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Nedashkovskaya O, Balabanova L, Otstavnykh N, Zhukova N, Detkova E, Seitkalieva A, Bystritskaya E, Noskova Y, Tekutyeva L, Isaeva M. In-Depth Genome Characterization and Pan-Genome Analysis of Strain KMM 296, a Producer of Highly Active Alkaline Phosphatase; Proposal for the Reclassification of Cobetia litoralis and Cobetia pacifica as the Later Heterotypic Synonyms of Cobetia amphilecti and Cobetia marina, and Emended Description of the Species Cobetia amphilecti and Cobetia marina. Biomolecules 2024; 14:196. [PMID: 38397433 PMCID: PMC10887145 DOI: 10.3390/biom14020196] [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: 12/09/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of the mussel Crenomytilus grayanus, was investigated in detail due to its ability to produce a highly active alkaline phosphatase CmAP of the structural family PhoA. A previous taxonomic study allocated the strain to the species Cobetia marina, a member of the family Halomonadaceae of the class Gammaproteobacteria. However, 16S rRNA gene sequencing showed KMM 296's relatedness to Cobetia amphilecti NRIC 0815T. The isolate grew with 0.5-19% NaCl at 4-42 °C and hydrolyzed Tweens 20 and 40 and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C18:1 ω7c, C12:0 3-OH, C18:1 ω7c, C12:0, and C17:0 cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and also an unidentified aminolipid, phospholipid, and a few unidentified lipids. The major respiratory quinone was Q-8. According to phylogenomic and chemotaxonomic evidence, and the nearest neighbors, the strain KMM 296 represents a member of the species C. amphilecti. The genome-based analysis of C. amphilecti NRIC 0815T and C. litoralis NRIC 0814T showed their belonging to a single species. In addition, the high similarity between the C. pacifica NRIC 0813T and C. marina LMG 2217T genomes suggests their affiliation to one species. Based on the rules of priority, C. litoralis should be reclassified as a later heterotypic synonym of C. amphilecti, and C. pacifica is a later heterotypic synonym of C. marina. The emended descriptions of the species C. amphilecti and C. marina are also proposed.
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Affiliation(s)
- Olga Nedashkovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia; (L.B.); (N.O.); (A.S.); (E.B.); (Y.N.)
| | - Larissa Balabanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia; (L.B.); (N.O.); (A.S.); (E.B.); (Y.N.)
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, Ajax Bay 10, Russky Island, Vladivostok 690922, Russia;
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia; (L.B.); (N.O.); (A.S.); (E.B.); (Y.N.)
| | - Natalia Zhukova
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Ekaterina Detkova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Federal Research Centre “Fundamentals of Biotechnology”, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia;
| | - Aleksandra Seitkalieva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia; (L.B.); (N.O.); (A.S.); (E.B.); (Y.N.)
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, Ajax Bay 10, Russky Island, Vladivostok 690922, Russia;
| | - Evgenia Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia; (L.B.); (N.O.); (A.S.); (E.B.); (Y.N.)
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, Ajax Bay 10, Russky Island, Vladivostok 690922, Russia;
| | - Yulia Noskova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia; (L.B.); (N.O.); (A.S.); (E.B.); (Y.N.)
| | - Liudmila Tekutyeva
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, Ajax Bay 10, Russky Island, Vladivostok 690922, Russia;
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia; (L.B.); (N.O.); (A.S.); (E.B.); (Y.N.)
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Pentekhina I, Nedashkovskaya O, Seitkalieva A, Gorbach V, Slepchenko L, Kirichuk N, Podvolotskaya A, Son O, Tekutyeva L, Balabanova L. Chitinolytic and Fungicidal Potential of the Marine Bacterial Strains Habituating Pacific Ocean Regions. Microorganisms 2023; 11:2255. [PMID: 37764100 PMCID: PMC10535946 DOI: 10.3390/microorganisms11092255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Screening for chitinolytic activity in the bacterial strains from different Pacific Ocean regions revealed that the highly active representatives belong to the genera Microbulbifer, Vibrio, Aquimarina, and Pseudoalteromonas. The widely distributed chitinolytic species was Microbulbifer isolated from the sea urchin Strongylocentrotus intermedius. Among seventeen isolates with confirmed chitinolytic activity, only the type strain P. flavipulchra KMM 3630T and the strains of putatively new species Pseudoalteromonas sp. B530 and Vibrio sp. Sgm 5, isolated from sea water (Vietnam mollusc farm) and the sea urchin S. intermedius (Peter the Great Gulf, the Sea of Japan), significantly suppressed the hyphal growth of Aspergillus niger that is perspective for the biocontrol agents' development. The results on chitinolytic activities and whole-genome sequencing of the strains under study, including agarolytic type strain Z. galactanivorans DjiT, found the new functionally active chitinase structures and biotechnological potential.
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Affiliation(s)
- Iuliia Pentekhina
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Olga Nedashkovskaya
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Aleksandra Seitkalieva
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Vladimir Gorbach
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Lubov Slepchenko
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Natalya Kirichuk
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Anna Podvolotskaya
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Oksana Son
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Liudmila Tekutyeva
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Larissa Balabanova
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
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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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