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Zhong W, Agarwal V. Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty. Beilstein J Org Chem 2024; 20:1635-1651. [PMID: 39076296 PMCID: PMC11285056 DOI: 10.3762/bjoc.20.146] [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: 02/19/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
Microbulbifer is a genus of halophilic bacteria that are commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic novelty. In this review, we summarize the distribution of Microbulbifer bacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated from Microbulbifer strains. We argue that these bacteria have been hiding in plain sight, and contemporary efforts into their genome and metabolome mining are going to lead to a proliferation of Microbulbifer-derived natural products in the future. We also describe, where possible, the ecological interactions of these bacteria in marine microbiomes.
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Affiliation(s)
- Weimao Zhong
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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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.
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Wang J, Jin L, Wang J, Chan Z, Zeng R, Wu J, Qu W. The first complete genome sequence of Microbulbifer celer KCTC12973T, a type strain with multiple polysaccharide degradation genes. Mar Genomics 2022; 62:100931. [DOI: 10.1016/j.margen.2022.100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
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Biorefinery of exhausted olive pomace through the production of polygalacturonases and omega-3 fatty acids by Crypthecodinium cohnii. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Wang D, Wang J, Zeng R, Wu J, Michael SV, Qu W. The degradation activities for three seaweed polysaccharides of Shewanella sp. WPAGA9 isolated from deep-sea sediments. J Basic Microbiol 2021; 61:406-418. [PMID: 33729617 DOI: 10.1002/jobm.202000728] [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: 12/15/2020] [Revised: 02/03/2021] [Accepted: 03/01/2021] [Indexed: 11/06/2022]
Abstract
Seaweed oligosaccharides possess great bioactivities. However, different microbial strains are required to degrade multiple polysaccharides due to their limited biodegradability, thereby increasing the cost and complexity of production. Shewanella sp. WPAGA9 was isolated from deep-sea sediments in this study. According to the genomic and biochemical analyses, the extracellular fermentation broth of WPAGA9 had versatile degradation abilities for three typical seaweed polysaccharides including agar, carrageenan, and alginate. The maximum enzyme activities of the extracellular fermentation broth of WPAGA9 were 71.63, 76.4, and 735.13 U/ml for the degradation of agar, alginate, and carrageenan, respectively. Moreover, multiple seaweed oligosaccharides can be produced by the extracellular fermentation broth of WPAGA9 under similar optimum conditions. Therefore, WPAGA9 can simultaneously degrade three types of seaweed polysaccharides under similar conditions, thereby greatly reducing the production cost of seaweed oligosaccharides. This finding indicates that Shewanella sp. WPAGA9 is an ideal biochemical tool for producing multiple active seaweed oligosaccharides at low costs and is also an important participant in the carbon cycle process of the deep-sea environment.
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Affiliation(s)
- Dingquan Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Runying Zeng
- Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen, China
| | - Jie Wu
- Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen, China
| | - Shija V Michael
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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Cheng W, Yan X, Xiao J, Chen Y, Chen M, Jin J, Bai Y, Wang Q, Liao Z, Chen Q. Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12. Sci Rep 2020; 10:10920. [PMID: 32616809 PMCID: PMC7331586 DOI: 10.1038/s41598-020-67921-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 06/16/2020] [Indexed: 01/09/2023] Open
Abstract
Alginate-degrading bacteria or alginate lyases can be used to oligomerize alginate. In this study, an alginate-degrading bacterium with high alginolytic activity was successfully screened by using Sargassum fusiforme sludge. When the strain was grown on a plate containing sodium alginate, the transparent ring diameter (D) was 2.2 cm and the ratio (D/d) of transparent ring diameter to colony diameter (d) was 8.8. After 36 h in culture at a temperature of 28 °C shaken at 150 r/min, the enzymatic activity of the fermentation supernatant reached 160 U/mL, and the enzymatic activity of the bacterial precipitate harvested was 2,645 U/mL. The strain was named Cobetia sp. cqz5-12. Its genome is circular in shape, 4,209,007 bp in size, with a 62.36% GC content. It contains 3,498 predicted coding genes, 72 tRNA genes, and 21 rRNA genes. The functional annotations for the coding genes demonstrated that there were 181 coding genes in the genome related to carbohydrate transport and metabolism and 699 coding genes with unknown functions. Three putative coding genes, alg2107, alg2108 and alg2112, related to alginate degradation were identified by analyzing the carbohydrate active enzyme (CAZy) database. Moreover, proteins Alg2107 and Alg2112 were successfully expressed and exhibited alginate lyase activity.
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Affiliation(s)
- Wenwen Cheng
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Xuanyu Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Jiali Xiao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Yunyun Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Minghui Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Jiayi Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Yu Bai
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Qi Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Zhiyong Liao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China.
| | - Qiongzhen Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China.
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Chen YP, Wu HT, Wang GH, Wu DY, Hwang IE, Chien MC, Pang HY, Kuo JT, Liaw LL. Inspecting the genome sequence and agarases of Microbulbifer pacificus LD25 from a saltwater hot spring. J Biosci Bioeng 2019; 127:403-410. [DOI: 10.1016/j.jbiosc.2018.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 09/29/2018] [Accepted: 10/02/2018] [Indexed: 12/27/2022]
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Biochemical Reconstruction of a Metabolic Pathway from a Marine Bacterium Reveals Its Mechanism of Pectin Depolymerization. Appl Environ Microbiol 2018; 85:AEM.02114-18. [PMID: 30341080 DOI: 10.1128/aem.02114-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022] Open
Abstract
Pectin is a complex uronic acid-containing polysaccharide typically found in plant cell walls, though forms of pectin are also found in marine diatoms and seagrasses. Genetic loci that target pectin have recently been identified in two phyla of marine bacteria. These loci appear to encode a pectin saccharification pathway that is distinct from the canonical pathway typically associated with phytopathogenic terrestrial bacteria. However, very few components of the marine pectin metabolism pathway have been experimentally validated. Here, we biochemically reconstructed the pectin saccharification pathway from a marine Pseudoalteromonas sp. in vitro and show that it results in the production of galacturonate and the key metabolic intermediate 5-keto-4-deoxyuronate (DKI). We demonstrate the sequential de-esterification and depolymerization of pectin into oligosaccharides and the synergistic action of glycoside hydrolases (GHs) to fully degrade these oligosaccharides into monosaccharides. Furthermore, we show that this pathway relies on enzymes belonging to GH family 105 to carry out the equivalent chemistry afforded by an exolytic polysaccharide lyase (PL) and KdgF in the canonical pectin pathway. Finally, we synthesize our findings into a model of marine pectin degradation and compare it with the canonical pathway. Our results underline the shifting view of pectin as a solely terrestrial polysaccharide and highlight the importance of marine pectin as a carbon source for suitably adapted marine heterotrophs. This alternate pathway has the potential to be exploited in the growing field of biofuel production from plant waste.IMPORTANCE Marine polysaccharides, found in the cell walls of seaweeds and other marine macrophytes, represent a vast sink of photosynthetically fixed carbon. As such, their breakdown by marine microbes contributes significantly to global carbon cycling. Pectin is an abundant polysaccharide found in the cell walls of terrestrial plants, but it has recently been reported that some marine bacteria possess the genetic capacity to degrade it. In this study, we biochemically characterized seven key enzymes from a marine bacterium that, together, fully degrade the backbone of pectin into its constituent monosaccharides. Our findings highlight the importance of pectin as a marine carbon source available to bacteria that possess this pathway. The characterized enzymes also have the potential to be utilized in the production of biofuels from plant waste.
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Study on expression and action mode of recombinant alginate lyases based on conserved domains reconstruction. Appl Microbiol Biotechnol 2018; 103:807-817. [DOI: 10.1007/s00253-018-9502-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
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Poduval PB, Noronha JM, Bansal SK, Ghadi SC. Characterization of a new virulent phage ϕMC1 specific to Microbulbifer strain CMC-5. Virus Res 2018; 257:7-13. [DOI: 10.1016/j.virusres.2018.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/11/2018] [Accepted: 08/28/2018] [Indexed: 11/29/2022]
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Li S, Wang L, Chen X, Zhao W, Sun M, Han Y. Cloning, Expression, and Biochemical Characterization of Two New Oligoalginate Lyases with Synergistic Degradation Capability. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:75-86. [PMID: 29362921 DOI: 10.1007/s10126-017-9788-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/06/2017] [Indexed: 06/07/2023]
Abstract
Alginate, the most abundant carbohydrate presents in brown macroalgae, has recently gained increasing attention as an alternative biomass for the production of biofuel. Oligoalginate lyases catalyze the degradation of alginate oligomers into monomers, a prerequisite for bioethanol production. In this study, two new oligoalginate lyase genes, oalC6 and oalC17, were cloned from Cellulophaga sp. SY116, and expressed them in Escherichia coli. The deduced oligoalginate lyases, OalC6 and OalC17, belonged to the polysaccharide lyase (PL) family 6 and 17, respectively. Both showed less than 50% amino acid identity with all of the characterized oligoalginate lyases. Moreover, OalC6 and OalC17 could degrade both alginate polymers and oligomers into monomers in an exolytic mode. Substrate specificity studies demonstrated that OalC6 preferred α-L-guluronate (polyG) blocks, while OalC17 preferred poly β-D-mannuronate (polyM) blocks. The combination of OalC6 and OalC17 showed synergistic degradation ability toward both alginate polymers and oligomers. Finally, an efficient process for the production of alginate monomers was established by combining the new-isolated exotype alginate lyases (i.e., OalC6 and OalC17) and the endotype alginate lyase AlySY08. Overall, our work provides new insights for the development of novel biotechnologies for biofuel production from seaweed.
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Affiliation(s)
- Shangyong Li
- Department of Pharmacology, College of basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Linna Wang
- Yellow Sea Fisheries Research Institute, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xuehong Chen
- Department of Pharmacology, College of basic Medicine, Qingdao University, Qingdao, 266071, China.
| | - Wenwen Zhao
- Department of Pharmacology, College of basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Mi Sun
- Yellow Sea Fisheries Research Institute, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yantao Han
- Department of Pharmacology, College of basic Medicine, Qingdao University, Qingdao, 266071, China.
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