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Galisteo C, de la Haba RR, Sánchez-Porro C, Ventosa A. A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils. Front Microbiol 2023; 14:1192059. [PMID: 37228371 PMCID: PMC10203224 DOI: 10.3389/fmicb.2023.1192059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023] Open
Abstract
Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.
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Zhang L, Huang W, Ning W, Song B, Osman G, Zhu J, Wang W. Radiobacillus kanasensis sp. nov., a halotolerant bacterium isolated from woodland soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 36821360 DOI: 10.1099/ijsem.0.005718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
A novel Gram-positive, aerobic, rod-shaped, non-motile, endospore-forming salt-tolerant bacterium strain (80T), was isolated from woodland soil collected near Kanas lake in the Altay region of Xinjiang, PR China. The strain grew at 15-45 °C, pH6.0-9.0 and with 0-14 % (w/v) NaCl. The complete genome size of the novel strain was 4 031 766 bp including a circle chromosome and a circle plasmid. The genomic DNA G+C content was 38.99 mol %. Phylogenetic analysis based on 16S rRNA gene sequence and genome showed that strain 80T has the highest similarity to Radiobacillus deserti TKL69T. However, the novel strain showed an average nucleotide identity value of 78.65 % (lower than 95 %) and a digital DNA-DNA hybridization value of 22.30 % with R. deserti TKL69T based on the genome sequences. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17:0 and C16 : 1 ω7c alcohol. The only respiratory quinone was MK-7. The cell wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified glycolipids were identified as the major polar lipids. The phylogenetic, phenotypic and chemotaxonomic analyses showed that strain 80T represents a novel species of the genus Radiobacillus and the name Radiobacillus kanasensis sp. nov. is proposed. The type strain is 80T (=GDMCC 1.2844T=JCM 35077T).
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Affiliation(s)
- Lijuan Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Wei Huang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Wang Ning
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Bo Song
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Ghenijan Osman
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Jing Zhu
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Wei Wang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:microorganisms10122355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
| | - Mohammad J. Taherzadeh
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
- Correspondence:
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Liu Y, Chen T, Cui X, Xu Y, Hu S, Zhao Y, Zhang W, Liu G, Zhang G. Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated S9-5T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. A polyphasic study confirmed the affiliation of the strain with the genus
Sphingomonas
. Strain S9-5T was an aerobic, Gram-stain-negative, non-spore-forming, non-motile and rod-shaped bacterium that could grow at 10–40 °C, pH 5–8 and with 0–9 % (w/v) NaCl. Q-10 was its predominant respiratory menaquinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and eight unidentified lipids comprised the polar lipids of strain S9-5T. Its major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and C16 : 0. The G+C content was 65.75mol%. Phylogenetic analysis based on 16S rRNA sequences showed that strain S9-5T was phylogenetically closely related to
Sphingomonas panaciterrae
DCY91T (98.17 %),
Sphingomonas olei
K-1-16T (98.11 %) and
Sphingomonas mucosissima
DSM 17494T (97.39 %). The average nucleotide identity values among strain S9-5T and
Sphingomonas panaciterrae
DCY91T,
Sphingomonas olei
K-1-16T and
Sphingomonas mucosissima
DSM 17494T were 78.82, 78.87 and 78.29 %, respectively. Based on the morphological, physiological and chemotaxonomic data, strain S9-5T (=JCM 34750T=GDMCC 1.2714T) should represent a novel species of the genus
Sphingomonas
, for which we propose the name Sphingomonas radiodurans sp. nov.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Xiaowen Cui
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Yeteng Xu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Shixin Hu
- Institute of Applied Magnetics, Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Lanzhou University, Lanzhou 730000, PR China
| | - Yidan Zhao
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
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