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Oren A, Göker M. Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38546332 PMCID: PMC10995726 DOI: 10.1099/ijsem.0.006229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Indexed: 04/07/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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Huang XX, Xu L, Sun JQ. Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878379 DOI: 10.1099/ijsem.0.005140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic, spore-forming, motile with unipolar biflagella, rod-shaped, indole acetic acid-producing bacterium, named LD4P30T, was isolated from a root of Suaeda salsa collected in Inner Mongolia, northern China. Strain LD4P30T grew at pH 6.0-11.0 (optimum, pH 7.0), 10-40 °C (35 °C) and in the presence of 1-15% (w/v) NaCl (5%). The strain was positive for oxidase and negative for catalase. The major cellular fatty acids of strain LD4P30T were iso-C15:0, C15:1 ω5c and anteiso-C15:0; the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol; and menaquinone-7 was the only respiratory quinone. The genomic DNA G+C content was 36.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain LD4P30T clustered with Gracilibacillus thailandensis TP2-8T, Gracilibacillus saliphilus YIM 91119T and Gracilibacillus lacisalsi BH312T, and showed 99.0, 98.9, 98.0 and <97.7% 16S rRNA gene similarity to G. thailandensis TP2-8T, G. saliphilus YIM 91119T, G. lacisalsi BH312T and all other current type strains, respectively. The digital DNA-DNA hybridization and average nucleotide identity based on blast values between strain LD4P30T and G. saliphilus YIM 91119T, G. thailandensis TP2-8T and G. lacisalsi BH312T were 44.9, 44.7 and 44.4%, and 91.1, 91.0 and 90.8%, respectively. Based on its phenotypic, physiological and phylogenetic characteristics, strain LD4P30T represents a novel species, for which the name Gracilibacillus suaedae is proposed. The type strain is LD4P30T (=CGMCC 1.17697T=KCTC 82375T).
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Affiliation(s)
- Xiao-Xian Huang
- Lab for Microbial Resources, Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ji-Quan Sun
- Lab for Microbial Resources, Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
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Deutch CE, Farden AM, DiCesare ES. Characterization of β-galactosidase and α-galactosidase activities from the halophilic bacterium Gracilibacillus dipsosauri. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01657-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Gracilibacillus dipsosauri strain DD1 is a salt-tolerant Gram-positive bacterium that can hydrolyze the synthetic substrates o-nitrophenyl-β-d-galactopyranoside (β-ONP-galactose) and p-nitrophenyl-α-d-galactopyranoside (α-PNP-galactose). The goals of this project were to characterize the enzymes responsible for these activities and to identify the genes encoding them.
Methods
G. dipsosauri strain DD1 was grown in tryptic soy broth containing various carbohydrates at 37 °C with aeration. Enzyme activities in cell extracts and whole cells were measured colorimetrically by hydrolysis of synthetic substrates containing nitrophenyl moieties. Two enzymes with β-galactosidase activity and one with α-galactosidase activity were partially purified by ammonium sulfate fractionation, ion-exchange chromatography, and gel-filtration chromatography from G. dipsosauri. Coomassie Blue-stained bands corresponding to each activity were excised from nondenaturing polyacrylamide gels and subjected to peptide sequencing after trypsin digestion and HPLC/MS analysis.
Result
Formation of β-galactosidase and α-galactosidase activities was repressed by d-glucose and not induced by lactose or d-melibiose. β-Galactosidase I had hydrolytic and transgalactosylation activity with lactose as the substrate but β-galactosidase II showed no activity towards lactose. The α-galactosidase had hydrolytic and transgalactosylation activity with d-melibiose but not with d-raffinose. β-Galactosidase I had a lower Km with β-ONP-galactose as the substrate (0.693 mmol l−1) than β-galactosidase II (1.662 mmol l−1), was active at more alkaline pH, and was inhibited by the product d-galactose. β-Galactosidase II was active at more acidic pH, was partially inhibited by ammonium salts, and showed higher activity with α-PNP-arabinose as a substrate. The α-galactosidase had a low Km with α-PNP-galactose as the substrate (0.338 mmol l−1), a pH optimum of about 7, and was inhibited by chloride-containing salts. β-Galactosidase I activity was found to be due to the protein A0A317L6F0 (encoded by gene DLJ74_04930), β-galactosidase II activity to the protein A0A317KZG3 (encoded by gene DLJ74_12640), and the α-galactosidase activity to the protein A0A317KU47 (encoded by gene DLJ74_17745).
Conclusions
G. dipsosauri forms three intracellular enzymes with different physiological properties which are responsible for the hydrolysis of β-ONP-galactose and α-PNP-galactose. BLAST analysis indicated that similar β-galactosidases may be formed by G. ureilyticus, G. orientalis, and G. kekensis and similar α-galactosidases by these bacteria and G. halophilus.
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Deutch CE, Yang S. Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant α-amylase. Antonie Van Leeuwenhoek 2020; 113:1049-1059. [PMID: 32318981 DOI: 10.1007/s10482-020-01417-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/09/2020] [Indexed: 11/26/2022]
Abstract
Gracilibacillus dipsosauri is a moderately-halophilic Gram-positive bacterium which forms an extracellular α-amylase that is induced by starch, repressed by D-glucose, and active in 2.0 M KCl. Previous studies showed that while enzyme activity could be measured with the synthetic substrate 2-chloro-4-nitrophenyl-α-D-maltotrioside (CNPG3), other assays were inconsistent and the protein showed aberrant mobility during nondenaturing gel electrophoresis. To clarify the properties of this enzyme, the genome of G. dipsosauri was sequenced and was found to be 4.19 Mb in size with an overall G+C content of 36.9%. A gene encoding an α-amylase composed of 691 amino acids was identified. The protein was a member of the glycosyl hydrolase 13 family, which had a molecular mass of 77,396 daltons and a pI of 4.39 due to an unusually large number of aspartate and glutamate residues (95/691 or 13.7%). BLAST analysis of the amino acid sequence revealed significant matches to other proteins with cyclodextrin glycosyltransferase activity. Partial purification of the protein from G. dipsosauri showed that fractions catalyzing the hydrolysis of CNPG3 and p-nitrophenyl-D-maltoheptoside also catalyzed the formation of β-cyclodextrin but not α-cyclodextrin or γ-cyclodextrin. Formation of β-cyclodextrin was not stimulated by high salt concentrations but did occur with rice, potato, wheat, and corn starches and amylopectin. These studies explain the unusual features of the α-amylase from G. dipsosauri and indicate it should be classified as EC 2.4.1.19. The availability of the complete genomic sequence of G. dipsosauri will provide the basis for studies on other enzymes from this halophile which may be useful for biotechnology.
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Affiliation(s)
- Charles E Deutch
- Microbion Research, 8931 W. Deanna Dr., Peoria, AZ, 85382, USA.
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, 85306, USA.
| | - Shanshan Yang
- Bioinformatics Core Facility, Knowledge Enterprise, Arizona State University, Tempe, AZ, 85281, USA
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Liu Z, Fu T, Hu C, Shen D, Macchioni N, Sozzi L, Chen Y, Liu J, Tian X, Ge Q, Feng Z, Liu H, Zhang Z, Pan J. Microbial community analysis and biodeterioration of waterlogged archaeological wood from the Nanhai No. 1 shipwreck during storage. Sci Rep 2018; 8:7170. [PMID: 29740020 PMCID: PMC5940862 DOI: 10.1038/s41598-018-25484-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/09/2018] [Indexed: 01/16/2023] Open
Abstract
Wooden shipwrecks are a significant part of the underwater cultural heritage. In 2007, the Nanhai No. 1 shipwreck was salvaged from the seabed and moved into the Marine Silk Road Museum, where it is still stored in a water tank. We analysed the microbial communities colonizing the hull surface of the Nanhai No. 1 shipwreck during storage. Six samples exposed to air were collected from different spots of the ship that exhibited obvious microbial plaques. High-throughput sequencing revealed the bacterial community includes both aquatic and terrestrial species, while in the fungal community, Fusarium was the most abundant genus across all samples and accounted for 84.91% to 98.40% of the total community composition. Two Fusarium species were isolated from the samples and were identified as F. solani and F. oxysporum. Both of the isolates were able to degrade cellulose, but only F. solani had the ability to degrade lignin. Antimicrobial efficacy in inhibiting the growth of Fusarium was assessed with five kinds of biocides, and isothiazolinones exhibited specific inhibition of Fusarium growth. These results provide critical background information to protect and reduce the biodegradation and destruction of this important historical shipwreck, and inform efforts to protect other similar artifacts.
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Affiliation(s)
- Zijun Liu
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Tongtong Fu
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Cuiting Hu
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Dawa Shen
- Chinese Academy of Cultural Heritage, Beijing, 100029, P.R. China
| | - Nicola Macchioni
- CNR-IVALSA, Via Madonna del Piano 10, 1-50019, Sesto Fiorentino, Italy
| | - Lorena Sozzi
- CNR-IVALSA, Via Madonna del Piano 10, 1-50019, Sesto Fiorentino, Italy
| | - Yue Chen
- Chinese Academy of Cultural Heritage, Beijing, 100029, P.R. China
| | - Jie Liu
- Chinese Academy of Cultural Heritage, Beijing, 100029, P.R. China
| | - Xingling Tian
- Chinese Academy of Cultural Heritage, Beijing, 100029, P.R. China
| | - Qinya Ge
- Chinese Academy of Cultural Heritage, Beijing, 100029, P.R. China
| | - Zhengteng Feng
- Maritime Silk Road Museum, Yangjiang, Guangdong province, 529500, P.R. China
| | - Huiru Liu
- Maritime Silk Road Museum, Yangjiang, Guangdong province, 529500, P.R. China
| | - Zhiguo Zhang
- National Center of Underwater Cultural Heritage, Beijing, 100192, P.R. China.
| | - Jiao Pan
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, P.R. China.
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Oh YJ, Lee HW, Lim SK, Kwon MS, Lee J, Jang JY, Park HW, Nam YD, Seo MJ, Choi HJ. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J Microbiol 2016; 54:588-593. [PMID: 27572507 DOI: 10.1007/s12275-016-6349-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/03/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
Abstract
A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)).
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Affiliation(s)
- Young Joon Oh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hae-Won Lee
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Min-Sung Kwon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jieun Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Ja-Young Jang
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hae Woong Park
- Advanced Process Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Korea Food Research Institute, Seongnam, 13539, Republic of Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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Hirota K, Hanaoka Y, Nodasaka Y, Yumoto I. Gracilibacillus alcaliphilus sp. nov., a facultative alkaliphile isolated from indigo fermentation liquor for dyeing. Int J Syst Evol Microbiol 2014; 64:3174-3180. [DOI: 10.1099/ijs.0.060871-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively alkaliphilic, lactic-acid-producing and halophilic strain, designated SG103T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample for dyeing prepared in a laboratory. 16S rRNA gene sequence phylogeny suggested that SG103T is a member of the genus
Gracilibacillus
with the closest relatives being ‘Gracilibacillus
xinjiangensis’ J2 (similarity: 97.06 %),
Gracilibacillus thailandensis
TP2-8T (97.06 %) and
Gracilibacillus halotolerans
NNT (96.87 %). Cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. The strain grew at temperatures between 13 and 48 °C with the optimum at 39 °C. It grew in the range pH 7–10 with the optimum at pH 9. The isoprenoid quinone detected was menaquinone-7 (MK-7) and the DNA G+C content was 41.3 mol%. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Unlike other reported species of the genus
Gracilibacillus
, the strain lacked diphosphatidylglycerol as a major polar lipid. DNA–DNA hybridization experiments with strains exhibiting greater than 96.87 % 16S rRNA gene sequence similarity, ‘G. xinjiangensis’ J2,
G. thailandensis
TP2-8T and
G. halotolerans
NNT, revealed 2±4 %, 4±9 % and 3±2 % relatedness, respectively. On the basis of the differences in phenotypic and chemotaxonomic characteristics, and the results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from reported species of the genus
Gracilibacillus
, strain SG103T merits classification as a members of a novel species, for which the name Gracilibacillus
alcaliphilus sp. nov. is proposed. The type strain is SG103T ( = JCM 17253T = NCIMB 14683T).
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Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshiko Hanaoka
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshinobu Nodasaka
- Laboratory of Electron Microscopy, Graduate School of Dentistry, Hokkaido University, Kita-ku, Sapporo 060-8586, Japan
| | - Isao Yumoto
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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