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Sorour AA, Khairy H, Zaghloul EH, Zaghloul HAH. Microbe- plant interaction as a sustainable tool for mopping up heavy metal contaminated sites. BMC Microbiol 2022; 22:174. [PMID: 35799112 PMCID: PMC9261045 DOI: 10.1186/s12866-022-02587-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 06/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phytoremediation is a green technology that removes heavy metal (HM) contamination from the environment by using HM plant accumulators. Among soil microbiota, plant growth promoting bacteria (PGPR) have a role influencing the metal availability and uptake. METHODS This current study evaluates the plant growth promoting qualities of microbial flora isolated from rhizosphere, plant roots, and marine aquatic HMs polluted environments in Alexandria through several biochemical and molecular traits. Metal contents in both collected soils and plant tissues were measured. Transcript levels of marker genes (HMA3 and HMA4) were analyzed. RESULTS Three terrestrial and one aquatic site were included in this study based on the ICP-MS identification of four HMs (Zn, Cd, Cu, and Ni) or earlier reports of HMs contamination. Using the VITEK2 bacterial identification system, twenty-two bacteria isolated from these loci were biochemically described. Pseudomonas and Bacillus were the most dominant species. Furthermore, the soil microbiota collected from the most contaminated HMs site with these two were able to enhance the Helianthus annuus L. hyper-accumulation capacity significantly. Specifically, sunflower plants cultivated in soils with HMs adapted bacteria were able to accumulate about 1.7-2.5-folds more Zn and Cd in their shoots, respectively. CONCLUSION The influence of PGPR to stimulate crop growth under stress is considered an effective strategy. Overall, our findings showed that plants cultivated in HMs contaminated sites in the presence of PGPR were able to accumulate significant amounts of HMs in several plant parts than those cultivated in soils lacking microbiota.
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Affiliation(s)
- Ahmed A Sorour
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharam Bek, Alexandria, 21511, Egypt
| | - Heba Khairy
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharam Bek, Alexandria, 21511, Egypt
| | - Eman H Zaghloul
- National Institute of Oceanography and Fisheries, NIOF, Cairo, Egypt
| | - Heba A H Zaghloul
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharam Bek, Alexandria, 21511, Egypt.
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A Novel Microbial Zearalenone Transformation through Phosphorylation. Toxins (Basel) 2021; 13:toxins13050294. [PMID: 33919181 PMCID: PMC8143168 DOI: 10.3390/toxins13050294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
Zearalenone (ZEA) is a mycotoxin widely occurring in many agricultural commodities. In this study, a purified bacterial isolate, Bacillus sp. S62-W, obtained from one of 104 corn silage samples from various silos located in the United States, exhibited activity to transform the mycotoxin ZEA. A novel microbial transformation product, ZEA-14-phosphate, was detected, purified, and identified by HPLC, LC-MS, and NMR analyses. The isolate has been identified as belonging to the genus Bacillus according to phylogenetic analysis of the 16S rRNA gene and whole genome alignments. The isolate showed high efficacy in transforming ZEA to ZEA-14-phosphate (100% transformation within 24 h) and possessed advantages of acid tolerance (work at pH = 4.0), working under a broad range of temperatures (22–42 °C), and a capability of transforming ZEA at high concentrations (up to 200 µg/mL). In addition, 23 Bacillus strains of various species were tested for their ZEA phosphorylation activity. Thirteen of the Bacillus strains showed phosphorylation functionality at an efficacy of between 20.3% and 99.4% after 24 h incubation, suggesting the metabolism pathway is widely conserved in Bacillus spp. This study established a new transformation system for potential application of controlling ZEA although the metabolism and toxicity of ZEA-14-phosphate requires further investigation.
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Behera BK, Chakraborty HJ, Patra B, Rout AK, Dehury B, Das BK, Sarkar DJ, Parida PK, Raman RK, Rao AR, Rai A, Mohapatra T. Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India. Front Microbiol 2020; 11:556136. [PMID: 33178147 PMCID: PMC7596357 DOI: 10.3389/fmicb.2020.556136] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/22/2020] [Indexed: 01/21/2023] Open
Abstract
In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus-Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.
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Affiliation(s)
- Bijay Kumar Behera
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Hirak Jyoti Chakraborty
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Biswanath Patra
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Budheswar Dehury
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Dhruba Jyoti Sarkar
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Pranaya Kumar Parida
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Rohan Kumar Raman
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Genetic Clearness Novel Strategy of Group I Bacillus Species Isolated from Fermented Food and Beverages by Using Fibrinolytic Enzyme Gene Encoding a Serine-Like Enzyme. J Nucleic Acids 2019; 2019:5484896. [PMID: 31236291 PMCID: PMC6545797 DOI: 10.1155/2019/5484896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/28/2019] [Indexed: 11/18/2022] Open
Abstract
Fibrinolytic enzyme gene (fibE) is widely conserved among Bacillus spp. belonging to group I species. This is encoding a serine-like enzyme (FibE) secreted in extracellular medium. This present work aims to assess the molecular usefulness of this novel conserved housekeeping gene among group I Bacillus spp. to identify and discriminate some related strains in traditional fermented food and beverages in Republic of Congo. First of all 155 isolates have been screened for enzymatic activities using caseinolytic assays. PCR techniques and nested PCR method using specific primers and correlated with 16S RNA sequencing were used. Blotting techniques have been performed for deep comparison with molecular methods. As a result B. amyloliquefaciens (1), B. licheniformis (1), B. subtilis (1), B. pumilus (3), B. altitudinis (2), B. atrophaeus (1), and B. safensis (3) have been specifically identified among 155 isolates found in fermented food and beverages. Genetic analysis and overexpression of glutathione S-transferases (GSTs) fused to mature protein of FibE in Escherichia coli BL21 and TOP10 showed 2-fold higher enzymatic activities by comparison with FibE wild type one. Immunodetection should be associated but this does not clearly discriminate Bacillus belonging to group I.
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Davidson P, Eutsey R, Redler B, Hiller NL, Laub MT, Durand D. Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes. PLoS Genet 2018; 14:e1007470. [PMID: 30212463 PMCID: PMC6136694 DOI: 10.1371/journal.pgen.1007470] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
The evolution of signal transduction pathways is constrained by the requirements of signal fidelity, yet flexibility is necessary to allow pathway remodeling in response to environmental challenges. A detailed understanding of how flexibility and constraint shape bacterial two component signaling systems is emerging, but how new signal transduction architectures arise remains unclear. Here, we investigate pathway remodeling using the Firmicute sporulation initiation (Spo0) pathway as a model. The present-day Spo0 pathways in Bacilli and Clostridia share common ancestry, but possess different architectures. In Clostridium acetobutylicum, sensor kinases directly phosphorylate Spo0A, the master regulator of sporulation. In Bacillus subtilis, Spo0A is activated via a four-protein phosphorelay. The current view favors an ancestral direct phosphorylation architecture, with the phosphorelay emerging in the Bacillar lineage. Our results reject this hypothesis. Our analysis of 84 broadly distributed Firmicute genomes predicts phosphorelays in numerous Clostridia, contrary to the expectation that the Spo0 phosphorelay is unique to Bacilli. Our experimental verification of a functional Spo0 phosphorelay encoded by Desulfotomaculum acetoxidans (Class Clostridia) further supports functional phosphorelays in Clostridia, which strongly suggests that the ancestral Spo0 pathway was a phosphorelay. Cross complementation assays between Bacillar and Clostridial phosphorelays demonstrate conservation of interaction specificity since their divergence over 2.7 BYA. Further, the distribution of direct phosphorylation Spo0 pathways is patchy, suggesting multiple, independent instances of remodeling from phosphorelay to direct phosphorylation. We provide evidence that these transitions are likely the result of changes in sporulation kinase specificity or acquisition of a sensor kinase with specificity for Spo0A, which is remarkably conserved in both architectures. We conclude that flexible encoding of interaction specificity, a phenotype that is only intermittently essential, and the recruitment of kinases to recognize novel environmental signals resulted in a consistent and repeated pattern of remodeling of the Spo0 pathway. Survival in a changing world requires signal transduction circuitry that can evolve to sense and respond to new environmental challenges. The Firmicute sporulation initiation (Spo0) pathway is a compelling example of a pathway with a circuit diagram that has changed over the course of evolution. In Clostridium acetobutylicum, a sensor kinase directly activates the master regulator of sporulation, Spo0A. In Bacillus subtilis, Spo0A is activated indirectly via a four-protein phosphorelay. These early observations suggested that the ancestral Spo0A was directly phosphorylated by a kinase in the earliest spore-former and that the Spo0 phosphorelay arose later in Bacilli via gain of additional proteins and interactions. Our analysis, based on a much larger set of genomes, surprisingly reveals phosphorelays, not only in Bacilli, but in many Clostridia. These findings support a model wherein sporulation was initiated by a Spo0 phosphorelay in the ancestral spore-former and the direct phosphorylation Spo0 pathways, which are observed in distinct sets of Clostridial taxa, are the result of convergent, reductive evolution. Further, our evidence suggests that these remodeling events were mediated by changes in kinase specificity, implicating flexible pathway remodeling, potentially combined with the recruitment of kinases, in Spo0 pathway evolution.
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Affiliation(s)
- Philip Davidson
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rory Eutsey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Brendan Redler
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - N. Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania, United States of America
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dannie Durand
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Gao YC, Guo SH, Wang JN, Zhang W, Chen GH, Wang H, Du J, Liu Y, Naidu R. Novel Bacillus cereus strain from electrokinetically remediated saline soil towards the remediation of crude oil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:26351-26360. [PMID: 29981021 DOI: 10.1007/s11356-018-2495-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
A new strain SWH-15 was successfully isolated after initial electrokinetic remediation experiment using the same saline soil sampled from Shengli Oilfield, China. Four methods (morphological and biochemical characteristics, whole-cell fatty acid methyl esters (FAMEs) analysis, 16S rRNA sequence analysis and DNA G + C content and DNA-DNA hybridization analysis) were used to identify the taxonomic status of SWH-15 and confirmed that SWH-15 was a novel species of the Bacillus (B.) cereus group. Then, we assessed the degrading ability of the novel strain SWH-15 to crude oil through a microcosm experiment with four treatments, including control (CK), bioremediation using SWH-15 (Bio), electrokinetic remediation (EK), and combined bioremediation and electrokinetic remediation (Bio + EK). The results showed that the Bio + EK combined remediation treatment was more effective than the CK, Bio, and EK treatments in degrading crude oil contaminants. Bioaugmentation, by addition of the strain SWH-15 had synergistic effect with EK in Bio + EK treatment. Bacterial community analysis showed that electrokinetic remediation alone significantly altered the bacterial community of the saline soil. The addition of the strain SWH-15 alone had a weak effect on the bacterial community. However, the strain SWH-15 boosted the growth of other bacterial species in the metabolic network and weakened the impact of electrical field on the whole bacterial community structure in the Bio + EK treatment.
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Affiliation(s)
- Yong-Chao Gao
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Shu-Hai Guo
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China.
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China.
| | - Jia-Ning Wang
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Wen Zhang
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Guan-Hong Chen
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Hui Wang
- School of Resources and Environment, University of Jinan, Jinan, 250022, China
| | - Jianhua Du
- Global Centre for Environmental Remediation, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Yanju Liu
- Global Centre for Environmental Remediation, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Ravi Naidu
- Global Centre for Environmental Remediation, University of Newcastle, Callaghan, NSW, 2308, Australia
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Jacquemyn H, Lenaerts M, Tyteca D, Lievens B. Microbial diversity in the floral nectar of seven Epipactis (Orchidaceae) species. Microbiologyopen 2013; 2:644-58. [PMID: 23836678 PMCID: PMC3948608 DOI: 10.1002/mbo3.103] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/23/2013] [Accepted: 05/28/2013] [Indexed: 11/16/2022] Open
Abstract
Floral nectar of animal-pollinated plants is commonly infested with microorganisms, yet little is known about the microorganisms inhabiting the floral nectar of orchids. In this study, we investigated microbial communities occurring in the floral nectar of seven Epipactis (Orchidaceae) species. Culturable bacteria and yeasts were isolated and identified by partially sequencing the small subunit (SSU) ribosomal RNA (rRNA) gene and the D1/D2 domains of the large subunit (LSU) rRNA gene, respectively. Using three different culture media, we found that bacteria were common inhabitants of the floral nectar of Epipactis. The most widely distributed bacterial operational taxonomic units (OTUs) in nectar of Epipactis were representatives of the family of Enterobacteriaceae, with an unspecified Enterobacteriaceae bacterium as the most common. In contrast to previous studies investigating microbial communities in floral nectar, very few yeast species (mainly of the genus Cryptococcus) were observed, and most of them occurred in very low densities. Total OTU richness (i.e., the number of bacterial and yeast OTUs per orchid species) varied between 4 and 20. Cluster analysis revealed that microbial communities of allogamous species differed from those of autogamous and facultatively autogamous species. This study extends previous efforts to identify microbial communities in floral nectar and indicates that the floral nectar of the orchids investigated mainly contained bacterial communities with moderate phylogenetic diversity.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/growth & development
- Bacteria/isolation & purification
- Biodiversity
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fungi/classification
- Fungi/genetics
- Fungi/growth & development
- Fungi/isolation & purification
- Genes, rRNA
- Molecular Sequence Data
- Orchidaceae/microbiology
- Phylogeny
- Plant Nectar
- RNA, Bacterial/genetics
- RNA, Fungal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Hans Jacquemyn
- Plant Conservation and Population Biology Biology Department, KU LeuvenKasteelpark Arenberg 31, B-3001, Heverlee, Belgium
| | - Marijke Lenaerts
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Thomas More University College, De Nayer Campus Department of Microbial and Molecular Systems (MS), KU Leuven AssociationB-2860, Sint-Katelijne-Waver, Belgium
- Scientia Terrae Research InstituteB-2860 Sint-Katelijne-Waver, Belgium
| | - Daniel Tyteca
- Biodiversity Research Centre Earth and Life Institute, Université catholique de LouvainB-1348, Louvain-la-Neuve, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Thomas More University College, De Nayer Campus Department of Microbial and Molecular Systems (MS), KU Leuven AssociationB-2860, Sint-Katelijne-Waver, Belgium
- Scientia Terrae Research InstituteB-2860 Sint-Katelijne-Waver, Belgium
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Hassi M, Guendouzi SE, Haggoud A, David S, Ibnsouda S, Houari A, Iraqui M. Antimycobacterial activity of a Brevibacillus laterosporusstrain isolated from a moroccan soil. Braz J Microbiol 2012; 43:1516-22. [PMID: 24031983 PMCID: PMC3769022 DOI: 10.1590/s1517-838220120004000036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/07/2012] [Indexed: 11/30/2022] Open
Abstract
The treatment of tuberculosis has become more difficult with the worldwide spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis. Moreover, the prevalence of human disease caused by atypical mycobacteria has also increased in the past two decades and has further complicated the problem of the treatment of mycobacterial infections. It is therefore urgent to develop new highly active molecules against these bacteria. The present study reports the isolation from a Moroccan soil of a Bacillus strain that exhibits an important antimycobacterial activity. The strain was identified as Brevibacillus laterosporus using DNA sequencing of the 16S ribosomal RNA gene. The antimycobacterial activity was assigned to a substance with a protein nature. This nature was revealed using a liquid-liquid extraction with organic solvents, precipitation with ammonium sulfate and treatment with a protease. This study suggested the identification and the characterization of this active metabolite enabling therapeutic investigations further.
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Affiliation(s)
- Mohammed Hassi
- Laboratoire de Biotechnologie Microbienne, Faculté des Sciences et Techniques de Fès , B.P: 2202, Fès , Maroc
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9
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Eppinger M, Bunk B, Johns MA, Edirisinghe JN, Kutumbaka KK, Koenig SSK, Huot Creasy H, Rosovitz MJ, Riley DR, Daugherty S, Martin M, Elbourne LDH, Paulsen I, Biedendieck R, Braun C, Grayburn S, Dhingra S, Lukyanchuk V, Ball B, Ul-Qamar R, Seibel J, Bremer E, Jahn D, Ravel J, Vary PS. Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319. J Bacteriol 2011; 193:4199-213. [PMID: 21705586 PMCID: PMC3147683 DOI: 10.1128/jb.00449-11] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 06/10/2011] [Indexed: 11/20/2022] Open
Abstract
Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key species and of particular importance in understanding genome evolution, dynamics, and plasticity in the bacilli. B. megaterium is a commercially available, nonpathogenic host for the biotechnological production of several substances, including vitamin B(12), penicillin acylase, and amylases. Here, we report the analysis of the first complete genome sequences of two important B. megaterium strains, the plasmidless strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The 5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551 plasmids represent a combined 417 kb and 523 genes, one of the largest plasmid arrays sequenced in a single bacterial strain. We have documented extensive gene transfer between the plasmids and the chromosome. Each strain carries roughly 300 strain-specific chromosomal genes that account for differences in their experimentally confirmed phenotypes. B. megaterium is able to synthesize vitamin B(12) through an oxygen-independent adenosylcobalamin pathway, which together with other key energetic and metabolic pathways has now been fully reconstructed. Other novel genes include a second ftsZ gene, which may be responsible for the large cell size of members of this species, as well as genes for gas vesicles, a second β-galactosidase gene, and most but not all of the genes needed for genetic competence. Comprehensive analyses of the global Bacillus gene pool showed that only an asymmetric region around the origin of replication was syntenic across the genus. This appears to be a characteristic feature of the Bacillus spp. genome architecture and may be key to their sporulating lifestyle.
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Affiliation(s)
- Mark Eppinger
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Boyke Bunk
- German Collection for Microorganisms and Cell Cultures, Braunschweig 38124, Germany
| | - Mitrick A. Johns
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Janaka N. Edirisinghe
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Kirthi K. Kutumbaka
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Sara S. K. Koenig
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Heather Huot Creasy
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | | | - David R. Riley
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Sean Daugherty
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Madeleine Martin
- Technische Universität Braunschweig, Institute of Microbiology, Braunschweig 38106, Germany
| | - Liam D. H. Elbourne
- Macquarie University, Department of Chemistry and Biomolecular Sciences, Sydney 2109, Australia
| | - Ian Paulsen
- Macquarie University, Department of Chemistry and Biomolecular Sciences, Sydney 2109, Australia
| | - Rebekka Biedendieck
- Technische Universität Braunschweig, Institute of Microbiology, Braunschweig 38106, Germany
| | - Christopher Braun
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Scott Grayburn
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Sourabh Dhingra
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Vitaliy Lukyanchuk
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Barbara Ball
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Riaz Ul-Qamar
- Technische Universität Braunschweig, Institute of Microbiology, Braunschweig 38106, Germany
| | - Jürgen Seibel
- Julius-Maximilians-Universität Würzburg, Institute of Organic Chemistry, Würzburg 97074, Germany
| | - Erhard Bremer
- Philipps-Universität Marburg, Laboratory for Molecular Microbiology, Marburg 35043, Germany
| | - Dieter Jahn
- Technische Universität Braunschweig, Institute of Microbiology, Braunschweig 38106, Germany
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Patricia S. Vary
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
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