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Sharma D, Chetri PB, Ranga V, Sen S, Sarmah BK, Barooah M. Genomic analysis of acid tolerance genes and deciphering the function of ydaG gene in mitigating acid tolerance in Priestia megaterium. Front Microbiol 2024; 15:1414777. [PMID: 38966390 PMCID: PMC11222612 DOI: 10.3389/fmicb.2024.1414777] [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: 04/09/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
Adverse environmental conditions, such as acid stress, induce bacteria to employ several strategies to overcome these stressors. These strategies include forming biofilms and activating specific molecular pathways, such as the general stress response (GSR). The genome of Priestia megaterium strain G18 was sequenced using the Illumina NextSeq 500 system, resulting in a de novo assembly of 80 scaffolds. The scaffolded genome comprises 5,367,956 bp with a GC content of 37.89%, and was compared to related strains using the MiGA web server, revealing high similarity to P. megaterium NBRC 15308 and P. aryabhattai B8W22 with ANI scores of 95.4%. Phylogenetic and ribosomal multilocus sequence typing (rMLST) analyses, based on the 16S rRNA and ribosomal protein-encoding alleles, confirmed close relationships within the P. megaterium species. Functional annotation identified 5,484 protein-coding genes, with 72.31% classified into 22 COG categories, highlighting roles in amino acid transport, transcription, carbohydrate metabolism, and ribosomal structure. An in-depth genome analysis of P. megaterium G18 revealed several key genes associated with acid tolerance. Targeted inactivation of the ydaG gene from SigB regulon, a general stress response gene, significantly reduced growth under acidic conditions compared to the wild type. qRT-PCR analysis showed increased ydaG expression in acidic conditions, further supporting its role in acid stress response. Microscopic analysis revealed no morphological differences between wild-type and mutant cells, suggesting that ydaG is not involved in maintaining cellular morphology but in facilitating acid tolerance through stress protein production. This research contributes to understanding the molecular mechanisms underlying acid tolerance in soil bacteria, P. megaterium, shedding light on potential applications in agriculture and industry.
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Affiliation(s)
- Darshana Sharma
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Purna Bahadur Chetri
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Vipin Ranga
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Subhajit Sen
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Bidyut Kumar Sarmah
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Madhumita Barooah
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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Chowdhury N, Naorem RS, Hazarika DJ, Goswami G, Dasgupta A, Bora SS, Boro RC, Barooah M. An oxalate decarboxylase-like cupin domain containing protein is involved in imparting acid stress tolerance in Bacillus amyloliquefaciens MBNC. World J Microbiol Biotechnol 2024; 40:64. [PMID: 38189984 DOI: 10.1007/s11274-023-03870-3] [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: 04/27/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024]
Abstract
We report here the structural and functional properties of an oxalate decarboxylase (OxDC)-like cupin domain-containing protein of Bacillus amyloliquefaciens MBNC and its role in imparting tolerance to acid stress conditions. Quantitative real-time PCR (qPCR) analysis revealed 32-fold and 20-fold upregulation of the target gene [(OxDC')cupin] under acetic acid stress and hydrochloric acid stress, respectively, indicating its association with the acid stress response. Bacterial cells with targeted inactivation of the (OxDC')cupin gene using the pMUTIN4 vector system showed decreased growth and survival rate in acidic pH, with drastically reduced exopolysaccharide production. In Silico protein-protein interaction studies revealed seven genes (viz. glmS, nagA, nagB, tuaF, tuaF, gcvT, and ykgA) related to cell wall biosynthesis and biofilm production to interact with OxDC-like cupin domain containing protein. While all these seven genes were upregulated in B. amyloliquefaciens MBNC after 6 h of exposure to pH 4.5, the mutant cells containing the inactivated (OxDC')cupin gene displayed significantly lower expression (RQ: 0.001-0.02) (compared to the wild-type cells) in both neutral and acidic pH. Our results indicate that the OxDC-like cupin domain containing protein is necessary for cell wall biosynthesis and biofilm production in Bacillus amyloliquefaciens MBNC for survival in acid-stress conditions.
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Affiliation(s)
- Naimisha Chowdhury
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Romen Singh Naorem
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Dibya Jyoti Hazarika
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Gunajit Goswami
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Abhisek Dasgupta
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sudipta Sankar Bora
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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Guzmán-Moreno J, García-Ortega LF, Torres-Saucedo L, Rivas-Noriega P, Ramírez-Santoyo RM, Sánchez-Calderón L, Quiroz-Serrano IN, Vidales-Rodríguez LE. Bacillus megaterium HgT21: a Promising Metal Multiresistant Plant Growth-Promoting Bacteria for Soil Biorestoration. Microbiol Spectr 2022; 10:e0065622. [PMID: 35980185 PMCID: PMC9604106 DOI: 10.1128/spectrum.00656-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022] Open
Abstract
The environmental deterioration produced by heavy metals derived from anthropogenic activities has gradually increased. The worldwide dissemination of toxic metals in crop soils represents a threat for sustainability and biosafety in agriculture and requires strategies for the recovery of metal-polluted crop soils. The biorestoration of metal-polluted soils using technologies that combine plants and microorganisms has gained attention in recent decades due to the beneficial and synergistic effects produced by its biotic interactions. In this context, native and heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in the development of strategies for sustainable biorestoration of metal-contaminated soils. In this study, we present a genomic analysis and characterization of the rhizospheric bacterium Bacillus megaterium HgT21 isolated from metal-polluted soil from Zacatecas, Mexico. The results reveal that this autochthonous bacterium contains an important set of genes related to a variety of operons associated with mercury, arsenic, copper, cobalt, cadmium, zinc and aluminum resistance. Additionally, halotolerance-, beta-lactam resistance-, phosphate solubilization-, and plant growth-promotion-related genes were identified. The analysis of resistance to metal ions revealed resistance to mercury (HgII+), arsenate [AsO4]³-, cobalt (Co2+), zinc (Zn2+), and copper (Cu2+). Moreover, the ability of the HgT21 strain to produce indole acetic acid (a phytohormone) and promote the growth of Arabidopsis thaliana seedlings in vitro was also demonstrated. The genotype and phenotype of Bacillus megaterium HgT21 reveal its potential to be used as a model of both plant growth-promoting and metal multiresistant bacteria. IMPORTANCE Metal-polluted environments are natural sources of a wide variety of PGPB adapted to cope with toxic metal concentrations. In this work, the bacterial strain Bacillus megaterium HgT21 was isolated from metal-contaminated soil and is proposed as a model for the study of metal multiresistance in spore-forming Gram-positive bacteria due to the presence of a variety of metal resistance-associated genes similar to those encountered in the metal multiresistant Gram-negative Cupriavidus metallidurans CH34. The ability of B. megaterium HgT21 to promote the growth of plants also makes it suitable for the study of plant-bacteria interactions in metal-polluted environments, which is key for the development of techniques for the biorestoration of metal-contaminated soils used for agriculture.
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Affiliation(s)
- Jesús Guzmán-Moreno
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Luis Fernando García-Ortega
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - Lilia Torres-Saucedo
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Paulina Rivas-Noriega
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Rosa María Ramírez-Santoyo
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Lenin Sánchez-Calderón
- Laboratorio de Genómica Evolutiva, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Iliana Noemi Quiroz-Serrano
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Luz Elena Vidales-Rodríguez
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
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Effects of Feeding 5-Aminolevulinic Acid on Iron Status in Weaned Rats from the Female Rats during Gestation and Lactation. Animals (Basel) 2022; 12:ani12202869. [PMID: 36290255 PMCID: PMC9598332 DOI: 10.3390/ani12202869] [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: 09/23/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022] Open
Abstract
Using female Sprague−Dawley (SD) rats as a model, the current study aimed to investigate whether feeding 5-aminolevulinic acid (5-ALA) to female SD rats during gestation and lactation can affect the iron status of weaned rats and provide new ideas for the iron supplementation of piglets. A total of 27 pregnant SD rats were randomly assigned to three treatments in nine replicates, with one rat per litter. Dietary treatments were basal diet (CON), CON + 50 mg/kg 5-ALA (5-ALA50), and CON + 100 mg/kg 5-ALA (5-ALA100). After parturition, ten pups in each litter (a total of 270) were selected for continued feeding by their corresponding mother, and the pregnant rats were fed diets containing 5-ALA (0, 50 and 100 mg/kg diet) until the newborn pups were weaned at 21 days. The results showed that the number of red blood cells (RBCs) in weaned rats in the 5-ALA100 group was significantly higher (p < 0.05) than that in the CON or 5-ALA50 group. The diet with 5-ALA significantly increased (p < 0.05) the hemoglobin (HGB) concentration, hematocrit (HCT) level, serum iron (SI) content, and transferrin saturation (TSAT) level in the blood of weaned rats, as well as the concentration of Hepcidin in the liver and serum of weaned rats and the expression of Hepcidin mRNA in the liver of weaned rats, with the 5-ALA100 group having the highest (p < 0.05) HGB concentration in the weaned rats, and the 5-ALA50 group having the highest (p < 0.05) Hepcidin concentration in serum and in the expression of Hepcidin mRNA in the liver of weaned rats. The other indicators between the 5-ALA groups had no effects. However, the level of total iron binding capacity (TIBC) was significantly decreased (p < 0.05) in the 5-ALA50 group. Moreover, the iron content in the liver of weaned rats fed with 5-ALA showed an upward trend (p = 0.085). In addition, feeding a 5-ALA-supplemented diet could also significantly reduce (p < 0.05) the expression of TfR1 mRNA in the liver of weaning rats (p < 0.05), and the expression of Tfr1 was not affected between 5-ALA groups. In conclusion, dietary supplementation with 5-ALA could improve the blood parameters, increase the concentration of Hepcidin in the liver and serum, and affect the expression of iron-related genes in the liver of weaned rats. Moreover, it is appropriate to add 50 mg/kg 5-ALA to the diet under this condition.
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Romadanova NV, Tolegen AB, Kushnarenko SV, Zholdybayeva EV, Bettoni JC. Effect of Plant Preservative Mixture TM on Endophytic Bacteria Eradication from In Vitro-Grown Apple Shoots. PLANTS (BASEL, SWITZERLAND) 2022; 11:2624. [PMID: 36235489 PMCID: PMC9572907 DOI: 10.3390/plants11192624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Endophytic contaminants are a common problem for the in vitro propagation of woody plants and have significant economic repercussions for the conservation of plant genetic resources and commercial micropropagation. In this study, first, the microbial contamination that appeared around the base of in vitro-grown apple shoots was identified as Bacillus megaterium. Then, plant preservative mixture (PPMTM) was used as a bactericidal agent in plant tissue culture. Its efficacy for eradicating endophytic B. megaterium in in vitro cultures of apple was tested. In vitro-contaminated shoots were grown in tissue culture medium supplemented with 0.2% v/v PPMTM for 12 weeks and then transferred to medium without any PPMTM and cultured for 24 weeks. This study showed that PPMTM is an effective agent for controlling the growth of B. megaterium. Our results highlight the species-specific response of apple shoots to PPMTM. PPMTM was effective in controlling endogenous microbial contaminations from apple varieties 'Golden Delicious', 'Landsberger Renette', 'Suislepper', and 'Aport krovavo-krasnyi'; meanwhile, in 'KG 7' and 'Gold Rush', all the plants grown in the absence of PPMTM were still bacterially contaminated, even though they were pre-treated for 12 weeks in PPMTM-supplemented medium. These results therefore suggest the essentiality of further testing of extended incubation of PPMTM in these cultivars that had outbreaks of bacterial contamination.
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Affiliation(s)
- Natalya V. Romadanova
- Institute of Plant Biology and Biotechnology, 45 Timiryazev St., Almaty 050040, Kazakhstan
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Al-Farabi Av. 71, Almaty 050040, Kazakhstan
| | - Arman B. Tolegen
- Institute of Plant Biology and Biotechnology, 45 Timiryazev St., Almaty 050040, Kazakhstan
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Al-Farabi Av. 71, Almaty 050040, Kazakhstan
| | | | - Elena V. Zholdybayeva
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan
| | - Jean Carlos Bettoni
- The New Zealand Institute for Plant and Food Research Limited, Batchelar Road, Palmerston North 4410, New Zealand
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Miljaković D, Marinković J, Tamindžić G, Đorđević V, Tintor B, Milošević D, Ignjatov M, Nikolić Z. Bio-Priming of Soybean with Bradyrhizobium japonicum and Bacillus megaterium: Strategy to Improve Seed Germination and the Initial Seedling Growth. PLANTS (BASEL, SWITZERLAND) 2022; 11:1927. [PMID: 35893631 PMCID: PMC9332681 DOI: 10.3390/plants11151927] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Bio-priming is a new technique of seed treatment that improves seed germination, vigor, crop growth and yield. The objective of this study was to evaluate the effectiveness of Bradyrhizobium japonicum (commercial strains) and Bacillus megaterium (newly isolated strains) as a single inoculant and co-inoculant during seed bio-priming to improve seed germination and initial seedling growth of two soybean cultivars. The treated seeds were subjected to germination test (GT), cold test (CT) and accelerated aging test (AAT). B. megaterium significantly improved all parameters in GT and CT; final germination, shoot length, root length, root dry weight, and seedling vigor index in AAT, as compared to control. In addition, co-inoculation significantly increased all parameters except shoot dry weight in GT; all parameters in CT; germination energy, shoot length, root length, and seedling vigor index in AAT, in comparison to the control. Moreover, Br. japonicum significantly improved the germination energy, shoot length, shoot dry weight, root dry weight, and seedling vigor index in GT; all parameters in CT; shoot length, root length, and seedling vigor index in AAT, compared with non-primed seeds. Thus, B. megaterium strains could be used in soybean bio-priming as a potential single inoculant and co-inoculant, following proper field evaluation.
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Affiliation(s)
- Dragana Miljaković
- Department of Microbiological Preparations, Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (B.T.)
| | - Jelena Marinković
- Department of Microbiological Preparations, Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (B.T.)
| | - Gordana Tamindžić
- Laboratory for Seed Testing, Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (G.T.); (D.M.); (Z.N.)
| | - Vuk Đorđević
- Department of Legumes, Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia;
| | - Branislava Tintor
- Department of Microbiological Preparations, Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (B.T.)
| | - Dragana Milošević
- Laboratory for Seed Testing, Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (G.T.); (D.M.); (Z.N.)
| | - Maja Ignjatov
- Department of Vegetable and Alternative Crops, Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia;
| | - Zorica Nikolić
- Laboratory for Seed Testing, Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (G.T.); (D.M.); (Z.N.)
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Goswami G, Hazarika DJ, Chowdhury N, Bora SS, Sarmah U, Naorem RS, Boro RC, Barooah M. Proline confers acid stress tolerance to Bacillus megaterium G18. Sci Rep 2022; 12:8875. [PMID: 35614097 PMCID: PMC9133035 DOI: 10.1038/s41598-022-12709-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
Proline plays a multifunctional role in several organisms including bacteria in conferring protection under stress conditions. In this paper we report the role of proline in conferring acid tolerance to Bacillus megaterium G18. An acid susceptible mutant of B. megaterium G18 which required proline for its growth under acid stress condition was generated through Tn5 mutagenesis. Further, targeted inactivation of proC involved in osmo-adaptive proline synthesis in B. megaterium G18 resulted in the loss of ability of the bacterium to grow at low pH (pH 4.5). Exogenous supply of proline (1 mM) to the growth medium restored the ability of the mutant cells to grow at pH 4.5 which was not the same in case of other osmoprotectants tested. Proline was produced and secreted to extracellular medium by B. megaterium G18 when growing in low pH condition as evidenced by the use of Escherichia coli proline auxotrophs and HPLC analysis. Further, pHT01 vector based expression of full length proC gene in the ∆proC mutant cells restored the survival capacity of the mutant cells in acidic pH, suggesting that proline production is an important strategy employed by B. megaterium G18 to survive under acid stress induced osmotic stress.
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Affiliation(s)
- Gunajit Goswami
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Dibya Jyoti Hazarika
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Naimisha Chowdhury
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sudipta Sankar Bora
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Unmona Sarmah
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Romen Singh Naorem
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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Li D, Huang M, Dong S, Jin Y, Zhou R, Wu C. Comprehensive Transcriptomic Analysis of Heterotrophic Nitrifying Bacterium Klebsiella sp. TN-10 in Response to Nitrogen Stress. Microorganisms 2022; 10:microorganisms10020353. [PMID: 35208807 PMCID: PMC8876665 DOI: 10.3390/microorganisms10020353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 02/01/2023] Open
Abstract
Klebsiella sp. TN-10, a heterotrophic nitrifying bacterium, showed excellent nitrification ability under nitrogen stress. The strain was cultured under different nitrogen stress levels, including ammonium sulfate 0.5, 2.5, and 5 g/L, and samples were titled group-L, group-M, and group-H, respectively. In these three groups, the removed total nitrogen was 70.28, 118.33, and 157.18 mg/L after 12 h of cultivation, respectively. An RNA-Seq transcriptome analysis was used to describe key regulatory networks in response to nitrogen stress. The GO functional enrichment and KEGG enrichment analyses showed that differentially expressed genes (DEGs) participated in more pathways under higher nitrogen stress (group-H). Carbohydrate metabolism and amino acid metabolism were the most abundant subcategories, which meant these pathways were significantly influenced by nitrogen stress and could be related to nitrogen removal. In the nitrogen cycle, up-regulated gene2311 (narK, encodes major facilitator superfamily transporter) may accelerate the entry of nitrogen into the cells and subsequently contribute to the nitrogen utilization. In addition, the up-regulation of gene2312 (narG), gene2313 (narH), and gene2315 (narH) may accelerate denitrification pathways and facilitate nitrogen removal. The results presented in this study may play a pivotal role in understanding the regulation networks of the nitrifying bacterium TN-10 under nitrogen stress.
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Affiliation(s)
- Dan Li
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (D.L.); (Y.J.); (R.Z.)
| | - Mingquan Huang
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, China
- Correspondence: (M.H.); (C.W.)
| | - Shirong Dong
- Sichuan Fansaoguang Food Group Co., Ltd, Chengdu 611732, China;
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (D.L.); (Y.J.); (R.Z.)
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (D.L.); (Y.J.); (R.Z.)
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (D.L.); (Y.J.); (R.Z.)
- Correspondence: (M.H.); (C.W.)
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9
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Chowdhury N, Hazarika DJ, Goswami G, Sarmah U, Borah S, Boro RC, Barooah M. Acid tolerant bacterium Bacillus amyloliquefaciens MBNC retains biocontrol efficiency against fungal phytopathogens in low pH. Arch Microbiol 2022; 204:124. [PMID: 34997335 DOI: 10.1007/s00203-021-02741-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/28/2022]
Abstract
Soil pH conditions have important consequences for microbial community structure, their dynamics, ecosystem processes, and interactions with plants. Low soil pH affects the growth and functional activity of bacterial biocontrol agents which may experience a paradigm shift in their ability to act antagonistically against fungal phytopathogens. In this study, the antifungal activity of an acid-tolerant soil bacterium Bacillus amyloliquefaciens MBNC was evaluated under low pH and compared to its activity in neutral pH conditions. Bacterial supernatant from 3-day-old culture (approximately 11.2 × 108 cells/mL) grown in low pH conditions was found more effective against fungal pathogens. B. amyloliquefaciens MBNC harboured genes involved in the synthesis of secondary metabolites of which surfactin homologues, with varying chain length (C11-C15), were identified through High-Resolution Mass Spectroscopy. The pH of the medium influenced the production of these metabolites. Surfactin C15 was exclusive to the extract of pH 4.5; production of iturinA and surfactin C11 was detected only in pH 7.0, while surfactin C12, C13 and C14 were detected in extracts of both the pH conditions. The secretion of phytohormones viz. indole acetic acid and gibberellic acid by B. amyloliquefaciens MBNC was detected in higher amounts in neutral condition compared to acidic condition. Although, secretion of metabolites and phytohormones in B. amyloliquefaciens MBNC was influenced by the pH condition of the medium, the isolate retained its antagonistic efficiency against several fungal phyto-pathogens under acidic condition.
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Affiliation(s)
- Naimisha Chowdhury
- DBT-North East Centre for Agricultural Biotechnology, Jorhat, Assam, 785013, India.,Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Dibya Jyoti Hazarika
- DBT-North East Centre for Agricultural Biotechnology, Jorhat, Assam, 785013, India.,Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Gunajit Goswami
- DBT-North East Centre for Agricultural Biotechnology, Jorhat, Assam, 785013, India
| | - Unmona Sarmah
- DBT-North East Centre for Agricultural Biotechnology, Jorhat, Assam, 785013, India
| | - Shrutirupa Borah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Madhumita Barooah
- DBT-North East Centre for Agricultural Biotechnology, Jorhat, Assam, 785013, India. .,Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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Kang J, Zhou X, Zhang W, Pei F, Ge J. Transcriptomic analysis of bacteriocin synthesis and stress response in Lactobacillus paracasei HD1.7 under acetic acid stress. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112897] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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A pH-Dependent Gene Expression Enables Bacillus amyloliquefaciens MBNC to Adapt to Acid Stress. Curr Microbiol 2021; 78:3104-3114. [PMID: 34173842 DOI: 10.1007/s00284-021-02573-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
Acid tolerance response (ATR), a process by which bacteria optimize their growth conditions for cellular functions, is a well-characterized bacterial stress response. A bacterial isolate identified, as Bacillus amyloliquefaciens MBNC, was isolated from acidic soil and studied for its acid tolerance response under several range of acidic stress conditions imposed through inorganic acid, organic acid, acetate buffer, and soil extract. The ability of the B. amyloliquefaciens MBNC to tolerate extreme acidic conditions (pH 4.5) increased when exposed to moderate-acidic pH (pH 5.5). Along with ATR, the bacterial cell density was also critical to its ability to tolerate low pH as the cells of late log phase were more tolerant to low pH stress compared to the early log phase cells. A comparative expression study of 28 genes of B. amyloliquefaciens MBNC was assessed in cells grown in neutral (pH 7.0) and acidic condition (pH 4.5) through qRT-PCR. Among the 28 genes analyzed, 24 genes showed increased expression whereas the expression of 4 genes was downregulated under acid stress indicating to the involvement of the genes in acid stress response.
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12
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Zhang Z, Liang ZC, Liang XY, Zhang QH, Wang YJ, Zhang JH, De Liu S. Physarum polycephalum macroplasmodium exhibits countermeasures against TiO 2 nanoparticle toxicity: A physiological, biochemical, transcriptional, and metabolic perspective. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 279:116936. [PMID: 33773179 DOI: 10.1016/j.envpol.2021.116936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/02/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Concerns about the environmental and human health implications of TiO2 nanoparticles (nTiO2) are growing with their increased use in consumer and industrial products. Investigations of the underlying molecular mechanisms of nTiO2 tolerance in organisms will assist in countering nTiO2 toxicity. In this study, the countermeasures exhibited by the slime mold Physarum polycephalum macroplasmodium against nTiO2 toxicity were investigated from a physiological, transcriptional, and metabolic perspective. The results suggested that the countermeasures against nTiO2 exposure include gene-associated metabolic rearrangements in cellular pathways involved in amino acid, carbohydrate, and nucleic acid metabolism. Gene-associated nonmetabolic rearrangements involve processes such as DNA repair, DNA replication, and the cell cycle, and occur mainly when macroplasmodia are exposed to inhibitory doses of nTiO2. Interestingly, the growth of macroplasmodia and mammal cells was significantly restored by supplementation with a combination of responsive metabolites identified by metabolome analysis. Taken together, we report a novel model organism for the study of nTiO2 tolerance and provide insights into countermeasures taken by macroplasmodia in response to nTiO2 toxicity. Furthermore, we also present an approach to mitigate the effects of nTiO2 toxicity in cells by metabolic intervention.
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Affiliation(s)
- Zhi Zhang
- School of Food Science/School of Public Health/the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China; Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhi Cheng Liang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xiu Yi Liang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Qing Hai Zhang
- School of Food Science/School of Public Health/the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Ya Jie Wang
- School of Food Science/School of Public Health/the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Jian Hua Zhang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Shi De Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
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Vu DH, Wainaina S, Taherzadeh MJ, Åkesson D, Ferreira JA. Production of polyhydroxyalkanoates (PHAs) by Bacillus megaterium using food waste acidogenic fermentation-derived volatile fatty acids. Bioengineered 2021; 12:2480-2498. [PMID: 34115556 PMCID: PMC8806590 DOI: 10.1080/21655979.2021.1935524] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
High production costs still hamper fast expansion of commercial production of polyhydroxyalkanoates (PHAs). This problem is greatly related to the cultivation medium which accounts for up to 50% of the whole process costs. The aim of this research work was to evaluate the potential of using volatile fatty acids (VFAs), derived from acidogenic fermentation of food waste, as inexpensive carbon sources for the production of PHAs through bacterial cultivation. Bacillus megaterium could assimilate glucose, acetic acid, butyric acid, and caproic acid as single carbon sources in synthetic medium with maximum PHAs production yields of 9-11%, on a cell dry weight basis. Single carbon sources were then replaced by a mixture of synthetic VFAs and by a VFAs-rich stream from the acidogenic fermentation of food waste. After 72 h of cultivation, the VFAs were almost fully consumed by the bacterium in both media and PHAs production yields of 9-10%, on cell dry weight basis, were obtained. The usage of VFAs mixture was found to be beneficial for the bacterial growth that tackled the inhibition of propionic acid, iso-butyric acid, and valeric acid when these volatile fatty acids were used as single carbon sources. The extracted PHAs were revealed to be polyhydroxybutyrate (PHB) by characterization methods of Fourier-transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC). The obtained results proved the possibility of using VFAs from acidogenic fermentation of food waste as a cheap substrate to reduce the cost of PHAs production.
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Affiliation(s)
- Danh H Vu
- Swedish Centre for Resource Recovery, University of Borås, Sweden
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Sweden
| | | | - Dan Åkesson
- Swedish Centre for Resource Recovery, University of Borås, Sweden
| | - Jorge A Ferreira
- Swedish Centre for Resource Recovery, University of Borås, Sweden
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14
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The impact of cell structure, metabolism and group behavior for the survival of bacteria under stress conditions. Arch Microbiol 2020; 203:431-441. [PMID: 32975620 DOI: 10.1007/s00203-020-02050-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/28/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
Microbes from diverse types of habitats are continuously exposed to external challenges, which may include acidic, alkaline, and toxic metabolites stress as well as nutrient deficiencies. To promote their own survival, bacteria have to rapidly adapt to external perturbations by inducing particular stress responses that typically involve genetic and/or cellular changes. In addition, pathogenic bacteria need to sense and withstand these environmental stresses within a host to establish and maintain infection. These responses can be, in principle, induced by changes in bacterial cell structure, metabolism and group behavior. Bacterial nucleic acids may serve as the core part of the stress response, and the cell envelope and ribosomes protect genetic structures from damage. Cellular metabolism and group behavior, such as quorum sensing system, can play a more important role in resisting stress than we have now found. Since bacteria survival can be only appreciated if we better understand the mechanisms behind bacterial stress response, here we review how morphological and physiological features may lead to bacterial resistance upon exposure to particular stress-inducing factors.
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15
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Draft Genome Sequences of Pseudomonas koreensis Strain UASWS1668, Bacillus megaterium Strain UASWS1667, and Paenibacillus sp. Strain UASWS1643, Considered Potential Plant Growth-Promoting Rhizobacteria. Microbiol Resour Announc 2020; 9:9/33/e00768-20. [PMID: 32817155 PMCID: PMC7427193 DOI: 10.1128/mra.00768-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) include species in the genera Bacillus, Paenibacillus, and Pseudomonas. We report here the draft genome sequences of the strains Pseudomonas koreensis UASWS1668 and Bacillus megaterium UASWS1667, isolated from a horse chestnut tree, and Paenibacillus sp. strain UASWS1643, isolated from a tomato stem. Auxin production and phosphate solubilization were biochemically confirmed. Plant growth-promoting rhizobacteria (PGPR) include species in the genera Bacillus, Paenibacillus, and Pseudomonas. We report here the draft genome sequences of the strains Pseudomonas koreensis UASWS1668 and Bacillus megaterium UASWS1667, isolated from a horse chestnut tree, and Paenibacillus sp. strain UASWS1643, isolated from a tomato stem. Auxin production and phosphate solubilization were biochemically confirmed.
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Gaucher F, Kponouglo K, Rabah H, Bonnassie S, Ossemond J, Pottier S, Jardin J, Briard-Bion V, Marchand P, Blanc P, Jeantet R, Jan G. Propionibacterium freudenreichii CIRM-BIA 129 Osmoadaptation Coupled to Acid-Adaptation Increases Its Viability During Freeze-Drying. Front Microbiol 2019; 10:2324. [PMID: 31681198 PMCID: PMC6797830 DOI: 10.3389/fmicb.2019.02324] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022] Open
Abstract
Propionibacterium freudenreichii is a beneficial bacterium with documented effects on the gut microbiota and on inflammation. Its presence within the animal and human intestinal microbiota was correlated with immunomodulatory effects, mediated by both propionibacterial surface components and by secreted metabolites. It is widely implemented, both in the manufacture of fermented dairy products such as Swiss-type cheeses, and in the production of probiotic food complements, under the form of freeze-dried powders. The bottleneck of this drying process consists in the limited survival of bacteria during drying and storage. Protective pre-treatments have been applied to other bacteria and may, in a strain-dependent manner, confer enhanced resistance. However, very little information was yet published on P. freudenreichii adaptation to freeze-drying. In this report, an immunomodulatory strain of this probiotic bacterium was cultured under hyperosmotic constraint in order to trigger osmoadaptation. This adaptation was then combined with acid or thermal pre-treatment. Such combination led to accumulation of key stress proteins, of intracellular compatible solute glycine betaine, to modulation of the propionibacterial membrane composition, and to enhanced survival upon freeze-drying. This work opens new perspectives for efficient production of live and active probiotic propionibacteria.
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Affiliation(s)
- Floriane Gaucher
- UMR STLO, Agrocampus Ouest, INRA, Rennes, France
- Bioprox, Levallois-Perret, France
| | | | - Houem Rabah
- UMR STLO, Agrocampus Ouest, INRA, Rennes, France
- Bba, Pôle Agronomique Ouest, Régions Bretagne et Pays de la Loire, Rennes, France
| | - Sylvie Bonnassie
- UMR STLO, Agrocampus Ouest, INRA, Rennes, France
- Université de Rennes I, Rennes, France
| | | | - Sandrine Pottier
- CNRS, ISCR – UMR 6226, PRISM, BIOSIT – UMS 3480 Université de Rennes I, Rennes, France
| | | | | | | | | | | | - Gwénaël Jan
- UMR STLO, Agrocampus Ouest, INRA, Rennes, France
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