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Xie J, Yin D, Ou J, Lu B, Liao S, Yang D, Zhang H, Shen N. A new strain of Rhodococcus indonesiensis T22.7.1 T and its functional potential for deacetylation of chitin and chitooligsaccharides. Front Microbiol 2024; 15:1427143. [PMID: 39113839 PMCID: PMC11303147 DOI: 10.3389/fmicb.2024.1427143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction Chitin, abundant in marine environments, presents significant challenges in terms of transformation and utilization. A strain, T22.7.1T, with notable chitin deacetylation capabilities, was isolated from the rhizosphere of Acanthus ebracteatus in the North Sea of China. Comparative 16S rDNA sequence analysis showed that the new isolate had the highest sequence similarity (99.79%) with Rhodococcus indonesiensis CSLK01-03T, followed by R. ruber DSM 43338T, R. electrodiphilus JC435T, and R. aetherivorans 10bc312T (98.97%, 98.81%, and 98.83%, respectively). Subsequent genome sequencing and phylogenetic analysis confirmed that strain T22.7.1T belongs to the R. indonesiensis species. However, additional taxonomic characterization identified strain T22.7.1T as a novel type strain of R. indonesiensis distinct from CSLK01-03T. Methods This study refines the taxonomic description of R. indonesiensis and investigates its application in converting chitin into chitosan. The chitin deacetylase (RiCDA) activity of strain T22.7.1T was optimized, and the enzyme was isolated and purified from the fermentation products. Results Through optimization, the RiCDA activity of strain T22.7.1T reached 287.02 U/mL, which is 34.88 times greater than the original enzyme's activity (8.0 U/mL). The natural CDA enzyme was purified with a purification factor of 31.83, and the specific activity of the enzyme solution reached 1200.33 U/mg. RiCDA exhibited good pH and temperature adaptability and stability, along with a wide range of substrate adaptabilities, effectively deacetylating chitin, chitooligosaccharides, N-acetylglucosamine, and other substrates. Discussion Product analysis revealed that RiCDA treatment increased the deacetylation degree (DD) of natural chitin to 83%, surpassing that of commercial chitosan. Therefore, RiCDA demonstrates significant potential as an efficient deacetylation tool for natural chitin and chitooligosaccharides, highlighting its applicability in the biorefining of natural polysaccharides.
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Affiliation(s)
- Junjie Xie
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Doudou Yin
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Junchao Ou
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Bo Lu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Siming Liao
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Dengfeng Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Hongyan Zhang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Naikun Shen
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
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Islam MM, Mandal S. Unveiling growth-promoting attributes of peanut root endophyte Micromonospora sp. Arch Microbiol 2024; 206:182. [PMID: 38502250 DOI: 10.1007/s00203-024-03886-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/21/2024]
Abstract
In this study, 20 endophytic actinobacteria were isolated from different parts of peanut plants growing in cropland with low and high salt in West Bengal, India. The endophytes underwent a rigorous morphological, biochemical, and genetic screening process to evaluate their effectiveness in enhancing plant growth. About 20% of these isolates were identified as potential plant growth-promoting endophytic actinobacteria, which showed high 16S rRNA gene sequence similarity (up to 99-100%) with different species of Micromonospora. Among these isolates, Micromonospora sp. ASENR15 produced the highest levels of indole acetic acid (IAA) and gibberellic acid (GA), while Micromonospora sp. ASENL2, Micromonospora sp. ANENR4, and Micromonospora sp. ASENR12 produced the highest level of siderophore. Among these leaf and root endophytic Micromonospora, strain ANENR4 was tested for its plant growth-promoting attributes. ANENR4 can be transmitted into the roots of a healthy peanut plant, enhances growth, and colonize the roots in abundance, suggesting the potential agricultural significance of the strain. Moreover, the study is the first report of endophytic Micromonospora in peanuts with PGP effects. The outcomes of this study open avenues for further research on harnessing the benefits of this endophytic Micromonospora for optimizing plant growth in agriculture.
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Affiliation(s)
- Md Majharul Islam
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Xie J, Zhang H, Xu X, Li S, Jiang M, Jiang Y, Shen N. Streptomyces beihaiensis sp. nov., a chitin-degrading actinobacterium, isolated from shrimp pond soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37083594 DOI: 10.1099/ijsem.0.005857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
A Gram-stain-positive actinobacterium, designated strain GXMU-J5T, was isolated from a sample of shrimp pond soil collected in Tieshangang Saltern, Beihai, PR China. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces. The organism formed an extensively branched substrate mycelium, with abundant aerial hyphae that differentiated into spores. Phylogenetic analysis of 16S rRNA gene sequences showed that strain GXMU-J5T was most related to Streptomyces kunmingensis DSM 41681T (similarity 97.74 %) and Streptomyces endophyticus YIM 65594T (similarity 96.80 %). However, the values of digital DNA-DNA hybridization, average nucleotide identity and evolutionary distance of multilocus sequence analysis between strain GXMU-J5T and its closest relatives indicated that it represented a distinct species. Strain GXMU-J5T contained ll-diaminopimelic acid and the major whole-cell hydrolysates were xylose and galactose. The predominant menaquinones of strain GXMU-J5T were revealed as MK-9(H4), MK-9(H6) and MK-9(H8). The polar lipids consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides and phospholipids of unknown structure containing glucosamine. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The whole genome size of strain GXMU-J5T was 6.79 Mbp with a 71.39 mol% G+C content. Genomic analysis indicated that strain GXMU-J5T had the potential to degrade chitin. On the basis of these genotypic and phenotypic data, it is supported that strain GXMU-J5T represents a novel species of the genus Streptomyces, for which the name Streptomyces beihaiensis sp. nov. is proposed. The type strain is strain GXMU-J5T (=MCCC 1K08064T=JCM 35629T).
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Affiliation(s)
- Junjie Xie
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; No. 158, Daxue Xi Road, Nanning, PR China
| | - Hongyan Zhang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; No. 158, Daxue Xi Road, Nanning, PR China
| | - Xia Xu
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; No. 158, Daxue Xi Road, Nanning, PR China
| | - Shiyong Li
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; No. 158, Daxue Xi Road, Nanning, PR China
| | - Mingguo Jiang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; No. 158, Daxue Xi Road, Nanning, PR China
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China; No. 182, 121st Street, Kunming, PR China
| | - Naikun Shen
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; No. 158, Daxue Xi Road, Nanning, PR China
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Draft Genome Sequence of an Endophytic Micromonospora sp. Strain, ANENR4, Isolated from the Root of a Peanut Plant (Arachis hypogaea). Microbiol Resour Announc 2022; 11:e0065522. [PMID: 36264266 PMCID: PMC9671019 DOI: 10.1128/mra.00655-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The genus Micromonospora was found to occur in a diverse range of habitats. Here, we report the genome sequence of an endophytic strain of Micromonospora sp., ANENR4. ANENR4 was isolated from the healthy roots of a peanut (Arachis hypogaea) plant from Egra, West Bengal, India.
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Maiti PK, Mandal S. Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance. Sci Rep 2022; 12:8409. [PMID: 35589875 PMCID: PMC9120177 DOI: 10.1038/s41598-022-12427-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
The genus Lentzea is a rare group of actinobacteria having potential for the exploration of bioactive compounds. Despite its proven ability to produce compounds with medical relevance, Lentzea genome analysis remains unexplored. Here we show a detailed understanding of the genetic features, biosynthetic gene clusters (BGCs), and genetic clusters for carbohydrate-active enzymes present in the Lentzea genome. Our analysis determines the genes for core proteins, non-ribosomal peptide synthetase condensation domain, and polyketide synthases-ketide synthase domain. The antiSMASH-based sequence analysis identifies 692 BGCs among which 8% are identical to the BGCs that produce geosmin, citrulassin, achromosin (lassopeptide), vancosamine, anabaenopeptin NZ857/nostamide A, alkylresorcinol, BE-54017, and bezastatin. The remaining BGCs code for advanced category antimicrobials like calcium-dependent, glycosylated, terpenoids, lipopeptides, thiopeptide, lanthipeptide, lassopeptide, lingual antimicrobial peptide and lantibiotics together with antiviral, antibacterial, antifungal, antiparasitic, anticancer agents. About 28% of the BGCs, that codes for bioactive secondary metabolites, are exclusive in Lentzea and could lead to new compound discoveries. We also find 7121 genes that code for carbohydrate-degrading enzymes which could essentially convert a wide range of polymeric carbohydrates. Genome mining of such genus is very much useful to give scientific leads for experimental validation in the discovery of new-generation bioactive molecules of biotechnological importance.
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Affiliation(s)
- Pulak Kumar Maiti
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Whole-Genome Shotgun (WGS) Sequence of cis-Isoprene Polymer-Degrading Nocardia sp. strain BSTN01. Microbiol Resour Announc 2022; 11:e0117521. [PMID: 35286159 PMCID: PMC9022567 DOI: 10.1128/mra.01175-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Species belonging to the genus Nocardia are known to be facultative human pathogens. There are also reports of Nocardia species capable of degrading various forms of rubber. Here, we report the whole-genome shotgun (WGS) sequence of Nocardia sp. strain BSTN01, isolated from stored water in latex-collecting cups thrown away near a local rubber processing unit in Tripura, India.
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Assessment of VITEK® 2, MALDI-TOF MS and full gene 16S rRNA sequencing for aerobic endospore-forming bacteria isolated from a pharmaceutical facility. METHODS IN MICROBIOLOGY 2022; 194:106419. [DOI: 10.1016/j.mimet.2022.106419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 11/18/2022]
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Sarkar B, Mandal S. Gordonia sp. BSTG01 isolated from Hevea brasiliensis plantation efficiently degrades polyisoprene (rubber). 3 Biotech 2021; 11:508. [PMID: 34881168 DOI: 10.1007/s13205-021-03063-5] [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: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 12/17/2022] Open
Abstract
Polyisoprene is the principal constituent of rubber latex which has been estimated globally as one of the major solid wastes. Bacterial bioremediation of this solid waste remains a major point of interest for scientists. This study reports a Gram-positive, non-motile, non-spore-forming actinomycete Gordonia sp. BSTG01, isolated from the bark of Hevea brasiliensis of a rubber plantation garden can considerably degrade natural rubber (NR) and synthetic polyisoprene rubber (SR). Scanning electron microscopy showed adhesive colonization of strain BSTG01 on both natural and synthetic rubber surface, conflating into the rubber and forming a biofilm. Rubber-dependent growth of the strain was examined by the decrease of rubber mass and increase of its total protein content in a time-dependent manner. Degradation was also verified by Schiff's reagent which confirms the appearance of aldehydes in the culture media. Fourier transform infrared spectroscopy including the attenuated total reflectance with the NR and SR pieces overgrown by the isolate revealed variations of the overall chemicals arising on the polyisoprene backbone due to the degradation of rubber by the strain BSTG01. Isolate BSTG01 (MTCC 13159) is a strain of Gordonia and this is the first strain isolated from unexplored rubber plantation area with considerable rubber degradation properties. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03063-5.
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Affiliation(s)
- Biraj Sarkar
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019 India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019 India
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Maiti PK, Mandal S. Streptomyces himalayensis sp. nov. including Streptomyces himalayensis subsp. himalayensis subsp. nov. and Streptomyces himalayensis subsp. aureolus subsp. nov. isolated from Western Himalaya. Arch Microbiol 2021; 203:2325-2334. [PMID: 33649903 DOI: 10.1007/s00203-021-02232-7] [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: 08/18/2020] [Revised: 01/25/2021] [Accepted: 02/11/2021] [Indexed: 12/27/2022]
Abstract
Two novel actinobacteria, strain PSKA28T and PSKA54T were isolated from soil sample of Kashmir-Himalaya, India (latitude 34°-01' N; longitude 74°-47' E; altitude 5328 ft). Polyphasic-taxonomic analysis revealed that these strains belong to the genus Streptomyces. The 16S rRNA gene-sequence similarity of these strain were highest (98.6%) with that of the Streptomyces torulosus NRRLB-3889T. They showed 92.1% gyrB gene-sequence similarity but 92.9 and 94.6% rpoB gene-sequence similarity, respectively, with Streptomyces torulosus NRRLB-3889T. The sequence similarities were significantly lower than the recommended threshold value for novel taxonomic position and the 16S rRNA sequence-based phylogenetic analysis indicated that these two isolates are in distinct clade. Phylogenomic analysis with their genome sequences, conferred by Type Strain Genome Server separated them from rest of the Streptomyces type strains. The cell wall contained LL-diaminopimelic acid and the whole-cell hydrolysate contained glucose and ribose. Major fatty acid methyl esters were 15:0 anteiso, 16:0 iso and 17:0 anteiso. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization (dDDH) values as well as evolutionary distance based on multilocus sequence analysis, between closely related type strains and either of the strain PSKA28T or PSKA54T, were considerably lower than the recommended threshold value (< 70% dDDH or < 95-96% ANI/AAI or > 0.007 MLSA distance). Therefore, these isolates represent a novel Streptomyces species, for which we proposed the name Streptomyces himalayensis sp. nov. Genotypic and phenotypic analyses clearly split these strains into two closely related sub-clusters. Based on this, two novel subspecies Streptomyces himalayensis subsp. himalayensis subsp. nov. and Streptomyces himalayensis subsp. aureolus subsp. nov. are proposed, with type strains JCM33755T (= MTCC12933T, MCC4145T) and JCM33759T (= MTCC12938, MCC4180), respectively.
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Affiliation(s)
- Pulak Kumar Maiti
- Department of Microbiology, Laboratory of Molecular Bacteriology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Department of Microbiology, Laboratory of Molecular Bacteriology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Maiti PK, Mandal S. Streptomyces cupreus sp. nov., an antimicrobial producing actinobacterium isolated from Himalayan soil. Arch Microbiol 2021; 203:1601-1609. [PMID: 33415367 DOI: 10.1007/s00203-020-02160-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 11/26/2022]
Abstract
A novel actinobacterium, designated Streptomyces sp strain PSKA01T, was isolated from a soil sample of Kashmir Himalaya, India (latitude:34˚-01'N; longitude:74˚-47'E; altitude: 5328 ft). The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that PSKA01T was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces venetus CMU-AB225T (99.3%), Streptomyces levis NBRC 15423 T (99.3%), Streptomyces misionensis DSM 40306 T (99.2%), Streptomyces carpinensis NRRL B-16921 T (99.2%), Streptomyces purpurascens NBRC 13077 T (99.2%), and Streptomyces phaeoluteichromatogenes NRRL 5799 T (99.2%). A phylogenomic tree based on genome sequences of the isolated strains, conferred by Type Strain Genome Server (TYGS), separated them from rest of the Streptomyces. The cell wall contained LL-diaminopimelic acid and the whole-cell hydrolysates were xylose and rhamnose. Major fatty acid methyl esters (FAME) were observed as 16:0 iso and 17:0 anteiso. In addition to the differences in phenotypic characters, the average nucleotide identity (ANI), average amino acid identity (AAI), digital DNA-DNA hybridization (dDDH) values, tetranucleotide frequency correlation coefficient (TETRA), and multilocus sequence analysis (MLSA) between PSKA01T and closely related type strains were considerably lower than the recommended threshold value; therefore, this isolate represents a novel Streptomyces species, for which the name Streptomyces cupreus sp. nov. is proposed. The type strain is PSKA01T (= JCM 33752 T = MCC 4182 T).
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Affiliation(s)
- Pulak Kumar Maiti
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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