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An H, Ching XH, Cheah WJ, Lim WL, Ee KY, Chong CS, Lam MQ. Genomic analysis of a halophilic bacterium Nesterenkonia sp. CL21 with ability to produce a diverse group of lignocellulolytic enzymes. Folia Microbiol (Praha) 2025; 70:71-82. [PMID: 38842626 DOI: 10.1007/s12223-024-01178-9] [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: 11/25/2023] [Accepted: 05/26/2024] [Indexed: 06/07/2024]
Abstract
Halophilic bacteria are extremophiles that thrive in saline environment. Their ability to withstand such harsh conditions makes them an ideal choice for industrial applications such as lignocellulosic biomass degradation. In this study, a halophilic bacterium with the ability to produce extracellular cellulases and hemicellulases, designated as Nesterenkonia sp. CL21, was isolated from mangrove sediment in Tanjung Piai National Park, Malaysia. Thus far, studies on lignocellulolytic enzymes concerning bacterial species under this genus are limited. To gain a comprehensive understanding of its lignocellulose-degrading potential, the whole genome was sequenced using the Illumina NovaSeq 6000 platform. The genome of strain CL21 was assembled into 25 contigs with 3,744,449 bp and a 69.74% GC content and was predicted to contain 3,348 coding genes. Based on taxonomy analysis, strain CL21 shares 73.8 to 82.0% average nucleotide identity with its neighbouring species, below the 95% threshold, indicating its possible status as a distinct species in Nesterenkonia genus. Through in-depth genomic mining, a total of 81 carbohydrate-active enzymes were encoded. Among these, 24 encoded genes were identified to encompass diverse cellulases (GH3), xylanases (GH10, GH11, GH43, GH51, GH127 and CE4), mannanases (GH38 and GH106) and pectinases (PL1, PL9, and PL11). The production of lignocellulolytic enzymes was tested in the presence of several substrates. This study revealed that strain CL21 can produce a diverse array of enzymes which are active at different time points. By combining experimental data with genomic information, the ability of strain CL21 to produce lignocellulolytic enzymes has been elucidated, with potential applications in biorefinery industry.
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Affiliation(s)
- Hongxuan An
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
| | - Xin Huey Ching
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wai Jun Cheah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wei Lun Lim
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), 02600, Arau, Perlis, Malaysia
| | - Kah Yaw Ee
- Department of Agricultural and Food Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
- Centre for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Ming Quan Lam
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
- Centre for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
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Machin EV, Roldán DM, Menes RJ. Sphaerotilus uruguayifluvii sp. nov., a novel filamentous bacterium isolated from river water. Antonie Van Leeuwenhoek 2024; 117:96. [PMID: 38980405 DOI: 10.1007/s10482-024-01996-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/29/2024] [Indexed: 07/10/2024]
Abstract
Strain C29T, a Gram-staining-negative, straight rod occurring singly, in pairs or short chains, was isolated from floating filamentous biomass of the Uruguay River. The strain was catalase and oxidase positive, chemoorganotrophic, strictly aerobic, non-motile, and grew at pH 6.0-9.0, 15-45 °C, and 0-0.5% (w/v) NaCl. Polyhydroxybutyrate was accumulated in nutrient-limited conditions. Phylogenetic analysis based on the 16S rRNA gene revealed that strain C29T had the highest sequence similarity with Leptothrix discophora SS-1T (97.82%), Ideonella livida TBM-1T (97.82%), Vitreoscilla filiformis L1401-2T (97.52%), Sphaerotilus sulfidivorans D-501T (97.50%) and Sphaerotilus natans DSM 6575T (97.46%). Other type strains with validly published names had similarities below 97.46%. Further phylogenomic analysis showed that strain C29T was affiliated to the family Sphaerotilaceae. Average nucleotide identity (ANI) and in silico DNA-DNA hybridization (dDDH) values with its phylogenetic relatives were lower than 91 and 41%, respectively, revealing that strain C29T represented a new species. The DNA G + C content of strain C29T was 70.9%. The annotation of the genome of the novel strain shows it possessed genes for the degradation of aromatic compounds. It also contained genes that encode sigma factors involved in response regulation of stress resistance, which is an important function for adaptation and survival in natural niches. Based on the results of the phylogenetic and phenotypic analyses, we propose that strain C29T represents a novel species, for which the name Sphaerotilus uruguayifluvii sp. nov. is proposed. The type strain is C29T (= CCM 9043T = DSM 113250T).
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Affiliation(s)
- Eliana V Machin
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Diego M Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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Zhao A, Cai H, Huang Y, Yang Q, Zhu Z, Zhou Y, Jiang M, Jiang Y, Huang W. Nesterenkonia marinintestina sp. nov., isolated from the fish intestine. Arch Microbiol 2024; 206:110. [PMID: 38369673 DOI: 10.1007/s00203-023-03825-0] [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: 11/03/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 02/20/2024]
Abstract
A Gram-positive, aerobic, non-motile, irregular short rod, nonspore-forming actinobacterial strain, designated GX14115T, was isolated from fish intestine in Beihai City, Guangxi, China and subjected to a taxonomic polyphasic investigation. Colonies were yellow‒green, circular, smooth, central bulge, convex, opaque and 2.0-3.0 mm in diameter after growth on 2216E medium at 30 °C for 72 h. Growth occurred at 4-45 °C (optimum 30 °C), at pH 4.5-10.0 (optimum pH 7.5) and in the presence of 0-12% NaCl (w/v) (optimum 3.5%). Chemotaxonomic analysis showed that the main menaquinone of strain GX14115T was MK-7. The major cellular fatty acids were anteiso-C15:0 (44.8%), anteiso-C17:0 (20.5%), and iso-C15:0 (16%). The whole-cell sugars were galactose and xylose. The peptidoglycan type was L-Lys-Gly-D-Asp, and the polar lipids were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), one unknown phospholipid (UP), and one unknown glycolipid (UG). The DNA G + C content of the type of strain was 69.5 mol%. The 16S rRNA gene sequence analysis revealed that strain GX14115T is affiliated with the genus Nesterenkonia and is closely related to Nesterenkonia sandarakina YIM 70009T (96.5%) and Nesterenkonia lutea YIM 70081T (96.8%). The calculated results indicated that the average nucleotide identity (ANI) values of GX14115T were 74.49-74.78%, to the two aforementioned type strains, and the digital DNA-DNA hybridization (dDDH) values were 20.1-20.7%. Strain GX14115T was proposed as a novel species of the genus Nesterenkonia by the physiological, chemotaxonomic, and phylogenetic data, for whose the name is Nesterenkonia marinintestina sp. nov. The type of strain is GX14115T (= MCCC 1K06658T = KCTC 49495T).
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Affiliation(s)
- Aolin Zhao
- Guangxi Minzu University, Nanning, China
| | - Hanqin Cai
- Guangxi Minzu University, Nanning, China
| | - Ying Huang
- Guangxi Minzu University, Nanning, China
| | - Quan Yang
- Guangxi Minzu University, Nanning, China
| | | | - Yan Zhou
- Guangxi Minzu University, Nanning, China
| | | | - Yi Jiang
- Yunnan University, Kunming, China
| | - Wenshan Huang
- Guangxi Lvyounong Biological Technology, Guigang, China
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Song MH, Ma WL, Zhang N, He W, Wang HC, Wang S, Fan YL, Zhang DF. Description of Nesterenkonia aerolata sp. nov., an actinobacterium isolated from air of manufacturing shop in a pharmaceutical factory. Antonie Van Leeuwenhoek 2024; 117:8. [PMID: 38170331 DOI: 10.1007/s10482-023-01905-1] [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: 09/30/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024]
Abstract
During our studies on the microorganism diversity from air of manufacturing shop in a pharmaceutical factory in Shandong province, China, a Gram-stain-positive, aerobic, cocci-shaped bacterium, designated LY-0111T, was isolated from a settling dish. Strain LY-0111T grew at temperature of 10-42 °C (optimum 35 °C), pH of 5.0-10.0 (optimum pH 7.0) and NaCl concentration of 1-12% (optimum 0.5-3%, w/v). Based on the 16S rRNA gene sequence analysis, the strain shared the highest sequence similarities to Nesterenkonia halophila YIM 70179T (96.2%), and was placed within the radiation of Nesterenkonia species in the phylogenetic trees. The genome of the isolate was sequenced, which comprised 2,931,270 bp with G + C content of 66.5%. A supermatrix tree based on the gene set bac120 indicated that LY-0111T was close related to Nesterenkonia xinjiangensis YIM 70097T (16S rRNA gene sequence similarity 95.3%). Chemotaxonomic analysis indicated that the main respiratory quinones were MK-7, MK-8, and MK-9, the predominant cellular fatty acids were anteiso-C15:0 and iso-C15:0, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. According to the phenotypic, chemotaxonomic and phylogenetic features, strain LY-0111T is considered to represent a novel species, for which the name Nesterenkonia aerolata sp. nov. is proposed. The type strain is LY-0111T (= JCM 36375T = GDMCC 1.3945T). In addition, Nesterenkonia jeotgali was proposed as a later synonym of Nesterenkonia sandarakina, according to the ANI (96.8%) and dDDH (72.9%) analysis between them.
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Affiliation(s)
- Ming-Hui Song
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, People's Republic of China
| | - Wen-Long Ma
- Shaanxi Zhuzhijian Planning and Design Group Co., LTD, Xi'an, People's Republic of China
| | - Ning Zhang
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, People's Republic of China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, People's Republic of China
| | - Wei He
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Hong-Chuan Wang
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization/Heilongjiang Black Soil Conservation Engineering and Technology Research Center, Harbin, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China
| | - Yi-Ling Fan
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, People's Republic of China.
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, People's Republic of China.
- China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China.
| | - Dao-Feng Zhang
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China.
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Kaale SE, Machangu RS, Lyimo TJ. Molecular characterization and phylogenetic diversity of actinomycetota species isolated from Lake Natron sediments at Arusha, Tanzania. Microbiol Res 2024; 278:127543. [PMID: 37950928 DOI: 10.1016/j.micres.2023.127543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/13/2023]
Abstract
Soda lakes are naturally occurring ecosystems characterized by extreme environmental conditions especially high pH and salinity levels but harboring valuable microbial communities with medical and biotechnological potentials. Lake Natron is one of the soda lakes situated in eastern branch of the East African Gregory Rift valley, Tanzania. In this study, the taxonomy and phylogenetic diversity of Actinomycetota species were explored in Lake Natron using molecular techniques. The sequencing of their 16S rRNA gene resulted into 13 genera of phylum Actinomycetota namely Streptomyces, Microbacterium, Nocardiopsis, Gordonia, Dietzia, Micromonospora, Microcella, Pseudarthrobacter, Nocardioides, Actinotalea, Cellulomonas, Isoptericola, and Glutamicibacter. We describe for the first time, the isolation of Streptomyces lasalocidi, S. harbinensis, S. anthocyanicus, Microbacterium aureliae, Pseudarthrobacter sp., Nocardioides sp. and Glutamicibacter mishrai from soda lake habitats. It also reports for the first time, the isolation of Gordonia spp., Microcella sp. and Actinotalea sp. from an East African Soda Lake as well as isolation of S. pseudogriseolus, S. calidiresistens and Micromonospora spp. from a Tanzania soda lake. Furthermore, two putative novel species of the phylum Actinomycetota were identified. Given that Actinomycetota are known potential sources of important biotechnological compounds, we recommend the broadening of the scope of bioprospection in future to include the novel species from Lake Natron.
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Affiliation(s)
- Sadikiel E Kaale
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania; Department of Biochemistry and Molecular Biology, Saint Francis University College of Health and Allied Sciences, Ifakara-Morogoro, Tanzania
| | - Robert S Machangu
- Department of Microbiology, Saint Francis University College of Health and Allied Sciences, Ifakara-Morogoro, Tanzania
| | - Thomas J Lyimo
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania.
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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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Wang S, Sun L, Narsing Rao MP, Fang B, Li W. Comparative Genome Analysis of a Novel Alkaliphilic Actinobacterial Species Nesterenkonia haasae. Pol J Microbiol 2022; 71:453-461. [PMID: 36185029 PMCID: PMC9608169 DOI: 10.33073/pjm-2022-040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/31/2022] [Indexed: 11/24/2022] Open
Abstract
In the present study, a comparative genome analysis of the novel alkaliphilic actinobacterial Nesterenkonia haasae with other members of the genus Nesterenkonia was performed. The genome size of Nesterenkonia members ranged from 2,188,008 to 3,676,111 bp. N. haasae and Nesterenkonia members of the present study encode the essential glycolysis and pentose phosphate pathway genes. In addition, some Nesterenkonia members encode the crucial genes for Entner-Doudoroff pathways. Some Nesterenkonia members possess the genes responsible for sulfate/thiosulfate transport system permease protein/ ATP-binding protein and conversion of sulfate to sulfite. Nesterenkonia members also encode the genes for assimilatory nitrate reduction, nitrite reductase, and the urea cycle. All Nesterenkonia members have the genes to overcome environmental stress and produce secondary metabolites. The present study helps to understand N. haasae and Nesterenkonia members' environmental adaptation and niches specificity based on their specific metabolic properties. Further, based on genome analysis, we propose reclassifying Nesterenkonia jeotgali as a later heterotypic synonym of Nesterenkonia sandarakina.
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Affiliation(s)
- Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, BeijingPeople’s Republic of China,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, BeijingPeople’s Republic of China, S. Wang, Heilongjiang Academy of Black Soil Conservation and Utilization, Heilongjiang Academy of Agricultural Sciences, People’s Republic of China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, People’s Republic of China
| | - Lei Sun
- Heilongjiang Academy of Black Soil Conservation and Utilization, BeijingPeople’s Republic of China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, GuangzhouPeople’s Republic of China
| | - Bao‑zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, BeijingPeople’s Republic of China,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, GuangzhouPeople’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, BeijingPeople’s Republic of China,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, GuangzhouPeople’s Republic of China
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Comparative Analysis of the Endophytic Bacterial Diversity of Populus euphratica Oliv. in Environments of Different Salinity Intensities. Microbiol Spectr 2022; 10:e0050022. [PMID: 35587636 PMCID: PMC9241684 DOI: 10.1128/spectrum.00500-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Populus euphratica Oliv. has a high tolerance for drought, salinity, and alkalinity. The main purpose of this study is to explore the effects of environments of different salinity intensities on endophytic community structure and the possible roles of endophytes in the tolerance of host plants. The characterization of endogenous bacteria in diversity has been investigated by using the Illumina high-throughput sequencing technique. The research showed that endophytic bacteria of P. euphratica in an extremely saline environment had low species diversity, especially in sap tissue. The dominant phyla in all groups were Proteobacteria, Actinobacteria, and Bacteroidetes. Notably, Firmicutes (relative abundance >5%) was a different dominant phylum in the samples from the high-saline environment compared with the relatively low-saline-environment group. The linear discriminant analysis effect size (LEfSe) analysis found that there were significant differences in different saline environments of Cytophagaceae (family), Rhodobacteraceae (family), and Rhodobacterales (order). These results indicated that the composition of the endogenous bacterial community was related to the growth environment of host plants. The predictive analysis of KEGG pathways and enzymes showed that the abundance of some enzymes and metabolic pathways of endophytes of P. euphratica increased with the increase of soil salinity, and most of the enzymes were related to energy metabolism and carbohydrate metabolism. These findings suggested that the endogenous bacteria of the host plant had different expression mechanisms under different degrees of stress, and this mechanism was very obvious in the distribution of endophytes, while the function of the endogenous bacteria needs to be further explored. IMPORTANCE Euphrates poplar (Populus euphratica Oliv.), as the only tree species that grows in the desert, has tenacious vitality with the characteristics of cold tolerance, drought tolerance, salt-alkali tolerance, and wind-sand resistance. P. euphratica has a long growth cycle and a high growth rate, which can break wind, fix sand, green the environment, and protect farmland, making it an important afforestation tree species in arid and semiarid areas. The area of P. euphratica in Xinjiang accounts for 91.1% of its area in China. Studying the endophytic bacteria of P. euphratica can give people a systematic understanding of it and the adaptability of the endogenous flora to the host and special environments. In this study, by analyzing the endophytic bacteria of P. euphratica in different saline-alkali regions of Xinjiang, it was found that the bacteria in different tissues of P. euphratica changed with the change of soil salinity. Especially in the sap tissue of P. euphratica under extremely high salinity, the diversity of endogenous bacteria was significantly lower than that in other tissues. These differential bacteria under different salinities were mostly related to the stress resistance of themselves and the host. Not only that, we also selected a strain of Bacillus with high stress resistance from the tissues of P. euphratica, which can survive under the extreme conditions of 10% NaCl and pH 11. We obtained a genome completion map of this strain, named it Bacillus haynesii P19 (GenBank accession no. PRJNA648288), and tried to use it for fermentation but in a different work, so as to develop it into a promising industrial fermentation chassis bacterium. Therefore, this study was of great significance for the understanding of endophytic bacteria in P. euphratica and the acquisition of extremophilic microbial resources.
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Xie F, Pei S, Zhang Y, Tian Y, Zhang G. Nesterenkonia sedimenti sp. nov., isolated from marine sediment. Arch Microbiol 2021; 203:6287-6293. [PMID: 34609528 DOI: 10.1007/s00203-021-02596-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
A Gram-staining-positive actinobacteria strain, designated MY13T, was isolated from deep-sea sediment of the western Pacific Ocean and subjected to a taxonomic polyphasic investigation. Based on the results, cells were aerobic, irregular short rod, non-motile and non-spore-forming. Colonies were cream, circular, smooth, convex, opaque and 1.0-2.0 mm in diameter after growth on MZ2 medium at 40 °C for 72 h. Strain MY13T grew at 4-50 °C (optimum, 40 °C), pH 7-12 (pH 9) and 0.5-15% (w/v) NaCl (3.5%). The 16S rRNA gene sequence analysis revealed that strain MY13T is affiliated with the genus Nesterenkonia and closely related to Nesterenkonia populi GP10-3T (96.6%). Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) differentiated it from its closest relatives, with values ranging from 19.8% to 22.4% and 72.6% to 78.0%, respectively. Chemotaxonomic analysis showed that the major menaquinone of strain MY13T was MK-7; major cellular fatty acids were anteiso-C17:0, anteiso-C15:0 and iso-C16:0; whole-cell sugars were galactose and xylose; the peptidoglycan type was L-Lys-Gly-D-Asp; and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids, one unknown polar lipid and two unknown lipids. The G+C content of genomic DNA was 63.1 mol%. Based on the physiological, chemotaxonomic and phylogenetic data, strain MY13T is a novel species of the genus Nesterenkonia, for which the name Nesterenkonia sedimenti sp. nov. is proposed. The type strain is MY13T (= LMG 28111T = MCCC 1A09979T = JCM 19767T = CGMCC 1.12784T).
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Affiliation(s)
- Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Shengxiang Pei
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Yubian Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China.
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10
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Roldán DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB, Králová S, Sedláček I, Busse HJ, Menes RJ. Hymenobacter caeli sp. nov., an airborne bacterium isolated from King George Island, Antarctica. Int J Syst Evol Microbiol 2021; 71. [PMID: 34152267 DOI: 10.1099/ijsem.0.004838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod-shaped and Gram-stain-negative bacterial strain 9AT, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9AT belongs to the genus Hymenobacter and shows the highest similarity to Hymenobacter coccineus CCM 8649T (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9AT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth is observed at 0-20 °C (optimum 10 °C), pH 6.0-8.0 (optimum pH 7.0), and in the absence of NaCl. The predominant menaquinone of strain 9AT is MK-7 and the major fatty acids comprise Summed Feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 25.2 %), iso-C15 : 0 (23.2 %), C16 : 1 ω5c (11.6 %), Summed Feature 4 (anteiso-C17 : 1 B/iso-C17 : 1 I) (9.6 %) and anteiso-C15 : 0 (9.6 %). The polar lipid profile consists of the major lipid phosphatidylethanolamine and moderate to minor amounts of phosphatidylserine, unidentified aminolipids, aminophospholipids, aminophosphoglycolipids, polar lipids lacking a functional group and an unidentified phospholipid and a glycolipid. In the polyamine pattern sym-homospermidine is predominant. On the basis of the results obtained, strain 9AT is proposed as a novel species of the genus Hymenobacter, for which the name Hymenobacter caeli sp. nov. is suggested. The type strain is 9AT (=CCM 8971T=LMG 32109T=DSM 111653T).
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Affiliation(s)
- Diego M Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | | | | | | | - William B Whitman
- Microbiology Department, University of Georgia, Athens, Georgia, USA
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Masaryk University, Brno, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Masaryk University, Brno, Czech Republic
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Wien, Austria
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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11
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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: 1.5] [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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12
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Wang S, Sun L, Wei D, Salam N, Fang BZ, Dong ZY, Hao XY, Zhang M, Zhang Z, Li WJ. Nesterenkonia haasae sp. nov., an alkaliphilic actinobacterium isolated from a degraded pasture in Songnen Plain. Arch Microbiol 2020; 203:959-966. [PMID: 33104820 DOI: 10.1007/s00203-020-02073-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/12/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023]
Abstract
An alkaliphilic actinobacterial strain, designated Hz 6-5T, was isolated from saline-alkaline soil from Songnen Plain in north-eastern China. The isolate formed light yellow-colored colonies and its cells were Gram-staining positive, non-motile, and non-spore-forming short rods. The strain was aerobic with optimal growth at 33 °C, pH 9.0, and in the presence of 0.5% (w/v) NaCl or 3% (w/v) KCl. It was catalase-positive and oxidase-negative. The isolate had highest 16S rRNA gene sequence similarities to the type strains of the species Nesternkonia natronophila M8T (98.2%), N. salmonea GY074T (98.1%), and N. sphaerica GY239T (97.4%), and the isolate formed a subclade with the type strains of these species in the neighbor-joining tree based on the 16S rRNA gene sequences. The phylogenetic tree based on the phylogenomic analysis also showed the same results. The DNA‒DNA relatedness (DDH) values of isolate Hz 6-5T with N. natronophila M8T, N. halophila DSM 16378T, and N. halobia CGMCC 1.2323T were 21.2%, 36.5%, and 32.0%, respectively. The characteristic diamino acid of strain Hz 6-5T was found to be lysine. The respiratory quinones were MK-9, MK-8, MK-7(H4), MK-7(H2) and MK-7 and the major cellular fatty acids (> 10%) were anteiso-C15:0, anteiso-C17:0 and iso-C16:0. The polar lipids detected for strain Hz 6-5T were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid, and two unidentified phospholipids. The DNA G + C content of isolate Hz 6-5T was 60.8%. Based on the results of phylogenetic analysis supported by morphological, physiological, chemotaxonomic, and other differentiating phenotypic evidence, strain Hz 6-5T is considered to represent a novel species of the genus Nesterenkonia, for which the name Nesterenkonia haasae sp. nov. is proposed. The type strain is Hz 6-5T (=CPCC 205100T=NBRC 113521T).
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Affiliation(s)
- Shuang Wang
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China
| | - Lei Sun
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China
| | - Dan Wei
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Yu Hao
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China
| | - Mingyi Zhang
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China
| | - Zhe Zhang
- Institute of Rural Renewal, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Roldán DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB, Králová S, Sedláček I, Busse HJ, Menes RJ. Hymenobacter artigasi sp. nov., isolated from air sampling in maritime Antarctica. Int J Syst Evol Microbiol 2020; 70:4935-4941. [PMID: 32744985 DOI: 10.1099/ijsem.0.004362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod-shaped and Gram-stain-negative bacterial strain, 1BT, was isolated from an air sample collected at King George Island, maritime Antarctica. Strain 1BT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth of strain 1BT is observed at 0-20 °C (optimum, 10 °C), pH 6.0-8.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences places strain 1BT within the genus Hymenobacter and shows the highest similarity to Hymenobacter antarcticus VUG-A42aaT (97.5 %). The predominant menaquinone of strain 1BT is MK-7 and the major fatty acids (>10 %) comprise summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 32.5 %), iso-C15 : 0 (17.6 %) and anteiso C15 : 0 (12.3 %). The polar lipid profile consists of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids and one unidentified phospholipid. The DNA G+C content based on the draft genome sequence is 61.2 mol%. Based on the data from the current polyphasic study, 1BT represents a novel species of the genus Hymenobacter, for which the name Hymenobacter artigasi sp. nov. is suggested. The type strain is 1BT (=CCM 8970T=CGMCC 1.16843T).
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Affiliation(s)
- Diego M Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Nikos Kyrpides
- DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - Tanja Woyke
- DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - Nicole Shapiro
- DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - William B Whitman
- Microbiology Department, University of Georgia, Athens, GA 30602, USA
| | - Stanislava Králová
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czechia
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay
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14
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Bacillus natronophilus sp. nov., an alkaliphilic bacterium isolated from a soda lake. Int J Syst Evol Microbiol 2020; 70:562-568. [DOI: 10.1099/ijsem.0.003792] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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