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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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Gan L, Li X, Wang H, Peng B, Tian Y. Structural characterization and functional evaluation of a novel exopolysaccharide from the moderate halophile Gracilibacillus sp. SCU50. Int J Biol Macromol 2020; 154:1140-1148. [DOI: 10.1016/j.ijbiomac.2019.11.143] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022]
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Gracilibacillus salitolerans sp. nov., a moderate halophile isolated from saline soil in Northwest China. Int J Syst Evol Microbiol 2020; 70:3701-3710. [DOI: 10.1099/ijsem.0.004224] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A moderately halophilic strain, designated SCU50T, was recovered from a saline soil sample and characterized by a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain SCU50T belonged to the genus
Gracilibacillus
and was most closely related to
Gracilibacillus thailandensis
TP2-8T (98.1 % similarity) and
Gracilibacillus orientalis
XH-63T (97.7 %). Genomic average nucleotide identity and digital DNA–DNA hybridization analyses confirmed the separate species status of the new isolate relative to other recognized
Gracilibacillus
species. The genome size was about 5.09 Mbp and the DNA G+C content was 36.7 mol%. The strain grew optimally at 10–15 % (w/v) NaCl, pH 6.5–7.5 and 25–30 °C. It contained anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 as the dominant fatty acids and menaquinone-7 as the major respiratory quinone. The polar lipid profile was examined and found to comprise diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The cell-wall peptidoglycan type was A1γ based on meso-diaminopimelic acid. Combining the data from phenotypic, chemotaxonomic, genomic and phylogenetic characterization, it was concluded that strain SCU50T should be assigned as representing a novel species within the genus
Gracilibacillus
. Thus, a novel taxon named Gracilibacillus salitolerans sp. nov. was first established, with SCU50T (=CGMCC 1.17336T=KCTC 43107T) as the type strain.
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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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Pal Y, Mayilraj S, Paul M, Schumann P, Krishnamurthi S. Indiicoccus explosivorum gen. nov., sp. nov., isolated from an explosives waste contaminated site. Int J Syst Evol Microbiol 2019; 69:2555-2564. [PMID: 31287396 DOI: 10.1099/ijsem.0.003541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pink-pigmented, Gram-stain-positive, aerobic, coccoid-shaped bacterial strain, designated as S5-TSA-19T, was isolated from an explosives contaminated site in Panchkula, Haryana, India. The 16S rRNA gene sequencing blast analysis indicated that the strain is a member of the family Planococcaceae with the highest sequence similarity to Planomicrobium soli XN13T (96.1 %), followed by Planococcus maitriensis S1T (95.6 %), Planococcus plakortidis DSM 23997T (95.6 %), Planomicrobium flavidum ISL-41T (95.6 %), Planococcus rifietoensis M8T (95.5 %), Planococcus salinus LCB217T (95.5 %) and Planococcus maritimus DSM 17275T (95.5 %). Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences (based on a conserved set of 400 proteins) retrieved the strain in a distinct branch indicating a separate lineage within the family Planococcaceae. Strain S5-TSA-19T had a distinctive chemotaxonomic pattern comprising A4α type peptidoglycan based on l-Lys-d-Asp, iso-C15 : 0 as the major fatty acid, absence of phosphatidylethanolamine as a major lipid and MK-7 and MK-6 as the major menaquinones, differentiating it from the genera Planococcus and Planomicrobium, thus supporting the findings of molecular phylogeny. Further, strain S5-TSA-19T was able to biotransform hexahydro-1,3,5,-trinitro-1,2,5-triazine (RDX) into nitrite derivatives under aerobic conditions in 2-4 days, whereas the closest reference strains did not possess this property. On the basis of polyphasic taxonomic characterization and a phylogenomics approach, strain S5-TSA-19T is proposed as the type strain of a novel species in a novel genus for which the name Indiicoccus explosivorum gen. nov., sp. nov. is proposed (=JCM 31737T=KCTC 33871T=MTCC 12608T).
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Affiliation(s)
- Yash Pal
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A Chandigarh 160036, Chandigarh 160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A Chandigarh 160036, Chandigarh 160036, India.,Present address: Bentoli AgriNutrition India Pvt Ltd, Chennai, India
| | - Mohit Paul
- CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A Chandigarh 160036, Chandigarh 160036, India
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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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