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Dubey H, Pradeep AR, Neog K, Debnath R, Aneesha PJ, Shah SK, Kamatchi I, Ponnuvel KM, Ramesha A, Vijayan K, Nongthomba U, Bora U, Vankadara S, VijayaKumari KM, Arunkumar KP. Genome sequencing and assembly of Indian golden silkmoth, Antheraea assamensis Helfer (Saturniidae, Lepidoptera). Genomics 2024; 116:110841. [PMID: 38599255 DOI: 10.1016/j.ygeno.2024.110841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
Muga silkworm (Antheraea assamensis), one of the economically important wild silkmoths, is unique among saturniid silkmoths. It is confined to the North-eastern part of India. Muga silk has the highest value among the other silks. Unlike other silkmoths, A. assamensis has a low chromosome number (n = 15), and ZZ/ZO sex chromosome system. Here, we report the first high-quality draft genome of A. assamensis, assembled by employing the Illumina and PacBio sequencing platforms. The assembled genome of A. assamensis is 501.18 Mb long, with 2697 scaffolds and an N50 of 683.23 Kb. The genome encompasses 18,385 protein-coding genes, 86.29% of which were functionally annotated. Phylogenetic analysis of A. assamensis revealed its divergence from other Antheraea species approximately 28.7 million years ago. Moreover, an investigation into detoxification-related gene families, CYP450, GST, and ABC-transporter, revealed a significant expansion in A. assamensis as compared to the Bombyx mori. This expansion is comparable to Spodoptera litura, suggesting adaptive responses linked to the polyphagous behavior observed in these insects. This study provides valuable insights into the molecular basis of evolutionary divergence and adaptations in muga silkmoth. The genome assembly reported in this study will significantly help in the functional genomics studies on A. assamensis and other Antheraea species along with comparative genomics analyses of Bombycoidea insects.
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Affiliation(s)
- Himanshu Dubey
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - A R Pradeep
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - Kartik Neog
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India
| | - Rajal Debnath
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India; Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India
| | - P J Aneesha
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - Suraj Kumar Shah
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India
| | - Indumathi Kamatchi
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - K M Ponnuvel
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - A Ramesha
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | | | - Upendra Nongthomba
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Utpal Bora
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | | | - K M VijayaKumari
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India
| | - Kallare P Arunkumar
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India.
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Gogoi P, Boruah JLH, Yadav A, Debnath R, Saikia R. Comparative seasonal analysis of Eri silkworm (Samia ricini Donovan) gut composition: implications for lignocellulose degradation. Environ Sci Pollut Res Int 2023; 30:109198-109213. [PMID: 37768488 DOI: 10.1007/s11356-023-29893-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Conversion of biomass such as lignocelluloses to an alternative energy source can contribute to sustainable development. Recently, biomass-degrading enzymes are reported to be common resources in insect-microbe interacting systems. Northeast India harbors ample sericigenous insect resources which are exploited for their silk products. Samia ricini Donovan is an economically important poly-phytophagous silkmoth capable of digesting foliage from different plant species, suggesting the versatility of a robust gut system. Here, a gut bacterial profile was determined by 16S rRNA gene characterization across the holometabolous life cycle during the summer and winter seasons, revealing 3 phyla, 13 families, and 22 genera. Comparative analysis among the seasonal gut isolates revealed a high diversity in summer, predominated by the genus Bacillus due to its high occurrence in all developmental stages. Shannon's diversity index demonstrated the second and fourth instars of summer as well as the fifth instar of winter to be relatively better developmental stages for gut bacteria assembly. Bacterial community shifts in concert to host developmental changes were found to be apparent between early instars and late instars in summer, which differed from those of winter. Forty-three and twenty-nine gut bacterial isolates were found to be cellulolytic and xylanolytic enzyme producers, respectively. The present results illustrate the gut microbiota of S. ricini over the seasons and support the holometabolous life cycle effect as the most likely factor shaping the gut bacterial microbiota. These findings may provide leads for the development of new cleaner and environmentally friendly lignocellulose-degrading enzymes.
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Affiliation(s)
- Parishmita Gogoi
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
- Academy of Scientific and Innovative Research, Uttar Pradesh, Kamala Nehru Nagar, Sector 19, Ghaziabad, 201002, India
| | - Jyoti Lakshmi Hati Boruah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
| | - Archana Yadav
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
| | - Rajal Debnath
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, 560035, India
| | - Ratul Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India.
- Academy of Scientific and Innovative Research, Uttar Pradesh, Kamala Nehru Nagar, Sector 19, Ghaziabad, 201002, India.
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Saikia J, Kotoky R, Debnath R, Kumar N, Gogoi P, Yadav A, Saikia R. De novogenomic analysis ofEnterobacter asburiaeEBRJ12, a plant growth-promoting rhizobacteria isolated from the rhizosphere of Phaseolus vulgarisL. J Appl Microbiol 2023; 134:6965352. [PMID: 36728698 DOI: 10.1093/jambio/lxac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 02/03/2023]
Abstract
AIM Environmental stresses such as water deficit induced stress are one of the major limiting factors in crop production. However, some plant growth-promoting rhizobacteria (PGPR) can promote plant growth in such adverse condition. Therefore, the objective was to isolate rhizospheric bacteria from Phaseolus vulgaris L. growing in a drought-affected soil and to analyze its plant growth promoting (PGP) efficacy to black gram (Vigna mungo L.) and Bhut jolokia (Capsicum chinense Jacq.). Whole-genome sequencing of the potential bacteria was targeted to analyze the genetic potential of the isolate as a plant growth-promoting agent. METHODS AND RESULTS The isolate Enterobacter asburiae EBRJ12 was selected based on its PGP efficacy, which significantly improved plant growth and development. The genomic analysis revealed the presence of one circular chromosome of size 4.8 Mb containing 16 genes for osmotic stress regulation including osmotically inducible protein osmY, outer membrane protein A precursor ompA, aquaporin Z, and an operon for osmoprotectant ABC transporter yehZYXW. Moreover, the genome has a complete genetic cluster for biosynthesis of siderophore Enterobactin and siderophore Aerobactin.The PGP effects were verified with black gram and Bhut jolokia in pot experiments. The isolate significantly increased the shoot length by 35.0% and root length by 58.0% of black gram, while 41.0% and 57.0% of elevation in shoot and root length were observed in Bhut jolokia compared to non-inoculated plants. CONCLUSIONS The EBRJ12 has PGP features that could improve the growth in host plants, and the genomic characterization revealed the presence of genetic potential for plant growth promotion.
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Affiliation(s)
- Juthika Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Sciences and Technology, Jorhat 785006, India
| | - Rhitu Kotoky
- Regional Centre for Biotechnology, NCR-Delhi 121001, India
| | - Rajal Debnath
- Biological Sciences and Technology Division, CSIR-North East Institute of Sciences and Technology, Jorhat 785006, India.,Seribiotech Research Laboratory, Central Silk Board, Sarjapura Road Kodathi, Bangalore 560035, India
| | - Niraj Kumar
- Biological Sciences and Technology Division, CSIR-North East Institute of Sciences and Technology, Jorhat 785006, India.,Academy of Scientific and Innovative Research, Kamala Nehru Nagar, Sector 19, Ghaziabad 201002, India
| | - Priyanka Gogoi
- Biological Sciences and Technology Division, CSIR-North East Institute of Sciences and Technology, Jorhat 785006, India.,Academy of Scientific and Innovative Research, Kamala Nehru Nagar, Sector 19, Ghaziabad 201002, India
| | - Archana Yadav
- Biological Sciences and Technology Division, CSIR-North East Institute of Sciences and Technology, Jorhat 785006, India
| | - Ratul Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Sciences and Technology, Jorhat 785006, India.,Academy of Scientific and Innovative Research, Kamala Nehru Nagar, Sector 19, Ghaziabad 201002, India
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Debnath R, Das S, Mukhopadhyay A, Saha T. Enrichment of laccase production by Phoma herbarum isolate KU4 under solid-state fermentation by optimizing RSM coefficients using genetic algorithm. Lett Appl Microbiol 2021; 73:515-528. [PMID: 34263965 DOI: 10.1111/lam.13537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
The process parameters were optimized to obtain enhanced enzyme activity from the fungus Phoma herbarum isolate KU4 using rice straw and saw dust as substrate under solid-state fermentation using Response surface methodology (RSM). Genetic algorithm was used to validate the RSM for maximum laccase production. Six variables, viz., pH of the media, initial moisture content, copper sulphate concentration, concentration of tannic acid, inoculum concentration and incubation time were found to be effective and optimized for enhanced production. Maximum laccase production was achieved by RSM at pH 5·0 and 86% of initial moisture content of the culture medium, 150 µmol l-1 of CuSO4 , 1·5% tannic acid and 0·128 g inoculum g-1 dry substrate inoculum size on the fourth day of fermentation. The highest laccase activity was observed as 79 008 U g-1 , which is approximately sixfold enhanced production compared to the unoptimized condition (12 085·26 U g-1 ).
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Affiliation(s)
- R Debnath
- Department of Molecular Biology & Biotechnology, Faculty of Science, University of Kalyani, Kalyani, India
| | - S Das
- Department of Molecular Biology & Biotechnology, Faculty of Science, University of Kalyani, Kalyani, India
| | - A Mukhopadhyay
- Department of Computer Science & Engineering, Faculty of Engineering Technology & Management, University of Kalyani, Kalyani, West Bengal, India
| | - T Saha
- Department of Molecular Biology & Biotechnology, Faculty of Science, University of Kalyani, Kalyani, India
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Harrewijn A, Buzzell GA, Debnath R, Leibenluft E, Pine DS, Fox NA. Corrigendum to "Frontal alpha asymmetry moderates the relations between behavioral inhibition and social-effect ERN" [Biological Psychology (2019) 10-16]. Biol Psychol 2021; 161:108078. [PMID: 33810917 DOI: 10.1016/j.biopsycho.2021.108078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- A Harrewijn
- Department of Human Development and Quantitative Methodology, University of Maryland, 3304 Benjamin Building, College Park, MD, 20742-1131, USA; Emotion and Development Branch, National Institute of Mental Health (NIMH), 9000 Rockville Pike, Bethesda, MD, 20892, USA.
| | - G A Buzzell
- Department of Human Development and Quantitative Methodology, University of Maryland, 3304 Benjamin Building, College Park, MD, 20742-1131, USA
| | - R Debnath
- Department of Human Development and Quantitative Methodology, University of Maryland, 3304 Benjamin Building, College Park, MD, 20742-1131, USA
| | - E Leibenluft
- Emotion and Development Branch, National Institute of Mental Health (NIMH), 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - D S Pine
- Emotion and Development Branch, National Institute of Mental Health (NIMH), 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - N A Fox
- Emotion and Development Branch, National Institute of Mental Health (NIMH), 9000 Rockville Pike, Bethesda, MD, 20892, USA
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Harrewijn A, Buzzell GA, Debnath R, Leibenluft E, Pine DS, Fox NA. Frontal alpha asymmetry moderates the relations between behavioral inhibition and social-effect ERN. Biol Psychol 2018; 141:10-16. [PMID: 30599209 DOI: 10.1016/j.biopsycho.2018.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/29/2018] [Accepted: 12/23/2018] [Indexed: 12/22/2022]
Abstract
Behavioral inhibition (BI) is an early temperamental precursor of anxiety disorders, characterized by withdrawal from novel situations. Some but not all young children with BI go on to display anxiety disorders. Neural correlates, such as frontal alpha asymmetry or event-related negativity (ERN), could moderate the relations between early BI and later anxiety. The goal of this longitudinal study was to test frontal alpha asymmetry as a potential moderator of the relation between BI and later anxiety, and of the relation between BI and the social-effect ERN. 100 children were assessed for BI at ages 2 and 3, and we collected EEG during resting state and the social Flanker task at age 12. Frontal alpha asymmetry did not correlate with BI or anxiety, nor did it moderate the relation between early BI and later anxiety. However, frontal alpha asymmetry did moderate the relation between BI and the social-effect ERN. This suggests that, in adolescents who previously manifested BI, a pattern of resting EEG associated with avoidance predicts hypersensitivity to errors in a social context.
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Affiliation(s)
- A Harrewijn
- Department of Human Development and Quantitative Methodology, University of Maryland, 3304 Benjamin Building, College Park, MD, 20742-1131, USA; Emotion and Development Branch, National Institute of Mental Health (NIMH), 9000 Rockville Pike, Bethesda, MD, 20892, USA.
| | - G A Buzzell
- Department of Human Development and Quantitative Methodology, University of Maryland, 3304 Benjamin Building, College Park, MD, 20742-1131, USA
| | - R Debnath
- Department of Human Development and Quantitative Methodology, University of Maryland, 3304 Benjamin Building, College Park, MD, 20742-1131, USA
| | - E Leibenluft
- Emotion and Development Branch, National Institute of Mental Health (NIMH), 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - D S Pine
- Emotion and Development Branch, National Institute of Mental Health (NIMH), 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - N A Fox
- Department of Human Development and Quantitative Methodology, University of Maryland, 3304 Benjamin Building, College Park, MD, 20742-1131, USA
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Debnath R, Yadav A, Gupta VK, Singh BP, Handique PJ, Saikia R. Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang. Front Plant Sci 2016; 7:1345. [PMID: 27642287 PMCID: PMC5009118 DOI: 10.3389/fpls.2016.01345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/22/2016] [Indexed: 05/15/2023]
Abstract
Information on rhizosphere microbiome of endemic plants from high mountain ecosystems against those of cultivated plantations is inadequate. Comparative bacterial profiles of endemic medicinal plant Rhododendron arboreum Sm. subsp. delavayi rhizosphere pertaining to four altitudinal zonation Pankang Thang (PTSO), Nagula, Y-junction and Bum La (Indo-China border; in triplicates each) along cold adapted Eastern slope of Himalayan Tawang region, India is described here. Significant differences in DGGE profile between below ground bulk vs. rhizospheric community profile associated with the plant was identified. Tagged 16S amplicon sequencing from PTSO (3912 m) to Bum La (4509 m), revealed that soil pH, total nitrogen (TN), organic matter (OM) significantly influenced the underlying bacterial community structure at different altitudes. The relative abundance of Acidobacteria was inversely related to pH, as opposed to TN which was positively correlated to Acidobacteria and Proteobacteria abundance. TN was also the significant predictor for less abundant taxonomic groups Chloroflexi, Gemmatimonadetes, and Nitrospirae. Bum La soil harbored less bacterial diversity compared to other sites at lower altitudes. The most abundant phyla at 3% genetic difference were Acidobacteria, Actinobacteria, and Proteobacteria amongst others. Analysis of similarity indicated greater similarity within lower altitudinal than higher altitudinal group (ANOSIM, R = 0.287, p = 0.02). Constraining the ordination with the edaphic factor explained 83.13% of variation. Unique phylotypes of Bradyrhizobium and uncultured Rhizobiales were found in significant proportions at the four regions. With over 1% relative abundance Actinobacteria (42.6%), Acidobacteria (24.02%), Proteobacteria (16.00%), AD3 (9.23%), WPS-2 (5.1%), and Chloroflexi (1.48%) dominated the core microbiome.
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Affiliation(s)
- Rajal Debnath
- Microbial Biotechnology Group, Biological Science and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and TechnologyJorhat, India
| | - Archana Yadav
- Microbial Biotechnology Group, Biological Science and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and TechnologyJorhat, India
| | - Vijai K. Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, National University of Ireland GalwayGalway, Ireland
| | - Bhim P. Singh
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram UniversityAizawl, India
| | | | - Ratul Saikia
- Microbial Biotechnology Group, Biological Science and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and TechnologyJorhat, India
- *Correspondence: Ratul Saikia,
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Gohain A, Gogoi A, Debnath R, Yadav A, Singh BP, Gupta VK, Sharma R, Saikia R. Antimicrobial biosynthetic potential and genetic diversity of endophytic actinomycetes associated with medicinal plants. FEMS Microbiol Lett 2015; 362:fnv158. [PMID: 26347302 DOI: 10.1093/femsle/fnv158] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2015] [Indexed: 11/13/2022] Open
Abstract
Endophytic actinomycetes are one of the primary groups that share symbiotic relationships with medicinal plants and are key reservoir of biologically active compounds. In this study, six selective medicinal plants were targeted for the first time for endophytic actinomycetes isolation from Gibbon Wild Life Sanctuary, Assam, India, during winter and summer and 76 isolates were obtained. The isolates were found to be prevalent in roots followed by stem and leaves. 16S rRNA gene sequence analysis revealed 16 genera, including rare genera, Verrucosispora, Isoptericola and Kytococcus, which have never been previously reported as endophytic. The genus Streptomyces (66%) was dominant in both seasons. Shannon's diversity index showed that Azadirachta indica (1.49), Rauwolfia serpentina (1.43) and Emblica officinalis (1.24) were relatively good habitat for endophytic actinomycetes. Antimicrobial strains showed prevalence of polyketide synthase (PKS) type-II (85%) followed by PKS type-I (14%) encoded in the genomes. Expression studies showed 12-fold upregulation of PKSII gene in seventh day of incubation for Streptomyces antibioticus (EAAG90). Our results emphasize that the actinomycetes assemblages within plant tissue exhibited biosynthetic systems encoding for important biologically active compounds.
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Affiliation(s)
- Anwesha Gohain
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Animesh Gogoi
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Rajal Debnath
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Archana Yadav
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Bhim P Singh
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram 796004, India
| | - Vijai K Gupta
- Glyco-Biotechnology Group, Department of Biochemistry, National University of Ireland Galway, Galway H91CF50, Ireland
| | - Rajeev Sharma
- Centre for Bioinformatics Studies, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Ratul Saikia
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
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Sarma RK, Gogoi A, Dehury B, Debnath R, Bora TC, Saikia R. Community profiling of culturable fluorescent pseudomonads in the rhizosphere of green gram (Vigna radiata L.). PLoS One 2014; 9:e108378. [PMID: 25279790 PMCID: PMC4184808 DOI: 10.1371/journal.pone.0108378] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/20/2014] [Indexed: 11/25/2022] Open
Abstract
Study on microbial diversity in the unexplored rhizosphere is important to understand their community structure, biology and ecological interaction with the host plant. This research assessed the genetic and functional diversity of fluorescent pseudomonads [FP] in the green gram rhizophere. One hundred and twenty types of morphologically distinct fluorescent pseudomonads were isolated during vegetative as well as reproductive growth phase of green gram. Rep PCR, ARDRA and RISA revealed two distinct clusters in each case at 75, 61 and 70% similarity coefficient index respectively. 16S rRNA partial sequencing analysis of 85 distantly related fluorescent pseudomonads depicted Pseudomonas aeruginosa as the dominant group. Out of 120 isolates, 23 (19%) showed antagonistic activity towards phytopathogenic fungi. These bacterial isolates showed varied production of salicylic acid, HCN and chitinase, 2, 4-diacetylphloroglucinol (DAPG), phenazine-1-carboxylic acid (PCA) and pyoluteorin (PLT). Production efficiency of inherent level of plant growth promoting (PGP) traits among the 120 isolates demonstrated that 10 (8%) solubilised inorganic phosphates, 25 (20%) produced indoles and 5 (4%) retained ACC deaminase activity. Pseudomonas aeruginosa GGRJ21 showed the highest production of all antagonistic and plant growth promoting (PGP) traits. In a greenhouse experiment, GGRJ21 suppressed root rot disease of green gram by 28-93% (p = 0.05). Consistent up regulation of three important stress responsive genes, i.e., acdS, KatA and gbsA and elevated production efficiency of different PGP traits could promote GGRJ21 as a potent plant growth regulator.
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Affiliation(s)
- Rupak K Sarma
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Animesh Gogoi
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Budheswar Dehury
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Rajal Debnath
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Tarun C Bora
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Ratul Saikia
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
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Debnath R, Saikia R, Sarma RK, Yadav A, Bora TC, Handique PJ. Psychrotolerant antifungal Streptomyces isolated from Tawang, India and the shift in chitinase gene family. Extremophiles 2013; 17:1045-59. [PMID: 24085523 DOI: 10.1007/s00792-013-0587-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 09/16/2013] [Indexed: 10/26/2022]
Abstract
A total of 210 Streptomyces were isolated from the soil samples of Tawang, India where temperature varied from 5 °C during daytime to -2 °C during the night. Based on antifungal activity, a total of 33 strains, putatively Streptomyces spp., were selected. Optimal growth temperature for the 33 strains was 16 °C, with growth occurring down to 6 °C but not above 30 °C. Phylogenetic analysis based on 16S rDNA sequences revealed the taxonomic affiliation of the 33 strains as species of Streptomyces. To examine the relatedness of the chitinase genes from six strong antifungal Streptomyces strains, a phylogenetic tree was constructed using the catalytic domain nucleotide sequences and resulted in seven distinct monophyletic groups. A quantitative PCR study for chitinase expressing ability revealed that of the six antifungal strains tested, the strain Streptomyces roseochromogenus TSR12 was the most active producer of family 18 chitinase genes. Streptomyces strains with enhanced inhibitory potential usually encode a family 19 chitinase gene; however, our present study did not show expression of this family in the six strains tested.
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Affiliation(s)
- Rajal Debnath
- Biotechnology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785 006, Assam, India
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Sarma RK, Debnath R, Saikia R, Handique PJ, Bora TC. Phylogenetic analysis of alkaline proteinase producing fluorescent pseudomonads associated with green gram (Vigna radiata L.) rhizosphere. Folia Microbiol (Praha) 2012; 57:129-37. [PMID: 22374358 DOI: 10.1007/s12223-012-0097-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 01/11/2012] [Indexed: 12/01/2022]
Abstract
Fifty fluorescent pseudomonads were isolated from rhizospheric soil of green gram from nearby area of Kaziranga, Assam, India and assayed for their extracellular proteinase production. Out of these isolates, 20 were found to be prominent in proteinase production. Genetic diversity of the 20 isolates were analyzed through BOX-PCR fingerprinting and 16S rDNA-RFLP along with three reference strains, viz., Pseudomonas fluorescens (NCIM2099(T)), Pseudomonas aureofaciens (NCIM2026(T)), and Pseudomonas aeruginosa (MTCC2582(T)). BOX-PCR produced two distinct clusters at 56% similarity coefficient and seven distinct BOX profiles. 16S rDNA-RFLP with three tetra-cutters restriction enzymes (HaeIII, AluI, and MspI) revealed two major clusters A and B; cluster A contained only single isolate FPS9 while the rest of 22 isolates belonged to the cluster B. Based on phenotypic characters and 16S rDNA sequence similarity, all the eight highly proteinase-producing strains were affiliated with P. aeruginosa. The proteinase was extracted from two most prominent strains (KFP1 and KFP2), purified by a three-step process involving (NH(4))(2)SO(4) precipitation, gel filtration, and ion exchange chromatography. The enzyme had an optimal pH of 8.0 and exhibit highest activity at 60°C and 37°C by KFP1 and KFP2 respectively. The specific activities were recorded as 75,050 (for KFP1) and 81,320 U/mg (for KFP2). The purified enzyme was migrated as a single band on native and SDS-PAGE with a molecular mass of 32 kDa. Zn(2+), Cu(2+), and Ni(2+) ion inhibited the enzyme activity. Enzyme activity was also inhibited by EDTA established as their metallo-proteinase nature.
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Affiliation(s)
- Rupak K Sarma
- Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
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Debnath R, Chaudhuri J. Preparation of well-dispersed anatase phase stabilized titania semiconductor particulate for use in photo-electrochemistry. ACTA ACUST UNITED AC 1991. [DOI: 10.1007/bf00726916] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Debnath R, Chaudhury J, Bera SC. Optical Properties and Nature of Coordination of Cu+ Ions in Calcium Metaphosphate Glass. phys stat sol (b) 1990; 157:723-733. [DOI: 10.1002/pssb.2221570225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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