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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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Boudjelal F, Zitouni A, Bouras N, Spröer C, Klenk HP, Smaoui S, Mathieu F. Rare Halophilic Nocardiopsis from Algerian Saharan Soils as Tools for Biotechnological Processes in Pharmaceutical Industry. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1061176. [PMID: 37284028 PMCID: PMC10241594 DOI: 10.1155/2023/1061176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/01/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023]
Abstract
The Sahara Desert, one of the most extreme ecosystems in the planet, constitutes an unexplored source of microorganisms such as mycelial bacteria. In this study, we investigated the diversity of halophilic actinobacteria in soils collected from five regions of the Algerian Sahara. A total of 23 halophilic actinobacterial strains were isolated by using a humic-vitamin agar medium supplemented with 10% NaCl. The isolated halophilic strains were subjected to taxonomic analysis using a polyphasic approach, which included morphological, chemotaxonomic, physiological (numerical taxonomy), and phylogenetic analyses. The isolates showed abundant growth in CMA (complex medium agar) and TSA (tryptic soy agar) media containing 10% NaCl, and chemotaxonomic characteristics were consistent with their assignment to the genus Nocardiopsis. Analysis of the 16S rRNA sequence of 23 isolates showed five distinct clusters and a similarity level ranging between 98.4% and 99.8% within the Nocardiopsis species. Comparison of their physiological characteristics with the nearest species showed significant differences with the closely related species. Halophilic Nocardiopsis isolated from Algerian Sahara soil represents a distinct phyletic line suggesting a potential new species. Furthermore, the isolated strains of halophilic Nocardiopsis were screened for their antagonistic properties against a broad spectrum of microorganisms by the conventional agar method (agar cylinders method) and found to have the capacity to produce bioactive secondary metabolites. Except one isolate (AH37), all isolated Nocardiopsis showed moderate to high biological activities against Pseudomonas syringae and Salmonella enterica, and some isolates showed activities against Agrobacterium tumefaciens, Serratia marcescens, and Klebsiella pneumoniae. However, no isolates were active against Bacillus subtilis, Aspergillus flavus, or Aspergillus niger. The obtained finding implies that the unexplored extreme environments such as the Sahara contain many new bacterial species as a novel drug source for medical and industrial applications.
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Affiliation(s)
- Farida Boudjelal
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
- Faculty of Biological Sciences (FSB), University of Sciences and Technologies Houari Boumediene (USTHB), BP 32 El Alia, Bab Ezzouar, 16111 Algiers, Algeria
| | - Abdelghani Zitouni
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Noureddine Bouras
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
- Laboratoire de Valorisation et Conservation des Écosystèmes Arides (LVCEA), Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaia, Ghardaia, Algeria
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Slim Smaoui
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177 3018 Sfax, Tunisia
| | - Florence Mathieu
- Laboratoire de Génie Chimique, UMR 5503 CNRS/INPT/UPS, INP-ENSAT, 1, Université de Toulouse, Avenue de l'Agrobiopôle, 31326 Castanet-Tolosan, France
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3
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Diversity of actinomycete and their metabolites isolated from Howz Soltan Lake, Iran. Arch Microbiol 2022; 205:24. [PMID: 36512155 DOI: 10.1007/s00203-022-03364-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Saline environments are largely unexplored sources of actinomycetes with the potential to produce biologically active secondary metabolites. A total of 34 actinomycete isolates from water, sediments and mostly rhizosphere (82%) were collected from different sites at Howz Soltan Lake in Iran. Based on phylogenetic analysis, the isolates belonged to the genera Streptomyces, Nocardia and Saccharomonospora. Cytotoxic assay revealed extract from isolate act9 as the most potent (19.716±5.72 µg/ml) against the MDA-MB-231 human breast cancer cell. Also, 38% of the isolates showed antimicrobial activity against some of the test microorganisms. The ethyl-acetate extract of isolate act18 showed the strongest antibacterial effect against Staphylococcus aureus and MRSA, and was further analyzed by GC/MS. Ar-tumerone (26.41%) and butyl isodecyl phthalate (21.77 %) were the main constituents detected in the extract. This is the first time Ar-tumerone is being detected in a prokaryote. Isolate act18 showed a high 16S rRNA sequence similarity to that of Streptomyces youssoufiensis DSM 41920. In addition, a number of the isolates produced different enzymes including lipase, amylase, protease, gelatinase, urease and lecithinase. Some of the isolates belonging to the genera Streptomyces and Nocardia exhibited plant growth promoting activity such as increased seed germination, stem length and the number of Echium leaves during the 20 days. Findings from this study indicated the diversity and biosynthetic potential of actinomycetes from saline environment.
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4
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Spiractinospora alimapuensis gen. nov., sp. nov., isolated from marine sediment of Valparaíso Bay (Chile) and proposal for reclassification of two species of the genus Nocardiopsis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005207] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An alkaliphilic actinobacterium, designated VN6-2T, was isolated from marine sediment collected from Valparaíso Bay, Chile. Strain VN6-2T formed yellowish-white branched substrate mycelium without fragmentation. Aerial mycelium was well developed, forming wavy or spiral spore chains. Strain VN6-2T exhibited a 16S rRNA gene sequence similarity of 93.9 % to
Salinactinospora qingdaonensis
CXB832T, 93.7 % to
Murinocardiopsis flavida
14-Be-013T, and 93.7 % to
Lipingzhangella halophila
14-Be-013T. Genome sequencing revealed a genome size of 5.9 Mb and an in silico G+C content of 69.3 mol%. Both of the phylogenetic analyses based on 16S rRNA gene sequences and the up-to-date bacterial core gene sequences revealed that strain VN6-2T formed a distinct monophyletic clade within the family
Nocardiopsaceae
. Chemotaxonomic assessment of strain VN6-2T showed that the major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0, and the predominant respiratory quinones were MK-9, MK-9(H2) and MK-9(H4). Whole-cell hydrolysates contained meso-diaminopimelic acid as the cell-wall diamino acid, and ribose and xylose as the diagnostic sugars. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, aminophospholipids, glycolipid and phospholipid. Based on the results of this polyphasic study, a novel genus, Spiractinospora gen. nov., is proposed within the family
Nocardiopsaceae
and the type species Spiractinospora alimapuensis gen. nov., sp. nov. The type strain is VN6-2T (CECT 30026T, CCUG 66258T). On the basis of the phylogenetic results herein, we also propose that Nocardiopsis arvandica and Nocardiopsis litoralis are later heterotypic synonyms of
Nocardiopsis sinuspersici
and
Nocardiopsis kunsanensis
, respectively, for which emended descriptions are given.
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Axenov-Gribanov DV, Morgunova MM, Vasilieva UA, Gamaiunov SV, Dmitrieva (Krasnova) ME, Pereliaeva EV, Belyshenko AY, Luzhetskyy AN. Composition of nutrient media and temperature of cultivation imposes effect on the content of secondary metabolites of Nocardiopsis sp. isolated from a Siberian Cave. 3 Biotech 2021; 11:386. [PMID: 34350091 PMCID: PMC8319253 DOI: 10.1007/s13205-021-02926-1] [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: 04/27/2021] [Accepted: 07/14/2021] [Indexed: 11/25/2022] Open
Abstract
Growth of human population leads to many global and medical problems. The problems include the crisis of health, antibiotic resistance, drug discovery, etc. Increasing antimicrobial resistance of microorganisms results in the need to screen natural products (incl. antibiotics and antimicrobial peptides) and their producers in different ecological niches. The purpose of this study was to estimate antibiotic activity and biotechnological potential of rare actinobacteria Nocardiopsis sp. The strain was isolated from Okhotnichya cave located in Siberia. Here, we cultivated the strain at 3 temperature modes (13 °C, 28 °C, 37 °C) in 11 liquid nutrient (rich and poor) media. Using modern assays of liquid chromatography and high-resolution mass spectrometry, we estimated the content and number of produced natural products, distribution of their masses, and potential rate of novel secondary metabolites. We demonstrated that minimal nutrient media with l-asparagine and SM25 media with malt extract were less productive at current experimental parameters. As it was shown, this strain was characterized by antibiotic properties against Bacillus subtilis when cultivated at 28 °C. Also, weak antibiotic activity of crude extracts was found in strain cultivation at 13 °C. Also, we detected a high number of novel amphiphilic and hydrophobic NPs produced by this strain. We demonstrated both the influence of the nutrient media composition and cultivation temperature on biosynthetic capabilities of rare strain Nocardiopsis sp. Finally, high level of natural products that were predicted as novel confirms high biotechnological value of rare genera of Actinobacteria that could be explained by the evolution of microorganisms in the isolated environment of cave ecosystem.
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Affiliation(s)
| | | | - Ulyana A. Vasilieva
- Irkutsk State University, 1 Karl Marx St, 664003 Irkutsk, Russia
- Siberian Institute of Plant Physiology and Biochemistry, 132 Lermontov Str, 664033 Irkutsk, Russia
| | - Stanislav V. Gamaiunov
- Irkutsk State University, 1 Karl Marx St, 664003 Irkutsk, Russia
- Speleology Club Arabica, 11 Berezovaya Rosha Str, 664043 Irkutsk, Russia
| | | | | | | | - Andriy N. Luzhetskyy
- Pharmaceutical Biotechnology, University of Saarland, Campus, C2.3, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, Campus, C2.3, 66123 Saarbrücken, Germany
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6
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Salam N, Xian WD, Asem MD, Xiao M, Li WJ. From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:132-147. [PMID: 37073336 PMCID: PMC10077289 DOI: 10.1007/s42995-020-00064-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
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Affiliation(s)
- Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
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7
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Pan HQ, Zhang DF, Li L, Jiang Z, Cheng J, Zhang YG, Wang HF, Hu JC, Li WJ. Nocardiopsis oceani sp. nov. and Nocardiopsis nanhaiensis sp. nov., actinomycetes isolated from marine sediment of the South China Sea. Int J Syst Evol Microbiol 2016; 65:3384-3391. [PMID: 26297579 DOI: 10.1099/ijsem.0.000425] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two actinomycete strains, designated 10A08AT and 10A08BT, were isolated from marine sediment samples of the South China Sea and their taxonomic positions were determined by a polyphasic approach. The two Gram-stain-positive, aerobic strains produced branched substrate mycelium and aerial hyphae, and no diffusible pigment was produced in the media tested. At maturity, spore chains were formed on aerial hyphae and all mycelium fragmented with age. Whole-cell hydrolysates of both strains contained meso-diaminopimelic acid and no diagnostic sugars. Their predominant menaquinones (>10 %) were MK-9(H4), MK-9(H6) and MK-10(H6) for strain 10A08AT and MK-9(H4), MK-9(H6), MK-10(H4) and MK-10(H6) for strain 10A08BT. The polar lipids detected from the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and unknown phosphoglycolipids and phospholipids. The major fatty acids (>10 %) of both strains were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The genomic DNA G+C contents of strains 10A08AT and 10A08BT were 70.9 and 71.6 mol%, respectively. On the basis of 16S rRNA gene sequence similarities, the two strains were shown to be most closely related to species of the genus Nocardiopsis. DNA–DNA hybridization relatedness values of < 70 % between these two isolates and their closest neighbour, Nocardiopsis terrae YIM 90022T, and between the two strains supported the conclusion that they represent two novel species. Based on phylogenetic analysis and phenotypic and genotypic data, it is concluded that the two isolates belong to the genus Nocardiopsis, and the names Nocardiopsis oceani sp. nov. (type strain 10A08AT = DSM 45931T = BCRC 16951T) and Nocardiopsis nanhaiensis sp. nov. (type strain 10A08BT = CGMCC 47227T = BCRC 16952T) are proposed.
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Affiliation(s)
- Hua-Qi Pan
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
| | - Dao-Feng Zhang
- State Key Laboratory of Biocontrol and Guangdong 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
| | - Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürumqi 830011, PR China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Juan Cheng
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürumqi 830011, PR China
| | - Hong-Fei Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürumqi 830011, PR China
| | - Jiang-Chun Hu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong 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.,Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürumqi 830011, PR China
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8
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Liu MJ, Zhu WY, Li J, Zhao GZ, Xiong Z, Park DJ, Hozzein WN, Kim CJ, Li WJ. Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota. Int J Syst Evol Microbiol 2015; 65:2562-2568. [PMID: 25948617 DOI: 10.1099/ijs.0.000304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete strain, designated YIM 690008T, was isolated from Daucus carota collected from South Korea and its taxonomic position was investigated by using a polyphasic approach. The strain grew well on most media tested and no diffusible pigment was produced. The aerial mycelium formed wrinkled single spores and short spore chains, some of which were branched. The whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, mannose, ribose, galactose and rhamnose. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-10(H8) and MK-10(H2). The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, some unknown phospholipids, glycolipids and polar lipids. The major fatty acids were i-C16 : 0, ai-C17 : 0 and C18 : 1ω9c. The DNA G+C content of the genomic DNA was 63.1 mol%. Phylogenetic analysis indicated that the isolate belongs to the family Nocardiopsaceae. However, based on phenotypic, chemotaxonomic and genotypic data, it was concluded that strain YIM 690008T represents a novel genus and novel species of the family Nocardiopsaceae, for which the name Actinorugispora endophytica gen. nov., sp. nov. (type strain YIM 690008T = DSM 46770T = JCM 30099T = KCTC 29480T) is proposed.
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Affiliation(s)
- Min-Jiao Liu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China.,Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, PR China
| | - Wen-Yong Zhu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infections Diseases, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, PR China
| | - Jie Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Guo-Zhen Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Zhi Xiong
- Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, PR China
| | - Dong-Jin Park
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Wael N Hozzein
- Bioproducts Research Chair (BRC), College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Chang-Jin Kim
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong 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
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9
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Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species: Incidence, ecological roles and adaptations. Microbiol Res 2015; 174:33-47. [PMID: 25946327 DOI: 10.1016/j.micres.2015.03.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/23/2022]
Abstract
Members of the genus Nocardiopsis are ecologically versatile and biotechnologically important. They produce a variety of bioactive compounds such as antimicrobial agents, anticancer substances, tumor inducers, toxins and immunomodulators. They also secrete novel extracellular enzymes such as amylases, chitinases, cellulases, β-glucanases, inulinases, xylanases and proteases. Nocardiopsis species are aerobic, Gram-positive, non-acid-fast, catalase-positive actinomycetes with nocardioform substrate mycelia and their aerial mycelia bear long chains of spores. Their DNA possesses high contents of guanine and cytosine. There is a marked variation in properties of the isolates obtained from different ecological niches and their products. An important feature of several species is their halophilic or halotolerant nature. They are associated with a variety of marine and terrestrial biological forms wherein they produce antibiotics and toxins that help their hosts in evading pathogens and predators. Two Nocardiopsis species, namely, N. dassonvillei and N. synnemataformans (among the thirty nine reported ones) are opportunistic human pathogens and cause mycetoma, suppurative infections and abscesses. Nocardiopsis species are present in some plants (as endophytes or surface microflora) and their rhizospheres. Here, they are reported to produce enzymes such as α-amylases and antifungal agents that are effective in warding-off plant pathogens. They are prevalent as free-living entities in terrestrial locales, indoor locations, marine ecosystems and hypersaline habitats on account of their salt-, alkali- and desiccation-resistant behavior. In such natural locations, Nocardiopsis species mainly help in recycling organic compounds. Survival under these diverse conditions is mediated by the production of extracellular enzymes, antibiotics, surfactants, and the accumulation of compatible solutes. The accommodative genomic features of Nocardiopsis species support their existence under the diverse conditions where they prevail.
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Affiliation(s)
- Tahsin Bennur
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Ameeta Ravi Kumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India.
| | - Vaishali Javdekar
- Department of Biotechnology, Abasaheb Garware College, Pune 411004, India.
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10
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Biodiversity of Halophilic and Halotolerant Actinobacteria. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Guo L, Tuo L, Habden X, Zhang Y, Liu J, Jiang Z, Liu S, Dilbar T, Sun C. Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 2015; 65:206-213. [DOI: 10.1099/ijs.0.055160-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain CA15-2T, was isolated from a soil sample collected from the rhizosphere of tamarisk in the Lop Nor region, Xinjiang, China, and was characterized by using a polyphasic taxonomic approach. Optimal growth occurred at 37 °C and pH 7.5–8.0 and with 5 % (w/v) NaCl. Strain CA15-2T formed white to pale-yellow branched substrate mycelium without fragmentation and sparse aerial mycelium with wavelike curves. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall but no diagnostic sugars. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid and other unidentified lipids. MK-9(H8), MK-10(H8) and MK-10(H6) were the predominant menaquinones. The major fatty acids were iso-C16 : 0 and C16 : 0. The G+C content of the genomic DNA was 69.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CA15-2T formed a distinct subclade in the family
Nocardiopsaceae
, with less than 95 % 16S rRNA gene sequence similarity to all known members of the family
Nocardiopsaceae
. On the basis of the evidence from our polyphasic study, a novel genus, Allosalinactinospora gen. nov., is proposed, with the type species Allosalinactinospora lopnorensis gen. nov., sp. nov. The type strain of Allosalinactinospora lopnorensis is strain CA15-2T ( = DSM 45697T = CGMCC 4.7074T).
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Affiliation(s)
- Lin Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Li Tuo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Xugela Habden
- College of Life Science and Chemistry, Xinjiang Normal University, Urumchi 830054, PR China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Jiameng Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Zhongke Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Shaowei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Tohty Dilbar
- College of Life Science and Chemistry, Xinjiang Normal University, Urumchi 830054, PR China
| | - Chenghang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
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12
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Hamedi J, Mohammadipanah F, Panahi HKS. Biotechnological Exploitation of Actinobacterial Members. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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13
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Antimicrobial and Biocatalytic Potential of Haloalkaliphilic Actinobacteria. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species as potential sources of diverse and novel extracellular enzymes. Appl Microbiol Biotechnol 2014; 98:9173-85. [PMID: 25269602 DOI: 10.1007/s00253-014-6111-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 01/10/2023]
Abstract
Members of the genus Nocardiopsis are generally encountered in locations that are inherently extreme. They are present in frozen soils, desert sand, compost, saline or hypersaline habitats (marine systems, salterns and soils) and alkaline places (slag dumps, lake soils and sediments). In order to survive under these severe conditions, they produce novel and diverse enzymes that allow them to utilize the available nutrients and to thrive. The members of this genus are multifaceted and release an assortment of extracellular hydrolytic enzymes. They produce enzymes that are cold-adapted (α-amylases), thermotolerant (α-amylases and xylanases), thermoalkalotolerant (cellulases, β-1,3-glucanases), alkali-tolerant thermostable (inulinases), acid-stable (keratinase) and alkalophilic (serine proteases). Some of the enzymes derived from Nocardiopsis species act on insoluble polymers such as glucans (pachyman and curdlan), keratin (feathers and prion proteins) and polyhydroxyalkanoates. Extreme tolerance exhibited by proteases has been attributed to the presence of some amino acids (Asn and Pro) in loop structures, relocation of multiple salt bridges to outer regions of the protein or the presence of a distinct polyproline II helix. The range of novel enzymes is projected to increase in the forthcoming years, as new isolates are being continually reported, and the development of processes involving such enzymes is envisaged in the future.
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Affiliation(s)
- Tahsin Bennur
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007, India
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15
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Isolation and characterization of novel alkali-halophilic actinomycetes from the Chilika brackish water lake, India. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0831-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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16
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Xu S, Yan L, Zhang X, Wang C, Feng G, Li J. Nocardiopsis fildesensis sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2014; 64:174-179. [DOI: 10.1099/ijs.0.053595-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A filamentous actinomycete strain, designated GW9-2T, was isolated from a soil sample collected from the Fildes Peninsula, King George Island, West Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew slowly on most media tested, producing small amounts of aerial mycelia and no diffusible pigments on most media tested. The strain grew in the presence of 0–12 % (w/v) NaCl (optimum, 2–4 %), at pH 9.0–11.0 (optimum, pH 9.0) and 10–37 °C (optimum, 28 °C). The isolate contained meso-diaminopimelic acid, no diagnostic sugars and MK-9(H4) as the predominant menaquinone. The major phospholipids were phosphatidylglycerol, phosphatidylcholine and phosphatidylmethylethanolamine. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, C18 : 1ω9c, iso-C15 : 0 and iso-C17 : 0. DNA–DNA relatedness was 37.6 % with
Nocardiopsis lucentensis
DSM 44048T, the nearest phylogenetic relative (97.93 % 16S rRNA gene sequence similarity). On the basis of the results of a polyphasic study, a novel species,
Nocardiopsis
fildesensis sp. nov., is proposed. The type strain is GW9-2T ( = CGMCC 4.7023T = DSM 45699T = NRRL B-24873T).
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Affiliation(s)
- Shanshan Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Lien Yan
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Xuan Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Chao Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Ge Feng
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Jing Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
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17
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Subramani R, Aalbersberg W. Culturable rare Actinomycetes: diversity, isolation and marine natural product discovery. Appl Microbiol Biotechnol 2013; 97:9291-321. [DOI: 10.1007/s00253-013-5229-7] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 11/30/2022]
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18
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Meena B, Rajan LA, Vinithkumar NV, Kirubagaran R. Novel marine actinobacteria from emerald Andaman & Nicobar Islands: a prospective source for industrial and pharmaceutical byproducts. BMC Microbiol 2013; 13:145. [PMID: 23800234 PMCID: PMC3695772 DOI: 10.1186/1471-2180-13-145] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 05/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Andaman and Nicobar Islands situated in the eastern part of Bay of Bengal are one of the distinguished biodiversity hotspot. Even though number of studies carried out on the marine flora and fauna, the studies on actinobacteria from Andaman and Nicobar Islands are meager. The aim of the present study was to screen the actinobacteria for their characterization and identify the potential sources for industrial and pharmaceutical byproducts. RESULTS A total of 26 actinobacterial strains were isolated from the marine sediments collected from various sites of Port Blair Bay where no collection has been characterized previously. Isolates were categorized under the genera: Saccharopolyspora, Streptomyces, Nocardiopsis, Streptoverticillium, Microtetraspora, Actinopolyspora, Actinokineospora and Dactylosporangium. Majority of the isolates were found to produce industrially important enzymes such as amylase, protease, gelatinase, lipase, DNase, cellulase, urease and phosphatase, and also exhibited substantial antibacterial activity against human pathogens. 77% of isolates exhibited significant hemolytic activity. Among 26 isolates, three strains (NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26) were found to generate appreciable extent of surfactant, amylase, cellulase and protease enzyme. NIOT-VKKMA02 produced surfactant using kerosene as carbon source and emulsified upto E(24)-63.6%. Moreover, NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26 synthesized 13.27 U/ml, 9.85 U/ml and 8.03 U/ml amylase; 7.75 U/ml, 5.01 U/ml and 2.08 U/ml of cellulase and 11.34 U/ml, 6.89 U/ml and 3.51 U/ml of protease enzyme, respectively. CONCLUSIONS High diversity of marine actinobacteria was isolated and characterized in this work including undescribed species and species not previously reported from emerald Andaman and Nicobar Islands, including Streptomyces griseus, Streptomyces venezuelae and Saccharopolyspora salina. The enhanced salt, pH and temperature tolerance of the actinobacterial isolates along with their capacity to secrete commercially valuable primary and secondary metabolites emerges as an attractive feature of these organisms. These results are reported for the first time from these emerald Islands and expand the scope to functionally characterize novel marine actinobacteria and their metabolites for the potential novel molecules of commercial interest.
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Affiliation(s)
- Balakrishnan Meena
- Andaman and Nicobar Centre for Ocean Science and Technology, ESSO-NIOT, Dollygunj, Port Blair, Andaman and Nicobar Islands 744 103, India.
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Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability. PLoS One 2013; 8:e61528. [PMID: 23626695 PMCID: PMC3634020 DOI: 10.1371/journal.pone.0061528] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/12/2013] [Indexed: 12/04/2022] Open
Abstract
The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111T. The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.
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20
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Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes. Extremophiles 2012; 17:1-13. [PMID: 23129307 DOI: 10.1007/s00792-012-0493-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/18/2012] [Indexed: 12/22/2022]
Abstract
More than 70 species of halotolerant and halophilic actinomycetes belonging to at least 24 genera have been validly described. Halophilic actinomycetes are a less explored source of actinomycetes for discovery of novel bioactive secondary metabolites. Degradation of aliphatic and aromatic organic compounds, detoxification of pollutants, production of new enzymes and other metabolites such as antibiotics, compatible solutes and polymers are other potential industrial applications of halophilic and halotolerant actinomycetes. Especially new bioactive secondary metabolites that are derived from only a small fraction of the investigated halophilic actinomycetes, mainly from marine habitats, have revealed the huge capacity of this physiological group in production of new bioactive chemical entities. Combined high metabolic capacities of actinomycetes and unique features related to extremophilic nature of the halophilic actinomycetes have conferred on them an influential role for future biotechnological applications.
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21
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Li J, Yang J, Zhu WY, He J, Tian XP, Xie Q, Zhang S, Li WJ. Nocardiopsis coralliicola sp. nov., isolated from the gorgonian coral, Menella praelonga. Int J Syst Evol Microbiol 2012; 62:1653-1658. [PMID: 21890725 DOI: 10.1099/ijs.0.035402-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinobacterial strain, SCSIO 10427T, was isolated from a gorgonian coral sample collected from Weizhou Island, Guangxi province, China, and its taxonomic position was investigated using a polyphasic approach. The organism was found to have a range of chemical and morphological properties consistent with its classification in the genus
Nocardiopsis
. Phylogenetic analysis indicated that 16S rRNA gene sequence similarity between strain SCSIO 10427T and type strains of other recognized members of the genus
Nocardiopsis
was lower than 98.4 %. Furthermore, phenotypic characteristics revealed that the strain differed from the currently recognized species of the genus
Nocardiopsis
. Therefore, strain SCSIO 10427T represents a novel species of the genus
Nocardiopsis
, for which the name Nocardiopsis coralliicola sp. nov. is proposed. The type strain is SCSIO 10427T ( = CCTCC AA 2011010T = DSM 45611T).
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Affiliation(s)
- Jie Li
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Jian Yang
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Wen-Yong Zhu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Jie He
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Xin-Peng Tian
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Qiong Xie
- State Key Lab of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, PR China
| | - Si Zhang
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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Fatty-acid compositions of marine isolates of the actinobacteria Nocardiopsis umidischolae KMM 7036 and Streptomyces sp. KMM 7210. Chem Nat Compd 2012. [DOI: 10.1007/s10600-012-0226-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chang X, Liu W, Zhang XH. Spinactinospora alkalitolerans gen. nov., sp. nov., an actinomycete isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61:2805-2810. [DOI: 10.1099/ijs.0.027383-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel marine actinomycete, designated CXB654T, was isolated from marine sediment collected at a depth of 17.5 m near the Yellow Sea Cold Water Mass, China. Optimal growth occurred at 37.0 °C, at pH 7.0–8.0 and in 3–8 % (w/v) NaCl. Strain CXB654T formed branched substrate mycelium without fragmentation. Abundant aerial mycelium differentiated into long or short chains of spores and spores were elliptical and cylindrical with spiny surfaces. Strain CXB654T contained meso-diaminopimelic acid as the diagnostic diamino acid, and ribose and glucose as the major whole-cell components. Phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. MK-10(H8), MK-10(H6) and MK-9(H8) were the predominant menaquinones. The major fatty acids were i-C16 : 0 (24.46 %), ai-C17 : 0 (20.66 %) and C18 : 0 (20.14 %). The DNA G+C content was 71.1 mol%. Comparative analysis of 16S rRNA gene sequences showed that the novel strain was most closely related to genera within the family Nocardiopsaceae, but formed a separate lineage. Highest sequence similarities were to Murinocardiopsis flavida DSM 45312T (96.6 %), Thermobifida halotolerans YIM 90462T (96.5 %) and Marinactinospora thermotolerans DSM 45154T (96.1 %). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain CXB654T was considered to represent a novel species in a new genus in the family Nocardiopsaceae, and the name Spinactinospora alkalitolerans gen. nov., sp. nov. is proposed; the type strain is CXB654T ( = DSM 45414T = LMG 25485T).
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Affiliation(s)
- Xianbo Chang
- College of Environmental and Material Engineering, Yantai University, Yantai, PR China
- Key Laboratory of Marine Genetics and Breeding for Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Wenzheng Liu
- Key Laboratory of Marine Genetics and Breeding for Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Xiao-Hua Zhang
- Key Laboratory of Marine Genetics and Breeding for Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
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Fang C, Zhang J, Pang H, Li Y, Xin Y, Zhang Y. Nocardiopsis flavescens sp. nov., an actinomycete isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61:2640-2645. [DOI: 10.1099/ijs.0.027987-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, aerobic bacterium, strain SA6T, was isolated from marine sediment taken at a depth of 20 cm on the seashore of Lianyungang, Jiangsu Province, China. Strain SA6T contained meso-diaminopimelic acid, no diagnostic sugars, type PIII phospholipids, and MK-10(H2) and MK-10(H4) as the predominant menaquinones. The organism showed a range of chemical and morphological properties consistent with its classification in the genus Nocardiopsis. The almost-complete 16S rRNA gene sequence of strain SA6T was aligned with corresponding sequences of representatives of the genus Nocardiopsis and related taxa by using two tree-making algorithms. Strain SA6T formed a distinct phyletic line within the evolutionary radiation occupied by the genus Nocardiopsis and was related most closely to the type strain of Nocardiopsis lucentensis. Strain SA6T could be distinguished from its nearest phylogenetic relatives in the genus Nocardiopsis based on DNA–DNA relatedness data and a combination of phenotypic properties. Strain SA6T should therefore be assigned to the genus Nocardiopsis as a representative of a novel species, for which the name Nocardiopsis flavescens sp. nov. is proposed. The type strain is SA6T ( = CGMCC 4.5723T = JCM 17424T).
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Affiliation(s)
- Caiyuan Fang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Jianli Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Huancheng Pang
- Institute of Agri-resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yuyi Li
- Institute of Agri-resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yabo Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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Abstract
A novel Gram-stain-positive, slightly halophilic, facultatively alkaliphilic, catalase-positive, oxidase-negative, endospore-forming, motile, rod-shaped, aerobic bacterium, designated strain JSM 082006T, was isolated from an oyster collected from Naozhou Island in the South China Sea. The isolate grew in 0–18 % (w/v) NaCl (optimum, 0.5–4.0 %), at pH 6.0–10.5 (optimum, pH 8.0) and at 15–45 °C (optimum, 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Strain JSM 082006T contained MK-7 as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C content was 40.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 082006T should be assigned to the genus Bacillus and that it was most closely related to the type strains of Bacillus barbaricus (sequence similarity 99.1 %) and Bacillus arsenicus (97.5 %), followed by those of Bacillus rigui (96.6 %) and Bacillus solisalsi (96.1 %). Phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data support the view that strain JSM 082006T represents a novel species of the genus Bacillus, for which the name Bacillus nanhaiensis sp. nov. is proposed; the type strain is JSM 082006T ( = DSM 23009T = KCTC 13712T).
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Kämpfer P, Schäfer J, Lodders N, Martin K. Murinocardiopsis flavida gen. nov., sp. nov., an actinomycete isolated from indoor walls. Int J Syst Evol Microbiol 2010; 60:1729-1734. [DOI: 10.1099/ijs.0.015990-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, mycelium-forming actinobacteria (strains 14-Be-013T and 02-Gi-014) were isolated from walls colonized with moulds and studied taxonomically. The isolates formed yellowish-pigmented substrate mycelium showing no fragmentation. Comparative analysis of 16S rRNA gene sequences showed that these bacteria are most closely related to genera within the family Nocardiopsaceae, but form a separate lineage within this family. Highest sequence similarities were to the type strains of Marinactinospora thermotolerans (96.0 % to 14-Be-013T), Nocardiopsis dassonvillei subsp. albirubida and Nocardiopsis lucentensis (both 95.3 % to 14-Be-013T). Whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall and no diagnostic sugars. Mycolic acids were absent. The major menaquinones were MK-10(H4), MK-11(H4) and MK-12(H2). The polar lipid profile consisted of phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown lipids. Major fatty acids iso-C16 : 0, anteiso-C17 : 0 and C18 : 1
ω9c supported the affiliation of these isolates to the family Nocardiopsaceae. Phenotypic analysis (including chemotaxonomy) further differentiated strains 14-Be-013T and 02-Gi-014 from the most closely related members of the genera Marinactinospora and Nocardiopsis. Since the two strains form a distinct lineage in the 16S rRNA gene sequence-based phylogenetic tree, the novel genus Murinocardiopsis gen. nov. with the type species Murinocardiopsis flavida sp. nov. is proposed. The type strain of Murinocardiopsis flavida is 14-Be-013T (=DSM 45312T =CCM 7612T).
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Affiliation(s)
- P. Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - J. Schäfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - N. Lodders
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - K. Martin
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV, Hans-Knöll-Institut für Naturstoff-Forschung eV, D-07745 Jena, Germany
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Bioprospecting microbial natural product libraries from the marine environment for drug discovery. J Antibiot (Tokyo) 2010; 63:415-22. [PMID: 20606699 DOI: 10.1038/ja.2010.56] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Marine microorganisms are fascinating resources due to their production of novel natural products with antimicrobial activities. Increases in both the number of new chemical entities found and the substantiation of indigenous marine actinobacteria present a fundamental difficulty in the future discovery of novel antimicrobials, namely dereplication of those compounds already discovered. This review will share our experience on the taxonomic-based construction of a highly diversified and low redundant marine microbial natural product library for high-throughput antibiotic screening. We anticipate that libraries such as these can drive the drug discovery process now and in the future.
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A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie van Leeuwenhoek 2010; 98:119-42. [PMID: 20582471 DOI: 10.1007/s10482-010-9460-2] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 05/14/2010] [Indexed: 11/26/2022]
Abstract
New structurally diverse natural products are discovered when novel screening procedures are introduced or when high quality biological materials from new sources are examined in existing screens, hence it is important to foster these two aspects of novelty in drug discovery programmes. Amongst prokaryotes, actinomycetes, notably streptomycetes, remain a rich source of new natural products though it has become increasingly difficult to find such metabolites from common actinomycetes as screening 'old friends' leads to the costly rediscovery of known compounds. The bioprospecting strategy which is the subject of this review is based upon the premise that new secondary metabolites can be found by screening relatively small numbers of dereplicated, novel actinomycetes isolated from marine sediments. The success of the strategy is exemplified by the discovery of a range of novel bioactive compounds, notably atrop-abyssomicin C and proximicins A, B and C from Verrucosispora strains isolated from sediment samples taken from the Sea of Japan and the Raune Fjord, respectively, and the dermacozines derived from Dermacoccus strains isolated from the Challenger Deep of the Mariana Trench in the Pacific Ocean. The importance of current advances in prokaryotic systematics in work of this nature is stressed and a plea made that resources be sought to train, support and employ the next generation of actinobacterial systematists.
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Nocardiopsis terrae sp. nov., a halophilic actinomycete isolated from saline soil. Antonie van Leeuwenhoek 2010; 98:31-8. [DOI: 10.1007/s10482-010-9425-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 03/03/2010] [Indexed: 10/19/2022]
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Chen YG, Zhang YQ, Yi LB, Li ZY, Wang YX, Xiao HD, Chen QH, Cui XL, Li WJ. Pontibacillus litoralis sp. nov., a facultatively anaerobic bacterium isolated from a sea anemone, and emended description of the genus Pontibacillus. Int J Syst Evol Microbiol 2010; 60:560-565. [DOI: 10.1099/ijs.0.009910-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, moderately halophilic, Gram-positive, endospore-forming, motile, catalase- and oxidase-positive, rod-shaped bacterium, strain JSM 072002T, was isolated from a sea anemone (Anthopleura xanthogrammica) collected from the South China Sea. Strain JSM 072002T was able to grow with 0.5–15 % (w/v) NaCl and at pH 6.0–10.0 and 15–50 °C; optimum growth was observed with 2–5 % (w/v) NaCl and at pH 7.5 and 35 °C. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The predominant respiratory quinone was menaquinone 7 and the genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 072002T should be assigned to the genus Pontibacillus and revealed relatively low 16S rRNA gene sequence similarities (<97 %) with the type strains of the three recognized Pontibacillus species (Pontibacillus chungwhensis BH030062T, 96.8 %; Pontibacillus marinus KCTC 3917T, 96.7 %; Pontibacillus halophilus JSM 076056T, 96.0 %). The combination of phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the view that strain JSM 072002T represents a novel species of the genus Pontibacillus, for which the name Pontibacillus litoralis sp. nov. is proposed. The type strain is JSM 072002T (=DSM 21186T=KCTC 13237T). An emended description of the genus Pontibacillus is also presented.
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Affiliation(s)
- Yi-Guang Chen
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Lang-Bo Yi
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Zhao-Yang Li
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Yong-Xiao Wang
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Huai-Dong Xiao
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Qi-Hui Chen
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Xiao-Long Cui
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Wen-Jun Li
- Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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