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Roman I, Fedorenko V, Gromyko O. Phylogenomic analyses of the genus Actinoplanes: description of four novel genera. Int J Syst Evol Microbiol 2024; 74. [PMID: 39046446 DOI: 10.1099/ijsem.0.006464] [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] [Indexed: 07/25/2024] Open
Abstract
The genus Actinoplanes comprises 57 species (in February 2024) that are important components of ecosystems and are widely used in biotechnology, especially pharmaceuticals. Phylogenetic analysis of the family Micromonosporaceae (based on the 16S rRNA gene sequence) allowed us to group members of different genera into separate clades; however, the genus Actinoplanes was divided into three separate clades. Such phylogenetic heterogeneity could be due to the limitations of 16S rRNA gene analysis. In response to this heterogeneity, genomic phylogeny was performed. Phylogenomic reconstruction based on 324 single-copy orthologous genes allowed us to divide the genus Actinoplanes first into four clades and then, based on average nucleotide identity analysis, into five clades. Finally, chemotaxonomic analysis of each clade confirmed each clade's distinctiveness and the necessity to reclassify the genus Actinoplanes. The obtained data allowed us to divide the genus Actinoplanes into five genera: Actinoplanes, Paractinoplanes, Winogradskya, Symbioplanes and Amorphoplanes.
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Affiliation(s)
- Ivan Roman
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Oleksandr Gromyko
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
- Microbial Culture Collection of Antibiotic Producers, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
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Yushchuk O, Binda E, Rückert-Reed C, Berini F, Fedorenko V, Kalinowski J, Marinelli F. Actinoplanes oblitus sp. nov., producing the glycopeptide antibiotic A477. Int J Syst Evol Microbiol 2024; 74. [PMID: 38190227 DOI: 10.1099/ijsem.0.006225] [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] [Indexed: 01/09/2024] Open
Abstract
In 1973, Eli Lilly and Company described the filamentous actinomycete producing the glycopeptide antibiotic A477 as an Actinoplanes species on the basis of its morphological and physiological features and deposited it as NRRL 3884T. In this paper, we report that the phylogenetic analysis based on the 16S rRNA gene sequence and the whole genome phylogenomic study indicate that NRRL 3884T forms a distinct monophyletic line within the genus Actinoplanes, being most closely related to Actinoplanes octamycinicus NBRC 14524T [99.6 % 16S rRNA gene similarity, 89.4 % average nucleotide identity (ANI), 46.0 % digital DNA-DNA hybridization (dDDH)] and Actinoplanes ianthinogenes NBRC 13996T (98.8 % 16S rRNA gene similarity, 89.0 % ANI, 47.0 % dDDH). NRRL 3884T forms an extensively branched, non-fragmented vegetative mycelium; either sterile aerial hyphae or regular subglobose sporangia are formed depending on cultivation conditions. The cell wall contains meso-2,6-diaminopimelic acid and 2,6-diamino-3-hydroxypimelic acid and the diagnostic sugars are glucose, mannose and ribose with a minor amount of rhamnose. The predominant menaquinone (MK) is MK-9(H4), with minor amounts of MK-9(H2), MK-9(H6) and MK-9(H8). Mycolic acids are absent. The diagnostic phospholipids are diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids are anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0, with moderate amounts of anteiso-C15 : 0 and iso-C17 : 0. The genomic G+C content is 71.5 mol%. Significant differences in the genomic, morphological, chemotaxonomic and biochemical data between NRRL 3884T and the two most closely related Actinoplanes type strains clearly demonstrate that NRRL 3884T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes oblitus sp. nov. is proposed. The type strain is NRRL 3884T (=DSM 116196T).
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Affiliation(s)
- Oleksandr Yushchuk
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
- Ivan Franko National University of Lviv, Department of Genetics and Biotechnology, 79005 Lviv, Ukraine
| | - Elisa Binda
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
| | | | - Francesca Berini
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
| | - Victor Fedorenko
- Ivan Franko National University of Lviv, Department of Genetics and Biotechnology, 79005 Lviv, Ukraine
| | - Jörn Kalinowski
- Bielefeld University, Technology Platform Genomics, CeBiTec, 33615 Bielefeld, Germany
| | - Flavia Marinelli
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
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Yao H, Liu S, Liu T, Ren D, Yang Q, Zhou Z, Mao J. Screening of marine sediment-derived microorganisms and their bioactive metabolites: a review. World J Microbiol Biotechnol 2023; 39:172. [PMID: 37115432 DOI: 10.1007/s11274-023-03621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Marine sediments are one of the largest habitats on Earth, and their unique ecology, such as high salinity, high pressure, and hypoxia, may activate certain silent genes in marine microbes, resulting in microbes, enzymes, active products, and specific metabolic pathways that can adapt to these specific ecological environments. Marine sediment-derived microorganisms and their bioactive metabolites are of great significance and have potential commercial development prospects for food, pharmaceutical, chemical industries, agriculture, environmental protection and human nutrition and health. In recent years, although there have been numerous scientific reports surrounding marine sediment-derived microorganisms and their bioactive metabolites, a comprehensive review of their research progress is lacking. This paper presents the development and renewal of traditional culture-dependent and omics analysis techniques and their application to the screening of marine sediment-derived microorganisms producing bioactive substances. It also highlights recent research advances in the last five years surrounding the types, functional properties and potential applications of bioactive metabolites produced by marine sediment-derived microorganisms. These bioactive metabolites mainly include antibiotics, enzymes, enzyme inhibitors, sugars, proteins, peptides, and some other small molecule metabolites. In addition, the review ends with concluding remarks on the challenges and future directions for marine sediment-derived microorganisms and their bioactive metabolites. The review report not only helps to deepen the understanding of marine sediment-derived microorganisms and their bioactive metabolites, but also provides some useful information for the exploitation and utilization of marine microbial resources and the mining of new compounds with potential functional properties.
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Affiliation(s)
- Hongli Yao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Department of Biology and Food Engineering, Bozhou University, Bozhou, 236800, Anhui, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Tiantian Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Dongliang Ren
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qilin Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhilei Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China.
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China.
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Ding LM, Ding PZ, Liu WL, Shen HL, Xia ZF, Wan CX, Zhang LL. Three novel Actinoplanes species isolated by using polyaspartic acid as a water-retaining agent for the enrichment in situ. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749688 DOI: 10.1099/ijsem.0.005705] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Three novel actinomycete strains, designated TRM66264-DLMT, TRM88002T and TRM88003T, were isolated by using polyaspartic acid as a water-retaining agent for the enrichment in situ. The 16S rRNA gene sequence and phylogenetic analyses of three strains indicated that they belonged to the genus Actinoplanes. The phylogenetically closest strains of TRM66264-DLMT, TRM88002T and TRM88003T were Actinoplanes bogorensis LIPI11-2-Ac043T (98.4 %), Actinoplanes abujensis A4029T (98.0 %) and Actinoplanes ferrugineus IFO15555T (98.1 %), respectively. The major polar lipids of strains TRM66264-DLMT and TRM88002T were phosphatidylethanolamine and disphosphatidylglycerol, while strain TRM88003T only had phosphatidylethanolamine. The predominant menaquinones of strain TRM66264-DLMT were identified as MK-9(H4) and MK-9 (H6). Strains TRM88002T and TRM88003T had MK-9(H4). The cell-wall peptidoglycan of three strains contained meso-diaminopimelic acid. The whole-cell sugars of strain TRM66264-DLMT were identified as arabinose, glucose, galactose and xylose. Strains TRM88002T and TRM88003T mainly had arabinose and glucose. The DNA G+C content of strains TRM66264-DLMT, TRM88002T and TRM88003T were 70.48, 70.46 and 70.64 mol%, respectively. Genotypic and phenotypic analysis confirmed that all three strains sre new members of the genus Acinoplanes. Therefore, it is proposed that strains TRM66264-DLMT, TRM88002T and TRM88003T represent three novel species of the genus Actinoplanes, for which the names Actinoplanes polyasparticus sp. nov. (type strain TRM66264-DLMT=CCTCC AA 2021015T=LMG 32389T), Actinoplanes hotanensis sp. nov. (type strain TRM88002T=CCTCC AA 2021036T=LMG 32621T) and Actinoplanes aksuensis sp. nov. (type strain TRM88003T=CCTCC AA 2021037 T=LMG 32622T) are proposed.
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Affiliation(s)
- La-Mei Ding
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - Pei-Zhi Ding
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - Wen-Long Liu
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - Hong-Ling Shen
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - Zhan-Feng Xia
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - Chuan-Xing Wan
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - Li-Li Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
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Saeng-In P, Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat S. Actinoplanes lichenicola sp. nov. and Actinoplanes ovalisporus sp. nov., isolated from lichen in Thailand. Int J Syst Evol Microbiol 2021; 71. [PMID: 34319866 DOI: 10.1099/ijsem.0.004921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two actinobacteria, designated as strain LDG1-01T and LDG1-06T, were isolated from lichen samples collected in Thailand. Results of morphological characterization, chemotaxonomic studies and 16S rRNA gene analysis indicated that both strains were members of the genus Actinoplanes. MK-9(H4) was found as the major menaquinone. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were observed as the polar lipids, but differences in minor unidentified polar lipids were found between the strains. Results of comparative genome analysis based on average nucleotide identity and digital DNA-DNA hybridization calculations revealed that both strains showed values below 95 and 70 %, respectively, from each other and closely related Actinoplanes type strains. Based on data from this polyphasic study, strains LDG1-01T and LDG1-06T represent novel species of the genus Actinoplanes. The names proposed are Actinoplanes lichenicola sp. nov. (type strain, LDG1-01T (=JCM 33066T=TISTR 2982T) and Actinoplanes ovalisporus sp. nov. (type strain, LDG1-06T=JCM 33067T=TISTR 2983T).
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Affiliation(s)
- Patcharin Saeng-In
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pawina Kanchanasin
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Ma Q, Zhang Q, Jiang X, Kong D, Han X, Xue H, Zhou Y, Zhang Y, Zhang W, Ruan Z. Actinoplanes solisilvae sp. nov., Isolated from Birch Forest Soil. Curr Microbiol 2020; 77:3799-3806. [PMID: 32915290 DOI: 10.1007/s00284-020-02192-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 09/01/2020] [Indexed: 11/25/2022]
Abstract
A novel actinomycete, designated strain LAM7112T, was isolated from soil sample collected from a birch forest in Xinjiang Uygur Autonomous Region, China. The new isolate was found to be able to grow at 20-45 °C (optimum: 35 °C), pH 5.0-10.0 (optimum: 7.0) and in the presence of 0-10.0% (optimum: 3.0%) (w/v) NaCl. The isolate formed very scantily irregular sporangia containing motile spores on the substrate mycelium. Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolate was closely related to members of the family Micromonosporaceae, with highest similarites to Actinoplanes ferrugineus X-14695T (97.4%), Micromonospora zamorensis DSM 45600T (97.3%) and Micromonospora aurantiaca ATCC 27029T (97.3%). In the phylogenetic trees, strain LAM7112T formed a stable phylogenetic subclade within the genus Actinoplanes. The genomic DNA G + C content was 70.0 mol%. The major fatty acids (> 10%) were determined to be iso-C16:0, anteiso-C15:0 and anteiso-C17:0. The predominant menaquinones were identified as MK-9 (H2), MK-9 (H4) and MK-9 (H6). The major polar lipids were found to be diphosphatidylglycerol, phosphatidylinositol and phosphatidylethanolamine. The diagnostic amino acid of the cell wall peptidoglycan was determined to be meso-diaminopimelic acid. The diagnostic sugars in cell hydrolysates were determined to be glucose and ribose. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM7112T (= CGMCC 4.7580T = JCM 32512T) is proposed to represent the type strain of a novel species of the genus Actinoplanes, for which the name Actinoplanes solisilvae is proposed.
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Affiliation(s)
- Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qi Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science, Xinjiang Normal University, Ürümqi, 830046, Xinjiang, China
- Xinjiang Urumqi Maternal and Child Care Hospital, Ürümqi, 830001, Xinjiang, China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiying Xue
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, Tibet, China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Wei Zhang
- College of Life Science, Xinjiang Normal University, Ürümqi, 830046, Xinjiang, China.
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, Tibet, China.
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Actinoplanes deserti sp. nov., isolated from a desert soil sample. Antonie van Leeuwenhoek 2018; 111:2303-2310. [PMID: 29974366 DOI: 10.1007/s10482-018-1121-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
A novel actinomycete, designated strain YIM CF22T, was isolated from a desert soil sample collected from Turpan in Xinjiang Uyghur Autonomous Region, north-western China. The taxonomic position of the strain YIM CF22T is described based on a polyphasic approach. Strain YIM CF22T was found to form irregular sporangia on agar media. It contains meso-diaminopimelic acid in the cell wall peptidoglycan. The major menaquinone was identified as MK-9(H4); the polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified phospholipids and two unidentified glycolipids. The whole cell sugars were found to be ribose, mannose, galactose, glucose and xylose. The major cellular fatty acids were found to be (> 5%) iso-C16:0 (43.5%), anteiso-C17:0 (10.2%), iso-C15:0 (7.1%), C17:1 ω8c (6.3%) and iso H-C16:1 (5.9%). The G+C content was determined to be 70.8%. 16S rRNA gene sequence analysis of strain YIM CF22T showed high similarity (97.0%) to Actinoplanes rishiriensis NBRC 108556T. The strain also showed high 16S rRNA gene sequence similarities to Verrucosispora sediminis CGMCC 4.3550T (96.9%) and Micromonospora tulbaghiae DSM 45142T (96.8%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM CF22T clusters with A. rishiriensis NBRC 108556T, Actinoplanes globisporus JCM 3186T and Actinoplanes rhizophilus NEAU-A-2T. Based on the differential phenotypic characteristics and the results of DNA-DNA relatedness and phylogenetic analysis, it is proposed that strain YIM CF22T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes deserti sp. nov. is proposed. The type strain is YIM CF22T (= KCTC 39543T = CCTCC AB2018113T).
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Jiang ZK, Tuo L, Huang DL, Osterman IA, Tyurin AP, Liu SW, Lukyanov DA, Sergiev PV, Dontsova OA, Korshun VA, Li FN, Sun CH. Diversity, Novelty, and Antimicrobial Activity of Endophytic Actinobacteria From Mangrove Plants in Beilun Estuary National Nature Reserve of Guangxi, China. Front Microbiol 2018; 9:868. [PMID: 29780376 PMCID: PMC5945994 DOI: 10.3389/fmicb.2018.00868] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 04/16/2018] [Indexed: 11/13/2022] Open
Abstract
Endophytic actinobacteria are one of the important pharmaceutical resources and well known for producing different types of bioactive substances. Nevertheless, detection of the novelty, diversity, and bioactivity on endophytic actinobacteria isolated from mangrove plants are scarce. In this study, five different mangrove plants, Avicennia marina, Aegiceras corniculatum, Kandelia obovota, Bruguiera gymnorrhiza, and Thespesia populnea, were collected from Beilun Estuary National Nature Reserve in Guangxi Zhuang Autonomous Region, China. A total of 101 endophytic actinobacteria strains were recovered by culture-based approaches. They distributed in 7 orders, 15 families, and 28 genera including Streptomyces, Curtobacterium, Mycobacterium, Micrococcus, Brevibacterium, Kocuria, Nocardioides, Kineococcus, Kytococcus, Marmoricola, Microbacterium, Micromonospora, Actinoplanes, Agrococcus, Amnibacterium, Brachybacterium, Citricoccus, Dermacoccus, Glutamicibacter, Gordonia, Isoptericola, Janibacter, Leucobacter, Nocardia, Nocardiopsis, Pseudokineococcus, Sanguibacter, and Verrucosispora. Among them, seven strains were potentially new species of genera Nocardioides, Streptomyces, Amnibacterium, Marmoricola, and Mycobacterium. Above all, strain 8BXZ-J1 has already been characterized as a new species of the genus Marmoricola. A total of 63 out of 101 strains were chosen to screen antibacterial activities by paper-disk diffusion method and inhibitors of ribosome and DNA biosynthesis by means of a double fluorescent protein reporter. A total of 31 strains exhibited positive results in at least one antibacterial assay. Notably, strain 8BXZ-J1 and three other potential novel species, 7BMP-1, 5BQP-J3, and 1BXZ-J1, all showed antibacterial bioactivity. In addition, 21 strains showed inhibitory activities against at least one "ESKAPE" resistant pathogens. We also found that Streptomyces strains 2BBP-J2 and 1BBP-1 produce bioactive compound with inhibitory activity on protein biosynthesis as result of translation stalling. Meanwhile, Streptomyces strain 3BQP-1 produces bioactive compound inducing SOS-response due to DNA damage. In conclusion, this study proved mangrove plants harbored a high diversity of cultivable endophytic actinobacteria, which can be a promising source for discovery of novel species and bioactive compounds.
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Affiliation(s)
- Zhong-ke Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Tuo
- Research Center for Medicine and Biology, Zunyi Medical University, Zunyi, China
| | - Da-lin Huang
- College of Basic Medical Sciences, Guilin Medical University, Guilin, China
| | - Ilya A. Osterman
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anton P. Tyurin
- Gause Institute of New Antibiotics, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Shao-wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dmitry A. Lukyanov
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga A. Dontsova
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vladimir A. Korshun
- Gause Institute of New Antibiotics, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Fei-na Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Cheng-hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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