1
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Ouchene R, Zaatout N, Suzuki MT. An Overview on Nocardiopsis Species Originating From North African Biotopes as a Promising Source of Bioactive Compounds and In Silico Genome Mining Analysis of Three Sequenced Genomes. J Basic Microbiol 2024; 64:e2400046. [PMID: 38934516 DOI: 10.1002/jobm.202400046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/21/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024]
Abstract
Actinobacteria are renowned for their prolific production of diverse bioactive secondary metabolites. In recent years, there has been an increasing focus on exploring "rare" genera within this phylum for biodiscovery purposes, notably the Nocardiopsis genus, which will be the subject of the present study. Recognizing the absence of articles describing the research process of finding bioactive molecules from the genus Nocardiopsis in North African environments. We, therefore, present a historical overview of the discoveries of bioactive molecules of the genus Nocardiopsis originating from the region, highlighting their biological activities and associated reported molecules, providing a snapshot of the current state of the field, and offering insights into future opportunities and challenges for drug discovery. Additionally, we present a genome mining analysis of three genomes deposited in public databases that have been reported to be bioactive. A total of 36 biosynthetic gene clusters (BGCs) were identified, including those known to encode bioactive molecules. Notably, a substantial portion of the BGCs showed little to no similarity to those previously described, suggesting the possibility that the analyzed strains could be potential producers of new compounds. Further research on these genomes is essential to fully uncovering their biotechnological potential. Moving forward, we discuss the experimental designs adopted in the reported studies, as well as new avenues to guide the exploration of the Nocardiopsis genus in North Africa.
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Affiliation(s)
- Rima Ouchene
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
- CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Sorbonne Université, Paris, France
| | - Nawel Zaatout
- Faculty of Natural and Life Sciences, University of Batna, Batna, Algeria
| | - Marcelino T Suzuki
- CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Sorbonne Université, Paris, France
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2
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Bhairamkar S, Kadam P, Anjulal H, Joshi A, Chaudhari R, Bagul D, Javdekar V, Zinjarde S. Comprehensive updates on the biological features and metabolic potential of the versatile extremophilic actinomycete Nocardiopsis dassonvillei. Res Microbiol 2024; 175:104171. [PMID: 37995890 DOI: 10.1016/j.resmic.2023.104171] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Nocardiopsis dassonvillei prevails under harsh environmental conditions and the purpose of this review is to highlight its biological features and recent biotechnological applications. The organism prevails in salt-rich soils/marine systems and some strains endure extreme temperatures and pH. A few isolates are associated with marine organisms and others cause human diseases. Comparative genomic analysis indicates its versatility in producing biotechnologically relevant metabolites. Antimicrobial, cytotoxic, anticancer and growth promoting biomolecules are obtained from this organism. It also synthesizes biotechnologically important enzymes. Bioactive compounds and enzymes obtained from this actinomycete provide evidence regarding its metabolic competence and its potential economic value.
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Affiliation(s)
- Shivani Bhairamkar
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Pratik Kadam
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - H Anjulal
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Avani Joshi
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Riddhi Chaudhari
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Dimpal Bagul
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Vaishali Javdekar
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Smita Zinjarde
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India.
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3
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Mo P, Li K, Zhou J, Zhou F, He J, Zou W, Gao J. Nocardiopsis changdeensis sp. nov., an endophytic actinomycete isolated from the roots of Eucommia ulmoides Oliv. J Antibiot (Tokyo) 2023; 76:191-197. [PMID: 36747085 DOI: 10.1038/s41429-023-00596-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/19/2022] [Accepted: 01/06/2023] [Indexed: 02/08/2023]
Abstract
Strain Mg02T was isolated from roots of Eucommia ulmoides Oliv. collected from Changde City, Hunan Province, China. Strain Mg02T, which exhibited distinct chemotaxonomic characteristics of the genus Nocardiopsis: cell-wall chemotype III/C, i.e., meso-diaminopimelic acid as diagnostic amino acid in whole-cell hydrolysates and menaquinone MK-10 with variable degrees of saturation in the side chain as the predominant isoprenoid quinone, was investigated by a polyphasic approach to determine their taxonomic position. Sequence analysis of the 16S rRNA gene indicated that strain Mg02T is affiliated to the genus Nocardiopsis, having highest sequence similarity to Nocardiopsis flavescens CGMCC 4.5723T (99.1%) and <98.7% to other species of the genus Nocardiopsis with validly published names. Phylogenetic analysis of 16S rRNA gene indicated strain Mg02T formed a separate evolutionary clade, suggesting that it could be a novel Nocardiopsis species. Phylogenomic analysis showed that strain Mg02T was closely related to N. flavescens CGMCC 4.5723T and distinct from the latter according to the clustering patterns. The Average Nucleotide Identity and digital DNA-DNA hybridization values between strain Mg02T and N. flavescens CGMCC 4.5723T were far below the species-level thresholds. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, we think that strain Mg02T should represent a novel Nocardiopsis species, for which the name Nocardiopsis changdeensis sp. nov. is proposed. The type strain is Mg02T (=MCCC 1K06174T = JCM 34709T).
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Affiliation(s)
- Ping Mo
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for health aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for wetland biology and Environmental Ecology, College of life and environmental sciences, Hunan University of Arts and Science, Changde, 415000, Hunan, China
| | - Kaiqin Li
- Hunan Institute of Agricultural Biotechnology, Changsha, 410000, Hunan, China
| | - Jinhua Zhou
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for health aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for wetland biology and Environmental Ecology, College of life and environmental sciences, Hunan University of Arts and Science, Changde, 415000, Hunan, China
| | - Fumin Zhou
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for health aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for wetland biology and Environmental Ecology, College of life and environmental sciences, Hunan University of Arts and Science, Changde, 415000, Hunan, China
| | - Jiang He
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for health aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for wetland biology and Environmental Ecology, College of life and environmental sciences, Hunan University of Arts and Science, Changde, 415000, Hunan, China
| | - Wansheng Zou
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for health aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for wetland biology and Environmental Ecology, College of life and environmental sciences, Hunan University of Arts and Science, Changde, 415000, Hunan, China.
| | - Jian Gao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
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4
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Mo P, Chen Y, Zou F, Zhou J, Zou W, Gao J. Nocardiopsis eucommiae sp. nov., a novel endophytic actinomycete isolated from leaves of Eucommia ulmoides Oliv. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748480 DOI: 10.1099/ijsem.0.005654] [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: 12/24/2022] Open
Abstract
A novel Gram-stain-positive, endophytic actinobacterium, designated strain HDS5T, was isolated from leaves of Eucommia ulmoides Oliv. collected from Changde City, Hunan Province, PR China. Strain HDS5T produced yellowish oil green substrate mycelia on Gause's synthetic medium, which also carried yellowish oil green aerial hyphae, fragmenting into rod-shaped elements with smooth surfaces. Strain HDS5T grew at pH 5.0-11.0 (optimum, pH 7), at 20-40 °C (optimum, 28 °C) and in the presence of 0-8.0% NaCl (w/v; optimum, 0-1.0 %). Whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic amino acid and no diagnostic sugars. The predominant fatty acids were iso-C16:0 and C18 : 1 ω9c. The menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). Strain HDS5T showed high 16S rRNA gene sequence similarity to Nocardiopsis prasina DSM 43845T (99.72 %), Nocardiopsis ganjiahuensis DSM 45031T (99.31 %), Nocardiopsis exhalans JCM 11759T (99.17 %), Nocardiopsis alba DSM 43377T (99.11 %), Nocardiopsis metallicus KBS6T (99.11 %), Nocardiopsis valliformis DSM 45023T (99.04 %), Nocardiopsis listeri NBRC 13360T (98.97 %), Nocardiopsis lucentensis DSM 44048T (98.83 %), Nocardiopsis terrae YIM 90022T (98.83 %) and <98.7 % similarities to other type strains. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences showed that strain HDS5T was closely related to N. prasina DSM 43845T. However, the average nucleotide identity based on blast and digital DNA-DNA hybridization values between them were determined to be 90.1 and 40.9 %, respectively, below the threshold of 95-96 and 70 % for the delineation of prokaryotic genomic species, suggesting that strain HDS5T represents a novel Nocardiopsis species. Furthermore, the morphological and physio-biochemical characteristics were sufficient to distinguish strain HDS5T from N. prasina DSM 43845T. Consequently, based on phenotypic and genotypic characteristics, strain HDS5T represents a new Nocardiopsis species, for which the name Nocardiopsis eucommiae sp. nov. is proposed. The type strain is HDS5T (=MCCC 1K06172T=JCM 34707T).
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Affiliation(s)
- Ping Mo
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for Health Aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for Wetland Biology and Environmental Ecology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, Hunan, PR China
| | - Yazhi Chen
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for Health Aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for Wetland Biology and Environmental Ecology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, Hunan, PR China
| | - Fumin Zou
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for Health Aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for Wetland Biology and Environmental Ecology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, Hunan, PR China
| | - Jinhua Zhou
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for Health Aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for Wetland Biology and Environmental Ecology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, Hunan, PR China
| | - Wansheng Zou
- State Key Laboratory of Development Biology of Freshwater Fish Sub-Center for Health Aquaculture, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, Changde Key Innovation Team for Wetland Biology and Environmental Ecology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, Hunan, PR China
| | - Jian Gao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, PR China
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5
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Camacho Pozo MI, Wieme AD, Pérez SR, Llauradó Maury G, Snauwaert C, Lescaylle Veranes Y, Peña Zamora L, Schumann P, Vandamme P. Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018. Int J Syst Evol Microbiol 2020; 70:6172-6179. [PMID: 33095134 DOI: 10.1099/ijsem.0.004514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An actinomycete, strain D1T, was isolated from a freshwater sediment sample collected from the San Pablo river in the La Risueña community, Santiago de Cuba province, Cuba. The strain was identified as a member of the genus Nocardiopsis by means of a polyphasic taxonomic study. It produced a light yellow non-fragmented substrate mycelium, a white well-developed aerial mycelium and straight to flexuous hyphae. No specific spore chains were observed. Strain D1T contained meso-diaminopimelic acid, no diagnostic sugars, and MK-10(H2), MK-10(H4), MK-10 and MK-10(H6) as predominant menaquinones, but not phosphatidylcholine as diagnostic polar lipid of the genus Nocardiopsis. The predominant fatty acids were iso-C16 : 0, 10-methyl-C18 : 0 and anteiso-C17 : 0. Strain D1T showed the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis synnematoformans DSM 44143T (99.8 %), Nocardiopsis dassonvillei subsp. albirubida NBRC 13392T (99.8 %) and Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T (99.6 %). A genomic OrthoANIu value between D1T and N. dassonvillei subsp. dassonvillei DSM 43111T of 97.63 % and a dDDH value of 78.9 % indicated that strain D1T should be classified in N. dassonvillei. However, phenotypic characteristics distinguished strain D1T from its nearest neighbour taxon. On basis of these results we propose to classify strain D1T (=LMG 30468T=CECT 30033T) as a representative of a novel subspecies of the genus Nocardiopsis, for which the name Nocardiopsis dassonvillei subsp. crassaminis subsp. nov. is proposed. In addition, the genomic distance between N. dassonvillei subsp. albirubida NBRC 13392T and N. dassonvillei subsp. dassonvillei DSM 43111T as determined through OrthoANIu (93.64 %) and dDDH (53.40 %), along with considerable phenotypic and chemotaxonomic differences reported in earlier studies, indicated that the classification of this taxon as Nocardiopsis alborubida Grund and Kroppenstedt 1990 is to be preferred over its classification as N. dassonvillei subsp. albirubida Evtushenko et al. 2000.
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Affiliation(s)
- Miladis Isabel Camacho Pozo
- Center for Industrial Biotechnology Studies, Faculty of Exact and Natural Sciences. University of Oriente, Patricio Lumumba, Santiago de Cuba 90500, Cuba
| | - Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35. B-9000 Ghent, Belgium
| | - Suyén Rodríguez Pérez
- Laboratory of Antibodies and Experimental Biomodels, Prolongation of 23th street and Caney highway, Vista Alegre, Santiago de Cuba, Cuba
| | - Gabriel Llauradó Maury
- Center for Industrial Biotechnology Studies, Faculty of Exact and Natural Sciences. University of Oriente, Patricio Lumumba, Santiago de Cuba 90500, Cuba
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35. B-9000 Ghent, Belgium
| | - Yaneisy Lescaylle Veranes
- Center for Industrial Biotechnology Studies, Faculty of Exact and Natural Sciences. University of Oriente, Patricio Lumumba, Santiago de Cuba 90500, Cuba
| | - Leonor Peña Zamora
- Center for Industrial Biotechnology Studies, Faculty of Exact and Natural Sciences. University of Oriente, Patricio Lumumba, Santiago de Cuba 90500, Cuba
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35. B-9000 Ghent, Belgium.,BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35. B-9000 Ghent, Belgium
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6
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Subramani R, Sipkema D. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs 2019; 17:E249. [PMID: 31035452 PMCID: PMC6562664 DOI: 10.3390/md17050249] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
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Affiliation(s)
- Ramesh Subramani
- School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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7
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Han J, Gao QX, Zhang YG, Li L, Mohamad OAA, Rao MPN, Xiao M, Hozzein WN, Alkhalifah DHM, Tao Y, Li WJ. Transcriptomic and Ectoine Analysis of Halotolerant Nocardiopsis gilva YIM 90087 T Under Salt Stress. Front Microbiol 2018; 9:618. [PMID: 29651284 PMCID: PMC5884947 DOI: 10.3389/fmicb.2018.00618] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/16/2018] [Indexed: 11/25/2022] Open
Abstract
The genus Nocardiopsis is an unique actinobacterial group that widely distributed in hypersaline environments. In this study, we investigated the growth conditions, transcriptome analysis, production and accumulation of ectoine by Nocardiopsis gilva YIM 90087T under salt stress. The colony color of N. gilva YIM 90087T changed from yellow to white under salt stress conditions. Accumulation of ectoine and hydroxyectoine in cells was an efficient way to regulate osmotic pressure. The ectoine synthesis was studied by transferring the related genes (ectA, ectB, and ectC) to Escherichia coli. Transcriptomic analysis showed that the pathways of ABC transporters (ko02010) and glycine, serine, and threonine metabolism (ko00260) played a vital role under salt stress environment. The ectABC from N. gilva YIM 90087T was activated under the salt stress. Addition of exogenous ectoine and hydroxyectoine were helpful to protect N. gilva YIM 90087T from salt stress.
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Affiliation(s)
- Jian Han
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China.,Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Quan-Xiu Gao
- Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
| | - Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
| | - Osama A A Mohamad
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China.,Institute for Post Graduate Environmental Studies, Environmental Science Department, Arish University, North Sinai, Egypt
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wael N Hozzein
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni Suef, Egypt.,Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Dalal H M Alkhalifah
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Yong Tao
- Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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8
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Muangham S, Suksaard P, Mingma R, Matsumoto A, Takahashi Y, Duangmal K. Nocardiopsissediminis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2016; 66:3835-3840. [PMID: 27381319 DOI: 10.1099/ijsem.0.001273] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A filamentous actinomycete, designated strain 1SS5-02T, was isolated from mangrove sediment collected from Ranong province, Thailand. The strain formed aerial and substrate mycelia composed of long, branched hyphae. Aerial mycelia differentiated into non-motile, rod-shaped spores. The organism contained meso-diaminopimelic acid and no diagnostic sugars in whole-cell hydrolysates. The predominant menaquinones were MK-11(H4), MK-11(H6) and MK-11(H8). Polar lipids comprised phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids and four unidentified lipids. The major fatty acids were iso-C16 : 0, C18 : 1ω9c, 10-methyl C18 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 73.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1SS5-02T belonged to the genus Nocardiopsis. The strain showed the highest degree of 16S rRNA gene sequence similarity with 'Nocardiopsis mangrovei' HA11166 (97.9 %) and Nocardiopsis trehalosi VKM Ac-942T (97.8 %). However, strain 1SS5-02T could be distinguished from its nearest phylogenetic relatives in the genus Nocardiopsis on the basis of DNA-DNA relatedness values and the combination of phenotypic properties. On the basis of polyphasic taxonomy, strain 1SS5-02T is considered to represent a novel species of the genus Nocardiopsis, for which the name Nocardiopsis sediminis sp. nov. is proposed. The type strain is 1SS5-02T (=BCC 75410T=NBRC 110934T).
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Affiliation(s)
- Supattra Muangham
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Paweena Suksaard
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Ratchanee Mingma
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kannika Duangmal
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
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9
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Zhang YG, Liu Q, Wang HF, Park DJ, Guo JW, Kim CJ, Zhang YM, Li WJ. Nocardiopsis ansamitocini sp. nov., a new producer of ansamitocin P-3 of the genus Nocardiopsis. Int J Syst Evol Microbiol 2015; 66:230-235. [PMID: 26486850 DOI: 10.1099/ijsem.0.000703] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An alkalitolerant actinomycete strain, designated EGI 80425T, capable of producing ansamitocin P-3, was isolated from a saline-alkali soil sample of Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80425T formed non-fragmented substrate mycelia and white aerial hyphae with long spore chains. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and rhamnose as the major sugar. The major fatty acids were anteiso-C17 : 0, iso-C16 : 0 and C18 : 1ω9c. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-10(H8) and MK-9(H4). The G+C content of the genomic DNA of strain EGI 80425T was 70.2 mol%. Strain EGI 80425T showed highest 16S rRNA gene sequence similarity to Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T (96.44 %). Phylogenetic analysis showed that strain EGI 80425T clustered with the members of the genus Nocardiopsis. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain EGI 80425T represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis ansamitocini sp. nov. is proposed. The type strain is EGI 80425T ( = CGMCC 9969T = KCTC 39605T).
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Affiliation(s)
- Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Qing Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China.,Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Hong-Fei Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Dong-Jin Park
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Jian-Wei Guo
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China.,Key Laboratory of Higher Quality and Efficient Cultivation and Security Control of Crops for Yunnan Province, Honghe University, Mengzi 661100, PR China
| | - Chang-Jin Kim
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Yuan-Ming Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China.,Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China
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