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Grabeck J, Mayer J, Miltz A, Casoria M, Quagliata M, Meinberger D, Klatt AR, Wielert I, Maier B, Papini AM, Neundorf I. Triazole-Bridged Peptides with Enhanced Antimicrobial Activity and Potency against Pathogenic Bacteria. ACS Infect Dis 2024. [PMID: 38885643 DOI: 10.1021/acsinfecdis.4c00078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
There are still no linear antimicrobial peptides (AMPs) available as a treatment option against bacterial infections. This is caused by several drawbacks that come with AMPs such as limited proteolytic stability and low selectivity against human cells. In this work, we screened a small library of rationally designed new peptides based on the cell-penetrating peptide sC18* toward their antimicrobial activity. We identified several effective novel AMPs and chose one out of this group to further increase its potency. Therefore, we introduced a triazole bridge at different positions to provide a preformed helical structure, assuming that this modification would improve (i) proteolytic stability and (ii) membrane activity. Indeed, placing the triazole bridge within the hydrophilic part of the linear analogue highly increased membrane activity as well as stability against enzymatic digestion. The new peptides, 8A and 8B, demonstrated high activity against several bacterial species tested including pathogenic N. gonorrhoeae and methicillin-resistant S. aureus. Since they exhibited significantly good tolerability against human fibroblast and blood cells, these novel peptides offer true alternatives for future clinical applications and are worth studying in more detail.
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Affiliation(s)
- Joshua Grabeck
- University of Cologne, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institute of Biochemistry, Zuelpicher Str. 47a, 50674 Cologne, Germany
| | - Jacob Mayer
- University of Cologne, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institute of Biochemistry, Zuelpicher Str. 47a, 50674 Cologne, Germany
| | - Axel Miltz
- University of Cologne, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institute of Biochemistry, Zuelpicher Str. 47a, 50674 Cologne, Germany
| | - Michele Casoria
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Denise Meinberger
- University of Cologne, Faculty of Medicine, Institute for Clinical Chemistry, Kerpener Str. 62, 50937 Cologne, Germany
| | - Andreas R Klatt
- University of Cologne, Faculty of Medicine, Institute for Clinical Chemistry, Kerpener Str. 62, 50937 Cologne, Germany
| | - Isabelle Wielert
- University of Cologne, Faculty of Mathematics and Natural Sciences, Department of Physics, Institute for Biological Physics, Zuelpicher Str. 47a, 50674 Cologne, Germany
| | - Berenike Maier
- University of Cologne, Faculty of Mathematics and Natural Sciences, Department of Physics, Institute for Biological Physics, Zuelpicher Str. 47a, 50674 Cologne, Germany
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Ines Neundorf
- University of Cologne, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institute of Biochemistry, Zuelpicher Str. 47a, 50674 Cologne, Germany
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Pan H, Wei L, Zhao H, Xiao Y, Li Z, Ding H. Perception of the Biocontrol Potential and Palmitic Acid Biosynthesis Pathway of Bacillus subtilis H2 through Merging Genome Mining with Chemical Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4834-4848. [PMID: 38401001 DOI: 10.1021/acs.jafc.3c06411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Bacillus has been widely studied for its potential to protect plants from pathogens. Here, we report the whole genome sequence of Bacillus subtilis H2, which was isolated from the tea garden soil of Guiyang Forest Park. Strain H2 showed a broad spectrum of antagonistic activities against many plant fungal pathogens and bacteria pathogens, including the rice blast fungus Magnaporthe oryzae, and showed a good field control effect against rice blast. The complete genome of B. subtilis H2 contained a 4,160,635-bp circular chromosome, with an average G + C content of 43.78%. Through the genome mining of strain H2, we identified 7 known antimicrobial compound biosynthetic gene clusters (BGCs) including sporulation killing factor, surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. Palmitic acid (PA), a secondary metabolite, was detected and identified in the H2 strain through genome mining analysis and gas chromatography-mass spectrometry (GC-MS). Additionally, we propose, for the first time, that the type II fatty acid synthesis (FAS) pathway in Bacillus is responsible for PA biosynthesis. This finding was confirmed by studying the antimicrobial activity of PA and conducting reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments. We also identified numerous genes associated with plant-bacteria interactions in the H2 genome, including more than 94 colonization-related genes, more than 34 antimicrobial genes, and more than 13 plant growth-promoting genes. These findings contribute to our understanding of the biocontrol mechanisms of B. subtilis H2 and have potential applications in crop disease control.
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Affiliation(s)
- Hang Pan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Longfeng Wei
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Hao Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Yang Xiao
- Institution of Supervision and Inspection Product Quality of Guizhou Province, Guiyang 550004, China
| | - Zhu Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Haixia Ding
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
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Guillén-Navarro K, López-Gutiérrez T, García-Fajardo V, Gómez-Cornelio S, Zarza E, De la Rosa-García S, Chan-Bacab M. Broad-Spectrum Antifungal, Biosurfactants and Bioemulsifier Activity of Bacillus subtilis subsp. spizizenii-A Potential Biocontrol and Bioremediation Agent in Agriculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:1374. [PMID: 36987062 PMCID: PMC10056679 DOI: 10.3390/plants12061374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
In this study, the antifungal, biosurfactant and bioemulsifying activity of the lipopeptides produced by the marine bacterium Bacillus subtilis subsp. spizizenii MC6B-22 is presented. The kinetics showed that at 84 h, the highest yield of lipopeptides (556 mg/mL) with antifungal, biosurfactant, bioemulsifying and hemolytic activity was detected, finding a relationship with the sporulation of the bacteria. Based on the hemolytic activity, bio-guided purification methods were used to obtain the lipopeptide. By TLC, HPLC and MALDI-TOF, the mycosubtilin was identified as the main lipopeptide, and it was further confirmed by NRPS gene clusters prediction based on the strain's genome sequence, in addition to other genes related to antimicrobial activity. The lipopeptide showed a broad-spectrum activity against ten phytopathogens of tropical crops at a minimum inhibitory concentration of 400 to 25 μg/mL and with a fungicidal mode of action. In addition, it exhibited that biosurfactant and bioemulsifying activities remain stable over a wide range of salinity and pH and it can emulsify different hydrophobic substrates. These results demonstrate the potential of the MC6B-22 strain as a biocontrol agent for agriculture and its application in bioremediation and other biotechnological fields.
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Affiliation(s)
- Karina Guillén-Navarro
- Grupo Académico de Biotecnología Ambiental, Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Tapachula, Carretera Antiguo Aeropuerto km 2.5, Tapachula 30700, Chiapas, Mexico; (K.G.-N.); (E.Z.)
| | - Tomás López-Gutiérrez
- Facultad de Ciencias Biologicas, Universidad Autónoma de Campeche, Av. Agustín Melgar s/n, Col. Buenavista, Campeche 24030, Campeche, Mexico
| | - Verónica García-Fajardo
- Grupo Académico de Biotecnología Ambiental, Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Tapachula, Carretera Antiguo Aeropuerto km 2.5, Tapachula 30700, Chiapas, Mexico; (K.G.-N.); (E.Z.)
| | - Sergio Gómez-Cornelio
- Ingeniería en Biotecnología, Universidad Politécnica del Centro, Carretera Federal Villahermosa-Teapa km 22.5, Villahermosa 86290, Tabasco, Mexico;
- Laboratorio de Nanotecnología-CICTAT, División Académica de Ingeniería y Arquitectura, Universidad Juárez Autónoma de Tabasco, Carr. Cunduacán-Jalpa de Méndez km 1, Cunduacán 86690, Tabasco, Mexico
| | - Eugenia Zarza
- Grupo Académico de Biotecnología Ambiental, Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Tapachula, Carretera Antiguo Aeropuerto km 2.5, Tapachula 30700, Chiapas, Mexico; (K.G.-N.); (E.Z.)
- Investigadora CONACyT—El Colegio de la Frontera Sur. Av. Insurgentes Sur 1582, Col. Crédito Constructor, Benito Juárez, Mexico City 03940, Mexico City, Mexico
| | - Susana De la Rosa-García
- Laboratorio de Microbiología Aplicada, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Cárdenas km 0.5, Villahermosa 86000, Tabasco, Mexico
| | - Manuel Chan-Bacab
- Departamento de Microbiología Ambiental y Biotecnología, Universidad Autónoma de Campeche, Av. Agustín Melgar s/n, Col. Buenavista, Campeche 24030, Campeche, Mexico
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Helfrich M, Entian KD, Stein T. Antibiotic profiling of wild-type bacilli led to the discovery of new lanthipeptide subtilin-producing Bacillus spizizenii strains whose 16S rDNA sequences differ from the B. spizizenii typing strain. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:839-850. [PMID: 35902452 PMCID: PMC9526687 DOI: 10.1007/s10123-022-00266-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/12/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022]
Abstract
Two dozen field-collected Bacillus and a dozen Bacillus spizizenii wild-type strains from strain collections were selected on the basis of their antagonistic properties against the Gram-positive strain Micrococcus luteus. Based on their genetic and antibiotic profiles, they were characterized (subtilin encoding spaS gene sequences, mass spectrometric, and quantitative-reversed phase liquid chromatographic analyses, as well as the presence of the lanthionine cyclase protein SpaC by western blotting), seven novel producers of the lanthipeptide subtilin. Phylogenetic analyses of the subtilin-producing wild-type strains based on their 16S rRNA sequences showed that all seven strains could be classified as B. spizizenii: The field-collected strains HS and N5, as well as strains DSM 618, 1087, 6395, 6405, and 8439 from the German Collection of Microorganisms and Cell Cultures. To the best of our knowledge, all B. spizizenii strains described so far are characterized by the fact that they can produce a lanthipeptide of the subtilin family. Both the lanthipeptide structures and the organization and sequences of the 16S rRNA-encoding genes suggest a subdivision of B. spizizenii into subspecies: The subtilin-producing B. spizizenii strains are distinctly different from the entianin-producing B. spizizenii typing strain TU-B-10 T (DSM 15029 T).
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Affiliation(s)
- Markus Helfrich
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
- Jennewein Biotechnologie GmbH, Maarweg 32, 53619, Rheinbreitbach, Germany
| | - Karl-Dieter Entian
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
| | - Torsten Stein
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany.
- Chemistry & Molecular Biotechnology, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany.
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Alajlani MM. Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role. Sci Rep 2022; 12:10521. [PMID: 35732659 PMCID: PMC9217942 DOI: 10.1038/s41598-022-13804-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
In a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.
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Affiliation(s)
- Muaaz Mutaz Alajlani
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, University of Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
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Alajlani MM. Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role. Sci Rep 2022; 12:10521. [DOI: https:/doi.org/10.1038/s41598-022-13804-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/27/2022] [Indexed: 08/08/2023] Open
Abstract
AbstractIn a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.
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Kamali M, Guo D, Naeimi S, Ahmadi J. Perception of Biocontrol Potential of Bacillus inaquosorum KR2-7 against Tomato Fusarium Wilt through Merging Genome Mining with Chemical Analysis. BIOLOGY 2022; 11:biology11010137. [PMID: 35053135 PMCID: PMC8773019 DOI: 10.3390/biology11010137] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 12/31/2022]
Abstract
Simple Summary Bacillus is a bacterial genus that is widely used as a promising alternative to chemical pesticides due to its protective activity toward economically important plant pathogens. Fusarium wilt of tomato is a serious fungal disease limiting tomato production worldwide. Recently, the newly isolated B. inaquosorum strain KR2-7 considerably suppressed Fusarium wilt of tomato plants. The present study was performed to perceive potential direct and indirect biocontrol mechanisms implemented by KR2-7 against this disease through genome and chemical analysis. The potential direct biocontrol mechanisms of KR2-7 were determined through the identification of genes involved in the synthesis of antibiotically active compounds suppressing tomato Fusarium wilt. Furthermore, the indirect mechanisms of this bacterium were perceived through recognizing genes that contributed to the resource acquisition or modulation of plant hormone levels. This is the first study that aimed at the modes of actions of B. inaquosorum against Fusarium wilt of tomatoes and the results strongly indicate that strain KR2-7 could be a good candidate for microbial biopesticide formulations to be used for biological control of plant diseases and plant growth promotion. Abstract Tomato Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), is a destructive disease that threatens the agricultural production of tomatoes. In the present study, the biocontrol potential of strain KR2-7 against Fol was investigated through integrated genome mining and chemical analysis. Strain KR2-7 was identified as B. inaquosorum based on phylogenetic analysis. Through the genome mining of strain KR2-7, we identified nine antifungal and antibacterial compound biosynthetic gene clusters (BGCs) including fengycin, surfactin and Bacillomycin F, bacillaene, macrolactin, sporulation killing factor (skf), subtilosin A, bacilysin, and bacillibactin. The corresponding compounds were confirmed through MALDI-TOF-MS chemical analysis. The gene/gene clusters involved in plant colonization, plant growth promotion, and induced systemic resistance were also identified in the KR2-7 genome, and their related secondary metabolites were detected. In light of these results, the biocontrol potential of strain KR2-7 against tomato Fusarium wilt was identified. This study highlights the potential to use strain KR2-7 as a plant-growth promotion agent.
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Affiliation(s)
- Maedeh Kamali
- College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China;
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology and School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
- Correspondence: ; Tel.: +852-3943-6298
| | - Shahram Naeimi
- Department of Biological Control Research, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran 19858-13111, Iran;
| | - Jafar Ahmadi
- Department of Genetics and Plant Breeding, Imam Khomeini International University, Qazvin 34149-16818, Iran;
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Essential-Oil-Loaded Nanoemulsion Lipidic-Phase Optimization and Modeling by Response Surface Methodology (RSM): Enhancement of Their Antimicrobial Potential and Bioavailability in Nanoscale Food Delivery System. Foods 2021; 10:foods10123149. [PMID: 34945700 PMCID: PMC8700816 DOI: 10.3390/foods10123149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/16/2023] Open
Abstract
Nanoencapsulation is an attractive technique used for incorporating essential oils in foods. Thus, our main goal was to formulate a novel nanoemulsion (NE) with nanoscale droplet size and lowest interfacial tension in the oil–water interface, contributing positively to the stability and the enhancement of essential oil potential. Thereby, response surface methodology (RSM), with mixture design was used to optimize the composition of the NE lipid phase. The essential oil combinations were encapsulated through high-pressure homogenization (HPH) with the binary emulsifier system (Tween 80: Gum Arabic). Then, the electrophoretic and physical properties were evaluated. We also conducted a follow-up stability and antimicrobial study that examined the stabilization mechanism of optimal NE. Thereafter, the effect of nanoencapsulation on the essential oil composition was assessed. The RSM results were best fitted into polynomial models with regression coefficient values of more than 0.95. The optimal NE showed a nanometer-sized droplet (270 nm) and lower interfacial tension (~11 mN/m), favoring negative ζ-potential (−15 mV), showing good stability under different conditions—it synergistically enhances the antimicrobial potential. GC-MS analysis showed that the use of HPH affected the active compounds, consistent with the differences in linalool and 2-Caren-10-al content. Hence, the novel nanometric delivery system contributes to food industry fortification.
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Clopés J, Winkler RG. Flagellar arrangements in elongated peritrichous bacteria: bundle formation and swimming properties. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:17. [PMID: 33683543 PMCID: PMC7940165 DOI: 10.1140/epje/s10189-021-00027-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/25/2021] [Indexed: 05/26/2023]
Abstract
The surface distribution of flagella in peritrichous bacterial cells has been traditionally assumed to be random. Recently, the presence of a regular grid-like pattern of basal bodies has been suggested. Experimentally, the manipulation of the anchoring points of flagella in the cell membrane is difficult, and thus, elucidation of the consequences of a particular pattern on bacterial locomotion is challenging. We analyze the bundle formation process and swimming properties of Bacillus subtilis-like cells considering random, helical, and ring-like arrangements of flagella by means of mesoscale hydrodynamics simulations. Helical and ring patterns preferentially yield configurations with a single bundle, whereas configurations with no clear bundles are most likely for random anchoring. For any type of pattern, there is an almost equally low probability to form V-shaped bundle configurations with at least two bundles. Variation of the flagellum length yields a clear preference for a single major bundle in helical and ring patterns as soon as the flagellum length exceeds the body length. The average swimming speed of cells with a single or two bundles is rather similar, and approximately [Formula: see text] larger than that of cells of other types of flagellar organization. Considering the various anchoring patterns, rings yield the smallest average swimming speed independent of the type of bundle, followed by helical arrangements, and largest speeds are observed for random anchoring. Hence, a regular pattern provides no advantage in terms of swimming speed compared to random anchoring of flagella, but yields more likely single-bundle configurations.
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Affiliation(s)
- Judit Clopés
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425, Jülich, Germany
- Institute for Theoretical Physics, RWTH Aachen University, 52074, Aachen, Germany
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425, Jülich, Germany.
- Institute for Theoretical Physics, RWTH Aachen University, 52074, Aachen, Germany.
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Isolation and characterization of a novel antimicrobial oxatetracyclo ketone from Bacillus stercoris MBTDCMFRI Ba37 isolated from the tropical estuarine habitats of Cochin. Mol Biol Rep 2021; 48:1299-1310. [PMID: 33590414 DOI: 10.1007/s11033-021-06146-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
Antimicrobial compounds from the safest source have gained greater relevance because of their wide spectrum of possible applications, especially in aquaculture industry, where pathogenic threat and antibacterial resistance are serious concerns. Bacillus stercoris MBTDCMFRI Ba37 isolated from mangrove environment of tropical estuarine habitats of Cochin exhibited a wide spectrum of antibacterial activity against major aquaculture pathogens belonging to genus Vibrio and Aeromonas. The structural characterization of the antibacterial compound from this strain may help in identifying their role as a biocontrol agent in aquaculture and allied sectors. The highest antibacterial activity was detected in 3rd day culture, grown in a modified Bacillus medium containing 1% of glycerol and 0.5% of glutamic acid at 30 °C, pH 8.0 and 15 ppt saline conditions. The inhibitory activity of the cell free supernatant was evident even at 20% v/v dilution. Preliminary studies on the nature of antibacterial action indicated that the bioactive principle is stable at temperatures up to 70 °C, between pH 6-9 and instable to lyzozyme and proteolytic enzymes. Bioassay guided purification followed by spectroscopic characterization of active fractions of B. stercoris MBTDCMFRI Ba37 revealed that the compound 1-(1-Hydroxyethyl)-1,7,10,12,13,15,17 heptamethyl-16-oxatetracyclo[8.7.0.02,3.012,13]heptadecan-5-one, is responsible for its major antibacterial activity. This is the first report on isolation and characterization of an antibacterial compound from the species B. stercoris. The results of this study indicated that B. stercoris MBTDCMFRI Ba37 has beneficial antibacterial properties which could be useful in developing novel antimicrobial therapeutics against a variety of aquaculture and other pathogens.
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Bacillus rugosus sp. nov. producer of a diketopiperazine antimicrobial, isolated from marine sponge Spongia officinalis L. Antonie van Leeuwenhoek 2020; 113:1675-1687. [PMID: 32939598 DOI: 10.1007/s10482-020-01472-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
A novel Gram-positive and endospore-forming bacterium assigned as strain SPB7T which is also a new source of a cyclic diketopiperazine (3S,6S)-3,6-diisobutylpiperazine-2,5-dione is described. A polyphasic (biochemical, phenotypic and genotypic) approach was used to clarify the taxonomic affiliation of this strain. The partial and complete 16S rRNA gene sequences revealed that strain SPB7T is a member of the Bacillus genus [showing high similarity (> 98.70%) with Bacillus spizizenii NRRL B-23049T, Bacillus tequilensis KCTC 13622T, Bacillus inaquosorum KCTC 13429T and Bacillus cabrialesii TE3T]. The maximum values for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (GGDC, Formula 2) of strain SPB7T was obtained for twenty-five strains of Bacillus spizizenii (ANI 95.01-95.48% and GGDC 62.70-60.00%). The whole-genome phylogenetic relationship showed that SPB7T formed an individual and separated clade with the Bacillus spizizenii group. Principal cellular fatty acids identified in strain SPB7T were anteiso C15:0, anteiso C17:0, iso C15:0, iso C17:0, C16:0, C10:0 3OH and iso C17:1 ϖ10c. Polar lipid profile showed presence of diphosphotidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and five unknown lipids. Cells were rod shaped, catalase, oxidase-positive and motile. Growth occurred at 20-45 °C (optimal 35 °C), at pH 6.0-10.0 (optimal pH 8) and 0-10% (w/v) NaCl (optimal 2%). The phenotypic, biochemical, and genotypic traits of strain SPB7T strongly supported its taxonomic affiliation as a novel species of the Bacillus genus, for which the name Bacillus rugosus sp. nov. is proposed. The type strain is SPB7T (= NRRL B-65559T, = CICC 24827T, = MCC 4185T).
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Dhruw C, Husain K, Kumar V, Sonawane VC. Novel xylanase producing Bacillus strain X2: molecular phylogenetic analysis and its application for production of xylooligosaccharides. 3 Biotech 2020; 10:328. [PMID: 32656061 PMCID: PMC7334322 DOI: 10.1007/s13205-020-02322-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 06/24/2020] [Indexed: 11/24/2022] Open
Abstract
A Bacillus strain X2 that produced extracellular endo-xylanase (GH 11) (EC: 3.2.1.8) was isolated from the soil of the Northeast India region. This aerobic culture was Gram positive and endospore forming. Chemotaxonomic characterization showed variance with the fatty acid profile of related species in the Bacillus subtilis group. In Bacillus strain X2, distinct occurrence of iso-C14:0 lipids is absent in other related species. The 16S rRNA gene sequence homology showed 99% similarity with Bacillus subtilis subsp. inaquosorum. The phylogenetic analysis by the multilocus sequence analysis (MLSA) of the nucleotide sequence of six concatenated genes (16S rRNA, groEL, gyrA, polC, purH and rpoB) resolved the taxonomic position of the Bacillus strain X2 in the Bacillus subtilis subsp. group. The MLSA showed that it is a member of a clade that includes Bacillus subtilis subsp. stercoris. In in silico DNA-DNA hybridization (DDH), the highest matching score was obtained with Bacillus subtilis subsp. stercoris (87%). The in silico DDH of the genome (G + C 43.7 mol %) shared 48.5%, with Bacillus subtilis subsp. inaquosorum. The MLSA phylogenetic tree and the highest degree of DNA hybridization, indicating that it belongs to the Bacillus subtilis subspecies stercoris.
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Affiliation(s)
- Chandrabhan Dhruw
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Khadim Husain
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Vyas Kumar
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
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13
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Xu S, Xie X, Zhao Y, Shi Y, Chai A, Li L, Li B. Whole-genome analysis of bacillus velezensis ZF2, a biocontrol agent that protects cucumis sativus against corynespora leaf spot diseases. 3 Biotech 2020; 10:186. [PMID: 32257742 DOI: 10.1007/s13205-020-2165-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/11/2020] [Indexed: 12/17/2022] Open
Abstract
Bacillus spp. have been widely described for their potentials to protect plants against pathogens. Here, we reported the whole genome sequence of Bacillus velezensis ZF2, which was isolated from the stem of a healthy cucumber plant. Strain ZF2 showed a broad spectrum of antagonistic activities against many plant bacterial and fungal pathogens, including the cucumber leaf spot fungus Corynespora cassiicola. The complete genome of B. velezensis ZF2 contained a 3,931,418-bp circular chromosome, with an average G + C content of 46.50%. Genome comparison revealed closest similarity between ZF2 and other B. velezensis strains. Genes homologous to 14 gene clusters for biosynthesis of secondary metabolites were identified in the ZF2 genome. Also identified were a number of genes involved in bacterial colonization, including the genes for motility, biofilm formation, flagella biosynthesis, and capsular biosynthesis. Numerous genes associated with plant-bacteria interactions, including cellulase or protease biosynthesis, and plant growth promotion were also identified in the ZF2 genome. Overall, our data will aid future studies of the biocontrol mechanisms of B. velezensis ZF2 and promote its application in vegetable disease control.
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Affiliation(s)
- Shuai Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xuewen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yurong Zhao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ali Chai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico. Int J Syst Evol Microbiol 2019; 69:3939-3945. [DOI: 10.1099/ijsem.0.003711] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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15
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Constraints on CaCO3 precipitation in superabsorbent polymer by aerobic bacteria. Appl Microbiol Biotechnol 2019; 104:365-375. [DOI: 10.1007/s00253-019-10215-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/08/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022]
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16
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Dunlap CA, Bowman MJ, Zeigler DR. Promotion of Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris to species status. Antonie van Leeuwenhoek 2019; 113:1-12. [PMID: 31721032 DOI: 10.1007/s10482-019-01354-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/26/2019] [Indexed: 12/12/2022]
Abstract
Bacillus subtilis currently encompasses four subspecies, Bacillus subtilis subsp. subtilis, Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris. Several studies based on genomic comparisons have suggested these subspecies should be promoted to species status. Previously, one of the main reasons for leaving them as subspecies was the lack of distinguishing phenotypes. In this study, we used comparative genomics to determine the genes unique to each subspecies and used these to lead us to the unique phenotypes. The results show that one difference among the subspecies is they produce different bioactive secondary metabolites. B. subtilis subsp. spizizenii is shown conserve the genes to produce mycosubtilin, bacillaene and 3,3'-neotrehalosadiamine. B. subtilis subsp. inaquosorum is shown conserve the genes to produce bacillomycin F, fengycin and an unknown PKS/NRPS cluster. B. subtilis subsp. stercoris is shown conserve the genes to produce fengycin and an unknown PKS/NRPS cluster. While B. subtilis subsp. subtilis is shown to conserve the genes to produce 3,3'-neotrehalosadiamine. In addition, we update the chemotaxonomy and phenotyping to support their promotion to species status.
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Affiliation(s)
- Christopher A Dunlap
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL, USA.
| | - Michael J Bowman
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL, USA
| | - Daniel R Zeigler
- Bacillus Genetic Stock Center, The Ohio State University, Columbus, OH, USA
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17
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Sharma R, Pielstick BA, Bell KA, Nieman TB, Stubbs OA, Yeates EL, Baltrus DA, Grose JH. A Novel, Highly Related Jumbo Family of Bacteriophages That Were Isolated Against Erwinia. Front Microbiol 2019; 10:1533. [PMID: 31428059 PMCID: PMC6690015 DOI: 10.3389/fmicb.2019.01533] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023] Open
Abstract
Erwinia amylovora is a plant pathogen from the Erwiniaceae family and a causative agent of the devastating agricultural disease fire blight. Here we characterize eight lytic bacteriophages of E. amylovora that we isolated from the Wasatch front (Utah, United States) that are highly similar to vB_EamM_Ea35-70 which was isolated in Ontario, Canada. With the genome size ranging from 271 to 275 kb, this is a novel jumbo family of bacteriophages. These jumbo bacteriophages were further characterized through genomic and proteomic comparison, mass spectrometry, host range and burst size. Their proteomes are highly unstudied, with over 200 putative proteins with no known homologs. The production of 27 of these putative proteins was confirmed by mass spectrometry analysis. These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea.
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Affiliation(s)
- Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brittany A Pielstick
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Kimberly A Bell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Tanner B Nieman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Olivia A Stubbs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Edward L Yeates
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - David A Baltrus
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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18
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Stein T. Oxygen-Limiting Growth Conditions and Deletion of the Transition State Regulator Protein Abrb in Bacillus subtilis 6633 Result in an Increase in Subtilosin Production and a Decrease in Subtilin Production. Probiotics Antimicrob Proteins 2019; 12:725-731. [DOI: 10.1007/s12602-019-09547-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Bahramisharif A, Rose LE. Efficacy of biological agents and compost on growth and resistance of tomatoes to late blight. PLANTA 2019; 249:799-813. [PMID: 30406411 DOI: 10.1007/s00425-018-3035-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/24/2018] [Indexed: 06/08/2023]
Abstract
This study identified biocontrol measures for improving plant quality and resistance under biotic stress caused by the most devastating pathogen in tomato production. The management of plant diseases are dependent on a variety of factors. Two important variables are the soil quality and its bacterial/fungal community. However, the interaction of these factors is not well understood and remains problematic in producing healthy crops. Here, the effect of oak-bark compost, Bacillus subtilis subsp. subtilis, Trichoderma harzianum and two commercial products (FZB24 and FZB42) were investigated on tomato growth, production of metabolites and resistance under biotic stress condition (infection with Phytophthora infestans). Oak-bark compost, B. subtilis subsp. subtilis, and T. harzianum significantly enhanced plant growth and immunity when exposed to P. infestans. However, the commercial products were not as effective in promoting growth, with FZB42 having the weakest protection. Furthermore, elevated levels of anthocyanins did not correlate with enhanced plant resistance. Overall, the most effective and consistent plant protection was obtained when B. subtilis subsp. subtilis was combined with oak-bark compost. In contrast, the combination of T. harzianum and oak-bark compost resulted in increased disease severity. The use of compost in combination with bio-agents should, therefore, be evaluated carefully for a reliable and consistent tomato protection.
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Affiliation(s)
- Amirhossein Bahramisharif
- Institute of Population genetics, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 26.03.00.25, 40225, Düsseldorf, Germany
- International Graduate School in Plant Sciences (iGRAD-Plant), Düsseldorf, Germany
| | - Laura E Rose
- Institute of Population genetics, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 26.03.00.25, 40225, Düsseldorf, Germany.
- International Graduate School in Plant Sciences (iGRAD-Plant), Düsseldorf, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
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20
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Abril AG, Rama JLR, Feijoo-Siota L, Calo-Mata P, Salazar S, Peix A, Velázquez E, Villa TG. Bacillus safensis subsp. osmophilus subsp. nov., isolated from condensed milk, and description of Bacillus safensis subsp. safensis subsp. nov. Int J Syst Evol Microbiol 2019; 69:189-195. [DOI: 10.1099/ijsem.0.003126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ana G. Abril
- 1Departmento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jose Luis R. Rama
- 1Departmento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Lucia Feijoo-Siota
- 1Departmento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- 2Departmento de Química Analítica, Nutrición y Bromatología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Sergio Salazar
- 3Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | - Alvaro Peix
- 3Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- 4Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Encarna Velázquez
- 4Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- 5Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Tomás G. Villa
- 1Departmento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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21
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The first report of antifungal lipopeptide production by a Bacillus subtilis subsp. inaquosorum strain. Microbiol Res 2018; 216:40-46. [DOI: 10.1016/j.micres.2018.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/17/2018] [Accepted: 08/01/2018] [Indexed: 12/18/2022]
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22
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Pinto C, Sousa S, Froufe H, Egas C, Clément C, Fontaine F, Gomes AC. Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. Stand Genomic Sci 2018; 13:30. [PMID: 30410642 PMCID: PMC6211603 DOI: 10.1186/s40793-018-0327-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 09/24/2018] [Indexed: 11/10/2022] Open
Abstract
Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321 is a naturally occurring strain in vineyard, with the ability to colonise grapevine and which unveils a naturally antagonistic potential against phytopathogens of grapevine, including those responsible for the Botryosphaeria dieback, a GTD disease. Herein we report the draft genome sequence of B. amyloliquefaciens subsp. plantarum Fito_F321, isolated from the leaf of Vitis vinifera cv. Merlot at Bairrada appellation (Cantanhede, Portugal). The genome size is 3,856,229 bp, with a GC content of 46.54% that contains 3697 protein-coding genes, 86 tRNA coding genes and 5 rRNA genes. The draft genome of strain Fito_F321 allowed to predict a set of bioactive compounds as bacillaene, difficidin, macrolactin, surfactin and fengycin that due to their antimicrobial activity are hypothesized to be of utmost importance for biocontrol of grapevine diseases.
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Affiliation(s)
- Cátia Pinto
- Biocant - Biotechnology Innovation Center, Cantanhede, Portugal
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP)- EA 4707, BP1039, Cedex 2 51687 Reims, France
| | - Susana Sousa
- Biocant - Biotechnology Innovation Center, Cantanhede, Portugal
| | - Hugo Froufe
- Biocant - Biotechnology Innovation Center, Cantanhede, Portugal
| | - Conceição Egas
- Biocant - Biotechnology Innovation Center, Cantanhede, Portugal
- Center for Neurosciences and Cell Biology (CNC), Faculty of Medicine, University of Coimbra, Polo I, 1st floor, Rua Larga, 3004-504 Coimbra, Portugal
| | - Christophe Clément
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP)- EA 4707, BP1039, Cedex 2 51687 Reims, France
| | - Florence Fontaine
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP)- EA 4707, BP1039, Cedex 2 51687 Reims, France
| | - Ana C Gomes
- Biocant - Biotechnology Innovation Center, Cantanhede, Portugal
- Center for Neurosciences and Cell Biology (CNC), Faculty of Medicine, University of Coimbra, Polo I, 1st floor, Rua Larga, 3004-504 Coimbra, Portugal
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23
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Daas MS, Rosana ARR, Acedo JZ, Douzane M, Nateche F, Kebbouche-Gana S, Vederas JC. Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough. Stand Genomic Sci 2018; 13:25. [PMID: 30344888 PMCID: PMC6186030 DOI: 10.1186/s40793-018-0331-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022] Open
Abstract
Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form parasporal crystals containing proteinaceous toxins. It is a member of the Bacillus cereus sensu lato, a group with low genetic diversity but produces several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from an oil-contaminated slough in Algeria, has strong antibacterial, antifungal and biosurfactant properties. Here, we report the 6.06 Mbp draft genome sequence of B. thuringiensis DNG9. The genome encodes several gene inventories for the biosynthesis of bioactive compounds such as zwittermycin A, petrobactin, insecticidal toxins, polyhydroxyalkanoates and multiple bacteriocins. We expect the genome information of strain DNG9 will provide another model system to study pathogenicity against insect pests, plant diseases, and antimicrobial compound mining and comparative phylogenesis among the Bacillus cereus sensu lato group.
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Affiliation(s)
- Mohamed Seghir Daas
- Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdes, 35000 Boumerdes, Algeria
- Food Technology Research Division, Institut National de la Recherche Agronomique d’Algérie, 16200, El Harrach, Algiers, Algeria
| | | | - Jeella Z. Acedo
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
| | - Malika Douzane
- Food Technology Research Division, Institut National de la Recherche Agronomique d’Algérie, 16200, El Harrach, Algiers, Algeria
| | - Farida Nateche
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology–Houari Boumediene, 16111, Bab Ezzouar, Algiers, Algeria
| | - Salima Kebbouche-Gana
- Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdes, 35000 Boumerdes, Algeria
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
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Zhang J, Lu L, Chen F, Chen L, Yin J, Huang X. Detoxification of diphenyl ether herbicide lactofen by Bacillus sp. Za and enantioselective characteristics of an esterase gene lacE. JOURNAL OF HAZARDOUS MATERIALS 2018; 341:336-345. [PMID: 28802244 DOI: 10.1016/j.jhazmat.2017.07.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 07/26/2017] [Accepted: 07/27/2017] [Indexed: 06/07/2023]
Abstract
A bacterial strain Za capable of degrading diphenyl ether herbicide lactofen was isolated and identified as Bacillus sp. This strain could degrade 94.8% of 50mgL-1 lactofen after 4days of inoculation in flasks. It was revealed that lactofen was initially hydrolyzed to desethyl lactofen, which was further transformed to acifluorfen, followed by the reduction of the nitro group to yield aminoacifluorfen. The phytotoxicity of the transformed product aminoacifluorfen to maize was decreased significantly compared with the lactofen. A gene lacE, encoding an esterase responsible for lactofen hydrolysis to desethyl lactofen and acifluorfen continuously, was cloned from Bacillus sp. Za. The deduced amino acid belonging to the esterase family VII contained a typical Ser-His-Asp/Glu catalytic triad and the conserved motifs GXSXG. The purified recombinant protein LacE displayed maximal esterase activity at 40°C and pH 7.0. Additionally, LacE had broad substrate specificity and was capable of hydrolyzing p-nitrophenyl esters. The enantioselectivity of LacE during lactofen degradation was further studied, and the results indicated that the (S)-(+)-lactofen was degraded faster than the (R)-(-)-lactofen, which could illustrate the reported phenomenon that (S)-(+)-lactofen was preferentially degraded in soil and sediment.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Luyao Lu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingling Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingang Yin
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xing Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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25
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Ernst FGM, Erber L, Sammler J, Jühling F, Betat H, Mörl M. Cold adaptation of tRNA nucleotidyltransferases: A tradeoff in activity, stability and fidelity. RNA Biol 2017; 15:144-155. [PMID: 29099323 DOI: 10.1080/15476286.2017.1391445] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Cold adaptation is an evolutionary process that has dramatic impact on enzymatic activity. Increased flexibility of the protein structure represents the main evolutionary strategy for efficient catalysis and reaction rates in the cold, but is achieved at the expense of structural stability. This results in a significant activity-stability tradeoff, as it was observed for several metabolic enzymes. In polymerases, however, not only reaction rates, but also fidelity plays an important role, as these enzymes have to synthesize copies of DNA and RNA as exact as possible. Here, we investigate the effects of cold adaptation on the highly accurate CCA-adding enzyme, an RNA polymerase that uses an internal amino acid motif within the flexible catalytic core as a template to synthesize the CCA triplet at tRNA 3'-ends. As the relative orientation of these residues determines nucleotide selection, we characterized how cold adaptation impacts template reading and fidelity. In a comparative analysis of closely related psychro-, meso-, and thermophilic enzymes, the cold-adapted polymerase shows a remarkable error rate during CCA synthesis in vitro as well as in vivo. Accordingly, CCA-adding activity at low temperatures is not only achieved at the expense of structural stability, but also results in a reduced polymerization fidelity.
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Affiliation(s)
- Felix G M Ernst
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
| | - Lieselotte Erber
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
| | - Joana Sammler
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
| | - Frank Jühling
- b INSERM Unit 1110 , Institute of Viral and Liver Diseases, University of Strasbourg , Strasbourg , France
| | - Heike Betat
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
| | - Mario Mörl
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
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26
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Ettelt V, Ekat K, Kämmerer PW, Kreikemeyer B, Epple M, Veith M. Streptavidin-coated surfaces suppress bacterial colonization by inhibiting non-specific protein adsorption. J Biomed Mater Res A 2017; 106:758-768. [DOI: 10.1002/jbm.a.36276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/10/2017] [Accepted: 10/16/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Volker Ettelt
- Laboratory of Biophysics, Faculty of Applied Natural Sciences; Westphalian University of Applied Sciences; Recklinghausen D-45665 Germany
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), Faculty of Chemistry; University of Duisburg-Essen; Essen D-45141 Germany
| | - Katharina Ekat
- Department Cell Biology; University Medical Center Rostock; Rostock D-18057 Germany
- Department of Operative Dentistry and Periodontology; University Medical Center Rostock; Rostock D-18057 Germany
| | - Peer W. Kämmerer
- Department of Oral, Maxillofacial and Plastic Surgery; University Medical Center Rostock; Rostock D-18057 Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, University Medical Center Rostock; Rostock D-18057 Germany
| | - Matthias Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), Faculty of Chemistry; University of Duisburg-Essen; Essen D-45141 Germany
| | - Michael Veith
- Laboratory of Biophysics, Faculty of Applied Natural Sciences; Westphalian University of Applied Sciences; Recklinghausen D-45665 Germany
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Guo LY, Ling SK, Li CM, Chen GJ, Du ZJ. Bacillus marinisedimentorum sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2017; 68:198-203. [PMID: 29134941 DOI: 10.1099/ijsem.0.002482] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, motile and facultatively anaerobic strain, designated NC2-31T, was isolated from sediment from the coast of Weihai, PR China. Optimal growth occurred at 37 °C, pH 7.5 and with 2.0-3.0 % (w/v) NaCl. MK-7 was the major respiratory quinone. Meso-diaminopimelic acid was a diagnostic diamino acid in the peptidoglycan. The major polar lipids of NC2-31T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The genomic DNA G+C content of the strain was 46.3 mol%. The predominant cellular fatty acids (>10.0 %) of NC2-31T were iso-C15 : 0 (18.9 %), anteiso-C15 : 0 (15.8 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) (15.3 %) and iso-C16 : 0 (10.3 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that NC2-31T should be classified as representing a member of the genus Bacillus. Based on data from the current polyphasic study, NC2-31T represents a novel species within the genus Bacillus, for which the name Bacillusmarinisedimentorum sp. nov. is proposed with type strain NC2-31T (=KCTC 33721T=MCCC 1K01239T).
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Affiliation(s)
- Ling-Yun Guo
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Si-Kai Ling
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Chang-Ming Li
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Guan-Jun Chen
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
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Hirota K, Nishita M, Matsuyama H, Yumoto I. Paralkalibacillus indicireducens gen., nov., sp. nov., an indigo-reducing obligate alkaliphile isolated from indigo fermentation liquor used for dyeing. Int J Syst Evol Microbiol 2017; 67:4050-4056. [DOI: 10.1099/ijsem.0.002248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8571, Japan
| | - Masatoshi Nishita
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan
| | - Hidetoshi Matsuyama
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan
| | - Isao Yumoto
- Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8571, Japan
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Spore Heat Activation Requirements and Germination Responses Correlate with Sequences of Germinant Receptors and with the Presence of a Specific spoVA2mob Operon in Foodborne Strains of Bacillus subtilis. Appl Environ Microbiol 2017; 83:AEM.03122-16. [PMID: 28130296 DOI: 10.1128/aem.03122-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/21/2017] [Indexed: 01/19/2023] Open
Abstract
Spore heat resistance, germination, and outgrowth are problematic bacterial properties compromising food safety and quality. Large interstrain variation in these properties makes prediction and control of spore behavior challenging. High-level heat resistance and slow germination of spores of some natural Bacillus subtilis isolates, encountered in foods, have been attributed to the occurrence of the spoVA2mob operon carried on the Tn1546 transposon. In this study, we further investigate the correlation between the presence of this operon in high-level-heat-resistant spores and their germination efficiencies before and after exposure to various sublethal heat treatments (heat activation, or HA), which are known to significantly improve spore responses to nutrient germinants. We show that high-level-heat-resistant spores harboring spoVA2mob required higher HA temperatures for efficient germination than spores lacking spoVA2mob The optimal spore HA requirements additionally depended on the nutrients used to trigger germination, l-alanine (l-Ala), or a mixture of l-asparagine, d-glucose, d-fructose, and K+ (AGFK). The distinct HA requirements of these two spore germination pathways are likely related to differences in properties of specific germinant receptors. Moreover, spores that germinated inefficiently in AGFK contained specific changes in sequences of the GerB and GerK germinant receptors, which are involved in this germination response. In contrast, no relation was found between transcription levels of main germination genes and spore germination phenotypes. The findings presented in this study have great implications for practices in the food industry, where heat treatments are commonly used to inactivate pathogenic and spoilage microbes, including bacterial spore formers.IMPORTANCE This study describes a strong variation in spore germination capacities and requirements for a heat activation treatment, i.e., an exposure to sublethal heat that increases spore responsiveness to nutrient germination triggers, among 17 strains of B. subtilis, including 9 isolates from spoiled food products. Spores of industrial foodborne isolates exhibited, on average, less efficient and slower germination responses and required more severe heat activation than spores from other sources. High heat activation requirements and inefficient, slow germination correlated with elevated resistance of spores to heat and with specific genetic features, indicating a common genetic basis of these three phenotypic traits. Clearly, interstrain variation and numerous factors that shape spore germination behavior challenge standardization of methods to recover highly heat-resistant spores from the environment and have an impact on the efficacy of preservation techniques used by the food industry to control spores.
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Fan B, Blom J, Klenk HP, Borriss R. Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an "Operational Group B. amyloliquefaciens" within the B. subtilis Species Complex. Front Microbiol 2017; 8:22. [PMID: 28163698 PMCID: PMC5247444 DOI: 10.3389/fmicb.2017.00022] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/04/2017] [Indexed: 11/13/2022] Open
Abstract
The plant growth promoting model bacterium FZB42T was proposed as the type strain of Bacillus amyloliquefaciens subsp. plantarum (Borriss et al., 2011), but has been recently recognized as being synonymous to Bacillus velezensis due to phylogenomic analysis (Dunlap C. et al., 2016). However, until now, majority of publications consider plant-associated close relatives of FZB42 still as "B. amyloliquefaciens." Here, we reinvestigated the taxonomic status of FZB42 and related strains in its context to the free-living soil bacterium DSM7T, the type strain of B. amyloliquefaciens. We identified 66 bacterial genomes from the NCBI data bank with high similarity to DSM7T. Dendrograms based on complete rpoB nucleotide sequences and on core genome sequences, respectively, clustered into a clade consisting of three tightly linked branches: (1) B. amyloliquefaciens, (2) Bacillus siamensis, and (3) a conspecific group containing the type strains of B. velezensis, Bacillus methylotrophicus, and B. amyloliquefaciens subsp. plantarum. The three monophyletic clades shared a common mutation rate of 0.01 substitutions per nucleotide position, but were distantly related to Bacillus subtilis (0.1 substitutions per nucleotide position). The tight relatedness of the three clusters was corroborated by TETRA, dDDH, ANI, and AAI analysis of the core genomes, but dDDH and ANI values were found slightly below species level thresholds when B. amyloliquefaciens DSM7T genome sequence was used as query sequence. Due to these results, we propose that the B. amyloliquefaciens clade should be considered as a taxonomic unit above of species level, designated here as "operational group B. amyloliquefaciens" consisting of the soil borne B. amyloliquefaciens, and plant associated B. siamensis and B. velezensis, whose members are closely related and allow identifying changes on the genomic level due to developing the plant-associated life-style.
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Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University Nanjing, China
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen Giessen, Germany
| | | | - Rainer Borriss
- Fachgebiet Phytomedizin, Institut für Agrar- und Gartenbauwissenschaften, Humboldt Universität zu BerlinBerlin, Germany; Nord Reet UGGreifswald, Germany
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Mohkam M, Nezafat N, Berenjian A, Mobasher MA, Ghasemi Y. Identification of Bacillus Probiotics Isolated from Soil Rhizosphere Using 16S rRNA, recA, rpoB Gene Sequencing and RAPD-PCR. Probiotics Antimicrob Proteins 2016; 8:8-18. [PMID: 26898909 DOI: 10.1007/s12602-016-9208-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Some Bacillus species, especially Bacillus subtilis and Bacillus pumilus groups, have highly similar 16S rRNA gene sequences, which are hard to identify based on 16S rDNA sequence analysis. To conquer this drawback, rpoB, recA sequence analysis along with randomly amplified polymorphic (RAPD) fingerprinting was examined as an alternative method for differentiating Bacillus species. The 16S rRNA, rpoB and recA genes were amplified via a polymerase chain reaction using their specific primers. The resulted PCR amplicons were sequenced, and phylogenetic analysis was employed by MEGA 6 software. Identification based on 16S rRNA gene sequencing was underpinned by rpoB and recA gene sequencing as well as RAPD-PCR technique. Subsequently, concatenation and phylogenetic analysis showed that extent of diversity and similarity were better obtained by rpoB and recA primers, which are also reinforced by RAPD-PCR methods. However, in one case, these approaches failed to identify one isolate, which in combination with the phenotypical method offsets this issue. Overall, RAPD fingerprinting, rpoB and recA along with concatenated genes sequence analysis discriminated closely related Bacillus species, which highlights the significance of the multigenic method in more precisely distinguishing Bacillus strains. This research emphasizes the benefit of RAPD fingerprinting, rpoB and recA sequence analysis superior to 16S rRNA gene sequence analysis for suitable and effective identification of Bacillus species as recommended for probiotic products.
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Affiliation(s)
- Milad Mohkam
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran
| | - Aydin Berenjian
- Faculty of Science and Engineering, School of Engineering, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Mohammad Ali Mobasher
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran.,Department of Medical Biotechnology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran. .,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
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Krawczyk AO, Berendsen EM, de Jong A, Boekhorst J, Wells-Bennik MHJ, Kuipers OP, Eijlander RT. A transposon present in specific strains ofBacillus subtilisnegatively affects nutrient- and dodecylamine-induced spore germination. Environ Microbiol 2016; 18:4830-4846. [DOI: 10.1111/1462-2920.13386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Antonina O. Krawczyk
- Laboratory of Molecular Genetics; University of Groningen; Nijenborgh 7 9747 AG Groningen the Netherlands
- Top Institute Food and Nutrition (TIFN); Nieuwe Kanaal 9A 6709 PA Wageningen the Netherlands
| | - Erwin M. Berendsen
- Laboratory of Molecular Genetics; University of Groningen; Nijenborgh 7 9747 AG Groningen the Netherlands
- Top Institute Food and Nutrition (TIFN); Nieuwe Kanaal 9A 6709 PA Wageningen the Netherlands
- NIZO Food Research B.V; Kernhemseweg 2 6718 ZB Ede the Netherlands
| | - Anne de Jong
- Laboratory of Molecular Genetics; University of Groningen; Nijenborgh 7 9747 AG Groningen the Netherlands
- Top Institute Food and Nutrition (TIFN); Nieuwe Kanaal 9A 6709 PA Wageningen the Netherlands
| | - Jos Boekhorst
- Top Institute Food and Nutrition (TIFN); Nieuwe Kanaal 9A 6709 PA Wageningen the Netherlands
- NIZO Food Research B.V; Kernhemseweg 2 6718 ZB Ede the Netherlands
| | - Marjon H. J. Wells-Bennik
- Top Institute Food and Nutrition (TIFN); Nieuwe Kanaal 9A 6709 PA Wageningen the Netherlands
- NIZO Food Research B.V; Kernhemseweg 2 6718 ZB Ede the Netherlands
| | - Oscar P. Kuipers
- Laboratory of Molecular Genetics; University of Groningen; Nijenborgh 7 9747 AG Groningen the Netherlands
- Top Institute Food and Nutrition (TIFN); Nieuwe Kanaal 9A 6709 PA Wageningen the Netherlands
| | - Robyn T. Eijlander
- Laboratory of Molecular Genetics; University of Groningen; Nijenborgh 7 9747 AG Groningen the Netherlands
- Top Institute Food and Nutrition (TIFN); Nieuwe Kanaal 9A 6709 PA Wageningen the Netherlands
- NIZO Food Research B.V; Kernhemseweg 2 6718 ZB Ede the Netherlands
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33
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Posada LF, Alvarez JC, Hu CH, de-Bashan LE, Bashan Y. Construction of probe of the plant growth-promoting bacteria Bacillus subtilis useful for fluorescence in situ hybridization. J Microbiol Methods 2016; 128:125-129. [PMID: 27263830 DOI: 10.1016/j.mimet.2016.05.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
Abstract
Strains of Bacillus subtilis are plant growth-promoting bacteria (PGPB) of many crops and are used as inoculants. PGPB colonization is an important trait for success of a PGPB on plants. A specific probe, based on the 16 s rRNA of Bacillus subtilis, was designed and evaluated to distinguishing, by fluorescence in situ hybridization (FISH), between this species and the closely related Bacillus amyloliquefaciens. The selected target for the probe was between nucleotides 465 and 483 of the gene, where three different nucleotides can be identified. The designed probe successfully hybridized with several strains of Bacillus subtilis, but failed to hybridize not only with B. amyloliquefaciens, but also with other strains such as Bacillus altitudinis, Bacillus cereus, Bacillus gibsonii, Bacillus megaterium, Bacillus pumilus; and with the external phylogenetic strains Azospirillum brasilense Cd, Micrococcus sp. and Paenibacillus sp. The results showed the specificity of this molecular probe for B. subtilis.
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Affiliation(s)
- Luisa F Posada
- Department of Process Engineering, Cra 49 #7 sur-50, Universidad EAFIT, Medellín, Colombia
| | - Javier C Alvarez
- Departament of Biological Sciences, Cra 49 #7 sur-50, Universidad EAFIT, Medellín, Colombia
| | - Chia-Hui Hu
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Luz E de-Bashan
- The Bashan Institute of Science, 1730 Post Oak Ct., AL 36830, USA; Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Av. IPN 195, La Paz, B.C.S. 23096, Mexico; Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Yoav Bashan
- The Bashan Institute of Science, 1730 Post Oak Ct., AL 36830, USA; Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Av. IPN 195, La Paz, B.C.S. 23096, Mexico; Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA.
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Guo X, Chen DD, Peng KS, Cui ZW, Zhang XJ, Li S, Zhang YA. Identification and characterization of Bacillus subtilis from grass carp (Ctenopharynodon idellus) for use as probiotic additives in aquatic feed. FISH & SHELLFISH IMMUNOLOGY 2016; 52:74-84. [PMID: 26988285 DOI: 10.1016/j.fsi.2016.03.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/04/2016] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Bacillus subtilis is widely used as probiotic species in aquaculture for water quality control, growth promoting, or immunity enhancing. The aim of this study is to find novel B. subtilis strains from fish as potential probiotics for aquaculture. Eleven B. subtilis isolates derived from the intestinal tract of grass carp were identified by gene sequencing and biochemical tests. These isolates were classified into 4 groups, and the representatives (GC-5, GC-6, GC-21 and GC-22) of each group were further investigated for antibiotic susceptibility, sporulation rate, biofilm formation, activity against pathogenic bacteria, resistance to stress conditions of intestinal tract (high percentage of bile and low pH) and high temperature, which are important for probiotics to be used as feed additives. Additionally, the adhesion properties of the 4 characterized strains were assessed using Caco-2 cell and gut mucus models. The results showed that the 4 strains differed in their capacities to adhere to intestinal epithelial cells and mucus. Furthermore, the strains GC-21 and GC-22 up-regulated the expression levels of IL-10 and TGF-β but down-regulated IL-1β, suggesting their potential anti-inflammatory abilities. Based on physiological properties of the 4 characterized B. subtilis strains, one or more strains may have potential to be used as probiotics in aquaculture.
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Affiliation(s)
- Xia Guo
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Dan-Dan Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Kai-Song Peng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Anhui Agricultural University, Hefei 230036, China
| | - Zheng-Wei Cui
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu-Jie Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Shanghai Ocean University, Shanghai 201306, China
| | - Shun Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yong-An Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Abstract
Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.
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Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis strain LM 4-2. Stand Genomic Sci 2015; 10:127. [PMID: 26664656 PMCID: PMC4674931 DOI: 10.1186/s40793-015-0118-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 12/03/2015] [Indexed: 11/26/2022] Open
Abstract
Bacillus subtilis LM 4–2, a Gram-positive bacterium was isolated from a molybdenum mine in Luoyang city. Due to its strong resistance to molybdate and potential utilization in bioremediation of molybdate-polluted area, we describe the features of this organism, as well as its complete genome sequence and annotation. The genome was composed of a circular 4,069,266 bp chromosome with average GC content of 43.83 %, which included 4149 predicted ORFs and 116 RNA genes. Additionally, 687 transporter-coding and 116 redox protein-coding genes were identified in the strain LM 4–2 genome.
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Piubeli F, de Lourdes Moreno M, Kishi LT, Henrique-Silva F, García MT, Mellado E. Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert. Indian J Microbiol 2015; 55:392-9. [PMID: 26543264 PMCID: PMC4627947 DOI: 10.1007/s12088-015-0539-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/13/2015] [Indexed: 10/23/2022] Open
Abstract
The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations .
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Affiliation(s)
- Francine Piubeli
- />Department of Genetics and Evolution (DGE), UFSCar, Via Washington Luis, Km. 235, São Carlos, SP Brazil
- />Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, C/Profesor García González, 2, 41012 Seville, Spain
| | - María de Lourdes Moreno
- />Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, C/Profesor García González, 2, 41012 Seville, Spain
| | - Luciano Takeshi Kishi
- />Department of Genetics and Evolution (DGE), UFSCar, Via Washington Luis, Km. 235, São Carlos, SP Brazil
| | - Flavio Henrique-Silva
- />Department of Genetics and Evolution (DGE), UFSCar, Via Washington Luis, Km. 235, São Carlos, SP Brazil
| | - María Teresa García
- />Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, C/Profesor García González, 2, 41012 Seville, Spain
| | - Encarnación Mellado
- />Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, C/Profesor García González, 2, 41012 Seville, Spain
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Mawlankar R, Thorat MN, Krishnamurthi S, Dastager SG. Bacillus cellulasensis sp. nov., isolated from marine sediment. Arch Microbiol 2015; 198:83-9. [DOI: 10.1007/s00203-015-1155-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/14/2015] [Accepted: 09/19/2015] [Indexed: 11/28/2022]
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40
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Diez V, Loznik M, Taylor S, Winn M, Rattray NJW, Podmore H, Micklefield J, Goodacre R, Medema MH, Müller U, Bovenberg R, Janssen DB, Takano E. Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block. ACS Synth Biol 2015; 4:796-807. [PMID: 25713978 DOI: 10.1021/sb500368w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A key problem in the engineering of pathways for the production of pharmaceutical compounds is the limited diversity of biosynthetic enzymes, which restricts the attainability of suitable traits such as less harmful byproducts, enhanced expression features, or different cofactor requirements. A promising synthetic biology approach is to redesign the biosynthetic pathway by replacing the native enzymes by heterologous proteins from unrelated pathways. In this study, we applied this method to effectively re-engineer the biosynthesis of hydroxyphenylglycine (HPG), a building block for the calcium-dependent antibiotic of Streptomyces coelicolor, a nonribosomal peptide. A key step in HPG biosynthesis is the conversion of 4-hydroxymandelate to 4-hydroxyphenylglyoxylate, catalyzed by hydroxymandelate oxidase (HmO), with concomitant generation of H2O2. The same reaction can also be catalyzed by O2-independent mandelate dehydrogenase (MdlB), which is a catabolic enzyme involved in bacterial mandelate utilization. In this work, we engineered alternative HPG biosynthetic pathways by replacing the native HmO in S. coelicolor by both heterologous oxidases and MdlB dehydrogenases from various sources and confirmed the restoration of calcium-dependent antibiotic biosynthesis by biological and UHPLC-MS analysis. The alternative enzymes were isolated and kinetically characterized, confirming their divergent substrate specificities and catalytic mechanisms. These results demonstrate that heterologous enzymes with different physiological contexts can be used in a Streptomyces host to provide an expanded library of enzymatic reactions for a synthetic biology approach. This study thus broadens the options for the engineering of antibiotic production by using enzymes with different catalytic and structural features.
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Affiliation(s)
| | | | | | | | | | - Helen Podmore
- ThermoFisher Scientific, 1 Boundary
Way, Hemel Hempstead, Herts, HP2 7GE, United Kingdom
| | | | | | | | - Ulrike Müller
- DSM Biotechnology Center, R&D, P.O. Box 1, 2600 AM Delft, The Netherlands
| | - Roel Bovenberg
- DSM Biotechnology Center, R&D, P.O. Box 1, 2600 AM Delft, The Netherlands
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Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00696-15. [PMID: 26159522 PMCID: PMC4490843 DOI: 10.1128/genomea.00696-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bacillus subtilis, which belongs to the phylum Firmicutes, is the most widely studied Gram-positive model organism. It is found in a wide variety of environments and is particularly abundant in soils and in the gastrointestinal tracts of ruminants and humans. Here, we present the complete genome sequence of the newly described B. subtilis strain UD1022. The UD1022 genome consists of a 4.025-Mbp chromosome, and other major findings from our analysis will provide insights into the genomic basis of it being a plant growth-promoting rhizobacterium (PGPR) with biocontrol potential.
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Involvement of Colonizing Bacillus Isolates in Glucovanillin Hydrolysis during the Curing of Vanilla planifolia Andrews. Appl Environ Microbiol 2015; 81:4947-54. [PMID: 25979899 DOI: 10.1128/aem.00458-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/11/2015] [Indexed: 11/20/2022] Open
Abstract
Vanilla beans were analyzed using biochemical methods, which revealed that glucovanillin disperses from the inner part to the outer part of the vanilla bean during the curing process and is simultaneously hydrolyzed by β-d-glucosidase. Enzymatic hydrolysis was found to occur on the surface of the vanilla beans. Transcripts of the β-d-glucosidase gene (bgl) of colonizing microorganisms were detected. The results directly indicate that colonizing microorganisms are involved in glucovanillin hydrolysis. Phylogenetic analysis based on 16S rRNA gene sequences showed that the colonizing microorganisms mainly belonged to the Bacillus genus. bgl was detected in all the isolates and presented clustering similar to that of the isolate taxonomy. Furthermore, inoculation of green fluorescent protein-tagged isolates showed that the Bacillus isolates can colonize vanilla beans. Glucovanillin was metabolized as the sole source of carbon in a culture of the isolates within 24 h. These isolates presented unique glucovanillin degradation capabilities. Vanillin was the major volatile compound in the culture. Other compounds, such as α-cubebene, β-pinene, and guaiacol, were detected in some isolate cultures. Colonizing Bacillus isolates were found to hydrolyze glucovanillin in culture, indirectly demonstrating the involvement of colonizing Bacillus isolates in glucovanillin hydrolysis during the vanilla curing process. Based on these results, we conclude that colonizing Bacillus isolates produce β-d-glucosidase, which mediates glucovanillin hydrolysis and influences flavor formation.
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Caamaño-Antelo S, Fernández-No I, Böhme K, Ezzat-Alnakip M, Quintela-Baluja M, Barros-Velázquez J, Calo-Mata P. Genetic discrimination of foodborne pathogenic and spoilage Bacillus spp. based on three housekeeping genes. Food Microbiol 2015; 46:288-298. [DOI: 10.1016/j.fm.2014.08.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/17/2014] [Indexed: 11/28/2022]
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Torres MJ, Petroselli G, Daz M, Erra-Balsells R, Audisio MC. Bacillus subtilis subsp. subtilis CBMDC3f with antimicrobial activity against Gram-positive foodborne pathogenic bacteria: UV-MALDI-TOF MS analysis of its bioactive compounds. World J Microbiol Biotechnol 2015; 31:929-40. [PMID: 25820813 DOI: 10.1007/s11274-015-1847-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/21/2015] [Indexed: 02/07/2023]
Abstract
In this work a new Bacillus sp. strain, isolated from honey, was characterized phylogenetically. Its antibacterial activity against three relevant foodborne pathogenic bacteria was studied; the main bioactive metabolites were analyzed using ultraviolet matrix assisted laser desorption-ionization mass spectrometry (UV-MALDI MS). Bacillus CBMDC3f was phylogenetically characterized as Bacillus subtilis subsp. subtilis after rRNA analysis of the 16S subunit and the gyrA gene (access codes Genbank JX120508 and JX120516, respectively). Its antibacterial potential was evaluated against Listeria monocytogenes (9 strains), B. cereus (3 strains) and Staphylococcus aureus ATCC29213. Its cell suspension and cell-free supernatant (CFS) exerted significant anti-Listeria and anti-S. aureus activities, while the lipopeptides fraction (LF) also showed anti-B. cereus effect. The UV-MALDI-MS analysis revealed surfactin, iturin and fengycin in the CFS, whereas surfactin predominated in the LF. The CFS from CBMDC3f contained surfactin, iturin and fengycin with four, two and four homologues per family, respectively, whereas four surfactin, one iturin and one fengycin homologues were identified in the LF. For some surfactin homologues, their UV-MALDI-TOF/TOF (MS/MS; Laser Induced Decomposition method, LID) spectra were also obtained. Mass spectrometry analysis contributed with relevant information about the type of lipopeptides that Bacillus strains can synthesize. From our results, surfactin would be the main metabolite responsible for the antibacterial effect.
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Affiliation(s)
- M J Torres
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Av.Bolivia 5150, 4400, Salta, Argentina
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45
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Webber DM, Hettiarachchy NS, Li R, Horax R, Theivendran S. Phenolic Profile and Antioxidant Activity of Extracts Prepared from Fermented Heat-Stabilized Defatted Rice Bran. J Food Sci 2014; 79:H2383-91. [DOI: 10.1111/1750-3841.12658] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/14/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel M. Webber
- College of Medicine; Dept. of Pediatrics; Univ. of Arkansas for Medical Sciences; 13 Children's Way Little Rock AR 72202 U.S.A
| | - Navam S. Hettiarachchy
- Dept. of Food Science; Dale Bumpers College of Agricultural, Food & Life Science; Univ. of Arkansas; 2650 N. Young Ave Fayetteville AR 72704 U.S.A
| | - Ruiqi Li
- Dept. of Food Science; Dale Bumpers College of Agricultural, Food & Life Science; Univ. of Arkansas; 2650 N. Young Ave Fayetteville AR 72704 U.S.A
| | - Ronny Horax
- Dept. of Food Science; Dale Bumpers College of Agricultural, Food & Life Science; Univ. of Arkansas; 2650 N. Young Ave Fayetteville AR 72704 U.S.A
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46
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Ashe S, Maji UJ, Sen R, Mohanty S, Maiti NK. Specific oligonucleotide primers for detection of endoglucanase positive Bacillus subtilis by PCR. 3 Biotech 2014; 4:461-465. [PMID: 28324377 PMCID: PMC4162904 DOI: 10.1007/s13205-013-0177-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/19/2013] [Indexed: 11/27/2022] Open
Abstract
A polymerase chain reaction (PCR) assay was developed for discrimination of Bacillus subtilis from other members of B. subtilis group as well as rapid identification from environmental samples. Primers ENIF and EN1R from endoglucanase gene were used to amplify a1311 bp DNA fragment. The specificity of the primers was tested with seven reference strains and 28 locally isolated strains of endoglucanase positive Bacillus species. The PCR product was only produced from B. subtilis. The results demonstrated high specificity of two oligonucleotides for B. subtilis. This species-specific PCR method provides a quick, simple, powerful and reliable alternative to conventional methods in the detection and identification of B. subtilis. To our knowledge this is the first report of a B. subtilis specific primer set.
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Affiliation(s)
- S Ashe
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar, 751002, Orissa, India
| | - U J Maji
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar, 751002, Orissa, India
| | - R Sen
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar, 751002, Orissa, India
| | - S Mohanty
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar, 751002, Orissa, India
| | - N K Maiti
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar, 751002, Orissa, India.
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Sirec T, Cangiano G, Baccigalupi L, Ricca E, Isticato R. The spore surface of intestinal isolates ofBacillus subtilis. FEMS Microbiol Lett 2014; 358:194-201. [DOI: 10.1111/1574-6968.12538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/14/2014] [Accepted: 07/14/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Teja Sirec
- Department of Biology; University of Naples Federico II; Naples Italy
| | | | | | - Ezio Ricca
- Department of Biology; University of Naples Federico II; Naples Italy
| | - Rachele Isticato
- Department of Biology; University of Naples Federico II; Naples Italy
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Alzahrani OM, Moir A. Spore germination and germinant receptor genes in wild strains of Bacillus subtilis. J Appl Microbiol 2014; 117:741-9. [PMID: 24916603 DOI: 10.1111/jam.12566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 11/25/2022]
Abstract
AIMS To compare the germination of laboratory and wild strains of Bacillus subtilis. METHODS AND RESULTS The spore germination of B. subtilis 168 (subsp. subtilis) was compared with that of the laboratory strain W23 (subsp. spizizenii) and desert-sourced isolates, including one member of subsp. subtilis (RO-NN-1), strains TU-B-10, RO-E-2, N10 and DV1-B-1, (all subsp. spizizenii), the B. mojavensis strain RO-H-1 and a B. subtilis natto strain. All germinated in L-alanine, although some were slower, and some 10-fold less sensitive to germinant. All germinated in calcium dipicolinate (CaDPA). Germination in asparagine, glucose, fructose + KCl was slow and incomplete in many of the strains, and decoating RO-NN-1 and W23 spores did not restore germination rates. Comparing the sequences of B. subtilis strains 168, RO-NN-1, W23, TU-B-10 and DV1-B-1, the operons encoding GerA, B and K germinant receptors were intact, although the two additional operons yndDEF and yfkQRST had suffered deletions or were absent in several spizizenii strains. CONCLUSIONS Wild strains possess an efficient germination machinery for L-alanine germination. AGFK germination is often less efficient, the gerB genes more diverged, and the two germinant receptor operons of unknown function have been lost from the genome in many subsp. spizizenii strains. SIGNIFICANCE AND IMPACT OF THE STUDY The two major subspecies of B. subtilis have conserved GerA receptor function, confirming its importance, at least in the natural environments of these strains.
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Affiliation(s)
- O M Alzahrani
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK; Department of Biotechnology, Taif University, Taif, Saudi Arabia
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Chandna P, Mayilraj S, Kuhad RC. Bacillus paraflexus sp. nov., isolated from compost. Int J Syst Evol Microbiol 2013; 63:4735-4743. [DOI: 10.1099/ijs.0.048223-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium capable of growing at 15–42 °C (optimum 30 °C) and at pH 5–11 (optimum pH 7) was isolated from compost. Its taxonomic position was deduced using a polyphasic approach and the strain was designated RC2T. 16S rRNA gene sequence analysis showed that the isolate belongs to the division
Firmicutes
, forming a clade within the cluster containing
Bacillus flexus
IFO 15715T, and showed highest similarity to
B. flexus
IFO 15715T (98.1 %). The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids of the novel strain were iso-C15:0 (36.83 %), anteiso-C15:0 (49.19 %) and C16:0 (5.19 %). DNA–DNA hybridization between strain RC2T and
B. flexus
DSM 1320T showed a level of relatedness of 54.5 %. The polar lipid profile of strain RC2T showed the presence of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was MK-7 and the G+C content of strain RC2T was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain RC2T was clearly distinguished from closely related members of the genus, and the strain is assigned to a novel species, for which the name Bacillus paraflexus sp. nov. is proposed. The type strain is RC2T ( = MTCC 9831T = MCC 2100T = KCTC 13724T = CCM 7754T).
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Affiliation(s)
- Piyush Chandna
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection (MTCC), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160 036, India
| | - Ramesh Chander Kuhad
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India
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Genomic insights into the taxonomic status of the three subspecies of Bacillus subtilis. Syst Appl Microbiol 2013; 37:95-9. [PMID: 24231292 DOI: 10.1016/j.syapm.2013.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 08/14/2013] [Accepted: 09/27/2013] [Indexed: 11/20/2022]
Abstract
Bacillus subtilis contains three subspecies, i.e., subspecies subtilis, spizizenii, and inaquosorum. As these subspecies are phenotypically indistinguishable, their differentiation has relied on phylogenetic analysis of multiple protein-coding gene sequences. B. subtilis subsp. inaquosorum is a recently proposed taxon that encompasses strain KCTC 13429(T) and related strains, which were previously classified as members of subspecies spizizenii. However, DNA-DNA hybridization (DDH) values among the three subspecies raised a question as to their independence. Thus, we evaluated the taxonomic status of subspecies inaquosorum using genome-based comparative analysis. In contrast to the previous experimental values of DDH, the inter-genomic relatedness inferred by average nucleotide identity (ANI) values indicated that subspecies inaquosorum and spizizenii were sufficiently different from subspecies subtilis and hence raised the possibility that the former two could be classified as separate species from B. subtilis. The genome-based tree also supported the separation of the two subspecies from B. subtilis. The exclusive presence of a subtilin synthesis system in subspecies spizizenii was a remarkable genetic characteristic that could even distinguish subspecies spizizenii from subspecies inaquosorum in addition to the low ANI values (<95%). Conclusively, the genome-based data obtained in this study demonstrated that subspecies inaquosorum and spizizenii are clearly distinguished from subspecies subtilis, and raises the possibility that these two subspecies could be classified as separate species from B. subtilis. In addition, the low ANI values between subspecies inaquosorum and spizizenii and the exclusive presence of subtilin synthesis genes in subspecies spizizenii also suggest circumscription of these two subspecies at the species level.
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