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Liu W, Cong B, Lin J, Zhao L, Liu S. Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment. BMC Genomics 2022; 23:713. [PMID: 36261793 PMCID: PMC9580203 DOI: 10.1186/s12864-022-08942-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated in order to understand nitrogen cycling involved in the deep-sea environment. RESULTS In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 and Halomonas profundus 13 genome sizes are 4,160,095 bp with a GC content of 62.5% and 5,251,450 bp with a GC content of 54.84%. Through a comparison of functional analyses, we predicted the possible C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 could use more carbon sources than Cobetia amphilecti N-80. The main genes associated with N metabolism in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, nosZ, and nirD. On the contrast, nirD, using NH4+ for energy, plays a main role in Cobetia amphilecti N-80. Both of them have the same genes for fixing inorganic carbon: icd, ppc, fdhA, accC, accB, accD, and accA. CONCLUSION In this study, the whole genomes of two strains were sequenced to clarify the basic characteristics of their genomes, laying the foundation for further studying nitrogen-metabolizing bacteria. Halomonas profundus 13 can utilize more carbon sources than Cobetia amphilecti N-80, as indicated by API as well as COG and KEGG prediction results. Finally, through the analysis of the nitrification and denitrification abilities as well as the inorganic carbon fixation ability of the two strains, the related genes were identified, and the possible metabolic pathways were predicted. Together, these results provide molecular markers and theoretical support for the mechanisms of inorganic carbon fixation by deep-sea microorganisms.
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Affiliation(s)
- Wenqi Liu
- School of Advanced Manufacturing, Fuzhou University, Fuzhou, 350108, China
| | - Bailin Cong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shenghao Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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Fernández-Juárez V, Jaén-Luchoro D, Brito-Echeverría J, Agawin NSR, Bennasar-Figueras A, Echeveste P. Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration. MICROBIAL ECOLOGY 2022; 83:296-313. [PMID: 33954842 DOI: 10.1007/s00248-021-01766-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Bacteria are essential in the maintenance and sustainment of marine environments (e.g., benthic systems), playing a key role in marine food webs and nutrient cycling. These microorganisms can live associated as epiphytic or endophytic populations with superior organisms with valuable ecological functions, e.g., seagrasses. Here, we isolated, identified, sequenced, and exposed two strains of the same species (i.e., identified as Cobetia sp.) from two different marine environments to different nutrient regimes using batch cultures: (1) Cobetia sp. UIB 001 from the endemic Mediterranean seagrass Posidonia oceanica and (2) Cobetia sp. 4B UA from the endemic Humboldt Current System (HCS) seagrass Heterozostera chilensis. From our physiological studies, both strains behaved as bacteria capable to cope with different nutrient and pH regimes, i.e., N, P, and Fe combined with different pH levels, both in long-term (12 days (d)) and short-term studies (4 d/96 h (h)). We showed that the isolated strains were sensitive to the N source (inorganic and organic) at low and high concentrations and low pH levels. Low availability of phosphorus (P) and Fe had a negative independent effect on growth, especially in the long-term studies. The strain UIB 001 showed a better adaptation to low nutrient concentrations, being a potential N2-fixer, reaching higher growth rates (μ) than the HCS strain. P-acquisition mechanisms were deeply investigated at the enzymatic (i.e., alkaline phosphatase activity, APA) and structural level (e.g., alkaline phosphatase D, PhoD). Finally, these results were complemented with the study of biochemical markers, i.e., reactive oxygen species (ROS). In short, we present how ecological niches (i.e., MS and HCS) might determine, select, and modify the genomic and phenotypic features of the same bacterial species (i.e., Cobetia spp.) found in different marine environments, pointing to a direct correlation between adaptability and oligotrophy of seawater.
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Affiliation(s)
- Víctor Fernández-Juárez
- Marine Ecology and Systematics (MarES), Department of Biology, University of the Balearic Islands, Palma, Spain.
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Jocelyn Brito-Echeverría
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Nona S R Agawin
- Marine Ecology and Systematics (MarES), Department of Biology, University of the Balearic Islands, Palma, Spain
| | | | - Pedro Echeveste
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
- Instituto Milenio de Oceanografía, Concepción, Chile
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Are the Closely Related Cobetia Strains of Different Species? Molecules 2021; 26:molecules26030690. [PMID: 33525723 PMCID: PMC7865433 DOI: 10.3390/molecules26030690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/12/2021] [Accepted: 01/26/2021] [Indexed: 11/17/2022] Open
Abstract
Marine bacteria of the genus Cobetia, which are promising sources of unique enzymes and secondary metabolites, were found to be complicatedly identified both by phenotypic indicators due to their ecophysiology diversity and 16S rRNA sequences because of their high homology. Therefore, searching for the additional methods for the species identification of Cobetia isolates is significant. The species-specific coding sequences for the enzymes of each functional category and different structural families were applied as additional molecular markers. The 13 closely related Cobetia isolates, collected in the Pacific Ocean from various habitats, were differentiated by the species-specific PCR patterns. An alkaline phosphatase PhoA seems to be a highly specific marker for C. amphilecti. However, the issue of C. amphilecti and C. litoralis, as well as C. marina and C. pacifica, belonging to the same or different species remains open.
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Balabanova L, Shkryl Y, Slepchenko L, Cheraneva D, Podvolotskaya A, Bakunina I, Nedashkovskaya O, Son O, Tekutyeva L. Genomic Features of a Food-Derived Pseudomonas aeruginosa Strain PAEM and Biofilm-Associated Gene Expression under a Marine Bacterial α-Galactosidase. Int J Mol Sci 2020; 21:ijms21207666. [PMID: 33081309 PMCID: PMC7593944 DOI: 10.3390/ijms21207666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
The biofilm-producing strains of P. aeruginosa colonize various surfaces, including food products and industry equipment that can cause serious human and animal health problems. The biofilms enable microorganisms to evolve the resistance to antibiotics and disinfectants. Analysis of the P. aeruginosa strain (serotype O6, sequence type 2502), isolated from an environment of meat processing (PAEM) during a ready-to-cook product storage (−20 °C), showed both the mosaic similarity and differences between free-living and clinical strains by their coding DNA sequences. Therefore, a cold shock protein (CspA) has been suggested for consideration of the evolution probability of the cold-adapted P. aeruginosa strains. In addition, the study of the action of cold-active enzymes from marine bacteria against the food-derived pathogen could contribute to the methods for controlling P. aeruginosa biofilms. The genes responsible for bacterial biofilm regulation are predominantly controlled by quorum sensing, and they directly or indirectly participate in the synthesis of extracellular polysaccharides, which are the main element of the intercellular matrix. The levels of expression for 14 biofilm-associated genes of the food-derived P. aeruginosa strain PAEM in the presence of different concentrations of the glycoside hydrolase of family 36, α-galactosidase α-PsGal, from the marine bacterium Pseudoalteromonas sp. KMM 701 were determined. The real-time PCR data clustered these genes into five groups according to the pattern of positive or negative regulation of their expression in response to the action of α-galactosidase. The results revealed a dose-dependent mechanism of the enzymatic effect on the PAEM biofilm synthesis and dispersal genes.
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Affiliation(s)
- Larissa Balabanova
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
- Correspondence: (L.B.); (Y.S.)
| | - Yuri Shkryl
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia
- Correspondence: (L.B.); (Y.S.)
| | - Lubov Slepchenko
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
| | - Daria Cheraneva
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
| | - Anna Podvolotskaya
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
| | - Irina Bakunina
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
| | - Olga Nedashkovskaya
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
| | - Oksana Son
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
| | - Liudmila Tekutyeva
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
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Thomas T, Elain A, Bazire A, Bruzaud S. Complete genome sequence of the halophilic PHA-producing bacterium Halomonas sp. SF2003: insights into its biotechnological potential. World J Microbiol Biotechnol 2019; 35:50. [PMID: 30852675 DOI: 10.1007/s11274-019-2627-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
Abstract
A halophilic Gram-negative eubacterium was isolated from the Iroise Sea and identified as an efficient producer of polyhydroxyalkanoates (PHA). The strain, designated SF2003, was found to belong to the Halomonas genus on the basis of 16S rRNA gene sequence similarity. Previous biochemical tests indicated that the Halomonas sp. strain SF2003 is capable of supporting various culture conditions which sometimes can be constraining for marine strains. This versatility could be of great interest for biotechnological applications. Therefore, a complete bacterial genome sequencing and de novo assembly were performed using a PacBio RSII sequencer and Hierarchical Genome Assembly Process software in order to predict Halomonas sp. SF2003 metabolisms, and to identify genes involved in PHA production and stress tolerance. This study demonstrates the complete genome sequence of Halomonas sp. SF2003 which contains a circular 4,36 Mbp chromosome, and replaces the strain in a phylogenetic tree. Genes related to PHA metabolism, carbohydrate metabolism, fatty acid metabolism and stress tolerance were identified and a comparison was made with metabolisms of relative species. Genes annotation highlighted the presence of typical genes involved in PHA biosynthesis such as phaA, phaB and phaC and enabled a preliminary analysis of their organization and characteristics. Several genes of carbohydrates and fatty acid metabolisms were also identified which provided helpful insights into both a better knowledge of the intricacies of PHA biosynthetic pathways and of production purposes. Results show the strong versatility of Halomonas sp. SF2003 to adapt to various temperatures and salinity which can subsequently be exploited for industrial applications such as PHA production.
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Affiliation(s)
- Tatiana Thomas
- Institut de Recherche Dupuy de Lôme (IRDL), UMR CNRS 6027, Université de Bretagne Sud, Rue Saint Maudé, Lorient, France
| | - Anne Elain
- Institut de Recherche Dupuy de Lôme (IRDL), UMR CNRS 6027, Université de Bretagne Sud, Rue Saint Maudé, Lorient, France
| | - Alexis Bazire
- Laboratoire de Biotechnologie et Chimie Marines, EA3884, IUEM, Université de Bretagne-Sud, Lorient, France
| | - Stéphane Bruzaud
- Institut de Recherche Dupuy de Lôme (IRDL), UMR CNRS 6027, Université de Bretagne Sud, Rue Saint Maudé, Lorient, France.
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Balabanova L, Podvolotskaya A, Slepchenko L, Eliseikina M, Noskova Y, Nedashkovskaya O, Son O, Tekutyeva L, Rasskazov V. Nucleolytic enzymes from the marine bacterium Cobetia amphilecti KMM 296 with antibiofilm activity and biopreservative effect on meat products. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.02.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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