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongguan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Natural Resource & Environmental Sciences, Zhejiang University, Hangzhou 310058, China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
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15
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Dunn MF, Becerra-Rivera VA. The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2671. [PMID: 37514285 PMCID: PMC10385936 DOI: 10.3390/plants12142671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.
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Affiliation(s)
- Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Víctor A Becerra-Rivera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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16
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Salazar B, Ortiz A, Keswani C, Minkina T, Mandzhieva S, Pratap Singh S, Rekadwad B, Borriss R, Jain A, Singh HB, Sansinenea E. Bacillus spp. as Bio-factories for Antifungal Secondary Metabolites: Innovation Beyond Whole Organism Formulations. MICROBIAL ECOLOGY 2023; 86:1-24. [PMID: 35604432 DOI: 10.1007/s00248-022-02044-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Several fungi act as parasites for crops causing huge annual crop losses at both pre- and post-harvest stages. For years, chemical fungicides were the solution; however, their wide use has caused environmental contamination and human health problems. For this reason, the use of biofungicides has been in practice as a green solution against fungal phytopathogens. In the context of a more sustainable agriculture, microbial biofungicides have the largest share among the commercial biocontrol products that are available in the market. Precisely, the genus Bacillus has been largely studied for the management of plant pathogenic fungi because they offer a chemically diverse arsenal of antifungal secondary metabolites, which have spawned a heightened industrial engrossment of it as a biopesticide. In this sense, it is indispensable to know the wide arsenal that Bacillus genus has to apply these products for sustainable agriculture. Having this idea in our minds, in this review, secondary metabolites from Bacillus having antifungal activity are chemically and structurally described giving details of their action against several phytopathogens. Knowing the current status of Bacillus secreted antifungals is the base for the goal to apply these in agriculture and it is addressed in depth in the second part of this review.
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Affiliation(s)
- Bruno Salazar
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México
| | - Aurelio Ortiz
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México
| | - Chetan Keswani
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Saglara Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Satyendra Pratap Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Bhagwan Rekadwad
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India
| | - Rainer Borriss
- Institut Für Agrar- Und Gartenbauwissenschaften, Fachgebiet Phytomedizin, Humboldt-Universität Zu Berlin, Lentze-Allee 55-57, 14195, Berlin, Germany
| | - Akansha Jain
- Division of Plant Biology, Bose Institute, CIT Road, Kankurgachi, Kolkata, India
| | - Harikesh B Singh
- Department of Biotechnology, GLA University, Mathura, 281406, India
| | - Estibaliz Sansinenea
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México.
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17
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Almadiy AA, Shaban AE, Ibrahim AM, Balhareth SM, El-Gioushy SF, Khater ESG. Partially substituting chemical NPK fertilizers and their impact on Eureka lemon trees (Citrus limon L. Burm) productivity and fruit quality. Sci Rep 2023; 13:10506. [PMID: 37380672 DOI: 10.1038/s41598-023-37457-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
The main aim of this study is to improve productivity, physical and chemical properties of the fruits and fruit quality of Eureka Lemon trees while lowering production costs by investigating the use of different NPK alternative sources (slow release, and bio) to reduce the use of chemical NPK fertilizers. Ten treatments of NPK fertilizers were applied. The results indicate that the highest values of yield (111.0 and 114.0 kg/tree) were found with 100% chemical NPK (control) for both first and second seasons, respectively. The lemon fruit weight ranged from 131.3 to 152.4 and 131.4 to 153.5 g for first and second seasons, respectively, for all treatments under study. The highest values of fruit length and fruit diameter were found with 100% chemical NPK (control) for both two seasons. The highest values of juice quality parameters (TSS, juice acidity, TSS/acid ratio and vitamin C concentration) responded favorably to higher chemical NPK treatment rates. The highest values of TSS, juice acidity, TSS/Acid ratio, and vitamin C concentration were 9.45%, 6.25%, 1.524 and 4.27 mg/100 g, respectively, were found with 100% chemical NPK (control) for both two seasons. Meanwhile, the lowest value of total sugar was found with 100% chemical NPK (control) for both two seasons.
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Affiliation(s)
- Abdulrhman A Almadiy
- Biology Department, Science and Art College, Najran University, Najran, Saudi Arabia.
| | - Ayman E Shaban
- Pomology Department, Faculty of Agriculture, Cairo University, Giza, 12511, Egypt
| | - Ammar M Ibrahim
- Biology Department, Science and Art College, Najran University, Najran, Saudi Arabia
| | - Salem M Balhareth
- Ministry of Environment and Water and Agriculture, Najran Horticulture Research Centre, Najran, Saudi Arabia
| | - Sherif F El-Gioushy
- Horticulture Department, Faculty of Agriculture, Benha University, Moshtohor, P.O. Box 13736, Toukh, Kalubia, Egypt.
| | - El-Sayed G Khater
- Agricultural and Biosystems Engineering Department, Faculty of Agriculture, Benha University, Moshtohor, P.O. Box 13736, Toukh, Kalubia, Egypt.
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18
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Bhadrecha P, Singh S, Dwibedi V. 'A plant's major strength in rhizosphere': the plant growth promoting rhizobacteria. Arch Microbiol 2023; 205:165. [PMID: 37012531 DOI: 10.1007/s00203-023-03502-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/18/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023]
Abstract
Human activities, industrialization and civilization have deteriorated the environment which eventually has led to alarming effects on plants and animals by heightened amounts of chemical pollutants and heavy metals in the environment, which create abiotic stress. Environmental conditions like drought, salinity, diminished macro-and micro-nutrients also contribute in abiotic stress, resulting in decrement of survival and growth of plants. Presence of pathogenic and competitive microorganisms, as well as pests lead to biotic stress and a plant alone can not defend itself. Thankfully, nature has rendered plant's rhizosphere with plant growth promoting rhizobacteria which maintain an allelopathic relationship with host plant to defend the plant and let it flourish in abiotic as well as biotic stress situations. This review discusses the mechanisms behind increase in plant growth via various direct and indirect traits expressed by associated microorganisms in the rhizosphere, along with their current scenario and promising future for sustainable agriculture. It also gives details of ten such bacterial species, viz. Acetobacter, Agrobacterium, Alcaligenes, Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Enterobacter and Frankia, whose association with the host plants is famed for enhancing plant's growth and survival.
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Affiliation(s)
- Pooja Bhadrecha
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, 140413, India
| | - Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, Gautam Budh Nagar, Uttar Pradesh, 203201, India
| | - Vagish Dwibedi
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, 140413, India.
- Thapar Institute of Engineering and Technology, Department of Biotechnology, 147004, PATIALA, India.
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Marfetán JA, Gallo AL, Farias ME, Vélez ML, Pescuma M, Ordoñez OF. Exiguobacterium sp. as a bioinoculant for plant-growth promotion and Selenium biofortification strategies in horticultural plants. World J Microbiol Biotechnol 2023; 39:134. [PMID: 36961610 DOI: 10.1007/s11274-023-03571-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/07/2023] [Indexed: 03/25/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) have a positive effect on plant development and being a promising way to enhance crop productivity and as substitution of chemical fertilizers. Selenium (Se) is an important trace element and its intake is usually lower than the daily minimum amount required for humans; hence, there is a demand on the design of Se biofortification strategies. Here, the genetic traits known to be associated with Plant-Growth Promotion (PGP) and Se biotransformation of Exiguobacterium sp. S17 were evaluated through genome analysis. Its growth-promoting capacity was tested through plant-growth promotion assays in laboratory and field conditions, using Brassica juncea (indian mustard), Beta vulgaris (chard), and Lactuca sativa (lettuce). Additionally, the Se biotransformation ability of Exiguobacterium sp. S17 was evaluated and the obtained selenized bacteria were tested in mustard plants. The sequenced bacteria genome revealed the presence of multiple genes involved in important functions regarding soil and plant colonization, PGP and Se biotransformation. Moreover, it was demonstrated that Exiguobacterium sp. S17 enhanced plant growth and could be useful to produce Se accumulation and biofortification in accumulator plants such as mustard. Thereby, Exiguobacterium sp. S17 might be used for developing new, sustainable, and environmentally friendly agro-technological strategies.
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Affiliation(s)
- Jorge A Marfetán
- Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Chubut, Argentina
- CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Ana L Gallo
- Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Chubut, Argentina
- Agencia Nacional de Promoción de la Investigación, El Desarrollo Tecnológico y la Innovación (Agencia I+D+I), Buenos Aires, Argentina
| | - Maria E Farias
- PROIMI Planta Piloto de Procesos Industriales Microbiológicos Av. Belgrano y Pasaje Caseros -(4000) - LIMLA Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas Tucumán, Argentina, CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
- PUNABIO SRL. Tucumán, Buenos Aires, Argentina
| | - Maria L Vélez
- Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Chubut, Argentina.
- CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
- Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), Esquel, Chubut, Argentina.
| | - Micaela Pescuma
- Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Chubut, Argentina
- CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Omar F Ordoñez
- Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Chubut, Argentina.
- CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
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20
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Xiang D, Yang X, Liu B, Chu Y, Liu S, Li C. Bio-priming of banana tissue culture plantlets with endophytic Bacillus velezensis EB1 to improve Fusarium wilt resistance. Front Microbiol 2023; 14:1146331. [PMID: 37007465 PMCID: PMC10064985 DOI: 10.3389/fmicb.2023.1146331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Tissue culture techniques have been routinely used for banana propagation and offered rapid production of planting materials with favorable genotypes and free of pathogenic microorganisms in the banana industry. Meanwhile, extensive scientific work suggests that micropropagated plantlets are more susceptible to Fusarium oxysporum f. sp. cubense (Foc), the deadly strain that causes Fusarium wilt of bananas than conventional planting material due to the loss of indigenous endophytes. In this study, an endophytic bacterium Bacillus velezensis EB1 was isolated and characterized. EB1 shows remarkable in vitro antagonistic activity against Foc with an inhibition rate of 75.43% and induces significant morphological and ultrastructural changes and alterations in the hyphae of Foc. Colony-forming unit (c.f.u.) counting and scanning electron microscopy (SEM) revealed that EB1 could colonize both the surface and inner tissues of banana tissue culture plantlets. Banana tissue culture plantlets of late rooting stage bioprimed with EB1 could efficiently ward off the invasive of Foc. The bio-priming effect could maintain in the acclimatized banana plants and significantly decrease the disease severity of Fusarium wilt and induce strong disease resistance by manipulating plant defense signaling pathways in a pot experiment. Our results provide the adaptability and potential of native endophyte EB1 in protecting plants from pathogens and infer that banana tissue culture plantlets bio-priming with endophytic microbiota could be a promising biological solution in the fight against the Fusarium wilt of banana.
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Affiliation(s)
- Dandan Xiang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaofang Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Bojing Liu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuanqi Chu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Siwen Liu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chunyu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Chunyu Li
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Zhao YQ, Hu KD, Yao GF, Wang SY, Peng XJ, Zhang H. A D-cysteine desulfhydrase, SlDCD2, participates in tomato fruit ripening by modulating ROS homoeostasis and ethylene biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad014. [PMID: 36968183 PMCID: PMC10031741 DOI: 10.1093/hr/uhad014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Hydrogen sulfide (H2S) is involved in multiple processes during plant growth and development. D-cysteine desulfhydrase (DCD) can produce H2S with D-cysteine as the substrate; however, the potential developmental roles of DCD have not been explored during the tomato lifecycle. In the present study, SlDCD2 showed increasing expression during fruit ripening. Compared with the control fruits, the silencing of SlDCD2 by pTRV2-SlDCD2 accelerated fruit ripening. A SlDCD2 gene-edited mutant was constructed by CRISPR/Cas9 transformation, and the mutant exhibited accelerated fruit ripening, decreased H2S release, higher total cysteine and ethylene contents, enhanced chlorophyll degradation and increased carotenoid accumulation. Additionally, the expression of multiple ripening-related genes, including NYC1, PAO, SGR1, PDS, PSY1, ACO1, ACS2, E4, CEL2, and EXP was enhanced during the dcd2 mutant tomato fruit ripening. Compared with the wild-type fruits, SlDCD2 mutation induced H2O2 and malondialdehyde (MDA) accumulation in fruits, which led to an imbalance in reactive oxygen species (ROS) metabolism. A correlation analysis indicated that H2O2 content was strongly positively correlated with carotenoids content, ethylene content and ripening-related gene expression and negatively correlated with the chlorophyll content. Additionally, the dcd2 mutant showed earlier leaf senescence, which may be due to disturbed ROS homeostasis. In short, our findings show that SlDCD2 is involved in H2S generation and that the reduction in endogenous H2S production in the dcd2 mutant causes accelerated fruit ripening and premature leaf senescence. Additionally, decreased H2S in the dcd2 mutant causes excessive H2O2 accumulation and increased ethylene release, suggesting a role of H2S and SlDCD2 in modulating ROS homeostasis and ethylene biosynthesis.
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Affiliation(s)
- Yu-Qi Zhao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Kang-Di Hu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Gai-Fang Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Si-Yue Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiang-Jun Peng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Hua Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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22
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Constantinescu-Aruxandei D, Oancea F. Closing the Nutrient Loop-The New Approaches to Recovering Biomass Minerals during the Biorefinery Processes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2096. [PMID: 36767462 PMCID: PMC9915181 DOI: 10.3390/ijerph20032096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The recovery of plant mineral nutrients from the bio-based value chains is essential for a sustainable, circular bioeconomy, wherein resources are (re)used sustainably. The widest used approach is to recover plant nutrients on the last stage of biomass utilization processes-e.g., from ash, wastewater, or anaerobic digestate. The best approach is to recover mineral nutrients from the initial stages of biomass biorefinery, especially during biomass pre-treatments. Our paper aims to evaluate the nutrient recovery solutions from a trans-sectorial perspective, including biomass processing and the agricultural use of recovered nutrients. Several solutions integrated with the biomass pre-treatment stage, such as leaching/bioleaching, recovery from pre-treatment neoteric solvents, ionic liquids (ILs), and deep eutectic solvents (DESs) or integrated with hydrothermal treatments are discussed. Reducing mineral contents on silicon, phosphorus, and nitrogen biomass before the core biorefinery processes improves processability and yield and reduces corrosion and fouling effects. The recovered minerals are used as bio-based fertilizers or as silica-based plant biostimulants, with economic and environmental benefits.
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Affiliation(s)
| | - Florin Oancea
- Department of Bioresources, Bioproducts Group, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania
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23
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Pereyra CM, Dal Lago CC, Creus CM, Pereyra MA. Azospirillum baldaniorum Sp 245 inoculation affects cell wall and polyamines metabolisms in cucumber seedling roots. FEMS Microbiol Lett 2023; 370:6998557. [PMID: 36690345 DOI: 10.1093/femsle/fnad005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 11/22/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Azospirillum baldaniorum Sp 245 is a model plant growth-promoting rhizobacterium. The first cross-talk with plants takes place within the roots. Roots cells growth is constrained by the primary cell wall (CW). Also, neighboring CW form the apoplast that should affect cells signaling and biochemical messages. Studies on CW phenolic composition ferulate (FA), diferulates (DFA) and p-coumarate and polyamines (PA) metabolisms of A. baldaniorum Sp 245- inoculated roots and on bacterial PA production in culture media should help to understand more about the mechanisms involved in Azospirillum-root association. For this purpose, CW-bound FA, DFA and p-coumarate contents, putrescine (put) and spermidine contents, diamine and polyamine oxidases activities, and H2O2 content of Cucumis sativus roots from dark grown seedlings inoculated with A. baldaniorum Sp 245 were determined. Also, bacterial PA production under constant agitation or static conditions was evaluated. Results showed lesser contents of all phenolics, and higher FA/DFA ratio in CW of inoculated roots that should be responsible for roots growth promotion. Also, the increased put content, DAO activity, and H2O2 production in the roots should be associated to A. baldaniorum Sp 245 growth promotion in early stages. Finally, the participation of both PA in A. baldaniorum Sp 245 biofilm formation was demonstrated.
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Affiliation(s)
| | - Claudia Cristina Dal Lago
- Instituto de Innovación para el Desarrollo Agroalimentario y Agroenergético Sostenible (IIDEAGROS)
- Grupo Innovación y desarrollo de alimentos regionales
| | - Cecilia Mónica Creus
- Instituto de Innovación para el Desarrollo Agroalimentario y Agroenergético Sostenible (IIDEAGROS)
- Laboratorio de Bioquímica Vegetal y Microbiana
| | - María Alejandra Pereyra
- Instituto de Innovación para el Desarrollo Agroalimentario y Agroenergético Sostenible (IIDEAGROS)
- Grupo Innovación y desarrollo de alimentos regionales
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24
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Sarkar AK, Sadhukhan S. Unearthing the alteration in plant volatiles induced by mycorrhizal fungi: A shield against plant pathogens. PHYSIOLOGIA PLANTARUM 2023; 175:e13845. [PMID: 36546667 DOI: 10.1111/ppl.13845] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Plants produce a large range of structurally varied low molecular weight secondary metabolites, which evaporate, known as volatile organic compounds (VOCs). Several of them are emitted in response to biotic stress as a defensive measure against pathogen attacks. Arbuscular Mycorrhizal Fungi (AMFs) can change the VOC pattern in parts of the plant and may promote plant defense via direct or indirect mechanisms. Mycorrhization of plants positively affects plant immunization along with growth and yield. The presence of AMF may raise the concentration of phenolic compounds and the activity of critical defense-related enzymes. AMF-induced changes in plant chemistry and associated volatile emissions lead to stronger immunity against pathogenic microorganisms. Despite substantial research into the origins of diversity in VOC-mediated plant communication, very little is known about the mechanism of influence of several AMFs on plant VOC emissions and modulation of plant immunization. Moreover, the molecular mechanism for VOC sensing in plants and mycorrhizal association is still unclear. In the present review, we have presented an up-to-date understanding of the cross-talk of AMF and VOC patterns in plants and the subsequent modulation of resistance against microbial pathogens.
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Affiliation(s)
- Anup Kumar Sarkar
- Department of Botany, Dukhulal Nibaran Chandra College, Murshidabad, West Bengal, India
- Plant Molecular Biology Laboratory, Department of Botany, Raiganj University, Uttar Dinajpur, West Bengal, India
| | - Sanjoy Sadhukhan
- Plant Molecular Biology Laboratory, Department of Botany, Raiganj University, Uttar Dinajpur, West Bengal, India
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25
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Antoszewski M, Mierek-Adamska A, Dąbrowska GB. The Importance of Microorganisms for Sustainable Agriculture-A Review. Metabolites 2022; 12:1100. [PMID: 36422239 PMCID: PMC9694901 DOI: 10.3390/metabo12111100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
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Affiliation(s)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
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New Insights into the Mechanism of Trichoderma virens-Induced Developmental Effects on Agrostis stolonifera Disease Resistance against Dollar Spot Infection. J Fungi (Basel) 2022; 8:jof8111186. [DOI: 10.3390/jof8111186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
Trichoderma is internationally recognized as a biocontrol fungus for its broad-spectrum antimicrobial activity. Intriguingly, the crosstalk mechanism between the plant and Trichoderma is dynamic, depending on the Trichoderma strains and the plant species. In our previous study, the Trichoderma virens 192-45 strain showed better pathogen inhibition through the secretive non-volatile and volatile substrates. Therefore, we studied transcriptional and metabolic responses altered in creeping bentgrass (Agrostis stolonifera L.) with T. virens colonization prior to a challenge with Clarireedia homoeocarpa. This fungal pathogen causes dollar spot on various turfgrasses. When the pathogen is deficient, the importance of T. virens to the enhancement of plant growth can be seen in hormonal production and microbe signaling, such as indole-3-acrylic acid. Therefore, these substrates secreted by T. virens and induced genes related to plant growth can be the ‘pre-defense’ for ensuing pathogen attacks. During C. homoeocarpa infection, the Trichoderma–plant interaction activates defense responses through the SA- and/or JA-dependent pathway, induced by T. virens and its respective exudates, such as oleic, citric, and stearic acid. Thus, we will anticipate a combination of genetic engineering and exogenous application targeting these genes and metabolites, which could make creeping bentgrass more resistant to dollar spot and other pathogens.
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Rajer FU, Samma MK, Ali Q, Rajar WA, Wu H, Raza W, Xie Y, Tahir HAS, Gao X. Bacillus spp.-Mediated Growth Promotion of Rice Seedlings and Suppression of Bacterial Blight Disease under Greenhouse Conditions. Pathogens 2022; 11:1251. [PMID: 36365003 PMCID: PMC9694674 DOI: 10.3390/pathogens11111251] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 07/30/2023] Open
Abstract
Rice (Oryza sativa L.) is a major cereal and staple food crop worldwide, and its growth and production are affected by several fungal and bacterial phytopathogens. Bacterial blight (BB) is one of the world's most devastating rice diseases, caused by Xanthomonas oryzae pv. oryzae (Xoo). In the current study, Bacillus atrophaeus FA12 and B. cabrialesii FA26 were isolated from the rice rhizosphere and characterized as having broad-range antifungal and antibacterial activities against various phytopathogens, including Xoo. In addition, the selected strains were further evaluated for their potent rice growth promotion and suppression efficacy against BB under greenhouse conditions. The result shows that FA12 and FA26, applied as seed inoculants, significantly enhanced the vigor index of rice seedlings by 78.89% and 108.70%, respectively. Suppression efficacy against BB disease by FA12 and FA26 reached up to 59.74% and 54.70%, respectively, in pot experiments. Furthermore, MALDI-TOF MS analysis of selected strains revealed the masses ranged from m/z 1040 to 1540, representing that iturins and fengycin are the major antimicrobial compounds in the crude extracts, which might have beneficial roles in rice defence responses against BB. In conclusion, FA12 and FA26 possess broad-range antagonistic activity and have the capability to promote plant growth traits. More importantly, applying these strains has a high potential for implementing eco-friendly, cost-effective, and sustainable management practices for BB disease.
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Affiliation(s)
- Faheem Uddin Rajer
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Pathology, Faculty of Crop Protection, Sindh Agriculture University, Tandojam 70060, Pakistan
| | - Muhammad Kaleem Samma
- Department of Biosciences, Shaheed Zulfiqar Ali Bhutto Institute of Science and Technology, Karachi 75600, Pakistan
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Waleed Ahmed Rajar
- Institute of Microbiology, University of Sindh, Jamshoro 76080, Pakistan
| | - Huijun Wu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Waseem Raza
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongli Xie
- State Key Laboratory of Plateau Ecology and Agriculture, Department of Grassland Science, College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Hafiz Abdul Samad Tahir
- Tobacco Research Institute, Pakistan Tobacco Board, Ministry of National Food Security and Research, Peshawar 25124, Pakistan
| | - Xuewen Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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28
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Jabborova D, Davranov K, Jabbarov Z, Bhowmik SN, Ercisli S, Danish S, Singh S, Desouky SE, Elazzazy AM, Nasif O, Datta R. Dual Inoculation of Plant Growth-Promoting Bacillus endophyticus and Funneliformis mosseae Improves Plant Growth and Soil Properties in Ginger. ACS OMEGA 2022; 7:34779-34788. [PMID: 36211029 PMCID: PMC9535732 DOI: 10.1021/acsomega.2c02353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Co-inoculation with beneficial microbes has been suggested as a useful practice for the enhancement of plant growth, nutrient uptake, and soil nutrients. For the first time in Uzbekistan the role of plant-growth-promoting Bacillus endophyticus IGPEB 33 and arbuscular mycorrhizal fungi (AMF) on plant growth, the physiological properties of ginger (Zingiber officinale), and soil enzymatic activities was studied. Moreover, the coinoculation of B. endophyticus IGPEB 33 and AMF treatment significantly increased the plant height by 81%, leaf number by 70%, leaf length by 82%, and leaf width by 40% compared to the control. B. endophyticus IGPEB 33 individually increased plant height significantly by 51%, leaf number by 56%, leaf length by 67%, and leaf width by 27% as compared to the control treatment. Compared to the control, B. endophyticus IGPEB 33 and AMF individually significantly increased chlorophyll a by 81-58%, chlorophyll b by 68-37%, total chlorophyll by 74-53%, and carotenoid content by 67-55%. However, combination of B. endophyticus IGPEB 33 and AMF significantly increased chlorophyll a by 86%, chlorophyll b by 72%, total chlorophyll by 82%, and carotenoid content by 83% compared to the control. Additionally, plant-growth-promoting B. endophyticus IGPEB 33 and AMF inoculation improved soil nutrients and soil enzyme activities compared to the all treatments. Co-inoculation with plant-growth-promoting B. endophyticus and AMF could be an alternative for the production of ginger that is more beneficial to soil nutrient deficiencies. We suggest that a combination of plant-growth-promoting B. endophyticus and AMF inoculation could be a more sustainable and eco-friendly approach in a nutrient-deficient soil.
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Affiliation(s)
- Dilfuza Jabborova
- Institute
of Genetics and Plant Experimental Biology, Uzbekistan Academy of Sciences, Kibray 111208, Uzbekistan
- Faculty
of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan
| | - Kakhramon Davranov
- Institute
of Microbiology of the Academy of Sciences of Uzbekistan, Tashkent 100174, Uzbekistan
| | - Zafarjon Jabbarov
- Faculty
of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan
| | - Subrata Nath Bhowmik
- Division
of Microbiology, ICAR-Indian Agricultural
Research Institute, Pusa,
New Delhi 110012, India
| | - Sezai Ercisli
- Department
of Horticulture, Agricultural Faculty, Ataturk
University, Erzurum 252240, Turkey
| | - Subhan Danish
- Department
of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Sachidanand Singh
- Department
of Biotechnology, Smt. S. S. Patel Nootan
Science & Commerce College, Sankalchand Patel University, Visnagar 384315, Gujarat, India
| | - Said E. Desouky
- Department
of Botany and Microbiology, Faculty of Science,
Al-azhar University, 11884 Nasr, Cairo, Egypt
| | - Ahmed M. Elazzazy
- Department
of Chemistry of Natural and Microbial Products, Pharmaceutical and Drug Industries Institute, National Research Centre, Dokki, Giza 12622, Egypt
| | - Omaima Nasif
- King Saud
University, Department of Physiology, College of Medicine and King
Khalid University Hospital, King Saud University, Medical City, P.O. Box 2925, Riyadh 11461, Saudi Arabia
| | - Rahul Datta
- Department
of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska 1, 61300 Brno, Czech Republic
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Tsotetsi T, Nephali L, Malebe M, Tugizimana F. Bacillus for Plant Growth Promotion and Stress Resilience: What Have We Learned? PLANTS (BASEL, SWITZERLAND) 2022; 11:2482. [PMID: 36235347 PMCID: PMC9571655 DOI: 10.3390/plants11192482] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 06/12/2023]
Abstract
The rhizosphere is a thin film of soil that surrounds plant roots and the primary location of nutrient uptake, and is where important physiological, chemical, and biological activities are occurring. Many microbes invade the rhizosphere and have the capacity to promote plant growth and health. Bacillus spp. is the most prominent plant growth promoting rhizobacteria due to its ability to form long-lived, stress-tolerant spores. Bacillus-plant interactions are driven by chemical languages constructed by a wide spectrum of metabolites and lead to enhanced plant growth and defenses. Thus, this review is a synthesis and a critical assessment of the current literature on the application of Bacillus spp. in agriculture, highlighting gaps that remain to be explored to improve and expand on the Bacillus-based biostimulants. Furthermore, we suggest that omics sciences, with a focus on metabolomics, offer unique opportunities to illuminate the chemical intercommunications between Bacillus and plants, to elucidate biochemical and molecular details on modes of action of Bacillus-based formulations, to generate more actionable insights on cellular and molecular events that explain the Bacillus-induced growth promotion and stress resilience in plants.
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Affiliation(s)
- Teboho Tsotetsi
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Lerato Nephali
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Motumiseng Malebe
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
- International R&D Division, Omnia Nutriology, Omnia Group (Pty) Ltd., Johannesburg 2021, South Africa
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Xie S, Jiang L, Wu Q, Wan W, Gan Y, Zhao L, Wen J. Maize Root Exudates Recruit Bacillus amyloliquefaciens OR2-30 to Inhibit Fusarium graminearum Infection. PHYTOPATHOLOGY 2022; 112:1886-1893. [PMID: 35297645 DOI: 10.1094/phyto-01-22-0028-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bacillus spp. can exert plant growth-promoting effects and biocontrol effects after effective colonization, and bacterial chemotaxis toward plant root exudates is the initial step to colonize. Under biotic stress, plants are able to alter their root exudates to attract or avoid different types of microbes. Hence, Bacillus chemotaxis toward root exudates after pathogen infection is crucial for exerting their beneficial effects. In this study, the Bacillus amyloliquefaciens OR2-30 strain, which exhibited greater chemotaxis ability toward maize root exudates after Fusarium graminearum infection, was screened from 156 rhizosphere microorganisms. The infected maize root exudates were further confirmed to improve the swarming and biofilm formation ability of the OR2-30 strain. Chemotaxis, swarming, and biofilm formation ability were able to influence bacterial colonization. Indeed, the the OR2-30 strain displayed more effective colonization ability in the maize rhizosphere after F. graminearum inoculation. Moreover, lipopeptides produced by OR2-30 were identified as iturins and responsible for suppressing F. graminearum growth. Further study showed that lipopeptides suppressed the growth of F. graminearum by inhibiting conidia formation and germination, inducing reactive oxygen species production and causing cell death in mycelium. Eventually, the OR2-30 strain increased maize resistance against F. graminearum. These results suggested that maize root exudates could recruit B. amyloliquefacines OR2-30 after F. graminearum infection, and that OR2-30 then suppresses the F. graminearum by producing lipopeptides, such as iturins, to protect maize.
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Affiliation(s)
- Shanshan Xie
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Lin Jiang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Qin Wu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Wenkun Wan
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yutian Gan
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Lingling Zhao
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Jiajia Wen
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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Wu X, Fan Y, Wang R, Zhao Q, Ali Q, Wu H, Gu Q, Borriss R, Xie Y, Gao X. Bacillus halotolerans KKD1 induces physiological, metabolic and molecular reprogramming in wheat under saline condition. FRONTIERS IN PLANT SCIENCE 2022; 13:978066. [PMID: 36035675 PMCID: PMC9404337 DOI: 10.3389/fpls.2022.978066] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Salt stress decreases plant growth and is a major threat to crop yields worldwide. The present study aimed to alleviate salt stress in plants by inoculation with halophilic plant growth-promoting rhizobacteria (PGPR) isolated from an extreme environment in the Qinghai-Tibetan Plateau. Wheat plants inoculated with Bacillus halotolerans KKD1 showed increased seedling morphological parameters and physiological indexes. The expression of wheat genes directly involved in plant growth was upregulated in the presence of KKD1, as shown by real-time quantitative PCR (RT-qPCR) analysis. The metabolism of phytohormones, such as 6-benzylaminopurine and gibberellic acid were also enhanced. Mining of the KKD1 genome corroborated its potential plant growth promotion (PGP) and biocontrol properties. Moreover, KKD1 was able to support plant growth under salt stress by inducing a stress response in wheat by modulating phytohormone levels, regulating lipid peroxidation, accumulating betaine, and excluding Na+. In addition, KKD1 positively affected the soil nitrogen content, soil phosphorus content and soil pH. Our findings indicated that KKD1 is a promising candidate for encouraging wheat plant growth under saline conditions.
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Affiliation(s)
- Xiaohui Wu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Plateau Ecology and Agriculture, Department of Grassland Science, College of Agricultural and Husbandry, Qinghai University, Xining, China
| | - Yaning Fan
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ruoyi Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Qian Zhao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Huijun Wu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Qin Gu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität, Berlin, Germany
- Nord Reet UG, Greifswald, Germany
| | - Yongli Xie
- State Key Laboratory of Plateau Ecology and Agriculture, Department of Grassland Science, College of Agricultural and Husbandry, Qinghai University, Xining, China
| | - Xuewen Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Gamboa-Becerra R, Desgarennes D, Molina-Torres J, Ramírez-Chávez E, Kiel-Martínez AL, Carrión G, Ortiz-Castro R. Plant growth-promoting and non-promoting rhizobacteria from avocado trees differentially emit volatiles that influence growth of Arabidopsis thaliana. PROTOPLASMA 2022; 259:835-854. [PMID: 34529144 DOI: 10.1007/s00709-021-01705-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Microbial volatile organic compounds (mVOCs) play important roles in inter- and intra-kingdom interactions, and they are also important as signal molecules in physiological processes acting either as plant growth-promoting or negatively modulating plant development. We investigated the effects of mVOCs emitted by PGPR vs non-PGPR from avocado trees (Persea americana) on growth of Arabidopsis thaliana seedlings. Chemical diversity of mVOCs was determined by SPME-GC-MS; selected compounds were screened in dose-response experiments in A. thaliana transgenic lines. We found that plant growth parameters were affected depending on inoculum concentration. Twenty-six compounds were identified in PGPR and non-PGPR with eight of them not previously reported. The VOCs signatures were differential between those groups. 4-methyl-2-pentanone, 1-nonanol, 2-phenyl-2-propanol and ethyl isovalerate modified primary root architecture influencing the expression of auxin- and JA-responsive genes, and cell division. Lateral root formation was regulated by 4-methyl-2-pentanone, 3-methyl-1-butanol, 1-nonanol and ethyl isovalerate suggesting a participation via JA signalling. Our study revealed the differential emission of volatiles by PGPR vs non-PGPR from avocado trees and provides a general view about the mechanisms by which those volatiles influence plant growth and development. Rhizobacteria strains and mVOCs here reported are promising for improvement the growth and productivity of avocado crop.
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Affiliation(s)
- Roberto Gamboa-Becerra
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico
| | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico
| | - Jorge Molina-Torres
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
| | - Enrique Ramírez-Chávez
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
| | - Ana L Kiel-Martínez
- Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico
| | - Gloria Carrión
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico.
| | - Randy Ortiz-Castro
- Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico.
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Koyro HW, Huchzermeyer B. From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity. PLANTS 2022; 11:plants11131654. [PMID: 35807605 PMCID: PMC9269222 DOI: 10.3390/plants11131654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022]
Abstract
Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.
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Affiliation(s)
- Hans-Werner Koyro
- Institute of Plantecology, Justus-Liebig-University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
- Correspondence:
| | - Bernhard Huchzermeyer
- Institute of Botany, Leibniz Universitaet Hannover, Herrenhaeuser Str. 2, 30416 Hannover, Germany; or
- AK Biotechnology, VDI-BV-Hannover, Hanomagstr. 12, 30449 Hannover, Germany
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Andleeb S, Shafique I, Naseer A, Abbasi WA, Ejaz S, Liaqat I, Ali S, Khan MF, Ahmed F, Ali NM. Molecular characterization of plant growth-promoting vermi-bacteria associated with Eisenia fetida gastrointestinal tract. PLoS One 2022; 17:e0269946. [PMID: 35704622 PMCID: PMC9200293 DOI: 10.1371/journal.pone.0269946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/31/2022] [Indexed: 11/18/2022] Open
Abstract
Earthworms are highly productive invertebrates and play a vital role in organic farming and improving soil structure and function. The gastrointestinal tract of earthworms possessed agricultural important bacteria. So, the current research aimed was to examine, screen, and identify the plant growth promoting bacteria existing in the digestive tract of Eisenia fetida called plant growth promoting vermi-bacteria. The plant growth promoting traits such as siderophore, phytohormone, and hydrolytic enzymes production, and phosphate solubiliation were assessed. Eleven vermi-bacteria i.e. Bacillus mycoides, B. aryabhattai, B. megaterium, Staphylococcus hominis, B. subtilis, B. spizizenii, B. licheniformis, B. mojavensis, B. toyonensis, B. anthracis, B. cereus, B. thuringiensis, and B. paranthracis were isolated and identified based on microscopic studies, biochemical tests, ribotyping, and agricultural traits. All vermi-bacteria are Gram-positive rods except Staphylococcus hominis and produce different compounds such as siderophore, indole acetic acid, catalase, oxidase, proteases, amylases, and lipases. All vermi-bacteria also act as phosphate solubilizers. Therefore, all isolated vermi-bacteria could be used as potential microbial biofertilizers to enhance crops production in Pakistan.
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Affiliation(s)
- Saiqa Andleeb
- Department of Zoology, Microbial Biotechnology and Vermi-Technology Laboratory, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- * E-mail: ,
| | - Irsa Shafique
- Department of Zoology, Microbial Biotechnology and Vermi-Technology Laboratory, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Anum Naseer
- Department of Zoology, Microbial Biotechnology and Vermi-Technology Laboratory, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Wajid Arshad Abbasi
- Department of CS&IT, Computational Biology and Data Analysis Laboratory, University of Azad Jammu & Kashmir, Muzaffarabad, Pakistan
| | - Samina Ejaz
- Department of Biochemistry, Islamia University Bahawalpur, Bahawalpur, Pakistan
| | - Iram Liaqat
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Shaukat Ali
- Department of Zoology, Government College University, Lahore, Pakistan
| | | | - Fayaz Ahmed
- Department of Zoology, Hazara University, Mansehra, KPK, Pakistan
| | - Nazish Mazhar Ali
- Department of Zoology, Government College University, Lahore, Pakistan
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35
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Ulrich K, Becker R, Behrendt U, Kube M, Schneck V, Ulrich A. Physiological and genomic characterisation of Luteimonas fraxinea sp. nov., a bacterial species associated with trees tolerant to ash dieback. Syst Appl Microbiol 2022; 45:126333. [DOI: 10.1016/j.syapm.2022.126333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022]
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36
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Copeland C. The feeling is mutual: Increased host putrescine biosynthesis promotes both plant and endophyte growth. PLANT PHYSIOLOGY 2022; 188:1939-1941. [PMID: 35355052 PMCID: PMC8968283 DOI: 10.1093/plphys/kiac001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
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37
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Ivo Ganchev. Role of Multispecies Biofilms with a Dominance of Bacillus subtilis in the Rhizosphere. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021150061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hasan N, Khan IU, Farzand A, Heng Z, Moosa A, Saleem M, Canming T. Bacillus altitudinis HNH7 and Bacillus velezensis HNH9 promote plant growth through upregulation of growth-promoting genes in upland cotton. J Appl Microbiol 2022; 132:3812-3824. [PMID: 35244318 DOI: 10.1111/jam.15511] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
Abstract
AIMS The potential of endophytic Bacillus strains to improve plant growth and yield was evaluated. METHODS AND RESULTS Endophytic Bacillus altitudinis HNH7 and Bacillus velezensis HNH9 were evaluated for their growth-promoting traits. In an in vitro plate assay, HNH7 and HNH9 exhibited proteolytic, amylolytic, lipolytic, and cellulolytic activity. HNH7 and HNH9 were able to solubilize iron by producing siderophores but were unable to solubilize insoluble phosphate. PCR confirmed the presence of four growth-promoting genes viz. pvd, budA, asbA, and satA in the genome of HNH7, while HNH9 also possessed the same genes except for budA. In a greenhouse experiment, HNH7 and HNH9 promoted the growth of upland cotton plants by upregulating the expression of growth-linked genes, EXP6, ARF1, ARF18, IAA9, CKX6, and GID1b. However, the expression of genes involved in ethylene biosynthesis i.e., ERF and ERF17 was downregulated after treating the plants with HNH7 and HNH9 compared to the control. Furthermore, cotton plants treated with HNH7 and HNH9 exhibited a significantly higher rate of photosynthesis and stomatal conductance. CONCLUSION HNH7 and HNH9 showed a promising potential to promote the growth of cotton plants. SIGNIFICANCE AND IMPACT OF STUDY Research on plant growth-promoting Bacillus strains can lead to the formation of biofertilizers.
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Affiliation(s)
- Nadeem Hasan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Irfan Ullah Khan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ayaz Farzand
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Zhou Heng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Anam Moosa
- Department of Plant Pathology, The Islamia University of Bahawalpur, Pakistan
| | - Muhammad Saleem
- College of Electrical and Mechanical Engineering, NUST, Rawalpindi, Islamabad, Pakistan
| | - Tang Canming
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Mokabel S, Olama Z, Ali S, El-Dakak R. The Role of Plant Growth Promoting Rhizosphere Microbiome as Alternative Biofertilizer in Boosting Solanum melongena L. Adaptation to Salinity Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050659. [PMID: 35270129 PMCID: PMC8912713 DOI: 10.3390/plants11050659] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 05/07/2023]
Abstract
Recent ecological perturbations are presumed to be minimized by the application of biofertilizers as a safe alternative to chemical fertilizers. The current study aims to use bioinoculum (I) as an alternative biofertilizer and to alleviate salinity stress in the cultivar Solanum melongena L. Baldi. The salinity drench was 200 mM NaCl (S), which was used with different treatments (0; I; S; S + I) in pots prefilled with clay and sand (1:2). Results showed that salinity stress inhibited both plant fresh and dry weights, water content, and photosynthetic pigments. The content of root spermine (Spm), spermidine (Spd), and puterscine (Put) decreased. However, addition of the bioinoculum to salt-treated plants increased pigment content (80.35, 39.25, and 82.44% for chl a, chl b, and carotenoids, respectively). Similarly, K+, K+/Na+, Ca2+, P, and N contents were significantly enhanced. Increases were recorded for Spm + Spd and Put in root and shoot (8.4-F, 1.6-F and 2.04-F, 2.13-F, respectively). RAPD PCR showed gene expression upregulation of photosystem II D2 protein, glutathione reductase, glutathione-S-transferase, protease I, and protease II. The current work recommends application of the selected bioinoculum as a green biofertilizer and biopesticide. Additionally, the studied eggplant cultivar can be regarded as a source of salt tolerance genes in agricultural fields.
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Affiliation(s)
- Souhair Mokabel
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt; (S.M.); (Z.O.)
| | - Zakia Olama
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt; (S.M.); (Z.O.)
| | - Safaa Ali
- Nucleic Acid Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technology Applications (SRTA-City), Alexandria 21934, Egypt;
| | - Rehab El-Dakak
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt; (S.M.); (Z.O.)
- Correspondence:
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40
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Kashyap AS, Manzar N, Nebapure SM, Rajawat MVS, Deo MM, Singh JP, Kesharwani AK, Singh RP, Dubey SC, Singh D. Unraveling Microbial Volatile Elicitors Using a Transparent Methodology for Induction of Systemic Resistance and Regulation of Antioxidant Genes at Expression Levels in Chili against Bacterial Wilt Disease. Antioxidants (Basel) 2022; 11:antiox11020404. [PMID: 35204287 PMCID: PMC8869530 DOI: 10.3390/antiox11020404] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/05/2022] [Accepted: 02/09/2022] [Indexed: 12/10/2022] Open
Abstract
Microbial volatiles benefit the agricultural ecological system by promoting plant growth and systemic resistance against diseases without harming the environment. To explore the plant growth-promoting efficiency of VOCs produced by Pseudomonas fluorescens PDS1 and Bacillus subtilis KA9 in terms of chili plant growth and its biocontrol efficiency against Ralstonia solanacearum, experiments were conducted both in vitro and in vivo. A closure assembly was designed using a half-inverted plastic bottle to demonstrate plant–microbial interactions via volatile compounds. The most common volatile organic compounds were identified and reported; they promoted plant development and induced systemic resistance (ISR) against wilt pathogen R. solanacearum. The PDS1 and KA9 VOCs significantly increased defensive enzyme activity and overexpressed the antioxidant genes PAL, POD, SOD, WRKYa, PAL1, DEF-1, CAT-2, WRKY40, HSFC1, LOX2, and NPR1 related to plant defense. The overall gene expression was greater in root tissue as compared to leaf tissue in chili plant. Our findings shed light on the relationship among rhizobacteria, pathogen, and host plants, resulting in plant growth promotion, disease suppression, systemic resistance-inducing potential, and antioxidant response with related gene expression in the leaf and root tissue of chili.
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Affiliation(s)
- Abhijeet Shankar Kashyap
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.K.); (R.P.S.)
- Plant Pathology Laboratory, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (N.M.); (M.V.S.R.); (J.P.S.)
- Correspondence: (A.S.K.); (D.S.)
| | - Nazia Manzar
- Plant Pathology Laboratory, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (N.M.); (M.V.S.R.); (J.P.S.)
| | | | - Mahendra Vikram Singh Rajawat
- Plant Pathology Laboratory, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (N.M.); (M.V.S.R.); (J.P.S.)
| | - Man Mohan Deo
- Farm Machinery and Power, ICAR-Indian Institute of Pulses Research, Kanpur 208024, India;
| | - Jyoti Prakash Singh
- Plant Pathology Laboratory, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (N.M.); (M.V.S.R.); (J.P.S.)
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Amit Kumar Kesharwani
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.K.); (R.P.S.)
| | - Ravinder Pal Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.K.); (R.P.S.)
| | - S. C. Dubey
- Division of Plant Quarantine, ICAR-NBPGR, New Delhi 110012, India;
- Krishi Bhawan, Indian Council of Agricultural Research, New Delhi 110001, India
| | - Dinesh Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.K.); (R.P.S.)
- Correspondence: (A.S.K.); (D.S.)
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Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects. Microbiol Spectr 2022; 10:e0216921. [PMID: 35107331 PMCID: PMC8809340 DOI: 10.1128/spectrum.02169-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined Bacillus strains in the evolutionary tree. A comparative genomic analysis among Bacillus velezensis HNA3, Bacillus velezensis FZB42, Bacillus amyloliquefaciens DSM7, and Bacillus subtilis 168 showed that only HNA3 has one predicated secretory protein feruloyl esterase that catalyzes the hydrolysis of plant cell wall polysaccharides. The analysis of gene clusters revealed that whole biosynthetic gene clusters type Lanthipeptide was exclusively identified in HNA3 and might lead to the synthesis of new bioactive compounds. Twelve gene clusters were detected in HNA3 responsible for the synthesis of 14 secondary metabolites including Bacillaene, Fengycin, Bacillomycin D, Surfactin, Plipastatin, Mycosubtilin, Paenilarvins, Macrolactin, Difficidin, Amylocyclicin, Bacilysin, Iturin, Bacillibactin, Paenibactin, and others. HNA3 has 77 genes encoding for possible antifungal and antibacterial secreting carbohydrate active enzymes. It also contains genes involved in plant growth promotion, such as 11 putative indole acetic acid (IAA)-producing genes, spermidine and polyamine synthase genes, volatile compound producing genes, and multiple biofilm related genes. HNA3 also has 19 phosphatase genes involved in phosphorus solubilization. Our results provide insights into the genetic characteristics responsible for the bioactivities and potential application of HNA3 as plant growth-promoting strain in ecological agriculture. IMPORTANCE This study is the primary initiative to identify Bacillus velezensis HNA3 whole genome sequence and reveal its genomic properties as an effective biocontrol agent against plant pathogens and a plant growth stimulator. HNA3 genetic profile can be used as a reference for future studies that can be applied as a highly effective biofertilizer and biofungicide inoculum to improve agriculture productivity. HNA3 reclassified in the phylogenetic tree which may be helpful for highly effective strain engineering and taxonomy. The genetic comparison among HNA3 and closely similar species B. velezensis FZB42, B. amyloliquefaciens DSM7, and B. subtilis 168 demonstrates some distinctive genetic properties of HNA3 and provides a basis for the genetic diversity of the Bacillus genus, which allows developing more effective eco-friendly resources for agriculture and separation of Bacillus velezensis as distinct species in the phylogenetic tree.
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Bacterial Inoculant and Sucrose Amendments Improve the Growth of Rheum palmatum L. by Reprograming Its Metabolite Composition and Altering Its Soil Microbial Community. Int J Mol Sci 2022; 23:ijms23031694. [PMID: 35163617 PMCID: PMC8835959 DOI: 10.3390/ijms23031694] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/29/2023] Open
Abstract
Rheum palmatum L. is an important traditional Chinese medicinal herb now in demand worldwide. Recently, the theoretical framework suggested that sucrose triggers colonization of PGPM (plant growth-promoting microbes) in the rhizosphere, but their interactions on the plant remain largely unknown. Here, we applied three concentrations of both Bacillus amyloliquefaciens EZ99 inoculant (1.0 × 105, 1.0 × 106, and 1.0 × 107 colony-forming units (CFU)/mL, denoted as LB, MB, and HB, respectively) and sucrose (0.15, 1.5, and 15 g/L, denoted as LS, MS, and HS, respectively) to investigate their co-effects on R. palmatum in a field experiment. The results showed that LB + MS (1.0 × 105 CFU/mL Bacillus + 1.5 g/L sucrose) and LB + LS (1.0 × 105 CFU/mL Bacillus + 0.15 g/L sucrose) treatments significantly increased root fresh weight (p ≤ 0.05). Metabolite analysis revealed that the treatment LB + LS significantly increased the relative content of major active components in rhubarb, namely anthraquinones and phenolic compounds, by 1.5% and 2.3%. Although high sucrose addition increased the activities of certain soil enzymes, the LB + LS treatment significantly increased total potassium (TK), whereas it decreased available potassium (AK), which facilitated the potassium utilization in rhizosphere soil. Furthermore, rhizosphere microbiomes revealed that fungal diversity was augmented in LB + LS treatment, in which the common causative fungal pathogen Fusarium spp. showed an effective suppression. Additionally, the redundancy analysis and Spearman correlations revealed a positive relationship of Sphingomonas associated with change in potassium bioavailability. Altogether, our findings suggest that the combined application of a bacterial inoculant and sucrose can improve the growth and quality of R. palmatum, and stimulate uptake of plant nutrients that contribute to alter the microbial community for biocontrol potential. Hence, this work not only has broad application prospects across economical plants, but also emphasizes agroecological practices for sustainable agriculture.
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Genome analysis of Pseudomonas sp. 14A reveals metabolic capabilities to support epiphytic behavior. World J Microbiol Biotechnol 2022; 38:49. [DOI: 10.1007/s11274-022-03238-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
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Quintas-Nunes F, Rossi MJ, Nascimento FX. Genomic insights into the plant-associated lifestyle of Kosakonia radicincitans MUSA4, a diazotrophic plant-growth-promoting bacterium. Syst Appl Microbiol 2022; 45:126303. [DOI: 10.1016/j.syapm.2022.126303] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/06/2022] [Accepted: 01/18/2022] [Indexed: 11/27/2022]
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Bioactive Biomolecules from Plant Growth-Promoting Rhizobacteria (PGPR). Fungal Biol 2022. [DOI: 10.1007/978-3-031-04805-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Abdelmoaty S, Khandaker MM, Mahmud K, Majrashi A, Alenazi MM, Badaluddin NA. Influence of Trichoderma harzianum and Bacillus thuringiensis with reducing rates of NPK on growth, physiology, and fruit quality of Citrus aurantifolia. BRAZ J BIOL 2022; 82:e261032. [DOI: 10.1590/1519-6984.261032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/04/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract Continuous use of chemical fertilizers gradually shrinks the crop yield and quality, and these adverse effects can be reduced by adopting new sustainable practices such as the use of manure, biofertilizers, and nano fertilizers. Limited information is existed on the application of Trichoderma harzianum and Bacillus thuringiensis microbes to improve lemon seedlings growth, physiology, and fruit formation. Therefore, the current study is aimed to evaluate the effects of T. harzianum and B. thuringiensis microbes mixing with low levels of inorganic fertilizer (NPK) on the plant growth, development, and quality of limau nipis (key lemon) fruits. The lemon seedlings growing media were inoculated during transplanting with T. harzianum and B. thuringiensis at various NPK fertilizers under polybagged conditions. The seedlings were grown around eighteen (18) months after inoculation with biofertilizers followed by Randomized Complete Block Design (RCBD) with five (5) replications. The results showed that T. harzianum with 50 g of NPK treatment (T2) increased the seedling's height, branch number, leaf height, ground area, and absolute growth rate (AGR) plant height by 50.12%, 107.84%, 17.91%, 17.91%, 116.93%, and 56.02%, respectively, over the control treatment. The number of leaves (60.82%), leaf area (42.75%), stem diameter (27.34%), specific leaf area (SLA) (39.07%), leaf area index (LAI) (54.40%), and absolute growth rate for leaf number (73.86%), leaf area (306.85%) and stem diameter (46.8%) of lemon seedlings increased significantly with B. thuringiensis plus 50 g NPK treatment (T3). The applications of B. thuringiensis with 25 g NPK fertilizer treatment (T5) increased leaf fresh weight (LFW), leaf dry weight (LDW), leaf moisture content (LMC), specific leaf weight (SLW), leaf relative growth rate (RGR), and chlorophyll content by 96.45%, 56.78%, 13.60%, 24.76%, 45.45%, and 16.22%, respectively, over the control group. In addition, T5 treatment increased the fruits number, individual fruit weight, fruit diameter, fruit dimension, leaf total soluble solids (TSS), and fruit TSS content of lemon tress by 81.81%, 55.52%, 43.54%, 25.69%, 89.47%, and 70.78% compared to the control treatment. Furthermore, soil inoculation of B. thuringiensis significantly increased the pulp to peel ratio and juice content of lemon fruits. From this study, it can be concluded that soil inoculation of both T. harzianum and B. thuringiensis with 25-50% NPK during transplanting improved plant growth, physiology, and fruit quality of limau nipis trees.
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Affiliation(s)
| | | | - K. Mahmud
- Universiti Putra Malaysia, Malaysia; Universiti Putra Malaysia, Malaysia
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Kim J, Pham H, Baek Y, Jo I, Kim YH, Ha NC. Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering. Acta Crystallogr D Struct Biol 2022; 78:104-112. [PMID: 34981766 DOI: 10.1107/s2059798321011724] [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: 07/22/2021] [Accepted: 11/04/2021] [Indexed: 11/11/2022] Open
Abstract
The YxaL protein was isolated from the soil bacterium Bacillus velezensis and has been shown to promote the root growth of symbiotic plants. YxaL has further been suggested to act as an exogenous signaling protein to induce the growth and branching of plant roots. Amino acid sequence analysis predicted YxaL to exhibit an eight-bladed β-propeller fold stabilized by six tryptophan-docking motifs and two modified motifs. Protein engineering to improve its structural stability is needed to increase the utility of YxaL as a plant growth-promoting factor. Here, the crystal structure of YxaL from B. velezensis was determined at 1.8 Å resolution to explore its structural features for structure-based protein engineering. The structure showed the typical eight-bladed β-propeller fold with structural variations in the third and fourth blades, which may decrease the stability of the β-propeller fold. Engineered proteins targeting the modified motifs were subsequently created. Crystal structures of the engineered YxaL proteins showed that the typical tryptophan-docking interaction was restored in the third and fourth blades, with increased structural stability, resulting in improved root growth-promoting activity in Arabidopsis seeds. The work is an example of structure-based protein engineering to improve the structural stability of β-propellor fold proteins.
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Affiliation(s)
- Jiheon Kim
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Ha Pham
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu 42472, Republic of Korea
| | - Yeongjin Baek
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong Hak Kim
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu 42472, Republic of Korea
| | - Nam Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
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Gushgari-Doyle S, Schicklberger M, Li YV, Walker R, Chakraborty R. Plant Growth Promotion Diversity in Switchgrass-Colonizing, Diazotrophic Endophytes. Front Microbiol 2021; 12:730440. [PMID: 34867848 PMCID: PMC8633415 DOI: 10.3389/fmicb.2021.730440] [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: 06/24/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022] Open
Abstract
Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass (Panicum virgatum), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.
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Affiliation(s)
- Sara Gushgari-Doyle
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcus Schicklberger
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yifan V Li
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert Walker
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Jiang L, Lee MH, Kim CY, Kim SW, Kim PI, Min SR, Lee J. Plant Growth Promotion by Two Volatile Organic Compounds Emitted From the Fungus Cladosporium halotolerans NGPF1. FRONTIERS IN PLANT SCIENCE 2021; 12:794349. [PMID: 34925431 PMCID: PMC8678569 DOI: 10.3389/fpls.2021.794349] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Microbial volatiles have beneficial roles in the agricultural ecological system, enhancing plant growth and inducing systemic resistance against plant pathogens without being hazardous to the environment. The interactions of plant and fungal volatiles have been extensively studied, but there is limited research specifically elucidating the effects of distinct volatile organic compounds (VOCs) on plant growth promotion. The current study was conducted to investigate the impact of VOCs from Cladosporium halotolerans NGPF1 on plant growth, and to elucidate the mechanisms for the plant growth-promoting (PGP) activity of these VOCs. The VOCs from C. halotolerans NGPF1 significantly promoted plant growth compared with the control, and this PGP activity of the VOCs was culture medium-dependent. Headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) identified two VOC structures with profiles that differed depending on the culture medium. The two compounds that were only produced in potato dextrose (PD) medium were identified as 2-methyl-butanal and 3-methyl-butanal, and both modulated plant growth promotion and root system development. The PGP effects of the identified synthetic compounds were analyzed individually and in blends using N. benthamiana plants. A blend of the two VOCs enhanced growth promotion and root system development compared with the individual compounds. Furthermore, real-time PCR revealed markedly increased expression of genes involved in auxin, expansin, and gibberellin biosynthesis and metabolism in plant leaves exposed to the two volatile blends, while cytokinin and ethylene expression levels were decreased or similar in comparison with the control. These findings demonstrate that naturally occurring fungal VOCs can induce plant growth promotion and provide new insights into the mechanism of PGP activity. The application of stimulatory volatiles for growth enhancement could be used in the agricultural industry to increase crop yield.
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Affiliation(s)
- Lingmin Jiang
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
| | - Myoung Hui Lee
- Wheat Research team, National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
| | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
| | - Pyoung Il Kim
- Center for Industrialization of Agricultural and Livestock Microorganisms (CIALM), Jeongeup, South Korea
| | - Sung Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jiyoung Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
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50
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Santos AP, Muratore LN, Solé-Gil A, Farías ME, Ferrando A, Blázquez MA, Belfiore C. Extremophilic bacteria restrict the growth of Macrophomina phaseolina by combined secretion of polyamines and lytic enzymes. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00674. [PMID: 34603977 PMCID: PMC8473456 DOI: 10.1016/j.btre.2021.e00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Extremophilic microorganisms were screened as biocontrol agents against two strains of Macrophomina phaseolina (Mp02 and 06). Stenotrophomonas sp. AG3 and Exiguobacterium sp. S58 exhibited a potential in vitro antifungal effect on Mp02 growth, corresponding to 52.2% and 40.7% inhibition, respectively. This effect was confirmed by scanning electron microscopy, where images revealed marked morphological alterations in fungus hyphae. The bacteria were found to secrete lytic enzymes and polyamines. Exiguobacterium sp. S56a was the only strain able to reduce the growth of the two strains of M. phaseolina through their supernatant. Antifungal supernatant activity was correlated with the ability of bacteria to synthesize and excrete putrescine, and the exogenous application of this polyamine to the medium phenocopied the bacterial antifungal effects. We propose that the combined secretion of putrescine, spermidine, and lytic enzymes by extremophilic microorganism predispose these microorganisms to reduce the disease severity occasioned by M. phaseolina in soybean seedlings.
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Affiliation(s)
- Ana P. Santos
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán, Argentina
| | - Luciana Nieva Muratore
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán, Argentina
| | - Anna Solé-Gil
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (CSIC-UPV), Avenida de los naranjos s/n, 46022 Valencia, Spain
| | - María E. Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán, Argentina
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (CSIC-UPV), Avenida de los naranjos s/n, 46022 Valencia, Spain
| | - Miguel A. Blázquez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (CSIC-UPV), Avenida de los naranjos s/n, 46022 Valencia, Spain
| | - Carolina Belfiore
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán, Argentina
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