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Malesevic M, Stanisavljevic N, Matijasevic D, Curcic J, Tasic V, Tasic S, Kojic M. Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia. MICROBIAL ECOLOGY 2023; 86:2344-2356. [PMID: 37222803 DOI: 10.1007/s00248-023-02242-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023]
Abstract
The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.
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Affiliation(s)
- Milka Malesevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia.
| | - Nemanja Stanisavljevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Danka Matijasevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Jovana Curcic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Vukasin Tasic
- Faculty of Informatics and Computing, Singidunum University, Belgrade, Serbia
| | - Srdjan Tasic
- The Academy of Applied Technical and Preschool Studies, Nis, Serbia
| | - Milan Kojic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
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Lai R, Lin M, Yan Y, Jiang S, Zhou Z, Wang J. Comparative Genomic Analysis of a Thermophilic Protease-Producing Strain Geobacillus stearothermophilus H6. Genes (Basel) 2023; 14:466. [PMID: 36833392 PMCID: PMC9956924 DOI: 10.3390/genes14020466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The genus Geobacillus comprises thermophilic gram-positive bacteria which are widely distributed, and their ability to withstand high temperatures makes them suitable for various applications in biotechnology and industrial production. Geobacillus stearothermophilus H6 is an extremely thermophilic Geobacillus strain isolated from hyperthermophilic compost at 80 °C. Through whole-genome sequencing and genome annotation analysis of the strain, the gene functions of G. stearothermophilus H6 were predicted and the thermophilic enzyme in the strain was mined. The G. stearothermophilus H6 draft genome consisted of 3,054,993 bp, with a genome GC content of 51.66%, and it was predicted to contain 3750 coding genes. The analysis showed that strain H6 contained a variety of enzyme-coding genes, including protease, glycoside hydrolase, xylanase, amylase and lipase genes. A skimmed milk plate experiment showed that G. stearothermophilus H6 could produce extracellular protease that functioned at 60 °C, and the genome predictions included 18 secreted proteases with signal peptides. By analyzing the sequence of the strain genome, a protease gene gs-sp1 was successfully screened. The gene sequence was analyzed and heterologously expressed, and the protease was successfully expressed in Escherichia coli. These results could provide a theoretical basis for the development and application of industrial strains.
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Affiliation(s)
- Ruilin Lai
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China
- Key Laboratory of Agricultural Microbiome (MARA), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Min Lin
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China
- Key Laboratory of Agricultural Microbiome (MARA), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongliang Yan
- Key Laboratory of Agricultural Microbiome (MARA), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shijie Jiang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China
| | - Zhengfu Zhou
- Key Laboratory of Agricultural Microbiome (MARA), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jin Wang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China
- Key Laboratory of Agricultural Microbiome (MARA), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Lal R, Singh B, Sar P, Phale P. Microbiology in India: Status, Challenges, and Scope. Environ Microbiol 2022; 24:2607-2611. [PMID: 35411614 DOI: 10.1111/1462-2920.16005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Rup Lal
- The Energy & Resources Institute, New Delhi, 110003, India
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Pinaki Sar
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Prashant Phale
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
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Khaswal A, Chaturvedi N, Mishra SK, Kumar PR, Paul PK. Current status and applications of genus Geobacillus in the production of industrially important products-a review. Folia Microbiol (Praha) 2022; 67:389-404. [PMID: 35229277 DOI: 10.1007/s12223-022-00961-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/19/2022] [Indexed: 11/25/2022]
Abstract
The genus Geobacillus is one of the most important genera which mainly comprises gram-positive thermophilic bacterial strains including obligate aerobes, denitrifiers and facultative anaerobes having capability of endospore formation as well. The genus Geobacillus is widely distributed in nature and mostly abundant in extreme locations such as cool soils, hot springs, hydrothermal vents, marine trenches, hay composts and dairy plants. Due to plasticity towards environmental adaptation, the Geobacillus sp. shows remarkable genome diversification and acquired many beneficial properties, which facilitates their exploitation for many biotechnological applications. Many thermophiles are of biotechnological importance and having considerable interest in commercial applications for the production of industrially important products. Recently, due to catabolic versatility especially in the degradation of hemicellulose and starch containing agricultural waste and rapid growth rates, these microorganisms show potential for the production of biofuels, thermostable enzymes and bioremediation. This review mainly summarizes the status of Geobacillus sp. including its notable properties, biotechnological studies and its potential application in the production of industrially important products.
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Affiliation(s)
- Ashutosh Khaswal
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India
| | - Neha Chaturvedi
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India
| | - Santosh Kumar Mishra
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India.
| | - Priya Ranjan Kumar
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India
| | - Prabir Kumar Paul
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India
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The Alphabet of the Elementary Microbiology: Revisited. Indian J Microbiol 2021; 61:397-400. [PMID: 34629565 PMCID: PMC8492822 DOI: 10.1007/s12088-021-00987-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Abstract
With the advent of metagenomics, a quest began to identify the dynamics of the microbial communities in different ecological niches. Altogether, this has resulted in identification of microorganisms but is limited to only a small number of phylogenetic groups that can be easily cultured. The majority of metagenomic sequencing data remains unassigned to any known microbial group and is regarded as the "microbial dark matter." Our group is now working on integrating culturomics (isolation of pure cultures) and metagenomics from extreme environments, particularly from hot water springs and chemically contaminated soils. Our target is to culture the rare extremophiles with biotechnological significance by designing culture media based on inputs from metagenomics. While culturomics integrated with metagenomics has been extensively employed for updating the microbial catalog from the human gut, there is a need to extend this approach to extreme environmental settings to explore the microbial dark matter.
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Affiliation(s)
- Utkarsh Sood
- The Energy and Resources Institute, New Delhi, India
| | - Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhigrid.8195.5, New Delhi, India
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Singh P, Hira P, Rawat CD, Lal R, Sood U. Genome-based reclassification of Amycolatopsis eurytherma as a later heterotypic synonym of Amycolatopsis thermoflava. Int J Syst Evol Microbiol 2021; 71. [PMID: 33470925 DOI: 10.1099/ijsem.0.004642] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The present study was carried out to clarify the taxonomic assignment of two closely related Amycolatopsis species. Genomic information for 48 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Amycolatopsis eurytherma Kim et al. 2002 and Amycolatopsis thermoflava Chun et al. 1999, are conspecific. The 16S rRNA gene sequences of the two species possess 98.85 % sequence similarity. Further, whole-genome comparisons showed that A. eurytherma DSM 44348T and A. thermoflava N1165T shared 98.75 % average nucleotide identity, 98.63 % average amino acid identity and 87.8 % digital DNA-DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. eurytherma DSM 44348T and A. thermoflava N1165T formed a monophyletic clade. Based on this evidence we propose the reclassification of Amycolatopsis eurytherma Kim et al. 2002 as a later heterotypic synonym of Amycolatopsis thermoflava Chun et al. 1999.
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Affiliation(s)
- Priya Singh
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, New Delhi-110019, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, New Delhi-110021, India
| | - Charu Dogra Rawat
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi-110007, India
| | - Rup Lal
- The Energy and Resources Institute, Lodhi Road, New Delhi-110003, India
| | - Utkarsh Sood
- The Energy and Resources Institute, Lodhi Road, New Delhi-110003, India
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Patel SKS, Gupta RK, Kim SY, Kim IW, Kalia VC, Lee JK. Rhus vernicifera Laccase Immobilization on Magnetic Nanoparticles to Improve Stability and Its Potential Application in Bisphenol A Degradation. Indian J Microbiol 2020; 61:45-54. [PMID: 33505092 DOI: 10.1007/s12088-020-00912-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
In the present study, Rhus vernicifera laccase (RvLac) was immobilized through covalent methods on the magnetic nanoparticles. Fe2O3 and Fe3O4 nanoparticles activated by 3-aminopropyltriethoxysilane followed with glutaraldehyde showed maximum immobilization yields and relative activity up to 81.4 and 84.3% at optimum incubation and pH of 18 h and 5.8, respectively. The maximum RvLac loading of 156 mg/g of support was recorded on Fe2O3 nanoparticles. A higher optimum pH and temperature of 4.0 and 45 °C were noted for immobilized enzyme compared to values of 3.5 and 40 °C for free form, respectively. Immobilized RvLac exhibited better relative activity profiles at various pH and temperature ranges. The immobilized enzyme showed up to 16-fold improvement in the thermal stability, when incubated at 60 °C, and retained up to 82.9% of residual activity after ten cycles of reuses. Immobilized RvLac exhibited up to 1.9-fold higher bisphenol A degradation efficiency potential over free enzyme. Previous reports have demonstrated the immobilization of RvLac on non-magnetic supports. This study has demonstrated that immobilization of RvLac on magnetic nanoparticles is very efficient especially for achieving high loading, better pH and temperature profiles, and thermal- and solvents-stability, high reusability, and higher degradation of bisphenol A.
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Affiliation(s)
- Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Rahul K Gupta
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Sang-Yong Kim
- Department of Food Science and Biotechnology, Shin-Ansan University, Ansan, 15435 Republic of Korea
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Vipin C Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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Kondaveeti S, Patel SKS, Woo J, Wee JH, Kim SY, Al-Raoush RI, Kim IW, Kalia VC, Lee JK. Characterization of Cellobiohydrolases from Schizophyllum commune KMJ820. Indian J Microbiol 2020; 60:160-166. [PMID: 32255848 PMCID: PMC7105533 DOI: 10.1007/s12088-019-00843-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022] Open
Abstract
A novel cellobiohydrolase (CBH)-generating fungi have been isolated and categorized as Schizophyllum commune KMJ820 based on morphology and rDNA gene sequence. Cellulose powder was used as carbon source, the total enzyme activity was 11.51 U/ml is noted; which is among the highest amounts of CBH-generating microbes studied. CBH have been purified to homogenize, with pursual of serial chromatography using S. commune supernatants and two different CBHs were found; CBH 1 and 2. The filtered CBHs showed greater activity (V max = 51.4 and 20.8 U/mg) in contrast to CBHs from earlier studies. The MW (molecular weights) of S. commune CBH 1 and 2 were verified to be approximately 50 kDa and 150 kDa, respectively, by size exclusion chromatography. Even though CBHs have been evaluated from other sources, but S. commune CBH is prominent in comparison to other CBHs by its high enzyme activity.
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Affiliation(s)
- Sanath Kondaveeti
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Janghun Woo
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Ji Hyang Wee
- Department of Food Science and Biotechnology, Shin-Ansan University, Ansan, 15435 Republic of Korea
| | - Sang-Yong Kim
- Department of Food Science and Biotechnology, Shin-Ansan University, Ansan, 15435 Republic of Korea
| | - Riyadh I. Al-Raoush
- Department of Civil and Architectural Engineering, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
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