1
|
Long M, Chen D, Fan H, Tang S, Gan Z, Xia H, Lu Y. Microbulbifer bruguierae sp. nov., isolated from sediment of mangrove plant Bruguiera sexangula, and comparative genomic analyses of the genus Microbulbifer. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240737 DOI: 10.1099/ijsem.0.006209] [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: 01/23/2024] Open
Abstract
A Gram-negative, non-motile, strictly aerobic, rod-shaped bacterium, designated as H12T, was isolated from the sediments of mangrove plant Bruguiera sexangula taken from Dapeng district, Shenzhen, PR China. The pairwise 16S rRNA gene sequence analysis showed that strain H12T shared high identity levels with species of the genus Microbulbifer, with the highest similarity level of 98.5 % to M. pacificus SPO729T, followed by 98.1 % to M. donghaiensis CN85T. Phylogenetic analysis using core-genome sequences showed that strain H12T formed a cluster with type species of M. pacificus SPO729T and M. harenosus HB161719T. The complete genome of strain H12T was 4 481 396 bp in size and its DNA G+C content was 56.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values among strain H12T and type species of genus Microbulbifer were below the cut-off levels of 95-96 and 70 %, respectively. The predominant cellular fatty acids of strain H12T were iso-C15 : 0 (22.5 %) and C18 : 1 ω7c (13.9 %). Ubiquinone-8 was detected as the major respiratory quinone. The polar lipids of strain H12T comprised one phosphatidylglycerol, one phosphatidylethanolamine, one unidentified aminoglycophospholipid, one unidentified glycophospholipid, three unidentified glycolipids, two unidentified aminolipids, and one unidentified lipid. Based on polyphasic evidence, strain H12T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer bruguierae sp. nov. is proposed. The type strain is H12T (=KCTC 92859T=MCCC 1K08451T). Comparative genomic analyses of strain H12T with strains of the genus Microbulbifer reveal its potential in degradation of pectin.
Collapse
Affiliation(s)
- Meng Long
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Dakun Chen
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
| | - Huimin Fan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Shaoshuai Tang
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Zhen Gan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
| | - Hongli Xia
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Yishan Lu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
| |
Collapse
|
2
|
Li Z, Du Z, Li H, Chen Y, Zheng M, Jiang Z, Du X, Ni H, Zhu Y. Characterisation of marine bacterium Microbulbifer sp. ALW1 with Laminaria japonica degradation capability. AMB Express 2022; 12:139. [DOI: 10.1186/s13568-022-01482-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/23/2022] [Indexed: 11/07/2022] Open
Abstract
AbstractMarine bacterium Microbulbifer sp. ALW1 was revealed to be able to effectively degrade Laminaria japonica thallus fragments into fine particles. Polysaccharide substrate specificity analysis indicated that ALW1 could produce extracellular alginate lyase, laminarinase, fucoidanase and cellulase. Based on alignment of the 16 S rRNA sequence with other reference relatives, ALW1 showed the closest relationship with Microbulbifer aggregans CCB-MM1T. The cell morphology and some basic physiological and biochemical parameters of ALW1 cells were characterised. ALW1 is a Gram-negative, rod- or oval-shaped, non-spore-forming and non-motile bacterium. The DNA–DNA relatedness values of ALW1 with type strains of M. gwangyangensis (JCM 17,800), M. aggregans (JCM 31,875), M. maritimus (JCM 12,187), M. okinawensis (JCM 16,147) and M. rhizosphaerae (DSM 28,920) were 28.9%, 43.3%, 41.2%, 35.4% and 45.6%, respectively. The major cell wall sugars of ALW1 were determined to be ribose and galactose, which differed from other closely related species. These characteristics indicated that ALW1 could be assigned to a separate species of the genus Microbulbifer. The complete genome of ALW1 contained one circular chromosome with 4,682,287 bp and a GC content of 56.86%. The putative encoded proteins were categorised based on their functional annotations. Phenotypic, physiological, biochemical and genomic characterisation will provide insights into the many potential industrial applications of Microbulbifer sp. ALW1.Key points.
Collapse
|
3
|
Microbulbifer okhotskensis sp. nov., isolated from a deep bottom sediment of the Okhotsk Sea. Arch Microbiol 2022; 204:548. [PMID: 35945400 DOI: 10.1007/s00203-022-03161-9] [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: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/02/2022]
Abstract
A Gram-negative, aerobic, non-motile bacterium КMM 9862T was isolated from a deep bottom sediment sample obtained from the Okhotsk Sea, Russia. Based on the 16S rRNA gene and whole genome sequences analyses the novel strain КMM 9862T fell into the genus Microbulbifer (class Gammaproteobacteria) sharing the highest 16S rRNA gene sequence similarities of 97.4% to Microbulbifer echini AM134T and Microbulbifer epialgicus F-104T, 97.3% to Microbulbifer pacificus SPO729T, 97.1% to Microbulbifer variabilis ATCC 700307T, and similarity values of < 97.1% to other recognized Microbulbifer species. The average nucleotide identity and digital DNA-DNA hybridization values between strain КMM 9862T and M. variabilis ATCC 700307T and M. thermotolerans DSM 19189T were 80.34 and 77.72%, and 20.2 and 19.0%, respectively. Strain КMM 9862T contained Q-8 as the predominant ubiquinone and C16:0, C16:1 ω7c, C12:0, and C10:0 3-OH as the major fatty acids. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, an unidentified aminolipid, two unidentified phospholipids, phosphatidic acid, and an unidentified lipid. The DNA G+C content of 49.8% was calculated from the genome sequence. On the basis of the phylogenetic evidence and distinctive phenotypic characteristics, the marine bacterium KMM 9862T is proposed to be classified as a novel species Microbulbifer okhotskensis sp. nov. The type strain of the species is strain KMM 9862T (= KACC 22804T).
Collapse
|
4
|
Park SL, Cho JY, Kim SH, Lee HJ, Kim SH, Suh MJ, Ham S, Bhatia SK, Gurav R, Park SH, Park K, Kim YG, Yang YH. Novel Polyhydroxybutyrate-Degrading Activity of the Microbulbifer Genus as Confirmed by Microbulbifer sp. SOL03 from the Marine Environment. J Microbiol Biotechnol 2022; 32:27-36. [PMID: 34750287 PMCID: PMC9628828 DOI: 10.4014/jmb.2109.09005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Ever since bioplastics were globally introduced to a wide range of industries, the disposal of used products made with bioplastics has become an issue inseparable from their application. Unlike petroleum-based plastics, bioplastics can be completely decomposed into water and carbon dioxide by microorganisms in a relatively short time, which is an advantage. However, there is little information on the specific degraders and accelerating factors for biodegradation. To elucidate a new strain for biodegrading poly-3-hydroxybutyrate (PHB), we screened out one PHB-degrading bacterium, Microbulbifer sp. SOL03, which is the first reported strain from the Microbulbifer genus to show PHB degradation activity, although Microbulbifer species are known to be complex carbohydrate degraders found in high-salt environments. In this study, we evaluated its biodegradability using solid- and liquid-based methods in addition to examining the changes in physical properties throughout the biodegradation process. Furthermore, we established the optimal conditions for biodegradation with respect to temperature, salt concentration, and additional carbon and nitrogen sources; accordingly, a temperature of 37°C with the addition of 3% NaCl without additional carbon sources, was determined to be optimal. In summary, we found that Microbulbifer sp. SOL03 showed a PHB degradation yield of almost 97% after 10 days. To the best of our knowledge, this is the first study to investigate the potent bioplastic degradation activity of Microbulbifer sp., and we believe that it can contribute to the development of bioplastics from application to disposal.
Collapse
Affiliation(s)
- Sol Lee Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jang Yeon Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Su Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hong-Ju Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Min Ju Suh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea,Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, Republic of Korea
| | - Ranjit Gurav
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - See-Hyoung Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong City 30016, Republic of Korea
| | - Kyungmoon Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong City 30016, Republic of Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea,Corresponding author Phone: +82-2-450-3936 Fax: +82-2-3437-8360 E-mail:
| |
Collapse
|
5
|
Cheng Y, Zhu S, Guo C, Xie F, Jung D, Li S, Zhang W, He S. Microbulbifer hainanensis sp. nov., a moderately halopilic bacterium isolated from mangrove sediment. Antonie van Leeuwenhoek 2021; 114:1033-1042. [PMID: 33844121 DOI: 10.1007/s10482-021-01574-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
A new bacterium was successfully isolated from a mangrove sediment sample in Haikou City, Hainan Province, China. The organism is a Gram-negative, rod-shaped, non-motile and strictly aerobic bacterium, named NBU-8HK146T. Strain NBU-8HK146T was able to grow at temperatures of 10-40 °C, at salinities of 0-11% (w/v) and at pH 5.5-9.5. Veoges-Proskauer, methyl red reaction and hydrolysis of Tween 20 were negative. Catalase and oxidase activities, H2S production, hydrolysis of starch, casein, Tweens 40, 60 and 80 were positive. The major cellular fatty acids were C16:0, iso-C15:0 and summed feature 9. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and two unidentified glycolipids. According to 16S rRNA gene sequence similarities, strain NBU-8HK146T shared 98.0%, 97.9%, 97.7%, 97.6% and 97.3% similarities to the species with validated name Microbulbifer taiwanensis CC-LN1-12T, Microbulbifer rhizosphaerae Cs16bT, Microbulbifer marinus Y215T, Microbulbifer donghaiensis CN85T and Microbulbifer aggregans CCB-MM1T, respectively. Phylogenetic analyses indicated that strain NBU-8HK146T formed a distinct lineage with strains Microbulbifer taiwanensis CC-LN1-12T and Microbulbifer marinus Y215T. Both digital DNA-DNA hybridization values (19.5-22.7%) and average nucleotide identity values (73.2-78.9%) between strain NBU-8HK146T and related species of genus Microbulbifer were below the species delineation cutoffs. The DNA G+C content was 58.9 mol%. Many proteins involving in the adaption of osmotic stress in the salt environment of mangrove were predicted in genome of strain NBU-8HK146T. From phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain NBU-8HK146T can be regarded as a new Microbulbifer species for which the name Microbulbifer hainanensis. The type strain is NBU-8HK146T (= KCTC 82226T = MCCC 1K04737T).
Collapse
Affiliation(s)
- Yuping Cheng
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Suting Zhu
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Chaobo Guo
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Feilu Xie
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Dawoon Jung
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Weiyan Zhang
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China.
| | - Shan He
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China.
| |
Collapse
|
6
|
Expression and Characterization of a Cold-Adapted Alginate Lyase with Exo/Endo-Type Activity from a Novel Marine Bacterium Alteromonas portus HB161718 T. Mar Drugs 2021; 19:md19030155. [PMID: 33802659 PMCID: PMC8002439 DOI: 10.3390/md19030155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
The alginate lyases have unique advantages in the preparation of alginate oligosaccharides and processing of brown algae. Herein, a gene alg2951 encoding a PL7 family alginate lyase with exo/endo-type activity was cloned from a novel marine bacterium Alteromonas portus HB161718T and then expressed in Escherichia coli. The recombinant Alg2951 in the culture supernatant reached the activity of 63.6 U/mL, with a molecular weight of approximate 60 kDa. Alg2951 exhibited the maximum activity at 25 °C and pH 8.0, was relatively stable at temperatures lower than 30 °C, and showed a special preference to poly-guluronic acid (polyG) as well. Both NaCl and KCl had the most promotion effect on the enzyme activity of Alg2951 at 0.2 M, increasing by 21.6 and 19.1 times, respectively. The TCL (Thin Layer Chromatography) and ESI-MS (Electrospray Ionization Mass Spectrometry) analyses suggested that Alg2951 could catalyze the hydrolysis of sodium alginate to produce monosaccharides and trisaccharides. Furthermore, the enzymatic hydrolysates displayed good antioxidant activity by assays of the scavenging abilities towards radicals (hydroxyl and ABTS+) and the reducing power. Due to its cold-adapted and dual exo/endo-type properties, Alg2951 can be a potential enzymatic tool for industrial production.
Collapse
|