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Shahid M, Singh BN, Verma S, Choudhary P, Das S, Chakdar H, Murugan K, Goswami SK, Saxena AK. Bioactive antifungal metabolites produced by Streptomyces amritsarensis V31 help to control diverse phytopathogenic fungi. Braz J Microbiol 2021; 52:1687-1699. [PMID: 34591293 PMCID: PMC8578481 DOI: 10.1007/s42770-021-00625-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/19/2021] [Indexed: 10/20/2022] Open
Abstract
Actinomycetes due to their unique repertoire of antimicrobial secondary metabolites can be an eco-friendly and sustainable alternative to agrochemicals to control plant pathogens. In the present study, antifungal activity of twenty different actinomycetes was evaluated via dual culture plate assay against six different phytopathogens, viz., Alternaria alternata, Aspergillus flavus, Fusarium oxysporum f. sp. lycopersici, Sarocladium oryzae, Sclerotinia sclerotiorum, and Rhizoctonia solani. Two potential isolates, Streptomyces amritsarensis V31 and Kribella karoonensis MSCA185 showing high antifungal activity against all six fungal pathogens, were further evaluated after extraction of bioactive metabolites in different solvents. Metabolite extracted from S. amritsarensis V31 in different solvents inhibited Rhizoctonia solani (7.5-65%), Alternaria alternata (5.5-52.7%), Aspergillus flavus (8-30.7%), Fusarium oxysporum f. sp. lycopersici (25-44%), Sarocladium oryzae (11-55.5%), and Sclerotinia sclerotiorum (29.7-40.5%); 1000 D diluted methanolic extract of S. amritsarensis V31 showed growth inhibition against R. solani (23.3%), A. flavus (7.7%), F. oxysporum (22.2%), S. oryzae (16.7%), and S. sclerotiorum (19.0%). Metabolite extracts of S. amritsarensis V31 significantly reduced the incidence of rice sheath blight both as preventive and curative sprays. Chemical profiling of the metabolites in DMSO extract of S. amritsarensis V31 revealed 6-amino-5-nitrosopyrimidine-2,4-diol as the predominant compound present. It was evident from the LC-MS analyses that S. amritsarensis V31 produced a mixture of potential antifungal compounds which inhibited the growth of different phytopathogenic fungi. The results of this study indicated that metabolite extracts of S. amritsarensis V31 can be exploited as a bio-fungicide to control phytopathogenic fungi.
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Affiliation(s)
- Mohammad Shahid
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India
| | - Bansh Narayan Singh
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India
| | - Shaloo Verma
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India
| | - Prassan Choudhary
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India
| | - Sudipta Das
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India
| | - Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India.
| | - Kumar Murugan
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India
| | - Sanjay Kumar Goswami
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India
- ICAR-Indian Institute of Sugarcane Research (IISR), Uttar Pradesh, Lucknow, 226002, India
| | - Anil Kumar Saxena
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Kushmaur, Mau, 275103, India
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Protection of surplus food from fungal spoilage using Streptomyces spp.: a green approach. Arch Microbiol 2020; 203:941-950. [PMID: 33089339 DOI: 10.1007/s00203-020-02087-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 10/06/2020] [Indexed: 02/04/2023]
Abstract
Consortia of Streptomyces spp. (colonies 169, 194, 165 and 130) used in this study are an efficient producer of secondary metabolites like chitinases and antifungal compounds, which may help in the protection of surplus food from spoilage. Qualitative screening for chitinase production and taxonomy of these colonies were undertaken in our previous studies. In the current study, GC-MS analysis of extract produced from the consortia of Streptomyces strains was done for the identification of antifungal compounds. Treatment of surplus food with activated consortia of Streptomyces spp. has protected powdered food for a month, whereas fresh food (unpowdered) was preserved for two days. A control sample of surplus food (untreated) was kept to check the contamination, which resulted in the growth of three fungi (FP-1, FG-1, and FB-1). Taxonomic characterization of fungi and identification of toxic compounds produced from them were done by ITS amplification and GC-MS analysis, respectively. The study shows that the secondary metabolites from Streptomyces spp. have the potential to protect the food from mycotoxin contamination. Based on literature reports, this is for the first time that bioactive compounds and chitinases produced from Streptomyces are being used for the protection and management of surplus food.
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Kumar P, Chauhan A, Kumar M, Kuanr BK, Solanki R, Kapur MK. Draft genome and secondary metabolite biosynthetic gene clusters of Streptomyces sp. strain 196. Mol Biol Rep 2020; 47:6741-6747. [PMID: 32888130 DOI: 10.1007/s11033-020-05731-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
Emergence of MDR 'superbugs' inflamed a severe sense of urgency amongst scientists aiming at the discovery of novel potential drug molecules. Bacteria of the genus Streptomyces are really worth investigating for their immense potential to produce natural compounds of pharmaceutical importance. In the present study, the genome of Streptomyces sp. strain 196 was sequenced, studied and secondary metabolite biosynthetic gene clusters (smBGCs) were detected. FAME analysis was used for taxonomic validation of strain 196. Genome of strain 196 was sequenced using the Illumina NextSeq system which has resulted in a draft genome of 7.4 Mb. Rapid annotation using subsystem technology (RAST) results revealed the presence of 6682 CDS, 64 tRNA genes and 7 rRNA genes. Comparative studies revealed that strain 196 have 93.5% nucleotide and 96% protein level similarities with Streptomyces rhizosphaericola 1AS2c. Genome mining using antiSMASH predicted the presence of BGCs responsible for diverse bioactive compound production. The detected gene clusters were two PKS-III, one PKS-I, five NRPS, two hybrid PKS-I/NRPS, one thiopeptide/LAP, and one bacteriocin types. Furthermore, many other types BGCs such as three ectoine, two siderophore, one arylpolyene, two butyrolactone, one lassopeptide, one lanthipeptide and one melanin were also found. The results of this study provides information about genome and BGCs of strain 196, this information is valuable for researchers who are interested in isolation of bioactive compounds and working on heterologous expression of cryptic BGCs for novel bioactive compounds production.
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Affiliation(s)
- Prateek Kumar
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110 019, India
| | - Anjali Chauhan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Munendra Kumar
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110 019, India
| | - Bijoy K Kuanr
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Renu Solanki
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Monisha Khanna Kapur
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110 019, India.
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Maurya S, Abraham JS, Somasundaram S, Toteja R, Gupta R, Makhija S. Indicators for assessment of soil quality: a mini-review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:604. [PMID: 32857216 DOI: 10.1007/s10661-020-08556-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/16/2020] [Indexed: 05/20/2023]
Abstract
Soil quality is the competence of soil to perform necessary functions that are able to maintain animal and plant productivity of the soil. Soil consists of various physical, chemical, and biological parameters, and all these parameters are involved in the critical functioning of soil. There is a need for continuous assessment of soil quality as soil is a complex and dynamic constituent of Earth's biosphere that is continuously changing by natural and anthropogenic disturbances. Any perturbations in the soil cause disturbances in the physical (soil texture, bulk density, etc.), chemical (pH, salinity, organic carbon, etc.), and biological (microbes and enzymes) parameters. These physical, chemical, and biological parameters can serve as indicators for soil quality assessment. However, soil quality assessment cannot be possible by evaluating only one parameter out of physical, chemical, or biological. So, there is an emergent need to establish a minimum dataset (MDS) which shall include physical, chemical, and biological parameters to assess the quality of the given soil. This review attempts to describe various physical, chemical, and biological parameters, combinations of which can be used in the establishment of MDS.
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Affiliation(s)
- Swati Maurya
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India
| | - Jeeva Susan Abraham
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India
| | - Sripoorna Somasundaram
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India
| | - Ravi Toteja
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India
| | - Renu Gupta
- Department of Zoology, Maitreyi College, University of Delhi, Bapu dham, Chanakyapuri, New Delhi, 110021, India
| | - Seema Makhija
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India.
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Potential applications of extracellular enzymes from Streptomyces spp. in various industries. Arch Microbiol 2020; 202:1597-1615. [PMID: 32451592 DOI: 10.1007/s00203-020-01898-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 01/21/2023]
Abstract
Extracellular enzymes produced from Streptomyces have the potential to replace toxic chemicals that are being used in various industries. The endorsement of this replacement has not received a better platform in developing countries. In this review, we have discussed the impact of chemicals and conventional practices on environmental health, and the role of extracellular enzymes to replace these practices. Burning of fossil fuels and agriculture residue is a global issue, but the production of biofuel using extracellular enzymes may be the single key to solve all these issues. We have discussed the replacement of hazardous chemicals with the use of xylanase, cellulase, and pectinase in food industries. In paper industries, delignification was done by the chemical treatment, but xylanase and laccase have the efficient potential to remove the lignin from pulp. In textile industries, the conventional method includes the chemicals which affect the nervous system and other organs. The use of xylanase, cellulase, and pectinase in different processes can give a safe and environment-friendly option to textile industries. Hazardous chemical pesticides can be replaced by the use of chitinase as an insecticide and fungicide in agricultural practices.
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Li X, Wang Z, Gan L, Tian Y. Draft genome sequence of Actinocorallia populi A251 T, an actinomycetes producing polyketides and nonribosomal polypeptides. 3 Biotech 2020; 10:79. [PMID: 32099730 PMCID: PMC6992827 DOI: 10.1007/s13205-020-2070-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
In this work, we present the draft genome sequence of Actinocorallia populi A251T consisting of 8,253,402 bp with a G + C content of 71.5 mol%. The genome sequence includes 3 5S rRNA genes, 54 tRNA genes, 28 snRNA genes and 19 CRISPRs in 26 contigs. Using the Rapid Annotation using Subsystem Technology, a total of 7766 coding DNA sequences, which were assigned to 436 subsystems, were found in the genome. And 6743 protein-coding sequences with designated functions were assigned to 19 categories in the Cluster of Orthologous Groups database. The genome contains 20 gene clusters responsible for the synthesis of secondary metabolites, including two type I polyketide synthase (PKS) gene clusters, two type III PKS gene clusters, three nonribosomal peptide synthetase (NRPS) gene clusters and two hybrid PKS/NRPS gene clusters. These results indicate that strain A251 has the ability to produce several nonribosomal polypeptides and diverse polyketides, which was verified by liquid chromatography-mass spectrometry analysis of the extraction from fermentation broth. In addition, lactones, indole and many unknown natural products are present in the metabolites. Bioactivity testing revealed anticancer and antidiabetic activities of the crude extract towards the cancer cell line HepG2. In summary, the genomic sequences and bioactive fermentation products demonstrate the potential of strain A251 in biotechnology.
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Affiliation(s)
- Xiaoguang Li
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, College of Biomass Science and Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065 People’s Republic of China
| | - Zhikuan Wang
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, College of Biomass Science and Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065 People’s Republic of China
| | - Longzhan Gan
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, College of Biomass Science and Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065 People’s Republic of China
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, College of Biomass Science and Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065 People’s Republic of China
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Deo D, Davray D, Kulkarni R. A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes. Microorganisms 2019; 7:E444. [PMID: 31614693 PMCID: PMC6843789 DOI: 10.3390/microorganisms7100444] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
Production of exopolysaccharides (EPS) is one of the unique features of Lactobacillus genus. EPS not only have many physiological roles such as in stress tolerance, quorum sensing and biofilm formation, but also have numerous applications in the food and pharmaceutical industries. In this study, we identified and compared EPS biosynthesis gene clusters in 106 sequenced Lactobacillus genomes representing 27 species. Of the 146 identified clusters, only 41 showed the typical generic organization of genes as reported earlier. Hierarchical clustering showed highly varied nature of the clusters in terms of the gene composition; nonetheless, habitat-wise grouping was observed for the gene clusters from host-adapted and nomadic strains. Of the core genes required for EPS biosynthesis, epsA, B, C, D and E showed higher conservation, whereas gt, wzx and wzy showed high variability in terms of the number and composition of the protein families. Analysis of the distribution pattern of the protein families indicated a higher proportion of mutually exclusive families in clusters from host-adapted and nomadic strains, whereas those from the free-living group had very few unique families. Taken together, this analysis highlights high variability in the EPS gene clusters amongst Lactobacillus with some of their properties correlated to the habitats.
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Affiliation(s)
- Dipti Deo
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412 115, India.
| | - Dimple Davray
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412 115, India.
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412 115, India.
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