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Zhuo Cai J, Lan Yu Y, Biao Yang Z, Xun Xu X, Chun Lv G, Lian Xu C, Yin Wang G, Qi X, Li T, Bon Man Y, Hung Wong M, Cheng Z. Synergistic improvement of humus formation in compost residue by fenton-like and effective microorganism composite agents. BIORESOURCE TECHNOLOGY 2024; 400:130703. [PMID: 38631654 DOI: 10.1016/j.biortech.2024.130703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/13/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
Improving the humification of compost through a synergistic approach of biotic and abiotic methods is of great significance. This study employed a composite reagent, comprising Fenton-like agents and effective microorganisms (EM) to improve humification. This composite reagent increased humic-acid production by 37.44 %, reaching 39.82 g kg-1, surpassing the control group. The composite reagent synergistically promoted micromolecular fulvic acid and large humic acid production. Collaborative mechanism suggests that Fenton-like agents contributed to bulk residue decomposition and stimulated the evolution of microbial communities, whereas EMs promoted highly aromatic substance synthesis and adjusted the microbial community structure. Sequencing analysis indicates the Fenton-like agent initiated compost decomposition by Firmicutes, and EM reduced the abundance of Virgibacillus, Lentibacillus, and Alcanivorax. Applied as an organic fertilizer in Brassica chinensis L. plantations, the composite reagent considerably improved growth and photosynthetic pigment content. This composite reagent with biotic and abiotic components provides a learnable method for promoting humification.
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Affiliation(s)
- Jun Zhuo Cai
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Ying Lan Yu
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Zhan Biao Yang
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Xiao Xun Xu
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Guo Chun Lv
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Chang Lian Xu
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Gui Yin Wang
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Xin Qi
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Ting Li
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China
| | - Yu Bon Man
- Consortium on Health, Environment, Education, and Research (CHEER), and Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
| | - Ming Hung Wong
- Consortium on Health, Environment, Education, and Research (CHEER), and Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
| | - Zhang Cheng
- School of Environmental Sciences, Sichuan Agricultural University, Chengdu, China.
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Subramanian P, Kim Y, Naito H, Asano T, Hamada M, Weon HY, Kwon SW, Heo J. Gracilibacillus salinarum sp. nov. and Gracilibacillus caseinilyticus sp. nov., halotolerant bacteria isolated from a saltern environment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787383 DOI: 10.1099/ijsem.0.005965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Two aerobic, Gram-stain-positive, spore-forming motile bacterial strains, designated SSPM10-3T and SSWR10-1T, were isolated from salterns in Jeollanam province of South Korea. Both strains were halotolerant and grew well in 5 % NaCl but not in 20 and 25% NaCl, respectively. Optimal growth was observed with 5 % NaCl, at 30 °C and at pH 7.0-8.0. On the basis of the results of phylogenetic analysis using 16S rRNA gene sequence, both the strains were placed within the genus Gracilibacillus with Gracilibacillus massiliensis (98.65 % similarity) as their nearest neighbour. Menaquinone-7 (MK-7) (97 %) was the major isoprenoid quinone in both strains and major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Orthologous average nucleotide identity with usearch (OrthoANIu) and digital DNA-DNA hybridisation (dDDH) percentage comparison indicated that SSPM10-3T and SSWR10-1T exhibited highest similarity with G. massiliensis Awa-1T at 74.27 % and 21.0 and 74.23 % and 20.0 %, respectively. The DNA G+C contents of the strains were 39.1 % (SSPM10-3T) and 38.5 % (SSWR10-1T). Members of the genus Gracilibacillus, both strains were distinct from each other with respect to their ability to produce urease, β-glucosidase, assimilation of inulin and methyl-α-d-glucopyranoside and degradation of casein. Compared with each other, ANI and d4 dDDH calculations were only 88.2 % and 36.3 %, well below the cut-off values for species delineation for each index. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics,SSPM10-3T and SSWR10-1T represent distinct novel species for which names Gracilibacillus salinarum SSPM10-3T and Gracilibacillus caseinilyticus SSWR10-1T are proposed. The type strains are SSPM10-3T (=KACC 21933T =NBRC 115502T) and SSWR10-1T (=KACC 21934T =NBRC 115503T).
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Affiliation(s)
- Parthiban Subramanian
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Hanako Naito
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Asano
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
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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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Oh YJ, Kim JY, Lim SK, Kwon MS, Choi HJ. Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi. J Microbiol 2021; 59:460-466. [PMID: 33907972 DOI: 10.1007/s12275-021-0513-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 11/25/2022]
Abstract
To date, all species in the genus Salicibibacter have been isolated in Korean commercial kimchi. We aimed to describe the taxonomic characteristics of two strains, NKC5-3T and NKC21-4T, isolated from commercial kimchi collected from various regions in the Republic of Korea. Cells of these strains were rod-shaped, Gram-positive, aerobic, oxidase- and catalase-positive, non-motile, halophilic, and alkalitolerant. Both strains, unlike other species of the genus Salicibibacter, could not grow without NaCl. Strains NKC5-3T and NKC21-4T could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and grow at pH 7.0-10.0 (optimum 8.5) and 8.0-9.0 (optimum 8.5), respectively; they showed 97.1% 16S rRNA gene sequence similarity to each other and were most closely related to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively). The genome of strain NKC5-3T was nearly 4.6 Mb in size, with 4,456 protein-coding sequences (CDSs), whereas NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs. OrthoANI values between the novel strains and S. kimchii NKC1-1T were far lower than the species demarcation threshold. NKC5-3T and NKC21-4T clustered together to form branches that were distinct from the other Salicibibacter species. The major fatty acids in these strains were anteiso-C15:0 and anteiso-C17:0, and the predominant menaquinone was menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and five unidentified phospholipids (PL), and those of NKC21-4T included DPG, PG, seven unidentified PLs, and an unidentified lipid. Both isolates had DPG, which is the first case in the genus Salicibibacter. The genomic G + C content of strains NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic analyses, strains NKC5-3T (= KACC 22040T = DSM 111417T) and NKC21-4T (= KACC 22041T = DSM 111418T) represent two novel species of the genus Salicibibacter, for which the names Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov. are proposed.
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Affiliation(s)
- Young Joon Oh
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon Yong Kim
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Min-Sung Kwon
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hak-Jong Choi
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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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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Oh YJ, Kim JY, Jo HE, Park HK, Lim SK, Kwon MS, Choi HJ. Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food. J Microbiol 2020; 58:387-394. [PMID: 32279278 DOI: 10.1007/s12275-020-9507-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/11/2020] [Accepted: 03/16/2020] [Indexed: 11/27/2022]
Abstract
Two bacterial strains designated NKC220-2T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic, oxidaseand catalase-positive, rod-shaped, spore-forming, non-motile, and halophilic bacteria. Both strains grew without NaCl, unlike type species in the genus Lentibacillus. The optimal pH for growth was 8.0, higher than that of the type species in the genus Lentibacillus, although growth was observed at pH 5.5-9.0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the two strains (99.3-99.9% similarity) are grouped within the genus Lentibacillus and most closely related to Lentibacillus juripiscarius IS40-3T (97.4-97.6% similarity) isolated from fish sauce in Thailand. OrthoANI value between two novel strains and Lentibacillus lipolyticus SSKP1-9T (79.5-79.6% similarity) was far lower than the species demarcation threshold. Comparative genomic analysis displayed differences between the two strains as well as among other strains belonging to Lentibacillus. Furthermore, each isolate had strain-specific groups of orthologous genes based on pangenome analysis. Genomic G + C contents of strains NKC-220-2T and NKC851-2 were 41.9 and 42.2 mol%, respectively. The strains contained meso-diaminopimelic acid in their cell walls, and the major menaquinone was menaquinone-7. Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified glycolipid, aminophospholipid, and phospholipid were the major polar lipid components of both strains. The major cellular fatty acids of the strains were anteiso-C15:0 and anteiso-C17:0. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic features, strains NKC220-2T and NKC851-2 represent novel species of the genus Lentibacillus, for which the name Lentibacillus cibarius sp. nov. is proposed. The type strain is NKC220-2T (= KACC 21232T = JCM 33390T).
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Affiliation(s)
- Young Joon Oh
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon Yong Kim
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hee Eun Jo
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Department of Animal Science and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyo Kyeong Park
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Min-Sung Kwon
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hak-Jong Choi
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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Oh YJ, Kim JY, Park HK, Jang JY, Lim SK, Kwon MS, Choi HJ. Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi. J Microbiol 2019; 57:997-1002. [PMID: 31659686 DOI: 10.1007/s12275-019-9421-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
A Gram-stain-positive, rod-shaped, alkalitolerant, and halophilic bacterium-designated as strain NKC3-5T-was isolated from kimchi that was collected from the Geumsan area in the Republic of Korea. Cells of isolated strain NKC3-5T were 0.5-0.7 μm wide and 1.4-2.8 μm long. The strain NKC3-5T could grow at up to 20.0% (w/v) NaCl (optimum 10%), pH 6.5-10.0 (optimum pH 9.0), and 25-40°C (optimum 35°C). The cells were able to reduce nitrate under aerobic conditions, which is the first report in the genus Salicibibacter. The genome size and genomic G + C content of strain NKC3-5T were 3,754,174 bp and 45.9 mol%, respectively; it contained 3,630 coding sequences, 16S rRNA genes (six 16S, five 5S, and five 23S), and 59 tRNA genes. Phylogenetic analysis based on 16S rRNA showed that strain NKC3-5T clustered with bacterium Salicibibacter kimchii NKC1-1T, with a similarity of 96.2-97.6%, but formed a distinct branch with other published species of the family Bacillaceae. In addition, OrthoANI value between strain NKC3-5T and Salicibibacter kimchii NKC1-1T was far lower than the species demarcation threshold. Using functional genome annotation, the result found that carbohydrate, amino acid, and vitamin metabolism related genes were highly distributed in the genome of strain NKC3-5T. Comparative genomic analysis revealed that strain NKC3-5T had 716 pan-genome orthologous groups (POGs), dominated with carbohydrate metabolism. Phylogenomic analysis based on the concatenated core POGs revealed that strain NKC3-5T was closely related to Salicibibacter kimchii. The predominant polar lipids were phosphatidylglycerol and two unidentified lipids. Anteiso-C15:0, iso-C17:0, anteiso-C17:0, and iso-C15:0 were the major cellular fatty acids, and menaquinone-7 was the major isoprenoid quinone present in strain NKC3-5T. Cell wall peptidoglycan analysis of strain NKC3-5T showed that meso-diaminopimelic acid was the diagnostic diamino acid. The phephenotypic, genomic, phylogenetic, and chemotaxonomic properties reveal that the strain represents a novel species of the genus Salicibibacter, for which the name Salicibibacter halophilus sp. nov. is proposed, with the type strain NKC3-5T (= KACC 21230T = JCM 33437T).
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Affiliation(s)
- Young Joon Oh
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon Yong Kim
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hyo Kyeong Park
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Ja-Young Jang
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Min-Sung Kwon
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hak-Jong Choi
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2019; 71. [PMID: 33787483 DOI: 10.1099/ijsem.0.004688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Jang JY, Oh YJ, Lim SK, Park HK, Lee C, Kim JY, Lee MA, Choi HJ. Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi. J Microbiol 2018; 56:880-885. [PMID: 30361979 DOI: 10.1007/s12275-018-8518-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
A moderately halophilic and alkalitolerant bacterial strain NKC1-1T was isolated from commercial kimchi in Korea. Strain NKC1-1T was Gram-stain-positive, aerobic, rod-shaped, non-motile, and contained diaminopimelic acid-type murein. Cell growth was observed in a medium containing 0-25% (w/v) NaCl (optimal at 10% [w/v]), at 20-40°C (optimal at 37°C) and pH 6.5-10.0 (optimal at pH 9.0). The major isoprenoid quinone of the isolate was menaquinone-7, and the major polar lipids were phosphatidylglycerol and unidentified phospholipids. Cell membrane of the strain contained iso-C17:0 and anteiso-C15:0 as the major fatty acids. Its DNA G + C content was 45.2 mol%. Phylogenetic analysis indicated the strain to be most closely related to Geomicrobium halophilum with 92.7-92.9% 16S rRNA gene sequence similarity. Based on polyphasic taxonomic evaluation with phenotypic, phylogenetic, and chemotaxonomic analyses, the strain represents a novel species in a new genus, for which the name Salicibibacter kimchii gen. nov., sp. nov. is proposed (= CECT 9537T; KCCM 43276T).
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Affiliation(s)
- Ja-Young Jang
- Research and Development Division, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Young Joon Oh
- Research and Development Division, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Research and Development Division, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hyo Kyeong Park
- Research and Development Division, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Changsu Lee
- Research and Development Division, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon Yong Kim
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Mi-Ai Lee
- Research and Development Division, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hak-Jong Choi
- Research and Development Division, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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Oh YJ, Jang JY, Lim SK, Kwon MS, Lee J, Kim N, Shin MY, Park HK, Seo MJ, Choi HJ. Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J Microbiol 2017; 55:933-938. [PMID: 29214493 DOI: 10.1007/s12275-017-7386-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 11/27/2022]
Abstract
A Gram-stain-positive, halophilic, rod-shaped, non-motile, spore forming bacterium, strain NKC1-2T, was isolated from kimchi, a Korean fermented food. Comparative analysis based on 16S rRNA gene sequence demonstrated that the isolated strain was a species of the genus Virgibacillus. Strain NKC1-2T exhibited high level of 16S rRNA gene sequence similarity with the type strains of Virgibacillus xinjiangensis SL6-1T (96.9%), V. sediminis YIM kkny3T (96.8%), and V. salarius SA-Vb1T (96.7%). The isolate grew at pH 6.5-10.0 (optimum, pH 8.5-9.0), 0.0-25.0% (w/v) NaCl (optimum, 10-15% NaCl), and 15-50°C (optimum, 37°C). The major menaquinone in the strain was menaquinone-7, and the main peptidoglycan of the strain was meso-diaminopimelic acid. The predominant fatty acids of the strain were iso-C14:0, anteisio-C15:0, iso- C15:0, and iso-C16:0 (other components were < 10.0%). The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G + C content of NKC1-2T was 42.5 mol%. On the basis of these findings, strain NKC1-2T is proposed as a novel species in the genus Virgibacillus, for which the name Virgibacillus kimchii sp. nov. is proposed (=KACC 19404T =JCM 32284T). The type strain of Virgibacillus kimchii is NKC1-2T.
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Affiliation(s)
- Young Joon Oh
- 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
| | - 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
| | - NamHee Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Mi-Young Shin
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Division of Animal Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyo Kyeong Park
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, 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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