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Sun YY, Chen RY, Zhou ZY, Gong Y, Du ZJ. Gilvimarinus gilvus sp. nov. and Gilvimarinus algae sp. nov., isolated from kelp seedlings. Int J Syst Evol Microbiol 2024; 74. [PMID: 39133214 DOI: 10.1099/ijsem.0.006490] [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: 08/13/2024] Open
Abstract
Two novel rod-shaped, strictly aerobic, non-motile and Gram-stain-negative bacterial strains, designated SDUM040013T and SDUM040014T, were isolated from kelp seedlings in Weihai, PR China. Cells of strain SDUM040013T were 0.3-0.4 µm wide and 0.8-1.8 µm long, catalase-positive and oxidase-positive. Growth of SDUM040013T was observed at 0-37 °C (optimum, 28-30 °C) and pH 5.5-9 (optimum, pH 8.0) and in the presence of 1-8 % (w/v) NaCl (optimum, 2 %). The DNA G+C content of strain SDUM040013T was 50.5 %. Strain SDUM040013T showed the highest 16S rRNA gene sequence similarity (97.1 %) to Gilvimarinus chinensis. Cells of strain SDUM040014T were 0.4-0.5 µm wide and 1.0-1.4 µm long, catalase-positive and oxidase-positive. Growth of SDUM040014T was observed at 4-40 °C (optimum, 28-30 °C) and pH 5.5-9 (optimum, pH 8.5) and in the presence of 0-8 % (w/v) NaCl (optimum, 2 %). The DNA G+C content of strain SDUM040014T was 56.5 %. Strain SDUM040014T showed the highest 16S rRNA gene sequence similarity (96.2%) to Gilvimarinus polysaccharolyticus. The isoprenoid quinone of both strains was Q-8 and the predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c) and C16 : 0. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. Given these phenotypic and chemotaxonomic properties, as well as phylogenetic data, strains SDUM040013T and SDUM040014T were considered to represent two novel species of the genus Gilvimarinus, for which the names Gilvimarinus gilvus sp. nov. and Gilvimarinus algae sp. nov. are proposed. The type strains are SDUM040013T (=KCTC 8123T=MCCC 1H01413T) and SDUM040014T (=KCTC 8124T=MCCC 1H01414T), respectively.
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Affiliation(s)
- Yang-Yang Sun
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Rui-Ying Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zi-Yang Zhou
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya Gong
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, Shandong, 264209, PR China
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Li F, Sun YY, Zhang YJ, Liu XJ, Du ZJ, Gong Y. Winogradskyella pelagia sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 39046891 DOI: 10.1099/ijsem.0.006470] [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: 07/27/2024] Open
Abstract
An orange-pigmented, Gram-stain-negative, strictly aerobic, non-flagellated and rod-shaped bacterium, designated strain DF17T, was isolated from coastal sediment collected from Jingzi Wharf, Weihai, PR China. The optimal growth conditions were determined to be at 30 °C, pH 7.5, and in 3 % (w/v) NaCl. According to phylogenetic analysis of the 16S rRNA gene sequence, strain DF17T showed the highest sequence similarity of 96.9 % to Winogradskyella aquimaris KCTC 23502T. The DNA G+C content was 35.8 mol%, and the major fatty acids were iso-C15 : 1 G, iso-C15 : 0, and iso-C17 : 0 3-OH. The major polar lipids were two aminoglycolipids, one phosphatidylethanolamine and four unidentified lipids. The predominant respiratory quinone was menaquinone-6 (MK-6). The average nucleotide identity, digital DNA-DNA hybridization, and amino acid identity values between strain DF17T and other Winogradskyella species were below the species delineation thresholds of 69.35-72.95 %, 16.9-19.6 % and 71.25-78.93 %, respectively. On the basis of its phenotypic, genetic and physiological characteristics, strain DF17T is suggested to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella pelagia sp. nov. is proposed. The type strain is DF17T (MCCC 1H00456T=KCTC 82421T).
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Affiliation(s)
- Fan Li
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Yang-Yang Sun
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
- Joint Science College, Shandong University, Weihai, Shandong 264209, PR China
| | - Ya-Jing Zhang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xin-Jiang Liu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai 264209, PR China
| | - Ya Gong
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai 264209, PR China
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An J, Yu Q, Xuan XQ, Zhang J, Du ZJ, Mu DS. Aequorivita sediminis sp. nov. and Aequorivita marina sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 38904664 DOI: 10.1099/ijsem.0.006423] [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: 06/22/2024] Open
Abstract
Two Gram-stain-negative, rod-shaped, non-motile, strictly aerobic strains, forming yellow colonies and designated F6058T and S2608T, were isolated from marine sediment collected in Weihai, PR China. Both strains grow at 4-40 °C (optimum, 30-33 °C), pH 6.0-7.5 (optimum, pH 6.5) and in the presence of 0-7.0 % (w/v) NaCl. The optimum NaCl concentrations for strains F6058T and S2608T were 2.0 % and 2.5 %, respectively. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strains F6058T and S2608T share an evolutionary lineage with members of the genus Aequorivita. The isolates exhibited a 16S rRNA gene sequence similarity of 96.7 % to each other. Strains F6058T exhibited the highest 16S rRNA gene sequence similarity to Aequorivita xiaoshiensis F64183T (98.8 %), and S2608T was most similar to Aequorivita capsosiphonis A71T (96.9 %). Iso-C15:0, anteiso-C15:0 and iso-C17:0 3-OH were the major fatty acids of strains F6058T and S2608T. The sole respiratory quinone of both isolates was menaquinone 6 (MK-6). The polar lipid profiles of the isolates both consisted of phosphatidylethanolamine and phosphoglycolipids; however, strain F6058T exhibited one glycolipid, one aminolipid and two unidentified polar lipids, and strain S2608T also had two glycolipids and one unidentified polar lipid. The DNA G+C contents of strains F6058T and S2608T were 34.6 % and 37.7 mol%, respectively. Based on their phenotypic, chemotaxonomic and genomic characteristics, strains F6058T and S2608T were considered to represent novel species of the genus Aequorivita, for which the names Aequorivita sediminis sp. nov. and Aequorivita marina sp. nov. were proposed. The type strains are F6058T (=KCTC 92653T=MCCC 1H01358T) and S2608T (KCTC 92652T=MCCC 1H01361T).
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Affiliation(s)
- Jing An
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Qian Yu
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Xiao-Qi Xuan
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Jing Zhang
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, PR China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, PR China
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Song Y, Yuan XY, Cong HY, Liu Y, Liu P, Wang MY, Du ZJ. Ottowia cancrivicina sp. nov., isolated from human stomach. Int J Syst Evol Microbiol 2024; 74. [PMID: 38728178 DOI: 10.1099/ijsem.0.006360] [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: 05/12/2024] Open
Abstract
A Gram-negative, facultative anaerobic, non-motile and rod-shaped bacterium, designated 10c7w1T, was isolated from a human gastrointestinal tract. Colonies on agar plates were small, circular, smooth and beige. The optimal growth conditions were determined to be 37 °C, pH 7.0-7.5 and 0 % (w/v) NaCl. Comparative analysis of complete 16S rRNA gene sequences revealed that strain 10c7w1T showed the highest sequence similarity of 95.8 % to Ottowia beijingensis MCCC 1A01410T, followed by Ottowia thiooxydans (95.2 %) JCM 11629T. The average amino acid identity values between 10c7w1T and O. beijingensis MCCC 1A01410T and O. thiooxydans JCM 11629T were above 60 % (71.4 and 69.5 %). The average nucleotide identity values between strain 10c7w1T and O. beijingensis MCCC 1A01410T and O. thiooxydans JCM 11629T were 76.9 and 72.5 %, respectively. The dominant fatty acids (≥10 %) were straight chain ones, with summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) and C16 : 00 being the most abundant. Q-8 was the only respiratory quinone. The major polar lipids of strain 10c7w1T were phosphatidylethanolamine, diphosphatidylglycerol and unknown lipids. The DNA G+C content of strain 10c7w1T was 63.6 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic data, strain 10c7w1T is considered to represent a novel species within the genus Ottowia, for which the name Ottowia cancrivicina sp. nov. is proposed. The type strain is 10c7w1T (=MCCC 1H01399T=KCTC 92200T).
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Affiliation(s)
- Yu Song
- Marie College, Shandong University, Weihai, Shandong, 264209, PR China
- Department of Central Lab, Weihai Municipal Hospital. Weihai, Shandong, 264200, PR China
| | - Xiao-Yan Yuan
- Department of Central Lab, Weihai Municipal Hospital. Weihai, Shandong, 264200, PR China
| | - Hai-Yan Cong
- Department of Central Lab, Weihai Municipal Hospital. Weihai, Shandong, 264200, PR China
| | - Yuan Liu
- Marie College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Peng Liu
- Department of Central Lab, Weihai Municipal Hospital. Weihai, Shandong, 264200, PR China
| | - Ming-Yi Wang
- Department of Central Lab, Weihai Municipal Hospital. Weihai, Shandong, 264200, PR China
| | - Zong-Jun Du
- Marie College, Shandong University, Weihai, Shandong, 264209, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, PR China
- Weihai Research Insitute of Industrial Technology of Shandong University, Weihai, 264209, PR China
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Li E, Liu K, Yang S, Li L, Ran K, Sun X, Qu J, Zhao L, Xin Y, Zhu F, Ma J, Song F, Li Z. Analysis of the complete genome sequence of Paenibacillus sp. lzh-N1 reveals its antagonistic ability. BMC Genomics 2024; 25:276. [PMID: 38481158 PMCID: PMC10938842 DOI: 10.1186/s12864-024-10206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Plant diseases caused by pathogenic fungi are devastating. However, commonly used fungicides are harmful to the environment, and some are becoming ineffective due to fungal resistance. Therefore, eco-friendly biological methods to control pathogenic fungi are urgently needed. RESULTS In this study, a strain, Paenibacillus sp. lzh-N1, that could inhibit the growth of the pathogenic fungus Mycosphaerella sentina (Fr) Schrorter was isolated from the rhizosphere soil of pear trees, and the complete genome sequence of the strain was obtained, annotated, and analyzed to reveal the genetic foundation of its antagonistic ability. The entire genome of this strain contained a circular chromosome of 5,641,488 bp with a GC content of 45.50%. The results of species identification show that the strain belongs to the same species as P. polymyxa Sb3-1 and P. polymyxa CJX518. Sixteen secondary metabolic biosynthetic gene clusters were predicted by antiSMASH, including those of the antifungal peptides fusaricidin B and paenilarvins. In addition, biofilm formation-related genes containing two potential gene clusters for cyclic lactone autoinducer, a gene encoding S-ribosylhomocysteine lyase (LuxS), and three genes encoding exopolysaccharide biosynthesis protein were identified. CONCLUSIONS Antifungal peptides and glucanase biosynthesized by Paenibacillus sp. lzh-N1 may be responsible for its antagonistic effect. Moreover, quorum sensing systems may influence the biocontrol activity of this strain directly or indirectly.
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Affiliation(s)
- Ee Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Kaiquan Liu
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 250353, Jinan, P. R. China
| | - Shuhan Yang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Ling Li
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 250353, Jinan, P. R. China
| | - Kun Ran
- Shandong Institute of Pomology, 271000, Taian, P. R. China
| | - Xiaoli Sun
- Shandong Institute of Pomology, 271000, Taian, P. R. China
| | - Jie Qu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Li Zhao
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Yuxiu Xin
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Feng Zhu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Jingfang Ma
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Feng Song
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China.
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China.
| | - Zhenghua Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China.
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China.
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Huang HJ, Zhang X, Sun XW, Chen B, Li XT, Zhou N, Abdugheni R, Cheng QY, Zhang TJ, Liu Y, Jiang Y, Deng Y, Liu SJ, Jiang CY. Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales. Arch Microbiol 2024; 206:141. [PMID: 38441685 DOI: 10.1007/s00203-024-03909-5] [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: 09/08/2023] [Revised: 01/26/2024] [Accepted: 02/24/2024] [Indexed: 03/07/2024]
Abstract
A strictly anaerobic, motile bacterium, designated as strain Ai-910T, was isolated from the sludge of an anaerobic digestion tank in China. Cells were Gram-stain-negative rods. Optimal growth was observed at 38 °C (growth range 25-42 °C), pH 8.5 (growth range 5.5-10.5), and under a NaCl concentration of 0.06% (w/v) (range 0-2.0%). Major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The respiratory quinone was MK-7. Using xylose as the growth substrate, succinate was produced as the fermentation product. Phylogenetic analysis based on the 16 S rRNA gene sequences indicated that strain Ai-910T formed a distinct phylogenetic lineage that reflects a new genus in the family Marinilabiliaceae, sharing high similarities to Alkaliflexus imshenetskii Z-7010T (92.78%), Alkalitalea saponilacus SC/BZ-SP2T (92.51%), and Geofilum rubicundum JAM-BA0501T (92.36%). Genomic similarity (average nucleotide identity and digital DNA-DNA hybridization) values between strain Ai-910T and its phylogenetic neighbors were below 65.27 and 16.90%, respectively, indicating that strain Ai-910T represented a novel species. The average amino acid identity between strain Ai-910T and other related members of the family Marinilabiliaceae were below 69.41%, supporting that strain Ai-910T was a member of a new genus within the family Marinilabiliaceae. Phylogenetic, genomic, and phenotypic analysis revealed that strain Ai-910T was distinguished from other phylogenetic relatives within the family Marinilabiliaceae. The genome size was 3.10 Mbp, and the DNA G + C content of the isolate was 42.8 mol%. Collectively, differences of the phenotypic and phylogenetic features of strain Ai-910T from its close relatives suggest that strain Ai-910T represented a novel species in a new genus of the family Marinilabiliaceae, for which the name Xiashengella succiniciproducens gen. nov., sp. nov. was proposed. The type strain of Xiashengella succiniciproducens is Ai-910T (= CGMCC 1.17893T = KCTC 25,304T).
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Affiliation(s)
- Hao-Jie Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Xi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Biao Chen
- Xuzhou Medical University, Xuzhou, 221004, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rashidin Abdugheni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu-Yin Cheng
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Tie-Jun Zhang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yao Liu
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yong Jiang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Ye Deng
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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Zhang J, Liang Q, Mu D, Lian F, Gong Y, Ye M, Chen G, Ye Y, Du Z. Cultivating the uncultured: Harnessing the "sandwich agar plate" approach to isolate heme-dependent bacteria from marine sediment. MLIFE 2024; 3:143-155. [PMID: 38827516 PMCID: PMC11139205 DOI: 10.1002/mlf2.12093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/18/2023] [Accepted: 10/10/2023] [Indexed: 06/04/2024]
Abstract
In the classical microbial isolation technique, the isolation process inevitably destroys all microbial interactions and thus makes it difficult to culture the many microorganisms that rely on these interactions for survival. In this study, we designed a simple coculture technique named the "sandwich agar plate method," which maintains microbial interactions throughout the isolation and pure culture processes. The total yield of uncultured species in sandwich agar plates based on eight helper strains was almost 10-fold that of the control group. Many uncultured species displayed commensal lifestyles. Further study found that heme was the growth-promoting factor of some marine commensal bacteria. Subsequent genomic analysis revealed that heme auxotrophies were common in various biotopes and prevalent in many uncultured microbial taxa. Moreover, our study supported that the survival strategies of heme auxotrophy in different habitats varied considerably. These findings highlight that cocultivation based on the "sandwich agar plate method" could be developed and used to isolate more uncultured bacteria.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | | | - Da‐Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
- Shandong University‐Weihai Research Institute of Industrial TechnologyWeihaiChina
| | | | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Mengqi Ye
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Guan‐Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Yuqi Ye
- Marine CollegeShandong UniversityWeihaiChina
| | - Zong‐Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
- Shandong University‐Weihai Research Institute of Industrial TechnologyWeihaiChina
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Zhang MD, Zhou ZY, Kou YY, Lu DC, Du ZJ. Brumimicrobium oceani sp. nov., isolated from coastal sediment saline lake and environmental adaptability analysis. Antonie Van Leeuwenhoek 2023; 116:1375-1384. [PMID: 37843738 DOI: 10.1007/s10482-023-01892-3] [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: 03/20/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
A novel Gram-stain-negative, aerobic, non-motile, rod-shaped and orange-colored bacterium, designated as strain C305T, was isolated from marine sediment of the coast area of Weihai, China. Strain C305T growth occurs at 4-40 °C (optimally at 30-33 °C), pH 6.0-9.0 (optimally at pH 8.0) and with 0.5-10.0% (w/v) NaCl (optimum 1.5-3.0%). No growth is observed without NaCl. The major cellular fatty acids of strain C305T were identified as iso-C15:0, iso-C15:1G and iso-C17:0 3-OH. The major respiratory quinone was found to be MK-6, and the DNA G + C content was determined to be 35.5 mol%. The predominant polar lipids were mainly phosphatidylethanolamines (PE), unidentified aminophospholipids (APL), andunidentified lipid (L2). Phylogenetic analysis based on 16S rRNA gene sequences revealed that C305T was a member of the genus Brumimicrobium and had a 16S rRNA gene sequence similarity values of 96.9-98.0% with recognized Brumimicrobium species. On the basis of the phylogenetic and phenotypic evidences, strain C305T represents a novel species of the genus Brumimicrobium, for which the name Brumimicrobium oceani sp. nov. is proposed. The type strain is C305T (= KCTC 62371 T = MCCC 1H00297T).
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Affiliation(s)
- Meng-Di Zhang
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
- Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zi-Yang Zhou
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Yi-Yu Kou
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - De-Chen Lu
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, People's Republic of China.
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Zhang J, Lian FB, Gao YZ, Du ZJ, Wang MY. Marinicella marina sp. nov. and Marinicella gelatinilytica sp. nov., isolated from coastal sediment, and genome analysis and habitat distribution of the genus Marinicella. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917552 DOI: 10.1099/ijsem.0.006130] [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: 11/04/2023] Open
Abstract
Three Marinicella strains, X102, S1101T and S6413T, were isolated from sediment samples from different coasts of Weihai, PR China. All strains were Gram-stain-negative, rod-shaped and non-motile. The predominant fatty acids of all strains were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and the major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strains X102 and S1101T shared 100 % 16S rRNA gene sequence similarity, and strains S1101T/X102 and S6413T had 95.4 % similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains S1101T and X102 were 99.9 and 99.2 %, respectively. Strain S1101T had ANI values of 69.1-72.9% and dDDH values of 17.9-20.5 % to members of the genus Marinicella. Strain S6413T had ANI values of 69.1-77.5% and dDDH values of 17.6-21.5 % to members of the genus Marinicella. The results of phylogenetic and comparative genomic analysis showed that the three strains belong to two novel species in the genus Marinicella, and strains X102 and S1101T represented one novel species, and strain S6413T represented another novel species. The result of BOX-PCR and genomic analysis showed that X102 and S1101T were not the same strain. The phylogenetic analyses and genomic comparisons, combined with phylogenetic, phenotypic and chemotaxonomic features, strongly supported that the three strains should be classified as representing two novel species of the genus Marinicella, for which the names Marinicella marina sp. nov. and Marinicella gelatinilytica sp. nov. are proposed, respectively. The type strains of the two novel species are S1101T (=KCTC 92642T=MCCC 1H01359T) and S6413T (=KCTC 92641T=MCCC 1H01362T), respectively. In addition, all previously described isolates of Marinicella were isolated from marine environments, but our study showed that Marinicella is also distributed in non-/low-saline habitats (e.g. animal gut, soil and indoor surface), which broadened our perception of the environmental distribution of Marinicella.
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Affiliation(s)
- Jing Zhang
- Weihai Municipal Hospital, Weihai, 264209, PR China
- Marine College, Shandong University, Weihai, 264209, PR China
| | - Feng-Bai Lian
- Marine College, Shandong University, Weihai, 264209, PR China
| | - Yi-Zhou Gao
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandon University, Weihai, 264209, PR China
| | - Ming-Yi Wang
- Weihai Municipal Hospital, Weihai, 264209, PR China
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Zhang J, Gao YZ, Du ZJ, Wang MY. Tumebacillus lacus sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2023; 73. [PMID: 37930355 DOI: 10.1099/ijsem.0.006153] [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: 11/07/2023] Open
Abstract
A Gram-stain-positive, aerobic, rod-shaped, endospore-forming and motile, by means of peritrichous flagella, bacterium, designated DT12T, was isolated from a lake water sample from Datun Lake of Yunnan Province, PR China. The results of phylogenetic analysis based on 16S rRNA gene sequence and the concatenated alignment of 120 ubiquitous single-copy proteins indicated that the novel strain represented a member of the genus Tumebacillus. The sole quinone was menaquinone-7 and the cell-wall peptidoglycan was type-A1γ. The major fatty acids (>10 %) of the novel strain were iso-C15 : 0 and anteiso-C15 : 0, while the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The results of phylogenetic analyses combined with phylogenetic, phenotypic and chemotaxonomic features, strongly supported the hypothesis that the strain should be classified as representing a novel species of the genus Tumebacillus, for which the name Tumebacillus lacus sp. nov. is proposed. The type strain is DT12T (=KCTC 33958T= MCCC 1H00320T). The genomic analysis revealed that DT12T has various biosynthetic gene clusters for secondary metabolites, and members of the genus Tumebacillus may represent a promising source of new natural products. Our study also showed that members of the genus Tumebacillus are widely distributed in a variety of habitats throughout the globe, particularly in soils, human-, animal- and plant-associated environments. Members of the genus Tumebacillus may have an important role in the growth and health of humans, plants and animals.
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Affiliation(s)
- Jing Zhang
- Weihai Municipal Hospital, Weihai, 264209, PR China
- Marine College, Shandong University, Weihai, 264209, PR China
| | - Yi-Zhou Gao
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandon University, Weihai, 264209, PR China
| | - Ming-Yi Wang
- Weihai Municipal Hospital, Weihai, 264209, PR China
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Zhang MD, Yue YY, Sun YY, Du ZJ. Marinihelvus fidelis gen. nov., sp. nov., isolated from marine sediment, and genomic comparison with multiple genera. Int J Syst Evol Microbiol 2023; 73. [PMID: 37982360 DOI: 10.1099/ijsem.0.006165] [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: 11/21/2023] Open
Abstract
A Gram-stain-negative, rod-shaped, non-gliding, non-flagellated, yellow, facultatively aerobic bacterial strain, designated as W260T, was isolated from marine sediment of Xiaoshi Island, Weihai, PR China. The cells of W260T were 0.3-0.5 µm wide and 1.5-2.0 µm long. Strain W260T grows optimally at a temperature of 33 °C (range, 15-37 °C), pH 8 (range, pH 6.5-9.5) and witha NaCl concentration of 3.0 % (w/v; range, 1-8 %). It has the highest sequence similarity to Thiohalobacter thiocyanaticus DSM 21152T (91.7 %), followed by Wenzhouxiangella marina MCCC 1K00261T (91.4 %) and Thiohalospira alkaliphila DSM 17116T (90.7 %). The similarity between strain W260T and the species Thiohalophilus thiocyanatoxydans DSM 16326T was 89.4 %. Genome sequencing revealed a genome size of 3 430 000 bp and a DNA G+C content of 64.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain W260T and W. marina MCCC 1K00261T were 69.6 and 16.1-20.6 %, respectively. The predominant quinone was ubiquitin-8, and the major fatty acids were iso-C14 : 0 and iso-C16 : 0. The polar lipids consisted of phosphatidylethanolamine, phospholipid, phosphatidylglycerol, diphosphatidylglycerol and four unidentified lipids. Based on phenotypic, phylogenetic and chemotaxonomic information, it was determined that strain W260T represents a novel genus and species and it was given the name Marinihelvus fidelis sp. nov. The type strain is W260T (=MCCC 1H00471T=KCTC 92639T).
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Affiliation(s)
- Meng-Di Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yu-Yan Yue
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yang-Yang Sun
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, Shandong, 264209, PR China
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Zhou ZY, An J, Jia YW, Xuan XQ, Du ZJ. Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37942742 DOI: 10.1099/ijsem.0.006155] [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: 11/10/2023] Open
Abstract
Two novel rod-shaped, Gram-stain-negative, aerobic and non-motile bacterial strains, designated M39T and C2-7T, were isolated from the coastal sediment of Xiaoshi Island, Weihai, PR China. Growth of strain M39T occurred at 15-37 °C, at pH 6.0-9.0 and in the presence of 1.0-9.0 % (w/v) NaCl. Strain C2-7T grew at 15-40 °C, at pH 6.0-8.0 and in the presence of 0.5-8.0 % (w/v) NaCl. Phylogenetic analysis based 16S rRNA gene sequences revealed that strains M39T and C2-7T belong to the phylum Bacteroidota. Based on the results of 16S rRNA gene sequence analysis, the closest relative of strain M39T was Robiginitalea marina KCTC 92035T (95.4 %), and the closest relative of strain C2-7T was Algoriphagus namhaensis DPG-3T (97.0 %). The percentage of conserved protein and average nucleotide identity values between strain M39T and some species of the genus Robiginitalea were 66.9-77.6% and 69.3-71.0 %, respectively, while those between strain C2-7T and some species of the genus Algoriphagus were 68.0-70.1% and 56.1-72.6 %, respectively. The major cellular fatty acids (>10 %) of strain M39T consisted of iso-C15 : 1 F, iso-C15 : 0 and iso-C17 : 0 3-OH, while those of strain C2-7T were iso-C15 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. MK-6 was the only respiratory quinone that was compatible with the genus of strain M39T. The predominant menaquinone of strain C2-7T was MK-7. The major polar lipids of strain M39T were phosphatidylethanolamine and glycolipids, and those of strain C2-7T were phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. The DNA G+C contents of strains M39T and C2-7T were 46.9 and 40.8 mol%, respectively. Based upon the results presented in this study, strains M39T and C2-7T represent novel species of the genera Robiginitalea and Algoriphagus, respectively, for which the names Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov. are proposed with the type strains M39T (=MCCC 1H00498T=KCTC 92014T) and C2-7T (=MCCC 1H00414T=KCTC 92027T).
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Affiliation(s)
- Zi-Yang Zhou
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Jing An
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Ya-Wei Jia
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Xiao-Qi Xuan
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, PR China
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Liu L, Liu Y, Liu S, Nikandrova AA, Imamutdinova AN, Lukianov DA, Osterman IA, Sergiev PV, Zhang B, Zhang D, Li F, Sun C. Bioprospecting for the soil-derived actinobacteria and bioactive secondary metabolites on the Western Qinghai-Tibet Plateau. Front Microbiol 2023; 14:1247001. [PMID: 37886074 PMCID: PMC10599150 DOI: 10.3389/fmicb.2023.1247001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Introduction The increase in incidence of multidrug-resistant bacteria and the inadequacy of new antimicrobial drugs have led to a widespread outbreak of bacterial antimicrobial resistance. To discover new antibiotics, biodiversity, and novelty of culturable actinobacteria dwelled in soil of the Western Qinghai-Tibet Plateau were investigated. By integrating antibacterial assay with omics tools, Amycolatopsis sp. A133, a rare actinobacterial strain and its secondary metabolites were further studied. Method Culture-dependent method was used to obtain actinobacterial strains from two soil samples collected from Ali region in Qinghai-Tibet Plateau. The cultural extractions of representative strains were assayed against "ESKAPE" pathogens by paper-disk diffusion method and the double fluorescent protein reporter "pDualrep2" system. An Amycolatopsis strain coded as A133 was prioritized and its secondary metabolites were further analyzed and annotated by omics tools including antiSMASH and GNPS (Global Natural Social Molecular Networking). The predicted rifamycin analogs produced by Amycolatopsis sp. A133 were isolated and identified by chromatographic separation, such as Sephadex LH-20 and HPLC, and spectral analysis, such as NMR and UPLC-HRESI-MS/MS, respectively. Results A total of 406 actinobacteria strains affiliated to 36 genera in 17 families of 9 orders were isolated. Out of 152 representative strains, 63 isolates exhibited antagonistic activity against at least one of the tested pathogens. Among them, 7 positive strains were identified by the "pDualrep2" system as either an inhibitor of protein translation or DNA biosynthesis. The cultural broth of Amycolatopsis sp. A133 exhibited a broader antimicrobial activity and can induce expression of TurboRFP. The secondary metabolites produced by strain A133 was annotated as rifamycins and zampanolides by antiSMASH and GNPS analysis. Five members of rifamycins, including rifamycin W, protorifamycin I, rifamycin W-M1, proansamycin B, and rifamycin S, were purified and identified. Rifamycin W-M1, was found as a new member of the naturally occurring rifamycin group of antibiotics. Discussion Assisted by omics tools, the successful and highly efficient discovery of rifamycins, a group of clinically used antibiotics from actinobacteria in Ali area encouraged us to devote more energy to explore new antibiotics from the soils on the Western Tibetan Plateau.
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Affiliation(s)
- Lifang Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuyu Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shaowei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arina N. Imamutdinova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Benyin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Dejun Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Feina Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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Zhang DD, Yue YY, Zhang MD, Du ZJ. Halocynthiibacter halioticoli sp. nov., isolated from the viscera of abalone Haliotis discus hannai. Arch Microbiol 2023; 205:350. [PMID: 37805946 DOI: 10.1007/s00203-023-03686-7] [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: 02/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
A Gram-stain-negative, rod-shaped, glide, non-flagellated, and facultatively anaerobic bacterial strain, designated as Z654T, was isolated from the gut of abalone Haliotis discus hannai from Rongcheng, Shandong province, China. Cells are 0.2-0.8 μm in width and 0.7-3.4 μm in length. Cells grew best at 30 °C (range, 15-37 °C), pH 7.0 (range, 6.0-8.5) and NaCl concentration of 2.0% (w/v) (range, 1-10%). According to the phylogenetic analysis of 16S rRNA gene sequence, the strain belongs to the genus Halocynthiibacter and the closest strain is Halocynthiibacter arcticus KCTC 42129 T (97.12%). The genome size of strain Z654T was 3,296,250 bp and the DNA G + C content was 54.2 mol%. The average nucleotide identity (ANI) scores and digital DNA-DNA hybridization (dDDH) scores with H. arcticus KCTC 42129 T were 70% and 14.6-18.2%, respectively. The predominant quinone was Q-10 and the major fatty acids were C18:0, C18:1 ω7c 11-methyl and summed feature 8. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid and unidentifed lipids. Based on the phenotypic, phylogenetic and chemotaxonomic data, strain Z654T was considered to represent a novel species of the genus Halocynthiibacter, for which the name Halocynthiibacte halioticoli sp. nov., is proposed. The type strain is Z654T (= MCCC 1H00503T = KCTC 92003 T).
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Affiliation(s)
- Dan-Dan Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Yu-Yan Yue
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Meng-Di Zhang
- Joint Science College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, People's Republic of China.
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Yue YY, Ye YQ, Zhou ZY, Zhang MD, Jia YW, Du ZJ. Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750765 DOI: 10.1099/ijsem.0.006039] [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: 09/27/2023] Open
Abstract
Two novel Gram-stain-negative, facultative anaerobic, chemoheterotrophic, non-motile and rod-shaped strains were isolated from intertidal sediment sampled at Xiaoshi Island, Weihai, PR China. Full sequence analysis of the 16S rRNA genes showed that the two strains were closely related to members of the genus Winogradskyella and the phylogenetic similarities to their closest relative, Winogradskyella aquimaris, were 96.7 and 95.8 %, respectively. The DNA G+C contents of strains 2Y89T and D23T were 33.3 and 35.1 mol%, respectively. The respiratory quinone detected in both strains was MK-6. The major fatty acids detected in strain 2Y89T were iso-C15 : 0 and iso-C15 : 1G, and in strain D23T they were iso-C15 : 1G, iso-C15 : 0 and iso-C17 : 03-OH. The principal polar lipids of strain 2Y89T mainly included phosphatidylethanolamine, aminoglycolipids, unidentified aminolipids, unidentified glycolipids and unidentified lipids; strain D23T was the same as strain 2Y89T except that it did not contain aminoglycolipids. Based on the phenotypic, chemical taxonomic, genotypic and phylogenetic features established in this study, we suggest that the new strains represent two novel species of the genus Winogradskyella, for which the names Winogradskyella vincentii sp. nov. (type strain 2Y89T=MCCC 1H00477T=KCTC 92034T) and Winogradskyella alexanderae sp. nov. (type strain D23T=MCCC 1H00462T=KCTC 92023T) are proposed.
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Affiliation(s)
- Yu-Yan Yue
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yu-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zi-Yang Zhou
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Meng-Di Zhang
- Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya-Wei Jia
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, 264209, PR China
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Zheng R, Ping XY, Fang Q, Lu DC, Du ZJ, Gong Y. Aliiroseovarius subalbicans sp. nov. and Aliiroseovarius sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 36827196 DOI: 10.1099/ijsem.0.005738] [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: 02/25/2023] Open
Abstract
Two novel strains (N1Y82T and N1F302T) were isolated from a marine sediment sample taken from the coastal zone of Weihai, PR China. Cells of the two strains were Gram-strain-negative, catalase-positive, oxidase-positive, non-motile and ovoid- to rod-shaped. Strain N1Y82T grew optimally at 16 °C, pH 7.5 and in the presence of 3.0 % (w/v) NaCl. Strain N1F302T grew optimally at 28 °C, pH 7.0-7.5 and in the presence of 2.0-2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strains N1Y82T and N1F302T belonged to the genus Aliiroseovarius, and were mostly related to Aliiroseovarius sediminilitoris KCTC 23959T with sequence similarity of 96.5 and 97.1 %, respectively. For these two novel strains, C18 : 1 ω7c was the major fatty acid, ubiquinone 10 was the predominant respiratory quinone, and phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and one unidentified phospholipid were the major polar lipids. The DNA G+C contents of strain N1Y82T and N1F302T were 61.3 and 59.0 %, respectively. Consequently, strains N1Y82T and N1F302T are considered to represent two novel species of the genus Aliiroseovarius, for which the names Aliiroseovarius subalbicans sp. nov. and Aliiroseovarius sediminis sp. nov. are proposed. The type strains are N1Y82T (=KCTC 82768T=MCCC 1H00524T) and N1F302T (=KCTC 82412T=MCCC 1H00525T), respectively.
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Affiliation(s)
- Rui Zheng
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xiu-Ya Ping
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Qi Fang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - De-Chen Lu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Ya Gong
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
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Description and Genomic Characterization of Oceaniferula flavus sp. nov., a Novel Potential Polysaccharide-Degrading Candidate of the Difficult-to-Cultivate Phylum Verrucomicrobiota Isolated from Seaweed. Mar Drugs 2022; 21:md21010031. [PMID: 36662204 PMCID: PMC9865893 DOI: 10.3390/md21010031] [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: 11/21/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
A novel strain, isolate 5K15T, which belongs to difficult-to-cultivate phylum Verrucomicrobiota, was recovered from kelp collected from Li Island, Rongcheng, China. The genome sequence of the strain (genome size 3.95 Mbp) showed the presence of four putative biosynthetic gene clusters (BGCs), namely, two terpene biosynthetic gene clusters, one aryl polyene biosynthetic cluster, and one type III PKS cluster. Genomic analysis revealed 79 sulfatase-encoded genes, 24 sulfatase-like hydrolase/transferase-encoded genes, and 25 arylsulfatase-encoded genes, which indicated the great potential of 5K15T to degrade sulfated polysaccharides. Comparative analysis of 16S rRNA gene sequence showed that the novel strain was most closely related to Oceaniferula marina N1E253T (96.4%). On the basis of evidence from a polyphasic study, it is proposed that the strain 5K15T (= KCTC 82748T = MCCC 1H00442T = SDUM 810003T) be classified as Oceaniferula flavus sp. nov. The strain has the ability of carbohydrate transport and metabolism. This ability allows it to survive in carbohydrate-rich materials such as kelp. It has the potential to be used in the marine drug industry using seaweed.
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Correia Costa I, Amorim de Oliveira M, Wosnick N, Ann Hauser-Davis R, Siciliano S, Nunes JLS. Elasmobranch-associated microbiota: a scientometric literature review. PeerJ 2022; 10:e14255. [PMID: 36345481 PMCID: PMC9636872 DOI: 10.7717/peerj.14255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Elasmobranchs provide greatly relevant ecosystem services for the balance of the environments in which they are inserted. In recent decades, sharp population declines have been reported for many species in different regions worldwide, making this taxonomic group currently one of the most threatened with extinction. This scenario is almost entirely due to excessive fishing pressure, but any contributing factor that may cause additional mortality to populations must be mapped and monitored. In a fast-changing world, emerging marine pollution associated with climate change display the potential to increase the spread of infectious agents. These can, in turn, lead to mortality events, both directly and indirectly, by reducing immune responses and the physical and nutritional condition of affected individuals. In this context, the present study aimed to analyze data concerning elasmobranch-associated microbiota, identifying study trends and knowledge gaps in order to direct future studies on this topic of growing relevance for the health of wild populations, as well as individuals maintained in captivity, considering the zoonotic potential of these microorganisms.
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Affiliation(s)
- Ivana Correia Costa
- Laboratório de Organismos Aquáticos, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
| | - Mariene Amorim de Oliveira
- Laboratório de Genética e Biologia Molecular, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
| | - Natascha Wosnick
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Salvatore Siciliano
- Departamento de Ciências Biológicas, Escola Nacional de Saúde Pública/FIOCRUZ, Rio de Janeiro, Brazil
| | - Jorge Luiz Silva Nunes
- Laboratório de Organismos Aquáticos, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
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19
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Xue JH, Zhang BN, Zhang F, Liu YY, Wu WJ, Wu ZM, Si Y, Yang PX, Xing X, Zhao LH. Comparative genomic analysis of the genus Marinomonas and taxonomic study of Marinomonas algarum sp. nov., isolated from red algae Gelidium amansii. Arch Microbiol 2022; 204:586. [PMID: 36048288 DOI: 10.1007/s00203-022-03215-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 11/02/2022]
Abstract
Members of the genus Marinomonas are known for their environmental adaptation and metabolically versatility, with abundant proteins associated with antifreeze, osmotic pressure resistance, carbohydrase and multiple secondary metabolites. Comparative genomic analysis focusing on secondary metabolites and orthologue proteins was conducted with 30 reference genome sequences in the genus Marinomonas. In this study, a Gram-stain-negative, rod-shaped, non-flagellated and strictly aerobic bacterium, designated as strain E8T, was isolated from the red algae (Gelidium amansii) in the coastal of Weihai, China. Optimal growth of the strain E8T was observed at temperatures 25-30 °C, pH 6.5-8.0 and 1-3% (w/v) NaCl. The DNA G + C content was 42.8 mol%. The predominant isoprenoid quinone was Q-8 and the major fatty acids were C16:0, summed feature 3 and summed feature 8. The major polar lipids were phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data obtained from this polyphasic taxonomic study, strain E8T should be considered as a novel species of the genus Marinomonas, for which the name Marinomonas algarum is proposed. The type strain is E8T (= KCTC 92201T = MCCC 1K07070T).
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Affiliation(s)
- Jian-Heng Xue
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Bei-Ning Zhang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Feng Zhang
- Weihai Ecological and Environmental Monitoring Center (Weihai Motor Vehicle Emission Monitoring Center), Weihai, 264209, Shandong, People's Republic of China
| | - Ying-Ying Liu
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Wen-Jie Wu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zhao-Ming Wu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Yue Si
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Peng-Xi Yang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Xiang Xing
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
| | - Li-Hua Zhao
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
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20
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Jiang Y, Zheng C, Yu T, Li J, Ai J, Li M, Liu X, Deng Z. Rhodococcus yananensis sp. nov., a novel denitrification actinobacterium isolated from microbial fermentation bed material from a pig farm. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005426] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An opaque, pink-coloured, gram-positive, aerobic bacteria (designated as FBM22-1T), was isolated from microbial fermentation bed material from a pig farm in northwestern China. Optimal growth occurred at 30–37 °C, pH 7.0 and with 0.5 % NaCl (w/v). The strain had nitrification and denitrification functions. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate belonged to the genus
Rhodococcus
. Strain FBM22-1T was closely related to
Rhodococcus zopfii
NBRC 100606T and
Rhodococcus rhodochrous
NBRC 16069T, with 16S rRNA gene sequence similarities of 97.9 and 97.7 %, respectively. The predominant menaquinone in strain FBM22-1T was MK-8(H2). The cellular fatty acids consisted primarily of C16 : 1ω7c and/or C16 : 1 ω6c, C16 : 0 and 10-methyl C18 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and glycolipid. The G+C content of strain FBM22-1T was 68.64 mol%. Based on the phenotypic, phylogenetic and chemotaxonomic characterization results, in combination with low values of digital DNA–DNA hybridization between strain FBM22-1T and its closest neighbours, FBM22-1T represents a novel species of the genus
Rhodococcus
, for which the name Rhodococcus yananensis sp. nov. is proposed; the type strain is FBM22-1T (=KCTC 49502T=CCTCC AB2020275T).
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Affiliation(s)
- Yingying Jiang
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan’an University, Yan’an 716000, PR China
- Shaanxi Key Laboratory of Research and Utilization of Resource Plants on the Loess Plateau, Yan'an University, Yan’an 716000, PR China
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Chaochao Zheng
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Tianfei Yu
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Jing Li
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Jiamin Ai
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Maiping Li
- Animal Husbandry and Veterinary Service Center, Yan’an 716000, PR China
| | - Xiaodong Liu
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan’an University, Yan’an 716000, PR China
- Shaanxi Key Laboratory of Research and Utilization of Resource Plants on the Loess Plateau, Yan'an University, Yan’an 716000, PR China
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Zhenshan Deng
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan’an University, Yan’an 716000, PR China
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
- Shaanxi Key Laboratory of Research and Utilization of Resource Plants on the Loess Plateau, Yan'an University, Yan’an 716000, PR China
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21
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Rhodohalobacter sulfatireducens sp. nov., isolated from a marine solar saltern. Arch Microbiol 2022; 204:457. [PMID: 35789432 DOI: 10.1007/s00203-022-03078-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/02/2022]
Abstract
A novel Gram-stain-negative, oxidase-positive, catalase-positive, non-motile, facultatively anaerobic, rod-shaped bacterium, designated WB101T, was isolated from a marine solar saltern located in Wendeng, PR China. Strain WB101T shared a high level of 16S rRNA gene sequence similarity with Rhodohalobacter barkolensis 15182T (93.5%), R. halophilus JZ3C29T (93.2%), and 'R. mucosus' 8A47T (92.1%). Strain WB101T formed a species-level branch within the genus Rhodohalobacter in both phylogenetic and phylogenomic topologies. The DNA G + C content was 42.0%. Strain WB101T was found to have menaquinone-7 as the only respiratory quinone. The dominant cellular fatty acid (≥ 10%) was iso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylcholine. Characterisation based on phylogenetic, physiological, and biochemical properties indicated that strain WB101T represents a novel species of the genus Rhodohalobacter, and the name Rhodohalobacter sulfatireducens sp. nov. is proposed. The type strain is WB101T (= KCTC 92204T = MCCC 1H00518T).
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22
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Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov. J Microbiol 2022; 60:678-688. [DOI: 10.1007/s12275-022-1581-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 11/27/2022]
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23
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Wang S, Chen GJ, Du ZJ. Microvenator marinus gen. nov., sp. nov., isolated from marine sediment, and description of Microvenatoraceae fam. nov. and Lujinxingiaceae fam. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005380] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, oxidase-negative and catalase-positive predatory bacillus, designated strain V1718T, was isolated from Xiaoshi Island, PR China. Strain V1718T was found to be closely related to
Lujinxingia sediminis
SEH01T, with 89.8 % similarity in the 16S rRNA gene sequence, followed by
Bradymonas sediminis
FA350T with a similarity of 88.4 %. Strain V1718T had the ability to prey on other bacteria, and selective predation on members of
Algoriphagus
,
Nocardioides
and
Bacillus
occurred with the strain. Growth was observed within the range of 20–45 °C (optimal at 37 °C), pH 6.5–9.0 (optimal at pH 8.0) and 1–10 % NaCl (optimal at 3–4 %, w/v). The predominant cellular fatty acids in strain V1718T were iso-C15 : 0 (53.0 %) and C16 : 0 (19.1 %). The major polar lipids present in the strain were phosphatidylglycerol and phosphatidylethanolamine, and the respiratory quinone was menaquinone MK-7. The complete genome sequence of strain V1718T was 5 847 748 bp with a G+C content of 55.2 mol%. The topology of the phylogenomic tree indicated that strain V1718T forms a separate branch in the same clade with the genus
Lujinxingia
and the family
Bradymonadaceae
. The average nucleotide identity and average amino acid identity values were 66.4 and 48.6 %, respectively, with
Bradymonas sediminis
FA350T (type species of
Bradymonas
) and 66.8 % and 48.9 % with
Lujinxingia litoralis
B210T (type species of
Lujinxingia
). The genes related to biosynthesis pathways of several important chemical compounds could not be found in the genome of strain V1718T, which was predicted to be the intrinsic reason for predation in this group. The physiological, biochemical and phylogenetic properties of strain V1718T suggest that it belongs to a novel family distinct from other culturable bradymonabacteria. The name Microvenator marinus gen. nov., sp. nov. is proposed, with strain V1718T (=KCTC 72082T=MCCC 1H00380T) as type strain; the name Microvenatoraceae fam. nov. is also proposed. Meanwhile, the genus
Lujinxingia
can also be taxonomic classified as Lujinxingiaceae fam. nov. Thus, two novel families and a novel genus of the order
Bradymonadales
are proposed in this paper.
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Affiliation(s)
- Shuo Wang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
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24
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Psychroserpens luteolus sp. nov., isolated from Gelidium, reclassification of Ichthyenterobacterium magnum as Psychroserpens magnus comb. nov., Flavihalobacter algicola as Psychroserpens algicola comb. nov., Arcticiflavibacter luteus as Psychroserpens luteus comb. nov. Arch Microbiol 2022; 204:279. [DOI: 10.1007/s00203-022-02895-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 11/02/2022]
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25
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Zhao LH, Wang ZJ, Song C, Xing X, Liu YY, Shi LF, Yu TT, Zhang YM, Zhu Q, Du ZJ. Fulvivirga marina sp. nov. and Fulvivirga sediminis sp. nov., two novel Bacteroidetes isolated from the marine sediment. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005308] [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
Two novel, designated strains 29W222T and 2943T, were isolated from the marine sediment from Aoshan Bay, Jimo, PR China. Growth was observed at pH 6.0–8.5 (optimum, pH 7.5) for strain 29W222T, and pH 5.5–8.5 (pH 7.0) for strain 2943T. Both strains displayed growth in 0.5–6 % NaCl with an optimum at 1 % for 29W222T; 0.5 % for 2943T. Both strains grew optimally at 33 °C. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that 29W222T and 2943T represented members of the genus
Fulvivirga
and strain 29W222T was most closely related to
Fulvivirga kasyanovii
KMM 6220T (97.9 % sequence similarity) and
Fulvivirga imtechensis
AK7T (95.0 %), and 2943T to
Fulvivirga imtechensis
AK7T (95.7 %) and
Fulvivirga kasyanovii
KMM 6220T (94.8 %). The genomic DNA G+C contents of 29W222T and 2943T were 39.9 and 37.7 mol%, respectively. The results of chemotaxonomic analysis indicated that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acid was iso-C15 : 0 for both strains. Average nucleotide identity and average amino acid identity values between strain 29W222T and
Fulvivirga kasyanovii
KMM 6220T were 78.9 and 83.6 %, respectively; the corresponding values between 2943T and
Fulvivirga imtechensis
AK7T were 69.8 and 63.6 %, respectively. Therefore, strains 29W222T and 2943T represent to two novel species of the genus
Fulvivirga
, for which the names Fulvivirga marina sp. nov. (29W222T=KCTC 62848T=MCCC 1K05194T) and Fulvivirga sediminis sp. nov. (2943T=KCTC 62847T= MCCC 1K05144T) are proposed, respectively.
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Affiliation(s)
- Li-Hua Zhao
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jie Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Cui Song
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xiang Xing
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Ying-Ying Liu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Li-Fang Shi
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Tong-Tong Yu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - You-Ming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Qian Zhu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
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26
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Yang M, Xue Q, Zuo Z, Zhou J, Zhang S, Li M, Zhou H, Zhang M, Kumar S, Li W, Chen G, Zhao D, Xiang H. Aliidiomarina halalkaliphila sp. nov., a haloalkaliphilic bacterium isolated from a soda lake in Inner Mongolia Autonomous Region, China. Int J Syst Evol Microbiol 2022; 72. [PMID: 35244531 PMCID: PMC9558577 DOI: 10.1099/ijsem.0.005263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A haloalkaliphilic strain (IM 1326T) was isolated from brine sampled at a soda lake in the Inner Mongolia Autonomous Region, China. Cells of the strain were rod-shaped and motile. Strain IM 1326T was able to grow at 4–42 °C (optimum, 37 °C) with 0–13.0 % (w/v) NaCl concentrations (optimum at 4.0–6.0 %) and at pH 7.5–11.0 (optimum at 9.0–10.0). The 16S rRNA gene phylogenetic analysis revealed that the isolate belongs to the genus Aliidiomarina and is closely related to the type strains of Aliidiomarina sanyensis (95.8 % sequence similarity), Aliidiomarina shirensis (95.7 %), Aliidiomarina iranensis (95.4 %) and Aliidiomarina haloalkalitolerans (95.3 %). The whole genome of strain IM 1326T was sequenced, and the genomic DNA G+C content was 49.7 mol%. Average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the isolate and the related Aliidiomarina species were 68.1–84.9 %, 76–78 % and 18.4–20.4 %, respectively. The respiratory quinone was ubiquinone-8. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminophospholipid. The predominant cellular fatty acids were summed feature 9 (10-methyl-C16 : 0/iso-C17 : 1 ω9c, 22.2 %), iso-C15 : 0 (16.1 %) and iso-C17 : 0 (13.1 %). Based on the results of phylogenetic analysis, genome relatedness, and the physiological and chemotaxonomic properties of the isolate, strain IM 1326T is considered to represent a novel species of the genus Aliidiomarina, for which the name Aliidiomarina halalkaliphila sp. nov. is proposed (type strain IM 1326T=CGMCC 1.17056T=JCM 34227T).
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Affiliation(s)
- Ming Yang
- Sichuan Normal University, Sichuan 610101, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Qiong Xue
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Zhenqiang Zuo
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Shengjie Zhang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Manqi Zhang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Sumit Kumar
- Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Wei Li
- Sichuan Normal University, Sichuan 610101, PR China
| | - Guiying Chen
- Sichuan Normal University, Sichuan 610101, PR China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
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27
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Shang DD, Yang GJ, Chen GJ, Du ZJ. Psychrobacter halodurans sp. nov. and Psychrobacter coccoides sp. nov., two new slightly halophilic bacteria isolated from marine sediment. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005173] [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
In this study, two bacterial strains designated F2608T and F1192T, isolated from marine sediment sampled in Weihai, PR China, were characterized using a polyphasic approach. Strains were aerobic, Gram-stain-negative and motile. According to the results of phylogenetic analyses based on their 16S rRNA genes, these two strains should be classified under the genus
Psychrobacter
and they both show <98.5% sequence similarity to their closest relative,
Psychrobacter celer
JCM 12601T. Moreover, strain F2608T showed 97.5% sequence similarity to strain F1192T. Strain F2608T grew at 4–37 °C (optimum, 30–33 °C) and at pH 6.0–9.0 (optimum, pH 6.5–7.0) in the presence of 0–12% (w/v) NaCl (optimum, 4.0–5.0%). Strain F1192T grew at 4–37 °C (optimum, 30 °C) and at pH 5.5–9.0 (optimum, pH 7.0–7.5) in the presence of 0.5–12% (w/v) NaCl (optimum, 3.0–4.0%). The genomic DNA G+C contents of strain F2608T and strain F1192T were 47.4 and 44.9 %, respectively. Genomic characteristics including average nucleotide identity and digital DNA–DNA hybridization values clearly separated strain F2608T from strain F1192T. The sole isoprenoid quinone in these two strains was ubiquinone 8 and the major cellular fatty acids (>10.0%) were C18:1
ω9c and C17:1
ω8c. The major polar lipids of these two strains were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Based on the results of polyphasic analysis, the two strains represent two novel species of the genus
Psychrobacter
, for which the names Psychrobacter halodurans sp. nov. and Psychrobacter coccoides sp. nov. are proposed. The type strains are F2608T (=MCCC 1K05774T=KCTC 82766T) and F1192T (=MCCC 1K05775T=KCTC 82765T), respectively.
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Affiliation(s)
- Dan-Dan Shang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Gui-Jun Yang
- Shandong University-Australia National University Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Guan-Jun Chen
- State key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
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28
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Yu Q, Qi Y, Pu J. Rheinheimera lutimaris sp. nov., a marine bacterium isolated from coastal sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34882530 DOI: 10.1099/ijsem.0.005143] [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-negative, aerobic, rod-shaped bacterium, designated strain YQF-2T, was isolated from coastal sediment sampled in Jiangsu Province and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 28 °C (range 4-38 °C) and pH 7 (pH 6-10). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YQF-2T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera pacifica KMM 1406T (98.6%), followed by Rheinheimera aestuarii H29T (98.4%), Rheinheimera japonica KMM 9513T (98.3%), Rheinheimera aquimaris SW-353T (98.3%), Rheinheimera hassiensis E48T (97.8%) and Rheinheimera muenzenbergensis E49T (97.7%). The 16S rRNA gene sequence identities between strain YQF-2T and other members of the genus Rheinheimera were below 97.2%. The digital DNA-DNA hybridization value between strain YQF-2T and R. pacifica KMM 1406T was 23.3±2.3%. The average nucleotide identity value between strain YQF-2T and R. pacifica KMM 1406T was 79.7%. The unique respiratory quinone was ubiquinone-8. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The strain had summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, C12:0 3-OH and iso-C17:0 3-OH as major fatty acids. The G+C content of the genomic DNA was 50.0 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-2T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera lutimaris sp. nov. is proposed, with the type strain YQF-2T (=KCTC 72184T=MCCC 1K03663T).
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Affiliation(s)
- Qunfang Yu
- Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Yanxiang Qi
- Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Jinji Pu
- Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
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Winogradskyella marina sp. nov., isolated from marine sediment. Arch Microbiol 2021; 203:5381-5386. [PMID: 34392381 DOI: 10.1007/s00203-021-02517-x] [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] [Received: 06/12/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/29/2022]
Abstract
A Gram-stain-negative, rod-shaped (0.3-0.6 × 0.9-2.2 µm), facultatively aerobic, non-motile and yellow-coloured bacterium, designated strain F6397T, was isolated from a marine sediment in Weihai, PR China. Growth of strain F6397T occurred at 4-37 °C (optimum, 30-33 °C), pH 6.0-9.0 (optimum, 7.5) and in the presence of 1-12% (optimum, 3.0%) (w/v) NaCl. Strain F6397T showed oxidase- and catalase-positive activities. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain was assigned to the genus Winogradskyella. Strain F6397T exhibited 95.5-98.1% sequence similarities to recognized species of the genus Winogradskyella. The average nucleotide identity (ANI) scores with Winogradskyella ludwigii HL116T, Winogradskyella litoriviva KMM 6491 T and Winogradskyella thalassocola KMM 3907 T were 80.1, 78.9 and 82.6%, respectively. The digital DNA-DNA hybridization (dDDH) scores were 23.5, 22.9 and 25.7%, respectively. The genomic DNA G + C content was 33.5 mol%. Strain F6397T contained iso-C15:0, iso-C15:1G, iso-C15:0 3-OH and iso-C17:0 3-OH as the predominant fatty acid and MK-6 as the predominant menaquinone. The polar lipid profiles contained phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. On the basis of the evidence presented in this study, strain F6397T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella marina sp. nov. is proposed. The type strain is F6397T (= KCTC 82422 T = MCCC 1H00438T).
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Oceaniferula marina gen.nov., sp.nov., an anti-fluoroquinolone bacterium isolated from marine sediment. Antonie van Leeuwenhoek 2021; 114:1855-1865. [PMID: 34468960 DOI: 10.1007/s10482-021-01645-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
A Gram-stain-negative, aerobic, rod-shaped, non-gliding and non-motile bacterium designated as N1E253T, was isolated from marine sediments collected from the coast of Weihai, PR China. N1E253T was found to grow at pH 7.0-9.0 (optimum, pH 7.5), 15-37 °C (optimum, 30 °C) in the presence of 1.5-5.0% (w/v) NaCl (optimum, 3.0%). The major polar lipids of strain N1E253T were phosphatidylethanolamine, diphosphatidylglycerol and one unidentified phospholipid. The sole respiratory quinone was MK-9. The major cellular fatty acids (> 10.0%) were iso-C14: 0, C16: 0 and Summed Feature 3 (C16:1 ω7c and/or C16:1 ω6c). The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this novel isolate to the family Verrucomicrobiaceae, with Persicirhabdus sediminis KCTC 22039 T being its closest relative with 92.1% sequence similarity. Genome sequencing revealed a genome size of 5,073,947 bp, DNA G + C content of 52.0% and two protein-coding genes related to the resistance of fluoroquinolones. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain N1E253T represents a novel species of a novel genus within the family Verrucomicrobiaceae, for which the name Oceaniferula marina gen. nov., sp. nov. is proposed. The type strain is N1E253T (= KCTC 72800 T = MCCC 1H00405T).
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Wang S, Mu DS, Li GY, Du ZJ. Description of Lujinxingia vulgaris sp. nov., isolated from coastal sediment via prey-traps. Antonie van Leeuwenhoek 2021; 114:1805-1818. [PMID: 34426860 DOI: 10.1007/s10482-021-01640-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/06/2021] [Indexed: 11/29/2022]
Abstract
Two Gram-stain negative, facultative anaerobic, oxidase-negative, catalase-positive bacilli, designated as strains TMQ4T and TMQ2, were isolated from Xiaoshi Island, China, using prey-traps. Growth was observed within the ranges 25-45 °C (optimally at 37 °C), pH 6.5-9.0 (optimally at pH 7.5-8.0) and 1-8% NaCl (optimally at 3-4%, w/v). The draft genome sequences of strains TMQ4T and TMQ2 contained 184 contigs of 5,609,735 bp with a G+C content of 64.4% and 148 contigs of 5,589,985 bp with a G+C content of 65.0%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Lujinxingia with the similarity of 98.9%. The phylogenetic and phylogenomic topologies and analyses demonstrated that both strains clustered together and differentiated from the closest neighbour, Lujinxingia sediminis SEH01T. Genomic analyses showed that two strains lost the biosynthesis pathway of several chemical compounds. Iso-C15:0 was contained in the predominant cellular fatty acids in both strains. The major polar lipids of both strains consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified lipids; and the respiratory quinone was menaquinone MK-7 for both strains. Both strains predated other bacteria, including Owenweeksia hongkongensis JCM 12287T and Paraliobacillus ryukyuensis DSM 15140T, and were lured with one prey Acinetobacter baumannii ATCC 19606T in prey-trap. Combining genomic analyses, two strains had the predatory indices of 2, similar to representative typical bacterial predators. The physiological, biochemical, and phylogenetic properties suggest that the two strains represent a novel species within the genus Lujinxingia. The name Lujinxingia vulgaris sp. nov. is proposed, with strain TMQ4T (= KCTC 62851T = MCCC 1H00392T) as type strain and strain TMQ2 (= KCTC 72,079 = MCCC 1H00381) as reference strain.
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Affiliation(s)
- Shuo Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Guang-Yu Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
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Sun XK, Zhang YN, Jia YY, Zhong YL, Chen GJ, Du ZJ. Palleronia sediminis sp. nov. and Flavivirga algicola sp. nov., two marine bacteria isolated from offshore areas near Weihai. Int J Syst Evol Microbiol 2021; 71. [PMID: 34370661 DOI: 10.1099/ijsem.0.004949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Two bacterial strains, designated SS33T and Y03T, were isolated from marine sediment and marine red alga collected on the coast of Weihai, PR China. Based on the results of 16S rRNA gene sequence analysis, strain SS33T was found to be closely related to Primorskyibacter marinus PX7T, Pelagivirga dicentrarchi YLY04T, Palleronia marisminoris DSM 26347T and Maribius pontilimi GH1-23T with 94.8, 94.6, 94.5 and 94.5 % sequence similarity; strain Y03T was found to be closest to Flavivirga aquimarina EC2D5T, Flavivirga eckloniae ECD14T and Flavivirga amylovorans JC2681T with 96.4, 96.1 and 96.0 % sequence similarity. Strain SS33T grew at 4-37 °C (optimum, 33 °C), at pH 6.0-9.5 (optimum, pH 7.5-8.0) and in the presence of 0-10 % (w/v) NaCl (optimum, 3.0 %). Chemotaxonomic analysis of strain SS33T showed that the predominant respiratory quinone was ubiquinone-10. The major fatty acids (>10.0 %) included C18 : 1 ω7c and C16 : 0. The major polar lipids included phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, one unidentified glycolipid, one unidentified polar lipid and two unidentified aminolipids. Strain Y03T grew at 15-40 °C (optimum, 28 °C), at pH 6.5-8.0 (optimum, pH 7.0) and in the presence of 0.5-9.0 % (w/v) NaCl (optimum, 2.0%). Chemotaxonomic analysis showed that the predominant respiratory quinone was menaquinone-6. The major fatty acids (>10.0 %) included iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids included phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and four unidentified polar lipids. Based on the polyphasic data, strain SS33T is considered to represent a novel species of the genus Palleronia, for which the name Palleronia sediminis sp. nov. is proposed, with the type strain SS33T (=KCTC 62986T=MCCC 1H00387T). Strain Y03T is considered to represent a novel species of the genus Flavivirga, for which the name Flavivirga algicola sp. nov. is proposed, with the type strain Y03T (=KCTC 72001T=MCCC 1H00386T).
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Affiliation(s)
- Xun-Ke Sun
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya-Ning Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yu-Yao Jia
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yan-Lin Zhong
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
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Jiang S, Lian FB, Sun YY, Zhang XK, Du ZJ. Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34398727 DOI: 10.1099/ijsem.0.004959] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3-0.4 µm wide, 2.0-2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4-40 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.5-8.0) and at NaCl concentrations of 1.0-10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c; 60.7 %), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9-95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2-80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae. Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner-Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae, for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).
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Affiliation(s)
- Shan Jiang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Feng-Bai Lian
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - You-Yang Sun
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xiao-Kui Zhang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong 264209, PR China.,State key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
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Gao C, Lun HY, Shang DD, Cai M, Ye MQ, Du ZJ. Gelidibacter maritimus sp. nov., isolated from marine sediment. Arch Microbiol 2021; 203:5117-5122. [PMID: 34309686 DOI: 10.1007/s00203-021-02478-1] [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: 03/24/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 10/20/2022]
Abstract
A Gram-stain-negative, yellow, strictly aerobic, non-flagellated, gliding, rod-shaped bacterial strain, was isolated from costal sediment, designated as F6074T. The strain F6074T grows optimally at 30 °C, pH 7.5, and 3.0% (w/v) NaCl. Cells of strain F6074T are 0.2-0.5 µm wide and 1.0-2.0 µm long. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain F6074T belonged to the genus Gelidibacter, with the highest sequence similarity to Gelidibacter japonicus JCM 31967T (98.0%), followed by G. flavus JCM 31135T (97.7%), and similarity between strain F6074T and the type species G. algens DSM 12408T was 96.0%. Genome sequencing results revealed a genome size of 47,07,621 bp. The DNA G + C content was 37.8 mol%. The ANI and dDDH values between strain F6074T and G. japonicus JCM 31967T were 83.9 and 27.8%, the values between strain F6074T and G. algens DSM 12408T were 77.5% and 31.5%, and the values between strain F6074T and G. flavus JCM 31135T were 84.3 and 27.9%, respectively. The predominant quinone was MK-6 and the major fatty acids were iso-C15:0, iso-C15:1G, iso-C17:0 3-OH, anteiso-C15:0 and summed feature 3. The polar lipids were consisted of phosphatidylethanolamine (PE), two unidentified aminolipids (AL) and three unidentified lipids (L1, L2, L3). Based on the phenotypic, phylogenetic and chemotaxonomic data, strain F6074T was considered to represent a novel species of the genus Gelidibacter, for which the name Gelidibacter maritimus sp. nov., is proposed. The type strain is F6074T (MCCC 1H00427T = KCTC 72942T).
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Affiliation(s)
- Cheng Gao
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - He-Yuan Lun
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Min Cai
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Meng-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China. .,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, People's Republic of China.
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China. .,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, People's Republic of China.
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Wang CN, Wang FQ, Liu Y, Wang MY, Du ZJ. Ostreibacterium oceani gen. nov., sp. nov., isolated from oyster, and description of Ostreibacteriaceae fam. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34228610 DOI: 10.1099/ijsem.0.004855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, short rod-shaped, facultatively anaerobic, non-motile, non-gliding, oxidase-positive and catalase-negative bacterium, designated ML27T, was isolated from oyster homogenate in Rushan, Weihai, PR China. Growth occurred at 20-33 °C (optimum, 30 °C), at pH 7.0-9.0 (optimum, pH 7.5-8.0) and in the presence of 1-6 % (w/v) NaCl (optimum, 3 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ML27T was 90.7 % similar to Suttonella ornithocola DSM 18249T, 89.2 % to Suttonella indologenes JCM 1478T and 88.2 % to Cardiobacterium hominis DSM 8339T; similarities to other species were less than 90 %. The average amino acid identity between strain ML27T, S. indologenes JCM 1478T, S. ornithocola DSM 18249T, C. hominis DSM 8339T and Dichelobacter nodosus ATCC 25549T were 46.23, 45.86, 45.54 and 45.84 %, respectively. Phylogenomic tree and phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate formed a novel family-level clade in the order Cardiobacteriales. The sole respiratory quinone was ubiquinone-7 (Q-7). The dominant cellular fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 46.3 %), C16 : 0 (17.8 %) and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 13.5 %). The DNA G+C content of strain ML27T was 45.6 mol%. Polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unidentified lipid. Comparative analyses of 16S rRNA gene sequences, genomic distinctiveness and characterization indicated that strain ML27T represents a novel species of a new genus within a novel family of the order Cardiobacteriales, for which the name Ostreibacterium oceani gen. nov., sp. nov. is proposed. The type strain of Ostreibacterium oceani is ML27T (=MCCC 1H00372T=KCTC 72155T). In addition, a novel family, Ostreibacteriaceae fam. nov., is proposed to accommodate the genus Ostreibacterium.
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Affiliation(s)
- Chao-Nan Wang
- Marine College, Shandong University, Weihai 264209, PR China
| | - Feng-Qing Wang
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, PR China
| | - Yuan Liu
- Marine College, Shandong University, Weihai 264209, PR China
| | - Ming-Yi Wang
- Department of Central Lab, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai 264200, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, PR China
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Zhu KL, Wang XQ, Zhang TS, Shang DD, Du ZJ. Salibaculum halophilum gen. nov., sp. nov. and Salibaculum griseiflavum sp. nov., in the family Rhodobacteraceae. Int J Syst Evol Microbiol 2021; 71. [PMID: 34170216 DOI: 10.1099/ijsem.0.004808] [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
Two Gram-stain-negative, moderately halophilic, non-motile, rod-shaped, pale yellow, and aerobic strains, designated WDS1C4T and WDS4C29T, were isolated from a marine solar saltern in Weihai, Shandong Province, PR China. Growth of strain WDS1C4T occurred at 10-45 °C (optimum, 37 °C), with 4-16 % (w/v) NaCl (optimum, 8 %) and at pH 6.5-9.0 (optimum, pH 7.5). Growth of strain WDS4C29T occurred at 10-45 °C (optimum, 40 °C), with 2-18 % (w/v) NaCl (optimum, 6 %) and at pH 6.5-9.0 (optimum, pH 7.5). Q-10 was the sole respiratory quinone of the two strains. The major polar lipids of strains WDS1C4T and WDS4C29T were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major cellular fatty acid in strains WDS1C4T and WDS4C29T was C18 : 1 ω7c, and the genomic DNA G+C contents of strains WDS1C4T and WDS4C29T were 67.6 and 63.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains WDS1C4T and WDS4C29T were members of the family Rhodobacteraceae and showed 94.3 and 95.3 % similarities to their closest relative, Celeribacter indicus, respectively. The similarity between WDS1C4T and WDS4C29T was 97.3 %. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing two novel species in a new genus for which the names Salibaculum halophilum gen. nov., sp. nov. (type species, type strain WDS1C4T=MCCC 1H00179T=KCTC 52542T) and Salibaculum griseiflavum sp. nov. (WDS4C29T=MCCC 1H00175T=KCTC 52541T) are proposed.
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Affiliation(s)
- Ke-Lei Zhu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xiao-Qun Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Tian-Shu Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
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Bo JS, Wang S, Song XZ, Du ZJ. Pontibaca salina sp. nov., isolated from marine sediment. Arch Microbiol 2021; 203:4493-4498. [PMID: 34148113 DOI: 10.1007/s00203-021-02434-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
A Gram-stain-negative, oval or short rod-shaped, non-motile, aerobic bacterium, designated strain S1109LT, was isolated from a marine sediment in Weihai, PR China. Cells were oxidase positive and catalase positive. Growth of strain S1109LT occurred at 10-40 °C (optimum, 30-33 °C), pH 6.5-10.0 (optimum, 7.0-8.0) and in the presence of 1-21% (optimum, 4-6%) (w/v) NaCl. 16S rRNA gene sequence phylogeny indicated that strain S1109LT was associated with the genus Pontibaca of the family Rhodobacteraceae because it showed the highest sequence similarity to Pontibaca methylaminivorans KCTC 22497T (97.5%). The average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) scores between strain S1109LT and Pontibaca methylaminivorans KCTC 22497T were 74.6% and 18.7%. The major cellular fatty acids of strain S1109LT were C19:0 cyclo ω8c and C18:1 ω7c. The polar lipids profiles of strain S1109LT were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and two unidentified lipids. Strain S1109LT contained ubiquinone-10 as the major respiratory quinone. The genomic DNA G + C content was 55.9 mol%. On the basis of the evidence presented in this study, strain S1109LT is considered to represent a novel species of the genus Pontibaca, for which the name Pontibaca salina sp. nov. is proposed. The type strain of is S1109LT (= KCTC 82411T = MCCC 1H00441T).
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Affiliation(s)
- Jin-Shuang Bo
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.,Department of Blood Transfusion, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, 264200, Shandong, People's Republic of China
| | - Shuai Wang
- Department of Clinical Laboratory, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, 264200, Shandong, People's Republic of China
| | - Xue-Zhen Song
- Department of Blood Transfusion, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, 264200, Shandong, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
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Jiang S, Sun YY, Lian FB, Zhang XK, Du ZJ. Stappia albiluteola sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34003740 DOI: 10.1099/ijsem.0.004807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain negative, rod-shaped, facultatively aerobic, pale-beige-coloured bacterial strain, designated F7233T, was isolated from coastal sediment sampled at Jingzi Bay, Weihai, PR China. Cells of strain F7233T were 0.3-0.4 µm wide, 1.2-1.4 µm wide long, non-spore-forming and motile with one flagellum. Optimum growth occurred at 30 °C, with 1.0 % (w/v) NaCl and at pH 6.5-7.0. Positive for nitrate reduction, hydrolysis of Tweens and oxidase activity. The sole respiratory quinone of strain F7233T was ubiquinone-10 and the predominant cellular fatty acid was summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified aminophospholipid. The G+C content of the chromosomal DNA was 63.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the newly isolate belonged to the genus Stappia, with 96.8 % sequence similarity to Stappia indica MCCC 1A01226T, 96.1 % similarity to Stappia stellulata JCM 20692T and 95.5% similarity to Stappia taiwanensis CC-SPIO-10-1T. On the basis of phylogenetic, phenotypic and chemotaxonomic data, it is considered that strain F7233T should represent a novel species within the genus Stappia, for which the name Stappia albiluteola sp. nov. is proposed. The type strain is F7233T (=MCCC 1H00419T=KCTC 72859T).
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Affiliation(s)
- Shan Jiang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - You-Yang Sun
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Feng-Bai Lian
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xiao-Kui Zhang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.,Marine College, Shandong University, Weihai, Shandong 264209, PR China
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Liu R, Lai Q, Gu L, Yan P, Shao Z. Croceimicrobium hydrocarbonivorans gen. nov., sp. nov., a novel marine bacterium isolated from a bacterial consortium that degrades polyethylene terephthalate. Int J Syst Evol Microbiol 2021; 71. [PMID: 33847553 DOI: 10.1099/ijsem.0.004770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1-8 %, at pH 6.5-8 and at temperatures of 10-40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae, and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA-DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).
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Affiliation(s)
- Renju Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,School of Environmental Science, Harbin Institute of Technology, Harbin, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Li Gu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Peisheng Yan
- School of Environmental Science, Harbin Institute of Technology, Harbin, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,School of Environmental Science, Harbin Institute of Technology, Harbin, PR China
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Moheibacter lacus sp. nov., Isolated from Freshwater Lake Sediment. Curr Microbiol 2021; 78:2160-2164. [PMID: 33813642 DOI: 10.1007/s00284-021-02465-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/15/2021] [Indexed: 10/21/2022]
Abstract
A Gram-stain-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-motile bacterium, designated BDHS18T, was isolated from the sediment of the Hasuhai Lake, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this strain belongs to the genus Moheibacter in the family Flavobacteriaceae and its closest relative was Moheibacter sediminis JCM 19634T (96.0%), followed by Moheibacter stercoris DSM 29388T (95.3%). Cells of strain BDHS18T were catalase-positive and oxidase-negative. Strain BDHS18T was found to grow optimally at 28-33 ℃, pH 7.5-8.0, and in the presence of approximately 1.0% (w/v) NaCl. Major cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, Summed feature 4 and Summed feature 9. The predominant respiratory quinone was MK-6. The predominant polar lipids in strain BDHS18T were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G + C content was 36.9 mol%. According to the phylogenetic analysis, physiological and phenotypic characteristics, strain BDHS18T represents a novel species of the genus Moheibacter, for which the name Moheibacter lacus sp. nov. is proposed. The type strain is BDHS18T (= KCTC 72160T = MCCC 1H00369T).
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Liu S, Wang T, Lu Q, Li F, Wu G, Jiang Z, Habden X, Liu L, Zhang X, Lukianov DA, Osterman IA, Sergiev PV, Dontsova OA, Sun C. Bioprospecting of Soil-Derived Actinobacteria Along the Alar-Hotan Desert Highway in the Taklamakan Desert. Front Microbiol 2021; 12:604999. [PMID: 33790875 PMCID: PMC8005632 DOI: 10.3389/fmicb.2021.604999] [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: 09/11/2020] [Accepted: 02/22/2021] [Indexed: 02/04/2023] Open
Abstract
Taklamakan desert is known as the largest dunefield in China and as the second largest shifting sand desert in the world. Although with long history and glorious culture, the Taklamakan desert remains largely unexplored and numerous microorganisms have not been harvested in culture or taxonomically identified yet. The main objective of this study is to explore the diversity, novelty, and pharmacological potential of the cultivable actinomycetes from soil samples at various sites along the Alar-Hotan desert highway in the Taklamakan desert. A total of 590 actinobacterial strains were recovered by the culture-dependent approach. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences unveiled a significant level of actinobacterial diversity with 55 genera distributed in 27 families of 12 orders. Thirty-six strains showed relatively low 16S rRNA similarities (<98.65%) with validly described species, among which four strains had already been characterized as novel taxa by our previous research. One hundred and forty-six actinobacterial isolates were selected as representatives to evaluate the antibacterial activities and mechanism of action by the paper-disk diffusion method and a double fluorescent protein reporter "pDualrep2" system, respectively. A total of 61 isolates exhibited antagonistic activity against the tested "ESKAPE" pathogens, among which seven strains could produce bioactive metabolites either to be able to block translation machinery or to induce SOS-response in the pDualrep2 system. Notably, Saccharothrix sp. 16Sb2-4, harboring a promising antibacterial potential with the mechanism of interfering with protein translation, was analyzed in detail to gain deeper insights into its bioactive metabolites. Through ultra-performance liquid chromatography (UPLC)-quadrupole time-of-flight (QToF)-MS/MS based molecular networking analysis and databases identification, four families of compounds (1-16) were putatively identified. Subsequent bioassay-guided separation resulted in purification of four 16-membered macrolide antibiotics, aldgamycin H (8), aldgamycin K (9), aldgamycin G (10), and swalpamycin B (11), and their structures were elucidated by HR-electrospray ionization source (ESI)-MS and NMR spectroscopy. All compounds 8-11 displayed antibacterial activities by inhibiting protein synthesis in the pDualrep2 system. In conclusion, this work demonstrates that Taklamakan desert is a potentially unique reservoir of versatile actinobacteria, which can be a promising source for discovery of novel species and diverse bioactive compounds.
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Affiliation(s)
- Shaowei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ting Wang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qinpei Lu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feina Li
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Gang Wu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhongke Jiang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xugela Habden
- College of Life Science, Xinjiang Normal University, Urumchi, China
| | - Lin Liu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaolin Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Dmitry A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga A. Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Li YX, Wang NN, Zhou YX, Lin CG, Wu JS, Chen XQ, Chen GJ, Du ZJ. Planococcus maritimus ML1206 Isolated from Wild Oysters Enhances the Survival of Caenorhabditis elegans against Vibrio anguillarum. Mar Drugs 2021; 19:md19030150. [PMID: 33809116 PMCID: PMC7999227 DOI: 10.3390/md19030150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
With the widespread occurrence of aquaculture diseases and the broad application of antibiotics, drug-resistant pathogens have increasingly affected aquatic animals’ health. Marine probiotics, which live under high pressure in a saltwater environment, show high potential as a substitute for antibiotics in the field of aquatic disease control. In this study, twenty strains of non-hemolytic bacteria were isolated from the intestine of wild oysters and perch, and a model of Caenorhabditis elegans infected by Vibrio anguillarum was established. Based on the model, ML1206, which showed a 99% similarity of 16S rRNA sequence to Planococcus maritimus, was selected as a potential marine probiotic, with strong antibacterial capabilities and great acid and bile salt tolerance, to protect Caenorhabditis elegans from being damaged by Vibrio anguillarum. Combined with plate counting and transmission electron microscopy, it was found that strain ML1206 could significantly inhibit Vibrio anguillarum colonization in the intestinal tract of Caenorhabditis elegans. Acute oral toxicity tests in mice showed that ML1206 was safe and non-toxic. The real-time qPCR results showed a higher expression level of genes related to the antibacterial peptide (ilys-3) and detoxification (ugt-22, cyp-35A3, and cyp-14A3) in the group of Caenorhabditis elegans protected by ML1206 compared to the control group. It is speculated that ML1206, as a potential probiotic, may inhibit the infection caused by Vibrio anguillarum through stimulating Caenorhabditis elegans to secrete antibacterial effectors and detoxification proteins. This paper provides a new direction for screening marine probiotics and an experimental basis to support the potential application of ML1206 as a marine probiotic in aquaculture.
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Affiliation(s)
- Ying-Xiu Li
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Nan-Nan Wang
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Yan-Xia Zhou
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Chun-Guo Lin
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Jing-Shan Wu
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Xin-Qi Chen
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
- Correspondence: (G.J.C.); (Z.-J.D.)
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
- Correspondence: (G.J.C.); (Z.-J.D.)
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Sulfitobacter algicola sp. nov., isolated from green algae. Arch Microbiol 2021; 203:2351-2356. [PMID: 33655407 DOI: 10.1007/s00203-021-02213-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/23/2020] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
A novel Gram-stain-negative, aerobic, non-flagellated, non-motile, oval-rod-shaped and light pink to light tawny-pigmented bacterial strain (designated 1151T) were isolated from marine green algae obtained from the coastal seawater of Weihai, China. Strain 1151T was found to grow at 15-37 °C (optimum, 33 °C), pH 7.0-9.5 (optimum, 7.5-8.5) and in the presence of 1-6% (w/v) NaCl (optimum, 3%). Cells were oxidase-positive and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 1151T was a member of the genus Sulfitobacter and exhibited the hightest sequence similarity to Sulfitobacter indolifex DSM 14862T (96.6%), followed by the sequence similarity to Sulfitobacter aestuarii hydD52T (96.5%) and Sulfitobacter profundi SAORIC-263T (96.5%). The average nucleotide identity and digital DDH values between strain 1151T and Sulfitobacter indolifex DSM 14862T were 69.9% and 20.9%, respectively. The average amino acid identity between strain 1151T and Sulfitobacter pontiacus DSM 10014T (type strain of the type species) was 62.3%. Q-10 was detected as the sole respiratory quinone. The dominant cellular fatty acids were sum feature 8 (C18: 1ω7c; 44.1%), C20: 1ω7c (29.7%) and C18: 0 (11.7%). The DNA G + C content of strain 1151T was 51.8 mol%. The polar lipids included phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), and three unidentified lipids (L1, L2 and L3). Based on the phylogenetic and phenotypic characteristics, strain 1151T is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter algicola sp. nov. is proposed. The type strain is 1151T (= KCTC 72513T = MCCC 1H00384T).
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Liu YL, Meng D, Wang F, Gong XF, Gu PF, Fan XY, Du ZJ, Zou JD, Li Q. Propylenella binzhouense gen. nov., sp. nov. isolated from activated sludge, and proposal of Propylenellaceae fam. nov. Antonie van Leeuwenhoek 2021; 114:225-233. [PMID: 33400070 DOI: 10.1007/s10482-020-01514-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 12/22/2020] [Indexed: 11/26/2022]
Abstract
A Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped, and aerobic bacterial strain (designated L72T) was isolated from propylene oxide saponification wastewater activated sludge obtained from a wastewater treatment facility in Binzhou (Shandong Province, PR China). Strain L72T grew between 25 and 40 °C (optimum growth at 30 °C). The pH range for growth was between 6.0 and 8.0 (optimum growth at pH 7.0). The range of NaCl concentrations for the growth of strain L72T was 0-3.0 % (w/v), with optimum growth at 1.0-2.0 % (w/v). The major cellular fatty acids of strain L72T were C19:0cyclo ω8c, C18:1ω7c, iso-C15:0, and anteiso-C15:0. Strain L72T contained Q-10 as the predominant respiratory quinone. The polar lipid profile was composed of Phosphatidylcholine, Glycolipid, Aminophospholipid, Phosphatidylethanolamine, Phosphatidylserine, Phosphatidyldimethylethanolamine, one unknown lipid (L) and two unidentified Phospholipids (PL). Genome sequencing revealed a genome size of 4,703,686 bp and a G + C content of 69.0 mol%. The 16S rRNA gene sequence similarities of strain L72T with other species were less than 94%. Phylogenetic analyses based on 16S rRNA gene sequences and genome data, revealed that strain L72T formed a distinct phylogenetic lineage within the order Hyphomicrobiales, separating them from members of all families. Strain L72T showed 70.7% average nucleotide identity and 18.6% digital DNA-DNA hybridization identity with the closely related species Rhodoligotrophos defluvii. Based on the phenotypic, phylogenetic and chemotaxonomic data, a new family Propylenellaceae fam. nov. comprising the genus Propylenella gen. nov. and species Propylenella binzhouense sp. nov. is proposed. The type strain is L72T (= CCTCC AB 2019081T = KCTC 72254T).
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Affiliation(s)
- Yu-Ling Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Dong Meng
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Fang Wang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Xiao-Fan Gong
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Peng-Fei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Xiang-Yu Fan
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, People's Republic of China
| | - Ji-Dong Zou
- Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250000, People's Republic of China.
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
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Feng X, Zou QH, Zhang XY, Ye MQ, Du ZJ. Oceanipulchritudo coccoides gen. nov., sp. nov., isolated from marine sediment within the family Puniceicoccaceae. Int J Syst Evol Microbiol 2020; 70:5654-5664. [PMID: 32931410 DOI: 10.1099/ijsem.0.004458] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic coccus, designated CK1056T, was isolated from coastal sediment of Xiaoshi Island, Weihai, PR China. Strain CK1056T was found to grow at 15-37 °C (optimum, 30 °C), with 0.5-6.5 % (w/v) NaCl (optimum, 3.5 %) and displayed alkaliphilic growth within the pH range of pH 6.5-10.0 (optimum, pH 8.0). The major fatty acids identified were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The main polar lipids consisted of aminophosphoglycolipid and phosphatidylethanolamine. The predominant respiratory quinone was MK-7. The G+C content of the genomic DNA was 54.0 mol%. The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this micro-organism to the family Puniceicoccaceae, with Coraliomargarita akajimensis KCTC 12865T as its closest relative with only 88.0 % sequence similarity. From the taxonomic data obtained in this study, we propose that the new marine isolate be placed into a novel species within a novel genus in the family Puniceicoccaceae, phylum Verrucomicrobia, for which the name Oceanipulchritudo coccoides gen. nov., sp. nov. is proposed. The type strain is CK1056T (=KCTC 72798T=MCCC 1H00425T).
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Affiliation(s)
- Xi Feng
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Qi-Hang Zou
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xiao-Yu Zhang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Meng-Qi Ye
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.,Marine College, Shandong University, Weihai, Shandong 264209, PR China
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Meng X, Chang YQ, Wang H, Du ZJ. Algibacillus agarilyticus gen. nov., sp. nov., isolated from the surface of the red algae Gelidium amansii. Int J Syst Evol Microbiol 2020; 71. [PMID: 33332262 DOI: 10.1099/ijsem.0.004558] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, strictly aerobic, coccoid and agar-hydrolysing bacterium, designated RQJ05T, was isolated from the marine red algae Gelidium amansii collected from the coastal area of Rizhao, PR China. Cells of strain RQJ05T were approximately 0.8-1.0×1.3-3.0 µm in size and motile by means of a polar flagellum. Growth occurred at 4-33 °C (optimum, 25-30 °C), pH 7.0-8.5 (optimum, pH 7.5-8.0) and in the presence of 1.0-7.0 % (w/v) NaCl (optimum, 2.0-3.0 %). Strain RQJ05T showed oxidase-positive and catalase-negative activities. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain RQJ05T formed a phylogenetic lineage with members of the family Alteromonadaceae and exhibited 16S rRNA gene sequence similarities of 92.6, 91.3, 90.2 and 90.1 % to Catenovulum maritimum Q1T, Catenovulum agarivorans YM01T, Paraphotobacterium marinum NSCS20N07DT and Algicola sagamiensis B-10-31T, respectively. The major cellular fatty acids of strain RQJ05T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids of strain RQJ05T were phosphatidylethanolamine, phosphatidylglycerol and two aminophospholipids. Strain RQJ05T contained Q-8 as the major respiratory quinone. The genomic DNA G+C content was 39.0 mol%. On the basis of genotypic, phenotypic and phylogenetic evidence, strain RQJ05T is presented as a representative of a novel species in a new genus, for which the name Algibacillus agarilyticus gen. nov., sp. nov. is proposed. The type strain is RQJ05T (=KCTC 62846T=MCCC 1H00352T).
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Affiliation(s)
- Xue Meng
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya-Qi Chang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Huan Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- State key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China.,Marine College, Shandong University, Weihai, Shandong, 264209, PR China
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Liu SW, Ye JJ, Lu QP, Cheema MT, Abbas M, Huang DL, Sajid I, Sun CH. Motilibacter deserti sp. nov. and Motilibacter aurantiacus sp. nov., two novel actinobacteria isolated from soil of Cholistan Desert and emended description of the genus Motilibacter. Syst Appl Microbiol 2020; 43:126150. [PMID: 33099259 DOI: 10.1016/j.syapm.2020.126150] [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] [Received: 04/21/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 02/03/2023]
Abstract
Two novel actinobacterial strains, designated as E257T and K478T, were isolated from hyper-arid soil samples collected in Cholistan Desert, Pakistan. Comparative analysis of 16S rRNA genes showed that strains E257T and K478T were assigned to the genus Motilibacter, being their closest relative M. rhizosphaerae RS-16T with 97.3% and 96.7% similarities, respectively. The sequence similarity between strain E257T and K478T was 98.9%. Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on multiple genes of conserved core proteins exhibited that these two strains belonged to the genus Motilibacter and formed a robust cluster separated from the two type species of the genus Motilibacter. Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), digital DNA-DNA hybridization (dDDH) values and Percentage of Conserved Proteins (POCP) calculated from the complete genome sequences indicated strains E257T and K478T were assigned into genus Motilibacter but clearly separated from each other and from the other species of the genus Motilibacter with values below the thresholds for species delineation. The two isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Motilibacter and also confirmed the differentiation from their closest species. The obtained results demonstrated that strains E257T and K478T represent two novel species of the genus Motilibacter, for which the names Motilibacter desertisp. nov. (type strain E257T = JCM 33651T = CGMCC 1.17159T) and Motilibacter aurantiacus sp. nov. (type strain K478T =JCM 33652T =CGMCC 1.17229T) are proposed.
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Affiliation(s)
- Shao-Wei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jing-Jing Ye
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; College of Basic Medical Sciences, Guilin Medical University, Guilin 541004, China
| | - Qin-Pei Lu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mohsin Tassawar Cheema
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quid-i-Azam Campus, Lahore 54590, Pakistan
| | - Muhammad Abbas
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quid-i-Azam Campus, Lahore 54590, Pakistan
| | - Da-Lin Huang
- College of Basic Medical Sciences, Guilin Medical University, Guilin 541004, China
| | - Imran Sajid
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quid-i-Azam Campus, Lahore 54590, Pakistan.
| | - Cheng-Hang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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48
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Zhao LH, Xing X, Liu YY, Sha S, Song C, Sun YH, Xianyu DW, Zhu Q. Aeromicrobium piscarium sp. nov., isolated from the intestine of Collichthys lucidus. Int J Syst Evol Microbiol 2020; 70:5280-5286. [DOI: 10.1099/ijsem.0.004407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, whitesmoke-coloured and aerobic bacterium, designated strain Co35T, was isolated from the intestine of Collichthys lucidus collected from the Jiangmen Guangdong Chinese White Dolphin Provincial Nature Reserve. Strain Co35T was able to grow at 15–35 °C (optimal 28 °C), at pH 7.0–8.5 (optimal 8.0) and with 0–9 % (w/v) NaCl (optimal 0.5–1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Co35T was a member of the genus
Aeromicrobium
within the family
Nocardioidaceae
. The genomic DNA G+C content of strain Co35T was 68.4 mol%. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 9 (MK-9), and the major fatty acids included 10-methyl C18 : 0. The polar lipids were found to consist of phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylinositol (PI), two unidentified phospholipids (PL1–2) and two unidentified glycolipids (GL1–2). On the basis of its phylogenetic, phenotypic, chemotaxonomic, genotypic and genomic characteristics presented in this study, strain Co35T represents a novel species in the genus
Aeromicrobium
, for which the name Aeromicrobium piscarium sp. nov. is proposed. The type strain is Co35T (=KCTC 49280T=MCCC 1K03754T).
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Affiliation(s)
- Li-Hua Zhao
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xiang Xing
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Ying-Ying Liu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Sha Sha
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Cui Song
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Yuan-Hao Sun
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Dai-Wei Xianyu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Qian Zhu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
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Zhang JY, Jiang XB, Zhu D, Wang XM, Du ZJ, Mu DS. Roseomonas bella sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2020; 70:5473-5478. [PMID: 32886590 DOI: 10.1099/ijsem.0.004436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31T, was isolated from sediment of Changqiaohai Lake, Yunnan Province, China. Growth occurred at 4-45 °C (optimum, 37 °C), at pH 6.5-9.5 (optimum, pH 8.0) and with 0-1 % (w/v) NaCl (optimum, 0 %). C18 : 1 ω7c/C18 : 1 ω6c and C16 : 0 were the predominant fatty acids. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidyldimethylethanolamine (PME) and one unidentified aminolipid (AL) were the major polar lipids. The G+C content of the genomic DNA was 71.5 %. 16S rRNA gene sequence comparisons indicated that strain CQN31T shared 96.8 % similarity with Roseomonas wooponensis JCM 19527T and 95.9 % with R. terricola EM0302T. Digital DNA-DNA hybridization values between strain CQN31T and Roseomonas stagni DSM 19981T, R. rosea DSM 14916T and R. mucosa NCTC 13291T were 21.0, 19.4 and 19.8 %, respectively. Average amino acid identity and average nucleotide identity values between strain CQN31T and R. stagni DSM 19981T, R. rosea DSM 14916T and R. mucosa NCTC 13291T were 73.7, 63.4 and 61.9 %, and 79.2, 77.1 and 77.5%, respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain CQN31T as a representative of a novel species in the genus Roseomonas, for which the name Roseomonas bella sp. nov. is proposed. The type strain is CQN31T (=KCTC 62447T=MCCC 1H00309T).
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Affiliation(s)
- Jin-Yu Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xiao-Bing Jiang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Di Zhu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xiao-Man Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China.,Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
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50
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Zhong XC, Xu W, Zhang Y, Zhang QQ, Du ZJ. Algibacter marinivivus sp. nov., isolated from the surface of a marine red alga. Int J Syst Evol Microbiol 2020; 70:5048-5053. [DOI: 10.1099/ijsem.0.004375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A Gram-stain-negative, non-flagellated bacterium, designated ZY111T, was isolated from the surface of a marine red alga, which was collected from the coast in Weihai, Shandong Province, PR China. Strain ZY111T exhibited growth at 4–37 °C (optimum, 25–28 °C) in the presence of 0–8.0 % (w/v) NaCl (optimum, 2.0–4.0% NaCl) and at pH 6.5–9.5 (optimum, pH 7.0–8.0). The 16S rRNA gene sequence analysis revealed that strain ZY111T belonged to the genus
Algibacter
, with
Algibacter amylolyticus
DSM 29199T as its closest relative (97.7 % similarity). The averagenucleotide identity value of strain ZY111T with
A. amylolyticus
DSM 29199T was 79.03 %. The digitalDNA–DNA hybridization value of strain ZY111T with
A. amylolyticus
DSM 29199T was 22.40 %. The dominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The sole respiratory quinone was determined to be menaquinone-6. The polar lipid profile of strain ZY111T consisted of phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids. The G+C content was 31.9 mol%. The phenotypic, chemotaxonomic and phylogenetic data clearly showed that strain ZY111T represents a novel species of the genus
Algibacter
, for which the name Algibacter marinivivus sp. nov. is proposed. The type strain is ZY111T (=KCTC 62373T=MCCC 1H00295T).
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Affiliation(s)
- Xian-Chun Zhong
- Marine College, Shandong University, Weihai 264209, PR China
| | - Wei Xu
- Marine College, Shandong University, Weihai 264209, PR China
| | - Yu Zhang
- Marine College, Shandong University, Weihai 264209, PR China
| | - Qi-Qing Zhang
- Marine College, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
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