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Ning S, Hou Q, Yang J, Ma C, Chen Y, Liu Y, Zhou H, Ma J, Huang Y, Cao L, Liu X, Pu J, Jin D, Lu S, Xu J. Planococcus shenhongbingii sp. nov., Planococcus shixiaomingii sp. nov. and Planococcus liqunii sp. nov., isolated from soil of the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2024; 74. [PMID: 39042107 DOI: 10.1099/ijsem.0.006465] [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: 07/24/2024] Open
Abstract
Six novel bacterial strains, designated N016T, N017, N022T, N028, N056T, and N064, were isolated from soil sampled on the Qinghai-Tibet Plateau. Cells were aerobic, orange or yellow, globular or rod-shaped, non-motile, non-spore-forming, Gram-stain-positive, catalase-positive and oxidase-negative. All the isolates were salt-tolerant and could grow in the range of 4-42 °C. Results of phylogenomic analyses based on 16S rRNA gene sequences and core genomic genes showed that the three pairs of strains (N016T/N017, N022T/N028, and N056T/N064) were closely related to the members of the genus Planococcus, and clustered with Planococcus ruber, Planococcus glaciei, and Planococcus chinensis. The digital DNA-DNA hybridization and average nucleotide identity values of the six novel strains with other members of the genus Planococcus were within the ranges of 18.7-53 % and 70.58-93.49 %, respectively, all below the respective recommended thresholds of 70.0 % and 95-96 %. The genomic DNA G+C content of the six strains ranged from 43.5 to 46.0 mol%. The major fatty acids of the six strains were anteiso-C15 : 0, iso-C14 : 0, and C16 : 1 ω7c alcohol. The predominant polar lipids of strains N016T, N022T, and N056T were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Menaquinones 7 and 8 were the respiratory quinones. The results of the above analyses indicated that the six strains represent three novel species of the genus Planococcus, for which the names Planococcus shenhongbingii sp. nov. (type strain N016T=GDMCC 1.4062T=JCM 36224T), Planococcus shixiaomingii sp. nov. (type strain N022T=GDMCC 1.4063T=JCM 36225T), and Planococcus liqunii sp. nov. (type strain N056T=GDMCC 1.4064T=JCM 36226T) are proposed.
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Affiliation(s)
- Shuo Ning
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Qiang Hou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Academy of Medical Sciences, Shanxi Medical University, Taiyuan 030001, PR China
| | - Jing Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Caiyun Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yulu Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yue Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Huimin Zhou
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jiajia Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Academy of Medical Sciences, Shanxi Medical University, Taiyuan 030001, PR China
| | - Yuyuan Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, Nanning 530021, PR China
| | - Linglin Cao
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaorui Liu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Shan Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Academy of Medical Sciences, Shanxi Medical University, Taiyuan 030001, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
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Ali A, Abbas S, Nawaz S, Man C, Liu YH, Li WJ, Ahmed I. Unraveling the draft genome and phylogenomic analysis of a multidrug-resistant Planococcus sp. NCCP-2050 T: a promising novel bacteria from Pakistan. 3 Biotech 2023; 13:325. [PMID: 37663752 PMCID: PMC10471537 DOI: 10.1007/s13205-023-03748-z] [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: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Planococcus is a genus of Gram-positive bacteria known for potential industrial and agricultural applications. Here, we report the first draft genome sequence and phylogenomic analysis of a CRISPR-carrying, multidrug-resistant, novel candidate Planococcus sp. NCCP-2050T isolated from agricultural soil in Pakistan. The strain NCCP-2050T exhibited significant resistance to various classes of antibiotics, including fluoroquinolones (i.e., ciprofloxacin, levofloxacin, ofloxacin, moxifloxacin, and bacitracin), cephalosporins (cefotaxime, ceftazidime, cefoperazone), rifamycins (rifampicin), macrolides (erythromycin), and glycopeptides (vancomycin). Planococcus sp. NCCP-2050T consists of genome size of 3,463,905 bp, comprised of 3639 annotated genes, including 82 carbohydrate-active enzyme genes and 39 secondary metabolite genes. The genome also contained 80 antibiotic resistance, 162 virulence, and 305 pathogen-host interaction genes along with two CRISPR arrays. Based on phylogenomic analysis, digital DNA-DNA hybridization, and average nucleotide identity values (i.e., 35.4 and 88.5%, respectively) it was suggested that strain NCCP-2050T might represent a potential new species within the genus Planococcus. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03748-z.
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Affiliation(s)
- Ahmad Ali
- National Culture Collection of Pakistan (NCCP), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Saira Abbas
- Department of Zoology, University of Science and Technology, Bannu, Pakistan
| | - Sadia Nawaz
- National Culture Collection of Pakistan (NCCP), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Cai Man
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 People’s Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 People’s Republic of China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People’s Republic of China
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), National Agricultural Research Centre (NARC), Islamabad, Pakistan
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Matthews A, Lima-Zaloumis J, Debes Ii RV, Boyer G, Trembath-Reichert E. Heterotrophic Growth Dominates in the Most Extremotolerant Extremophile Cultures. ASTROBIOLOGY 2023; 23:446-459. [PMID: 36723486 DOI: 10.1089/ast.2022.0100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Due to their ability to withstand "extreme" conditions, Earth's extremophilic organisms can constrain habitability windows for other planetary systems. However, there are many other considerations to microbial growth requirements beyond environmental extremes, such as nutrient availability. Here, we conduct a literature review of the most extremotolerant extremophiles in culture, since working with cultured organisms allows environmental and nutrient variables to be constrained with a high level of specificity. We generated a database that includes the isolation environment, carbon source(s) used, and growth preferences across temperature, pressure, salinity, and pH extremes. We found that the "most extreme" conditions were primarily sustained by heterotrophs, except for hyperthermophiles. These results highlight the importance of considering organic carbon availability when using extremophiles for habitability constraints. We also interrogated polyextreme potential across temperature, pressure, salinity, and pH conditions. Our findings suggest that the investigation of growth tolerance rather than growth optimum may reveal wider habitability parameters. Overall, these results highlight the potential polyextremes, environments, nutrient requirements, and additional analyses that could improve the application of cultured investigations to astrobiology questions.
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Affiliation(s)
- Adrianna Matthews
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | | | - R Vincent Debes Ii
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Grayson Boyer
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
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Moyo AC, Dufossé L, Giuffrida D, van Zyl LJ, Trindade M. Structure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South Africa. Microb Cell Fact 2022; 21:43. [PMID: 35305628 PMCID: PMC8933910 DOI: 10.1186/s12934-022-01752-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/26/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed that the culturing of the orange-pigmented Planococcus sp. CP5-4 isolate increased the evaporation rate of industrial wastewater brine effluent, which we attributed to the orange pigment. This demonstrated the potential application of this bacterium for industrial brine effluent management in evaporation ponds for inland desalination plants. Here we identified a C30-carotenoid biosynthetic gene cluster responsible for pigment biosynthesis in Planococcus sp. CP5-4 through isolation of mutants and genome sequencing. We further compare the core genes of the carotenoid biosynthetic gene clusters identified from different Planococcus species' genomes which grouped into gene cluster families containing BGCs linked to different carotenoid product chemotypes. Lastly, LC-MS analysis of saponified and unsaponified pigment extracts obtained from cultures of Planococcus sp. CP5-4, revealed the structure of the main (predominant) glucosylated C30-carotenoid fatty acid ester produced by Planococcus sp. CP5-4. RESULTS Genome sequence comparisons of isolated mutant strains of Planococcus sp. CP5-4 showed deletions of 146 Kb and 3 Kb for the non-pigmented and "yellow" mutants respectively. Eight candidate genes, likely responsible for C30-carotenoid biosynthesis, were identified on the wild-type genome region corresponding to the deleted segment in the non-pigmented mutant. Six of the eight candidate genes formed a biosynthetic gene cluster. A truncation of crtP was responsible for the "yellow" mutant phenotype. Genome annotation revealed that the genes encoded 4,4'-diapolycopene oxygenase (CrtNb), 4,4'- diapolycopen-4-al dehydrogenase (CrtNc), 4,4'-diapophytoene desaturase (CrtN), 4,4'- diaponeurosporene oxygenase (CrtP), glycerol acyltransferase (Agpat), family 2 glucosyl transferase 2 (Gtf2), phytoene/squalene synthase (CrtM), and cytochrome P450 hydroxylase enzymes. Carotenoid analysis showed that a glucosylated C30-carotenoid fatty acid ester, methyl 5-(6-C17:3)-glucosyl-5, 6'-dihydro-apo-4, 4'-lycopenoate was the main carotenoid compound produced by Planococcus sp. CP5-4. CONCLUSION We identified and characterized the carotenoid biosynthetic gene cluster and the C30-carotenoid compound produced by Planococcus sp. CP5-4. Mass-spectrometry guided analysis of the saponified and unsaponified pigment extracts showed that methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate esterified to heptadecatrienoic acid (C17:3). Furthermore, through phylogenetic analysis of the core carotenoid BGCs of Planococcus species we show that various C30-carotenoid product chemotypes, apart from methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate and 5-glucosyl-4, 4-diaponeurosporen-4'-ol-4-oic acid, may be produced that could offer opportunities for a variety of applications.
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Affiliation(s)
- Anesu Conrad Moyo
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa
- BioCiTi Laboratory, 4th Floor Block B, Bandwidth Barn, Woodstock Exchange Building, 66-68 Albert Road, Woodstock, Cape Town, 7925, South Africa
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, ESIROI Agroalimentaire, Université de La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 9, F-97744, Saint-Denis, France
| | - Daniele Giuffrida
- Università Degli Studi Di Messina, Dip. B.I.O.M.O.R.F, Polo Annunziata, 98168, Messina, ME, Italy
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa.
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López GD, Álvarez-Rivera G, Carazzone C, Ibáñez E, Leidy C, Cifuentes A. Bacterial Carotenoids: Extraction, Characterization, and Applications. Crit Rev Anal Chem 2021; 53:1239-1262. [PMID: 34915787 DOI: 10.1080/10408347.2021.2016366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Natural carotenoids are secondary metabolites that exhibit antioxidant, anti-inflammatory, and anti-cancer properties. These types of compounds are highly demanded by pharmaceutical, cosmetic, nutraceutical, and food industries, leading to the search for new natural sources of carotenoids. In recent years, the production of carotenoids from bacteria has become of great interest for industrial applications. In addition to carotenoids with C40-skeletons, some bacteria have the ability to synthesize characteristic carotenoids with C30-skeletons. In this regard, a great variety of methodologies for the extraction and identification of bacterial carotenoids has been reported and this is the first review that condenses most of this information. To understand the diversity of carotenoids from bacteria, we present their biosynthetic origin in order to focus on the methodologies employed in their extraction and characterization. Special emphasis has been made on high-performance liquid chromatography-mass spectrometry (HPLC-MS) for the analysis and identification of bacterial carotenoids. We end up this review showing their potential commercial use. This review is proposed as a guide for the identification of these metabolites, which are frequently reported in new bacteria strains.
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Affiliation(s)
- Gerson-Dirceu López
- Chemistry Department, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Universidad de los Andes, Bogotá, Colombia
- Physics Department, Laboratory of Biophysics, Universidad de los Andes, Bogotá, Colombia
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| | | | - Chiara Carazzone
- Chemistry Department, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Universidad de los Andes, Bogotá, Colombia
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| | - Chad Leidy
- Physics Department, Laboratory of Biophysics, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
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Wang Y, Ma L, He J, Liu Z, Weng S, Wang L, He J, Guo C. Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401 T, a new species isolated from Antarctic krill. BMC Microbiol 2021; 21:288. [PMID: 34686131 PMCID: PMC8532331 DOI: 10.1186/s12866-021-02347-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/06/2021] [Indexed: 11/12/2022] Open
Abstract
Background Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary metabolism of the extremophiles of Antarctic krill has received little attention. Results In this study, a new bacterial strain MSAK28401T from Antarctic krill was isolated and identified. The results of analysis on phenotypic, chemotaxonomic, and genomic characteristics showed that the strain MSAK28401T belongs to the genus Planococcus. Cells of this strain were coccoid (0.89–1.05 μm) and aerobic. The majority of the fatty acid content was C15:0 anteiso (37.67 ± 0.90%) followed by C16:1 ω7c alcohol (10.37 ± 1.22%) and C16:0 iso (9.36 ± 0.71%). The calculated average nucleotide identity and DNA–DNA hybridization values between the strain MSAK28401T and type strains P. citreus DSM 20549T and P. rifietoensis M8T were lower than 91 and 70%, respectively. The strain MSAK28401T (=KCTC 43283T and MCCC 1k05448T) represented a new member of the genus Planococcus and was named P. alpniumensis sp. nov. Moreover, genes involved in the degradation of aromatic compounds (e.g., salicylate, gentisate, and quinate) were found in the genome, implying that strain MSAK28401T has an aromatic compound as its potential metabolite. This work will help us understand the genomic characteristics and potential metabolic pathway of Planococcus from Antarctic krill. Conclusions This study reported the genomic information and phenotypic characteristics of the new strain P. alpniumensis MSAK28401T isolated from Antarctic krill, and provided the genome information of Planococcus strains for further studying the function roles in aromatic compound metabolism. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02347-3.
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Affiliation(s)
- Yuanyuan Wang
- State Key Laboratory for Biocontrol / Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China
| | - Lingbo Ma
- Key Laboratory of the East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Shanghai, 116023, People's Republic of China
| | - Jian He
- State Key Laboratory for Biocontrol / Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China
| | - Zixuan Liu
- State Key Laboratory for Biocontrol / Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China
| | - Shaoping Weng
- Guangdong Province Key Laboratory for Aquatic Economic Animals, and Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China
| | - Lumin Wang
- Key Laboratory of the East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Shanghai, 116023, People's Republic of China
| | - Jianguo He
- State Key Laboratory for Biocontrol / Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China.,Guangdong Province Key Laboratory for Aquatic Economic Animals, and Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China
| | - Changjun Guo
- State Key Laboratory for Biocontrol / Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China. .,Guangdong Province Key Laboratory for Aquatic Economic Animals, and Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China.
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Takemura M, Takagi C, Aikawa M, Araki K, Choi SK, Itaya M, Shindo K, Misawa N. Heterologous production of novel and rare C 30-carotenoids using Planococcus carotenoid biosynthesis genes. Microb Cell Fact 2021; 20:194. [PMID: 34627253 PMCID: PMC8502411 DOI: 10.1186/s12934-021-01683-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to solvents. A yellow marine bacterium Planococcus maritimus strain iso-3 was isolated from an intertidal sediment that looked industrially polluted, from the Clyde estuary in the UK. This bacterium was found to produce a yellow acyclic carotenoid with a basic carbon 30 (C30) structure, which was determined to be methyl 5-glucosyl-5,6-dihydro-4,4′-diapolycopenoate. In the present study, we tried to isolate and identify genes involved in carotenoid biosynthesis from this marine bacterium, and to produce novel or rare C30-carotenoids with anti-oxidative activity in Escherichia coli by combinations of the isolated genes. Results A carotenoid biosynthesis gene cluster was found out through sequence analysis of the P. maritimus genomic DNA. This cluster consisted of seven carotenoid biosynthesis candidate genes (orf1–7). Then, we isolated the individual genes and analyzed the functions of these genes by expressing them in E. coli. The results indicated that orf2 and orf1 encoded 4,4′-diapophytoene synthase (CrtM) and 4,4′-diapophytoene desaturase (CrtNa), respectively. Furthermore, orf4 and orf5 were revealed to code for hydroxydiaponeurosporene desaturase (CrtNb) and glucosyltransferase (GT), respectively. By utilizing these carotenoid biosynthesis genes, we produced five intermediate C30-carotenoids. Their structural determination showed that two of them were novel compounds, 5-hydroxy-5,6-dihydro-4,4′-diaponeurosporene and 5-glucosyl-5,6-dihydro-4,4′-diapolycopene, and that one rare carotenoid 5-hydroxy-5,6-dihydro-4,4′-diapolycopene is included there. Moderate singlet oxygen-quenching activities were observed in the five C30-carotenoids including the two novel and one rare compounds. Conclusions The carotenoid biosynthesis genes from P. maritimus strain iso-3, were isolated and functionally identified. Furthermore, we were able to produce two novel and one rare C30-carotenoids in E. coli, followed by positive evaluations of their singlet oxygen-quenching activities. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01683-3.
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Affiliation(s)
- Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan.
| | - Chiharu Takagi
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Mayuri Aikawa
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Kanaho Araki
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Seon-Kang Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Mitsuhiro Itaya
- Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University, Wakasato 4-17-1, Nagano, 380-8553, Japan
| | - Kazutoshi Shindo
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
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Sato Y, Okano K, Kimura H, Honda K. TEMPURA: Database of Growth TEMPeratures of Usual and RAre Prokaryotes. Microbes Environ 2021; 35. [PMID: 32727974 PMCID: PMC7511790 DOI: 10.1264/jsme2.me20074] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Growth temperature is one of the most representative biological parameters for characterizing living organisms. Prokaryotes have been isolated from various temperature environments and show wide diversity in their growth temperatures. We herein constructed a database of growth TEMPeratures of Usual and RAre prokaryotes (TEMPURA, http://togodb.org/db/tempura), which contains the minimum, optimum, and maximum growth temperatures of 8,639 prokaryotic strains. Growth temperature information is linked with taxonomy IDs, phylogenies, and genomic information. TEMPURA provides useful information to researchers working on biotechnological applications of extremophiles and their biomolecules as well as those performing fundamental studies on the physiological diversity of prokaryotes.
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Affiliation(s)
- Yu Sato
- International Center for Biotechnology, Osaka University
| | - Kenji Okano
- International Center for Biotechnology, Osaka University
| | - Hiroyuki Kimura
- Research Institute of Green Science and Technology, Shizuoka University.,Department of Geosciences, Faculty of Science, Shizuoka University
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University
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Genome Mining Reveals Two Missing CrtP and AldH Enzymes in the C30 Carotenoid Biosynthesis Pathway in Planococcus faecalis AJ003 T. Molecules 2020; 25:molecules25245892. [PMID: 33322786 PMCID: PMC7764019 DOI: 10.3390/molecules25245892] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
Planococcus faecalis AJ003T produces glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid as its main carotenoid. Five carotenoid pathway genes were presumed to be present in the genome of P. faecalis AJ003T; however, 4,4-diaponeurosporene oxidase (CrtP) was non-functional, and a gene encoding aldehyde dehydrogenase (AldH) was not identified. In the present study, a genome mining approach identified two missing enzymes, CrtP2 and AldH2454, in the glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid biosynthetic pathway. Moreover, CrtP2 and AldH enzymes were functional in heterologous Escherichia coli and generated two carotenoid aldehydes (4,4′-diapolycopene-dial and 4,4′-diaponeurosporene-4-al) and two carotenoid carboxylic acids (4,4′-diaponeurosporenoic acid and 4,4′-diapolycopenoic acid). Furthermore, the genes encoding CrtP2 and AldH2454 were located at a distance the carotenoid gene cluster of P. faecalis.
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Gan L, Li X, Tian Y, Peng B. Genomic insights into the salt tolerance and cold adaptation of Planococcus halotolerans SCU63 T. Arch Microbiol 2020; 202:2841-2847. [PMID: 32681430 DOI: 10.1007/s00203-020-01979-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/17/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022]
Abstract
Planococcus halotolerans, recently described as a novel species with SCU63T as the type strain, is capable of thriving in up to 15% NaCl and temperatures as low as 0 °C. To better understand its adaptation strategies at the genomic level, strain SCU63T was subjected to whole-genome sequencing and data mining. The high-quality assembly yielded 17 scaffolds with a genome size of 3,622,698 bp. Its genome harbors 3683 protein-coding sequences and 127 RNA genes, as well as three biosynthetic gene clusters and 25 genomic islands. The phylogenomic tree provided compelling insights into the evolutionary relationships of Planococcus. Comparative genomic analysis revealed key similarities and differences in the functional gene categories among Planococcus species. Strain SCU63T was shown to have diverse stress response systems for high salt and cold habitats. Further comparison with three related species showed the presence of numerous unique gene clusters in the SCU63T genome. The strain might serve as a good model for using extremozymes in various biotechnological processes.
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Affiliation(s)
- Longzhan Gan
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China.,Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China
| | - Xiaoguang Li
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China.,Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China
| | - Yongqiang Tian
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China. .,Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China.
| | - Biyu Peng
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China. .,Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China.
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11
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Sajjad W, Din G, Rafiq M, Iqbal A, Khan S, Zada S, Ali B, Kang S. Pigment production by cold-adapted bacteria and fungi: colorful tale of cryosphere with wide range applications. Extremophiles 2020; 24:447-473. [PMID: 32488508 PMCID: PMC7266124 DOI: 10.1007/s00792-020-01180-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022]
Abstract
Pigments are an essential part of everyday life on Earth with rapidly growing industrial and biomedical applications. Synthetic pigments account for a major portion of these pigments that in turn have deleterious effects on public health and environment. Such drawbacks of synthetic pigments have shifted the trend to use natural pigments that are considered as the best alternative to synthetic pigments due to their significant properties. Natural pigments from microorganisms are of great interest due to their broader applications in the pharmaceutical, food, and textile industry with increasing demand among the consumers opting for natural pigments. To fulfill the market demand of natural pigments new sources should be explored. Cold-adapted bacteria and fungi in the cryosphere produce a variety of pigments as a protective strategy against ecological stresses such as low temperature, oxidative stresses, and ultraviolet radiation making them a potential source for natural pigment production. This review highlights the protective strategies and pigment production by cold-adapted bacteria and fungi, their industrial and biomedical applications, condition optimization for maximum pigment extraction as well as the challenges facing in the exploitation of cryospheric microorganisms for pigment extraction that hopefully will provide valuable information, direction, and progress in forthcoming studies.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Ghufranud Din
- Department of Microbiology, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
| | - Awais Iqbal
- School of Life Sciences, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, People's Republic of China
| | - Suliman Khan
- The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sahib Zada
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
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12
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Zhang B, Yang R, Zhang G, Liu Y, Zhang D, Zhang W, Chen T, Liu G. Characteristics of Planococcus antioxidans sp. nov., an antioxidant-producing strain isolated from the desert soil in the Qinghai-Tibetan Plateau. Microbiologyopen 2020; 9:1183-1196. [PMID: 32162498 PMCID: PMC7294307 DOI: 10.1002/mbo3.1028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 02/19/2020] [Accepted: 02/24/2020] [Indexed: 01/01/2023] Open
Abstract
Strain Y74T was an isolate from the sandy soil in the town of Huatugou, Qinghai-Tibet Plateau, China. An analysis of this strain's phenotypic, chemotaxonomic, and genomic characteristics established the relationship of the isolate with the genus Planococcus. Strain Y74T was able to grow between 4 and 42°C (with an optimum temperature of 28°C) at pH values of 6-8.5 and in 0%-7% (w/v) NaCl. The dominant quinones were MK-8 and MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and an unknown phospholipid. The majority of the fatty acid content was anteiso-C15:0 (28.8%) followed by C16:1 ω7c alcohol (20.9%) and iso-C14:0 (13.4%). The 16S rRNA gene sequence similarity analysis demonstrated a stable branch formed by strain Y74T and Planococcus halotolerans SCU63T (99.66%). The digital DNA-DNA hybridization between these two strains was 57.2%. The G + C content in the DNA of Y74T was 44.5 mol%. In addition, the morphological, physiological, and chemotaxonomic pattern clearly differentiated the isolates from their known relatives. In conclusion, the strain Y74T (=JCM 32826T = CICC24461T ) represents a novel member of the genus Planococcus, for which the name Planococcus antioxidans sp. nov. is proposed. Strain Y74T was found to have potent antioxidant activity via its hydrogen peroxide tolerance and its 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity. The DPPH radical-scavenging activity was determined to be 40.2 ± 0.7%. The genomic analysis indicated that six peroxidases genes, one superoxide dismutase gene, and one dprA (DNA-protecting protein) are present in the genome of Y74T .
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Affiliation(s)
- Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Ruiqi Yang
- College of Geography and Environmental Engineering, Lanzhou City University, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Dongming Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
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Planococcus lenghuensis sp. nov., an oil-degrading bacterium isolated from petroleum-contaminated soil. Antonie van Leeuwenhoek 2020; 113:839-850. [PMID: 32114684 DOI: 10.1007/s10482-020-01394-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
Abstract
A Gram-staining-positive and aerobic coccus with the ability to degrade petroleum bacterium, designated Y42T, was isolated from the Lenghu oil field located in the northern margin of the Qaidam Basin. Phylogenetic and signature nucleotides analyses revealed that strain Y42T belongs to the genus Planococcus. The multiple sequence alignments of 16S rRNA and housekeeping genes showed that strain Y42T formed a distinct lineage with the other Planococcus clade. The average nucleotide identity (ANI) and DNA-DNA hybridization values (DDH) between strain Y42T and the reference strains were 69.5-70.1 and 19.4-21.7%, respectively, which values were below the threshold for species delineation. The major fatty acids of strain Y42T were anteiso-C15:0. The respiratory quinone was MK-7 (71.8%) as the predominant menaquinone followed the MK-6 (28.2%) and the cell-wall hydrolysates contained LL-diaminopimelic acid. The polar lipid was composed of diphosphatidyl glycerol, phosphatidyl glycerol, phosphoglycolipid, aminophospholipid and four unidentified lipids. The peptidoglycan type was A4α (L-Lys-D-Glu). The strain Y42T possessed larger genome (approximately 4 MB) and revealed obvious differences for the abundance of the COG categories compared with the other Planococcus bacteria. Also, the strain Y42T also possessed more unique orthologous proteins. The structural characteristics of the strain Y42T genome provided a competitive advantage for better survival in petroleum-polluted environments. Combined with the 16S rRNA gene and genome sequence, phenotypic as well as chemotaxonomic characterisations, strain Y42T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus lenghuensis sp. nov. be proposed. The type strain is Y42T (= CGMCC 1.15921T = JCM 32719T).
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Silva‐Castro GA, Moyo AC, Khumalo L, van Zyl LJ, Petrik LF, Trindade M. Factors influencing pigment production by halophilic bacteria and its effect on brine evaporation rates. Microb Biotechnol 2019; 12:334-345. [PMID: 30277309 PMCID: PMC6389849 DOI: 10.1111/1751-7915.13319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/12/2018] [Accepted: 09/04/2018] [Indexed: 11/29/2022] Open
Abstract
The disposal of reject brine, a highly concentrated waste by-product generated by various industrial processes, represents a major economic and environmental challenge. The common practice in dealing with the large amounts of brine generated is to dispose of it in a pond and allow it to evaporate. The rate of evaporation is therefore a key factor in the effectiveness of the management of these ponds. The addition of various dyes has previously been used as a method to increase the evaporation rate. In this study, a biological approach, using pigmented halophilic bacteria (as opposed to chemical dyes), was assessed. Two bacteria, an Arthrobacter sp. and a Planococcus sp. were selected due to their ability to increase the evaporation of synthetic brine. When using industrial brine, supplementation of the brine with an iron source was required to maintain the pigment production. Under these conditions, the Planococcus sp. CP5-4 produced a carotenoid-like pigment, which resulted in a 20% increase in the evaporation rate of the brine. Thus, the pigment production capability of halophilic bacteria could potentially be exploited as an effective step in the management of industrial reject brines, analogous to the crystallizer ponds used to mine salt from sea water.
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Affiliation(s)
- Gloria Andrea Silva‐Castro
- Institute of Microbial Biotechnology and Metagenomics (IMBM)Department of BiotechnologyUniversity of the Western Cape7535BellvilleCape TownSouth Africa
| | - Anesu Conrad Moyo
- Institute of Microbial Biotechnology and Metagenomics (IMBM)Department of BiotechnologyUniversity of the Western Cape7535BellvilleCape TownSouth Africa
| | - Londiwe Khumalo
- Institute of Microbial Biotechnology and Metagenomics (IMBM)Department of BiotechnologyUniversity of the Western Cape7535BellvilleCape TownSouth Africa
| | - Leonardo Joaquim van Zyl
- Institute of Microbial Biotechnology and Metagenomics (IMBM)Department of BiotechnologyUniversity of the Western Cape7535BellvilleCape TownSouth Africa
| | - Leslie F. Petrik
- Department of ChemistryUniversity of the Western Cape7535BellvilleCape TownSouth Africa
| | - Marla Trindade
- Institute of Microbial Biotechnology and Metagenomics (IMBM)Department of BiotechnologyUniversity of the Western Cape7535BellvilleCape TownSouth Africa
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Carotenoids from heterotrophic bacteria isolated from Fildes Peninsula, King George Island, Antarctica. ACTA ACUST UNITED AC 2019; 21:e00306. [PMID: 30705834 PMCID: PMC6348148 DOI: 10.1016/j.btre.2019.e00306] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 12/23/2022]
Abstract
Carotenoids are isoprenoid pigments used by pharmaceutical, cosmetic, food and feed industry as antioxidants and colorants. Although traditional sources of carotenoids are fruits, vegetables and chemical synthesis, prospecting for alternative sinks of common and/or unusual carotenoids is important for the development of natural carotenoid industry. In this work, 30 pigmented bacterial strains from Fildes Peninsula in King George Island, Antarctica, were isolated and identified by 16S rRNA gene sequencing and classified in three phyla, Bacteroidetes, Firmicutes and Actinobacteria. After cells extraction, ten different carotenoids were identified based on the chromatographic and spectroscopic characteristic obtained by HPLC-PDA and HPLC-PDA-APCI-MS analyses. Strains assigned to Bacteroidetes affiliated to Flavobacterium, Chryseobacterium and Zobellia genera, presented a pigment profile composed of zeaxanthin, β-cryptoxanthin and β-carotene. Firmicutes strains of Planococcus genus produced a C50 carotenoid, identified as C.p. 450 glucoside. Actinobacteria isolates were mainly assigned to Arthrobacter genus, and few to Salinibacterium and Cryobacterium genera. Arthrobacter strains produced C50 carotenoids such as decaprenoxanthin and its glucosylated derivatives, as well as some C40 carotenoids such as lycopene which is used as synthesis precursors of the C50 carotenoids. Salinibacterium and Cryobacterium genera produced C.p. 450 free form and its glucosylated derivatives. Although most isolates produce carotenoids similar in diversity and quantity than those already reported in the literature, novel sources for C50 carotenoids results from this work. According to their carotenoid content, all isolates could be promising candidates for carotenoids production.
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Gan L, Zhang Y, Zhang L, Li X, Wang Z, He L, Li Z, Tian Y. Planococcus halotolerans sp. nov., isolated from a saline soil sample in China. Int J Syst Evol Microbiol 2018; 68:3500-3505. [PMID: 30265231 DOI: 10.1099/ijsem.0.003019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, coccoid or short rod-shaped, moderate-orange-pigmented, halotolerant and psychrotolerant bacterium, designated strain SCU63T, was isolated from a saline soil sample in China, and characterized by a polyphasic taxonomic approach. 16S rRNA gene sequence similarity of strain SCU63T to species in the genera Planococcus and Planomicrobium ranged from 96.5 to 98.6 %. Phylogenetic trees as well as diagnostic signature nucleotides in the 16S rRNA gene sequence supported the view that this strain should be assigned to the genus Planococcus. Further, average nucleotide identity and digital DNA-DNA hybridization analyses confirmed the separate species status of strain SCU63T relative to the closely related taxa. The isolate grew at 0-40 °C (optimum, 30-35 °C), at pH 6.5-9.0 (pH 7.0-7.5) and in the presence of 0-15 % (w/v) NaCl (3 %). The principal fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C16 : 0 and iso-C14 : 0, and the dominant isoprenoid quinones were MK-8 and MK-7. The peptidoglycan type was determined to be A4α (l-Lys-d-Glu), and the polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and one unidentified lipid. The DNA G+C content was 44.6 mol%. Based on the genotypic, phenotypic and chemotaxonomic data, strain SCU63T can be classified as a novel species in the genus Planococcus, for which the name Planococcushalotolerans sp. nov. is proposed. The type strain is SCU63T (=CGMCC 1.13628T=KCTC 43001T).
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Affiliation(s)
- Longzhan Gan
- 1Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yi Zhang
- 2Chengdu Jinkai Biology Engineering Co., Ltd., Chengdu 611130, PR China
| | - Lingli Zhang
- 3Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Xiaoguang Li
- 1Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Zhikuan Wang
- 1Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Linling He
- 1Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Zhenjiang Li
- 2Chengdu Jinkai Biology Engineering Co., Ltd., Chengdu 611130, PR China
| | - Yongqiang Tian
- 1Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
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Gan L, Zhang H, Tian J, Li X, Long X, Zhang Y, Dai Y, Tian Y. Planococcus salinus sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. Int J Syst Evol Microbiol 2018; 68:589-595. [DOI: 10.1099/ijsem.0.002548] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Longzhan Gan
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Heming Zhang
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Jiewei Tian
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xiaoguang Li
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xiufeng Long
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & PeKing Union Medical College, Beijing 100050, PR China
| | - Yumei Dai
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, PR China
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Complete genome sequence of Planococcus faecalis AJ003 T, the type species of the genus Planococcus and a microbial C30 carotenoid producer. J Biotechnol 2018; 266:72-76. [PMID: 29237561 DOI: 10.1016/j.jbiotec.2017.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 11/23/2022]
Abstract
A novel type strain, Planococcus faecalis AJ003T, isolated from the feces of Antarctic penguins, synthesizes a rare C30 carotenoid, glycosyl-4,4'-diaponeurosporen-4'-ol-4-oic acid. The complete genome of P. faecalis AJ003T comprises a single circular chromosome (3,495,892 bp; 40.9% G + C content). Annotation analysis has revealed 3511 coding DNA sequences and 99 RNAs; seven genes associated with the MEP pathway and five genes involved in the carotenoid pathway have been identified. The functionality and complementation of 4,4'-diapophytoene synthase (CrtM) and two copies of heterologous 4,4'-diapophytoene desaturase (CrtN) involved in carotenoid biosynthesis were analyzed in Escherichia coli.
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See-Too WS, Ee R, Madhaiyan M, Kwon SW, Tan JY, Lim YL, Convey P, Pearce DA, Yin WF, Chan KG. Planococcus versutus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:944-950. [DOI: 10.1099/ijsem.0.001721] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Munusamy Madhaiyan
- Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link 117604, Singapore
| | - Soon-Wo Kwon
- National Agrobiodiversity Center, National Academy of Agricultural Science, Suwon 441-707, Republic of Korea
| | - Jia Yi Tan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yan Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Peter Convey
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - David A. Pearce
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Wai Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia
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